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Why is (in forensic genetics) in some cases more appropriate comparison of nuclear DNA but in some other cases comparison of mitochondrial DNA?
Is it because geneticists are sometimes unable to find nDNA or if nDNA is too damaged? Also could it be because of the structure of mtDNA (it's more protected against degradation, which is good for identifying old biological material)? I can't see any other advantages, since mitochondrial DNA mutations occur frequently, due to the lack of the error checking, but are there any that I am missing?
Thank you in advance.
mtDNA is present in a much higher copy number per cell than nuclear DNA.
According to this paper, there are approximately 4000 or so mitochondrial DNA copies per human muscle cell.
copy number of mtDNA per diploid nuclear genome in myocardium was 6970 ± 920, significantly higher than that in skeletal muscle, 3650 ± 620 (P = 0.006).
This makes it far more likely that a non-degraded copy of mtDNA exists, considering that there are normally only 2 or 4 copies of nuclear DNA per cell per locus for almost all kinds of cells.
Difficulties of sex determination from forensic bone degraded DNA: A comparison of three methods
Sex determination is of paramount importance in forensic anthropology. Numerous anthropological methods have been described, including visual assessments and various measurements of bones. Nevertheless, whatever the method used, the percentage of correct classification of a single bone usually varies between 80% and 95%, due to significant intra- and inter-population variations, and sometimes variations coming from secular trends. DNA is increasingly used in a forensic context. But forensic DNA extraction from bone raises several issues, because the samples are very often badly altered and/or in very small quantity. Nuclear DNA is difficult to get from degraded samples, according to low copy number, at least in comparison with mitochondrial DNA. In a forensic context (as in a paeleoanthropological context) DNA sex determination is usually complicated by the weak amount of DNA, the degraded nature of nucleic acids, the presence of enzymatic inhibitors in DNA extracts, the possible faint amplification of Y band and the risk of contamination during either excavation or manipulation of samples.
The aim of this work was to compare three methods of DNA sex determination from bones: procedure #1 using a single PCR amplification, procedure #2 using a double PCR amplification, and procedure #3 adding bleaching for decontamination of the bone, instead of simply rubbing the bone. These processes were applied to samples of bones (49 samples coming from 39 individuals) that were in various states of post mortem alteration.
The main results are the following. (i) No DNA could be extracted from three skulls (parietal bones, mastoid process), the compact bone of one rib, and the diaphysis of one femur (ii) there was a contamination in three skulls and (iii) the Y band did not appear in two male cases, with one of the three procedures (male tibia, procedure #2) and with procedures #2 and #3 (male femur).
This study emphasises the main issue while working with altered bones: the impossibility to extract DNA in some cases, and, worth of all, the contamination of the sample or the faint amplification of Y band which leads to a wrong sex answer. Multiple and significant precautions have to be taken to avoid such difficulties.
Interplay between mitochondria and nucleus may have implications for new treatment
Mitochondria, the 'batteries' that produce our energy, interact with the cell's nucleus in subtle ways previously unseen in humans, according to research published today in the journal Science.
The study, led by scientists at the University of Cambridge, suggests that matching mitochondrial DNA to nuclear DNA could be important when selecting potential donors for the recently-approved mitochondrial donation treatment, in order to prevent potential health problems later in life.
Almost all of the DNA that makes up the human genome -- the body's 'blueprint' -- is contained within our cells' nuclei. This is referred to as 'nuclear DNA'. Among other functions, nuclear DNA codes for the characteristics that make us individual as well as for the proteins that do most of the work in our bodies.
Our cells also contain mitochondria, often referred to as the 'batteries' that provide the energy for our cells to function. Each of these mitochondria is coded for by a tiny amount of 'mitochondrial DNA'. Mitochondrial DNA makes up only 0.1% of the overall human genome and is passed down exclusively from mother to child.
Until now, scientists had thought that mitochondria were readily interchangeable, serving only to power our bodies, and so an individual's mitochondria could be replaced with those from a donor with no consequences. However, in the first major population study to use data from the UK-wide 100,000 Genomes Project and its National Institute for Health Research (NIHR)-funded pilot project, researchers compared mitochondrial and nuclear DNA from tens of thousands of people and found that mitochondria may be fine-tuned to the nucleus.
The researchers studied over 1,500 mother-child pairs and found that just under a half (45%) of individuals within these pairs harboured mutations affecting at least 1% of their mitochondrial DNA. Mutations in certain parts of mitochondrial DNA were more likely to be transmitted, such as those in the so-called D-loop region, which controls how mitochondrial DNA copies itself. Conversely, mutations in other parts of mitochondrial DNA were more likely to be suppressed, such as the code for how mitochondria produce their own proteins.
"Children inherit their DNA exclusively from their mother and we wanted to see how this explains the origins of mitochondrial diseases," says first author Dr Wei Wei from the Medical Research Council (MRC) Mitochondrial Biology Unit and Department of Clinical Neurosciences at the University of Cambridge. "What we found was that there is some kind of selection taking place when mitochondrial DNA is transmitted down a generation, allowing some mutations to be passed on and others to be blocked."
Genetic variants that had previously been observed around the world were more likely to be passed on than completely new ones, the team found. This implies that there is a mechanism that filters the mitochondrial DNA when it is being passed down from mother to child, influencing the likelihood that a particular variant becomes established in the human population.
DNA can give us clues to our ancestry -- for example, the pattern of genetic variants in an individual's DNA might be more common in people of European ancestry than it is in people of Asian ancestry. In most people, genetic variants in both our nuclear and mitochondrial DNA come from the same part of the world. However, in around one in 40 people in the UK sample, the mitochondrial DNA and nuclear DNA did not have matching ancestries. For example, the nuclear DNA could be European whilst the mitochondrial DNA is Asian. This happens because at some point in the maternal lineage, there was a mother from a different ethnic background.
"As mitochondrial DNA has a much higher mutation rate than nuclear DNA, mutation of the mitochondrial genome is a common occurrence. We wanted to study the natural selective forces determining the fate of these mutations," says Dr Ernest Turro of the Department of Haematology and the MRC Biostatistics Unit, and one of the senior authors of this study.
"Our statistical analysis suggests that, in people with differing mitochondrial and nuclear ancestries, recent mitochondrial mutations are more likely to have been seen before in populations with the same nuclear ancestry than the same mitochondrial ancestry."
Crucially, these results suggest that changes in our mitochondrial DNA are shaped by our nuclear DNA.
"This discovery shows us that there's a subtle relationship between the mitochondria and nuclei in our cells that we're only just starting to understand," says Professor Patrick Chinnery, Head of the Department of Clinical Neurosciences at the University of Cambridge and Wellcome Trust Principal Research Fellow. "What this suggests to us is that swapping mitochondria might not be as straightforward as just changing the batteries in a device."
The evidence mirrors that from previous studies in fruit flies and mice, where a mismatch between their mitochondrial and nuclear DNA affected how long the organisms lived for and caused cardiovascular and metabolic complications later in life (diseases in humans that might include heart disease and type 2 diabetes, for example).
The findings could have implications for mitochondrial donation treatment (also known as mitochondrial replacement therapy), says Professor Chinnery, who previously worked with the team at Newcastle University pioneering this treatment. This technique is now licenced for use in the UK to prevent the transmission from mother to child of potentially devastating mitochondrial diseases. It involves substituting a mother's nuclear DNA into a donor egg while retaining the donor's mitochondria.
"Mitochondrial replacement therapy is an important new treatment to enable mothers to have children free from terrible mitochondrial diseases, which arise because of severe mutations in mitochondrial DNA," says Professor Chinnery.
"Our work suggests we'll need to look carefully at this new treatment to make sure it does not cause unexpected health problems further down the line. It may mean that doctors will need to match the nuclear genome and mitochondrial genome of mitochondrial donors, similar to an organ transplant."
The team has now begun work looking at those people whose mitochondrial DNA does not match their nuclear DNA to see if this mismatch increases the likelihood that they will be affected by health problems later in life.
The research is the first major population study to arise from data collected as part of the 100,000 Genomes Project, which collects genetic data from patients through the NHS with the aim of transforming the way people are cared for and providing a major new resource for medical research. Pilot data for the study was collected through the NIHR Cambridge Biomedical Research Centre.
"The involvement of the 100,00 Genomes Project in major discoveries demonstrates the importance of large-scale, carefully collected datasets with whole genome sequences, which provide new biological insights and pave the way for major healthcare transformations," says Professor Mark Caulfield, Chief Executive of Genomics England and Co-Director of the William Harvey Research Institute at Queen Mary University of London.
Forensic genetics- why is mtDNA comparison sometimes better than nDNA comparison? - Biology
Who are your ancestors?
For most of us, that’s a tricky question.
We might usually know who our parents are, as well as their parents, but it can quickly become cloudy.
We get different stories from mum and dad, and far more when you begin tracing grandparents, great-grandparents and so on. Soon you’ve got 16. 32. 64 leads, and no way of knowing how precise each one is.
Ancestry records can certainly help you kick-start your journey into your roots.
They’re ace for recent history - spotting the moment your dear old grandad first moved to London, or the exact day your great-grandparents from Devon got married.
The main issue with these records is that they mostly just confirm what you already knew…
What about your more distant ancestors?
Now, if you're just starting to wonder about your heritage, look no further than DNA testing. ts popularity has exploded in recent years, with the number of keen genealogists signing up for testing kits projected to double in 2021. This DNA boom has made exploring ancestry all the more accessible to you and I, and is fast becoming a common topic of casual conversation.
The DNA market is projected to double in 2021—for the 5th year in a row.
It’s no surprise that DNA tests are in high demand. The things you learn from them are irresistible:
Ancestry – Everything we’ve ever known about our heritage has come from our parents and grandparents. A Heritage DNA test can tell you so much more about who you are and where you’re from. Most companies offer this basic service, but some are far better than others.
Family History – This is part and parcel of Ancestry. If you’re keen on family mysteries, a DNA test can help you solve them. If your parents also have their DNA tested, you can sometimes sort out which genes you received from each side of the family.
Community – Uncovering your genetic heritage also you a deeper connection to the places that you’re “from.” On top of this, some of the best DNA test companies will connect you with people who share pieces of DNA with you. Many people use this feature to discover long-lost relatives.
Health Risks – Some DNA tests can reveal unique traits embedded in your genetic code that may put you at risk for certain health conditions. This can help you alter your lifestyle to try and prevent them.
Family Planning – A DNA test can help you ascertain which genes you may pass onto your children, for better or worse.
With so many people clamoring to get their hands on the benefits listed above, more and more DNA testing companies have been rising to meet them.
Each DNA test has different strengths and weaknesses, and each company spends millions on marketing to make sure you’ve heard of them.
Yet how do you know which DNA test is right for you?
That’s why we’ve compiled 3 of the most popular DNA tests, along with user reviews and criteria.
Yet first, let’s get started on the 3 Essential Tips You Must Know Before Buying a DNA Test…
Mistake #1: Don’t buy a brand by how “popular” it appears to be.
Some brands have a great marketing team with a massive advertising budget. You might see/hear their ads everywhere. That’s because they’re spending millions to make sure you’ve heard of them.
Despite the great marketing, some of those companies have subpar services at best. They’re more concerned with making a sale than they are with actually delivering a quality product.
To be clear, a popular company with great marketing does NOT necessarily mean that they have a bad service. A couple of them offer services that are quite good! But you shouldn’t assume that they have a great service just because they appear to be popular, and you also shouldn’t write off lesser-known companies—some of these are new up-and-coming services who will eventually rise to the top of the market. They give you a unique opportunity to get in on the ground floor—and potentially get added value for your money.
Mistake #2: Don’t buy the cheapest OR the most expensive genetic test you can find.
The old adage “You get what you pay for” applies here. However, price is a tricky quality to navigate.
On the one hand, you don’t want something too cheap. It’s doubtful that the cheapest Ancestry DNA test is the best DNA test, and will tend to give you very little information. These tests will tell you things you already know about yourself, like which continent your genes came from. Sometimes cheap tests are simply trying to undercut the market—They may be selling at a loss up front with the hopes that customers will buy more from them later.
On the other hand, you don’t want to get hoodwinked by an over-priced DNA test. Expensive DNA tests may have a great product, but you can often find a product of similar (or even better) quality at a cheaper price.
All in all, it behooves you strike a comfortable middle ground. In our experience, roughly £80-90 is a fair price for a quality DNA test (give or take a few pounds). Aiming for a test around this amount will help ensure that you get a good product without over-paying.
Mistake #3: Don’t confuse “Accuracy” with “Precision.”
Almost every DNA test company on the market claims to be the “most accurate.” They’re not lying. DNA tests are typically 99.9% accurate. However, they’re often not precise.
What’s the difference between Accuracy and Precision?
For something to be “accurate,” it just needs to be true. If you have European heritage and your Ancestry DNA test comes back with results that simply say “European,” then it’s an accurate test. It’s giving you results that are true, even if they’re not detailed.
For something to be “precise,” it has to be an exact expression of details. The most precise DNA tests currently on the market have at least 20 unique regions they use in their Ancestry reports. The best companies will have multiple regions on each continent in their reports (rather than having most of their tested regions all on the same continent).
However, you have to be wary of companies overselling how precise their tests are. Some companies claim to have hundreds of regions in their reports. In our experience, this is bending the truth a bit. Most of them really test for 20-30 regions, but then list the names of countries that are contained within those regions without actually distinguishing between them.
For example, if a DNA test determines that someone has Iberian Ancestry, one of these companies might list Spain and Portugal underneath and count those as 2 “regions” for marketing purposes even though they don’t give a percentage breakdown for how much Iberian Ancestry is Spanish or Portugese.
In other words, some companies can be a little misleading with their marketing.
The Top 3 DNA Tests According to Customers Like You
Now you know what to look out for, we want to reveal which DNA test is the highest-rated according to customers like you on top review platforms like Facebook and Google.
Without further ado, here are the top 3 DNA Tests according to real customers.
Customers Tended to Rank DNA Tests According to these 8 Factors:
STRs vs. SNPs: thoughts on the future of forensic DNA testing
Largely due to technological progress coming from the Human Genome and International HapMap Projects, the issue has been raised in recent years within the forensic DNA typing community of the potential for single nucleotide polymorphism (SNP) markers as possible replacements of the currently used short tandem repeat (STR) loci. Our human identity testing project team at the U.S. National Institute of Standards and Technology (NIST) has explored numerous SNP and STR loci and assays as well as developing miniSTRs for degraded DNA samples. Based on their power of discrimination, use in deciphering mixture components, and ability to be combined in multiplex assays in order to recover information from low amounts of biological material, we believe that STRs rather than SNPs will fulfill the dominant role in human identity testing for the foreseeable future. However, SNPs may play a useful role in specialized applications such as mitochondrial DNA (mtDNA) testing, Y-SNPs as lineage markers, ancestry informative markers (AIMs), the prediction of phenotypic traits, and other potential niche forensic casework applications.
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Figure 1 and table 1 show the results of comparisons between nc and mt genes with different methods of phylogenetic analysis. Figure 1 plots bootstrap support values for nc versus mt genes for all of the phylogenetic methods that we employed. Nine of nine panels show comparisons between nc genes and mt protein-coding genes (filled squares) five of nine panels also show comparisons between nc genes and mt RNA genes (open squares). Data points that fall on the diagonal lines correspond to cases where nc and mt bootstrap support percentages are equivalent. Data points above the diagonal lines show cases where mt support exceeds nc support. Data points below the diagonal lines show cases where nc support exceeds mt support. Table 1 summarizes the numbers of cases for which nc bootstrap support was higher for a benchmark clade, the numbers of cases for which bootstrap support was equal, and the numbers of cases for which mt bootstrap support exceeded nc support. Table 1 also shows mean bootstrap support (for all benchmark clades) for both nc and mt genes with different phylogenetic methods.
For comparisons between mt protein-coding genes and nc genes, there were 106 benchmark clades that were scored across 24 pairwise comparisons between individual nc and mt data sets. Support deriving from the nc genes exceeded support deriving from the mt protein-coding genes in 90–100 of the 106 cases with different phylogenetic methods ( fig. 1 and table 1 ). A dense concentration of data points (filled squares) below the diagonal lines is evident in all of the panels in figure 1 and illustrates the superior performance of the nc genes. Mean bootstrap support was always higher for the nc genes ( table 1 ). Whereas mean mt support ranged from 30.7% (parsimony with zero weight at third codon positions) to 43.8% (minimum evolution–Γ+I), nc support ranged from 84.3% (minimum evolution–Γ+I) to 89.6% (minimum evolution–HKY85). The difference in mean bootstrap ranged from 40.5% (minimum evolution–Γ+I vs. minimum evolution–Γ+I) to 56.0% (parsimony vs. parsimony with zero weight at third codon positions).
Mitochondrial RNA genes performed better than mt protein-coding genes in comparisons against the nc genes. Benchmark clades were scored across eight pairwise comparisons between individual nc and mt RNA data sets. Bootstrap support scores were higher for nc genes in 31–33 of the 42 cases ( fig. 1 and table 1 ). Mean support scores for nc genes were higher than those for mt RNA genes with all phylogenetic methods. Nevertheless, differences between means were always less than those for comparisons between nc genes and mt protein-coding genes. Differences in mean support ranged from 16.5% to 24.3% ( table 1 ).
In all comparisons between the 3 or 6 concatenated nc genes and the 12 concatenated mt protein-coding genes from complete mt genomes, both nc and mt genes showed increased support for all of the benchmark clades as a function of the number of resampled nucleotides. However, the nc genes were always more efficient than the mt genes in recovering benchmark clades ( figs. 2 and 3 ). This was especially noticeable for Cetartiodactyla, with both parsimony ( figs. 2A and 3A ) and minimum evolution ( figs. 2B and 3B ). The more controversial clades (Afrotheria Hippopotamidae + Cetacea) were also recovered with greater efficiency with the nc data ( figs. 2 and 3 ).
Among the data sets that included marsupial outgroups, Δ values for all substitutions were highest for the three nc genes. Furthermore, these values exceeded sequence divergence values for the intraplacental comparisons for all three nc genes ( table 2 ). Among the mt protein-coding genes, Δ values (all substitutions) were always less than the intraplacental divergences ( table 2 ).
Among nc genes, transitions and transversions showed positive Δ values both at first + second and at third positions. For transversions, Δ values both at first + second and at third positions were higher than intraplacental divergences. For transitions, Δ values at first + second positions were always higher than intraplacental divergences at third positions, transition Δ values were higher than intraplacental divergences for A2AB but lower than intraplacental divergences for IRBP and vWF.
Among mt protein-coding genes, transversion Δ values were higher than intraplacental divergences at first + second positions but lower than intraplacental divergences at third positions. Transition Δ values at first + second positions were lower than intraplacental divergence values except in one instance—the caniform-to-feliform divergence for COII. Third-position transitions of mt protein-coding genes were saturated (mean Δ value = −0.83 table 2 ).
With the introduction of next-generation sequencing (NGS), ancient DNA (aDNA) studies on humans have progressed from analyses of a few hundred basepairs of mitochondrial DNA to large-scale population genomic studies [1–3]. The feasibility of such projects ultimately rely on having access to many ancient samples with sufficient biomolecule preservation. In particular, owing to the indiscriminate nature of 'shotgun' sequencing, the proportion of DNA that derives from the target species—the endogenous DNA content—is a crucial factor. Because DNA degrades over time , and skeletal tissues are invaded by microbes, the endogenous DNA content is often very low in ancient samples (<1%) making genome-scale analyses impossible or, at best, very expensive . Thus, recent aDNA research on human remains has focused on identifying new suitable substrates [6–9] and optimizing DNA extraction methods [6, 10, 11], thereby increasing the success rate for identifying samples that are suitable for genome-scale analyses. Owing to high levels of endogenous DNA, the inner part of the petrous bone and the cementum layer in teeth roots are currently recognized as the optimal substrates for such research.
The petrous bone, part of the temporal bone, is the hardest and most dense bone in the mammal body . The otic capsule surrounds and protects the sensory organs of the inner ear, collectively known as the vestibulo-cochlear organ. Gamba et al.  compared DNA preservation in petrous bones and teeth from seven individuals, revealing that the endogenous DNA content in petrous bone exceeded the teeth by 5.2-fold on average. However, the teeth used in that comparison were not sampled specifically from the cementum layer, which is crucial to optimize the endogenous DNA yield [6, 9]. Pinhasi et al.  refined the petrous bone sampling and recent studies have confirmed that this bone preserves aDNA extremely well, even when the samples are from warmer climates like Africa , the Near East , or Oceania .
However, there are only two petrous bones in each skull, and sampling one leaves a visible hole in the inferior part of the skull. For precious ancient skulls this can be problematic. Moreover, the otic capsule is formed by endochondral ossification by week 18 during gestation  and strontium isotope ratios in petrous bone can therefore provide information on the geographic location of the child during pregnancy , as well as childhood stable isotopic dietary signals . If the entire otic capsule is used for DNA extraction, this information is lost. If sampling involves removal of a large part of the petrous bone, information on sex  and childhood disease  may be lost as well. Likewise, tooth sampling can be just as damaging, in particular when only one or a few teeth are preserved. In addition to the obvious decrease in exhibitional value caused by removing teeth from a skull, morphological studies of teeth can provide important keys to population affinities , and analyses of tooth wear can yield insights into the diet and age of an individual [22, 23]. Strontium isotope analyses of the enamel holds information on the geographic location during childhood [24, 25], and tooth calculus has proven an excellent resource for studying ancient proteomics . We note, however, that morphological and biomolecular analyses of tooth crowns do not have to be compromised by DNA sampling, if only sampling the root e.g., Damgaard et al. , and petrous bones can be sampled with careful drilling without affecting the external temporal bone, which is the part mainly used in morphological studies.
Regardless, when doing irreplaceable damage to precious material it is important that the arguments are based on solid scientific evidence, so the pros and cons can be evaluated with local archaeologists or museum curators before sampling each skeleton. The current literature does not allow for a direct comparison of DNA preservation in petrous bone and tooth cementum, when both these substrates are sampled optimally. To remedy this, we present a comparative analysis of DNA preservation in tooth cementum and petrous bone obtained from ancient human skulls, from across a range of different ages and preservation environments. The samples span four major time periods and locations (Table 1) (i) Bronze Age from Central Asia, (ii) Viking Age from England, (iii) Iron Age and (iv) Historical period from Denmark. We include samples that appear both poorly and well preserved (defined in method section), as well as petrous bones that have been cremated. In prehistorical times cremation was a common funerary practice in many cultures incouding those of the pre-Roman Iron Age in Scandinavia . This ritual has often left the petrous bones as the only surviving biological remains, and therefore the only substrate on which to attempt an aDNA extraction. Although the DNA backbone fragments faster during heating , it is possible that the dense structure of the petrous bone could have protected the DNA even under these extreme conditions. We set out to test that.
Selection, nuclear genetic variation, and mtDNA
Weaver and Roseman (2005) review the case for Neandertal extinction based on ancient mtDNA. They present simulations that demonstrate that a Neandertal contribution to the modern human mtDNA pool is very unlikely. These simulations are simpler than those carried out by Currat and Excoffier (2004), but considering the publication schedule of Current Anthropology, they were probably completed earlier. Their conclusion is the same: if mtDNA has not undergone a selective sweep, then Neandertals almost certainly became extinct without issue.
But that's not especially news: indeed, it was strongly suspected even before ancient Neandertal mtDNA sequences were discovered (e.g. Manderscheid and Rogers 1996). The question has been, and remains, is human mtDNA actually neutral? Or is its recent pattern of variation in living humans the result of recent selection within the human lineage? If there was a selective sweep in humans, then the mtDNA of Neandertals shouldn't look like modern human mtDNA for that reason. This wouldn't prove that Neandertals contributed other genes to later people, but it would make their mtDNA variation irrelevant to their ultimate fate.
Unlike most papers on the topic, Weaver and Roseman (2005) review this issue. On the basis of their review, they conclude that mtDNA is almost certainly neutral. Here's how they put it:
That does indeed seem unlikely, so it might seem that they have made a solid case.
But -- unsurprisingly to those who read the weblog often -- I think they have left out many important aspects of the story. There is a strong case for mtDNA selection, but Weaver and Roseman (2005) omit much of the data that point to that conclusion. And some of the data that they include actually indicates quite the opposite of what they claim.
They make a very common assumption -- one that is widespread in the human genetics literature -- but one that is nonetheless wrong: every expansion is the same expansion. A review of the sources that Weaver and Roseman (2005) cite shows quite the opposite: expansions are not all alike, and expansions estimated for nuclear DNA may actually prove that mtDNA was selected.
This is a very long post, and I have hidden most of it beneath the fold. Click on in if you want my take on selection on mtDNA.
Is it reasonable to think that mtDNA was selected?
Before embarking on a review of Weaver and Roseman's argument, it is important to tackle one central question: Is it even reasonable to think that mtDNA was selected?
If this were an unreasonable idea, there would be no point to arguing for it. So what reason might one have to think that a selective sweep of mtDNA might have happened?
Within the past 30,000 to 1 million years, human populations have changed radically in longevity (Caspari and Lee 2004), brain size (Lee and Wolpoff 2003 Ruff et al. 1997), diet, and energetics (Leonard and Robertson 1997 Sorensen and Leonard 2001). Human mtDNA variants have been found to be associated with chronic diseases of aging , brain disorders (Zhu et al. 2004), performance in athletes (Niemi and Majamaa 2005), and longevity itself (Niemi et al. 2005). The present pattern of variation also appears to be correlated with climate (Ruiz-Pesini et al. 2004), and may affect the dietary energetics and insulin metabolism (Lowell and Schulman 2005).
Simply put, variation in mtDNA is a strong target for further research into the effects of aging, metabolism, and disorders of the brain for a reason: it impacts all these areas strongly.
Together, these facts strongly suggest that human mtDNA may have undergone multiple adaptive substitutions within the past million years. They don't prove that such selection happened, but they give abundant reason to suppose that it might have. Indeed, Ruiz-Pesini et al. (2004) suggest that adaptive selection has happened on mtDNA in some regions of the world in recent times. This suggestion is fully consistent with -- and even foreshadows -- the idea that mtDNA underwent many adaptive substitutions during human evolution.
In fact, this is exactly the same logic by which many nuclear genes have been asserted to have been positively selected recently in human evolution. Consider the case of FoxP2. Enard et al. (2002) proposed that this gene had undergone a selective sweep within the past 200,000 years in humans, and Klein (2002) made it the centerpiece of his argument that language had evolved recently at the origin of modern humans. Like mtDNA, FoxP2 is strongly out of mutation-drift equilibrium. But human FoxP2 shows many fewer amino acid substitutions compared to chimpanzees than does human mtDNA (2 for FoxP2, 50-60 for mtDNA), meaning that the possibility of selection on human mtDNA should be greater, not less. And FoxP2 is only one functional gene mtDNA contains 13 peptide-coding regions (Arnason et al. 1996), selection on any one of which would affect the entire molecule.
So what exactly is the difference that leads the same people to say that FoxP2 is selected and mtDNA is not? There is no statistical test of selection that shows FoxP2 to be selected and mtDNA not. Human mtDNA completely fails standard tests of neutrality such as Tajima's D (Merriwether et al. 1991), the ratio of synonymous to nonsynonymous substitutions (Wise et al. 1998), and comparison of within-species to between-species diversity (Wise et al. 1997).
In fact, the only difference I can find is that there is a literature that assumes mtDNA neutrality and attempts to use its variation to determine what kind of neutral event could explain its variation without selection. The only kind of event that suffices is a massive expansion of the human population -- estimated to be a hundred-fold or greater -- from an initial effective population size of fewer than 10,000 individuals to many millions (Harpending et al. 1998 1993 Sherry et al. 1994). This event is proposed to have occurred anytime from 40,000 years ago to as much as 150,000 years ago or longer -- although the data indicates that it must have occurred earlier in Africa and later in Europe and East Asia.
There is no history of such an assumption for FoxP2 (although it might equally be suggested to represent such an event), therefore its variation is logically assumed to represent a selective sweep.
Thus, the issue of mtDNA selection cannot be separated from the issue of population expansion. It should be noted that an expansion of the human population does not disprove the hypothesis that a selective sweep occurred, but it does provide an alternative hypothesis that might explain the pattern of variation (although not the involvement of mtDNA in energy metabolism, diseases of aging, brain disorders, etc.).
Happily, we can test this alternative. Other genes, in particular, all neutral regions of the nuclear genome, must reflect the same demographic history as mtDNA. Thus, these genes should also show evidence of a massive population expansion.
What's an order of magnitude between friends?
Here's what Weaver and Roseman (2005:681-682) say about nuclear genomic evidence for population expansions:
The microsatellite study they cite is the review by Zhivotovsky et al. (2003). Here's what Weaver and Roseman (2005:681) say:
Here are the actual figures from Zhivotovsky et al. (2003:1179):
|Estimated expansion time (kya)||4.3||35.3||25.3||17.6|
|Effective population size before growth||2609||1883||1760||1688|
In short, these populations are all estimated to have expanded from an effective size of less than 2000 at a time between 17,000 and 35,000 years ago (except hunter-gatherers, who are estimated to have expanded 4300 years ago).
Weaver and Roseman (2005:681) cite a wide range of estimates for mtDNA expansion times: from 200,000 to 40,000 years ago. This range of estimates is wide mainly because of uncertainty about the mtDNA mutation rate. In their simulations, Weaver and Roseman (2005:679) assume a growth starting at 40,000 years ago this is at or near the latest possible date of expansion for Europe only from other studies (e.g. Harpending et al. 1993 Sherry et al. 1994). Weaver and Roseman (2005:679) assume a preexpansion female effective size of 1000.
Compared to these mtDNA estimates, the microsatellite estimates are not so bad. They are more recent than the most recent possible for mtDNA by a factor of two, but their preexpansion population size is consistent.
What about the SNPs? The autosomal and X chromosomal SNP study they refer to is Marth et al. (2004). Weaver and Roseman (2005:681) say this:
Here are the actual figures from Marth et al. (2004:360), for the best-fit models (bottleneck for European and Asian, expansion for Africa), with generations converted to years (assuming 20-year generations):
|Original population size||10,000||10,000||10,000|
|Final population size||20,000||25,000||18,000|
The sharp-eyed will notice a couple of things about these tables. First, the initial population size between the microsatellite estimates and the SNP estimates is different by an order of magnitude. Now, that has an immense effect on the coalescence times expected for autosomal genes. The initial effective size of 10,000 in the SNP study recognizes that autosomal genes have coalescence times ranging from as little as 200,000 years (or less) to as ancient as 3 million years (or older). This range of dates is simply inconsistent with a long-term effective size of 1000-2000. This inconsistency alone means that the microsatellite estimates must be wrong.
This is a more severe problem than it might appear, because the signature for population expansion from the microsatellites requires a very, very small initial population size. This is because the estimates are based on the variance of allele size taken among sites -- meaning that different loci must have nearly exactly the same coalescent time to show a sign of population expansion (Kimmel et al. 1998 Zhivotovsky et al. 2000). The methods used to substantiate an expansion on microsatellite data simply lack the power to detect an expansion from a initial size as great as 10,000.
In other words, expansions are not all alike: the "expansions" estimated for the SNPs lie outside the statistical power of microsatellites entirely the expansions estimated to explain microsatellite data are absolutely inconsistent with the large initial population size estimated for SNP data. Both these kinds of loci are autosomal: their evolution -- if neutral -- must follow precisely the same constraints.
Of course, the dates are also different, by a factor of three or more. But the other key difference is that these SNPs indicate not a simple expansion, but a bottleneck.
Can this bottleneck be consistent with the diversity of mtDNA? On the surface, it might seem that a post-bottleneck expansion and an expansion are the same thing. And Fay and Wu (1999) showed that certain kinds of bottlenecks might be consistent with mtDNA disequilibrium and nuclear DNA equilibrium. But the bottleneck estimated by Marth et al. (2004) is much less severe than the simulations of Fay and Wu (1999): [CORRECTION 9/5/05: these bottlenecks simulated by Fay and Wu (1999) are] three times longer (30,000 years) and involves one-half to one-third the population size during the bottleneck. In contrast, the simulations that are most consistent with the estimates of Marth et al. (2004) show that no large effect is expected upon mtDNA variation.
The same conclusion may be drawn from the simulations presented by Ambrose (1998), who tested whether a bottleneck associated with the Toba volcanic event 71,000 years ago might be consistent with human mtDNA variation. These simulations found that such a bottleneck could not be excluded by mtDNA variation. But they also found that the bottleneck could not by itself explain the pattern of mtDNA variation. Instead, a more ancient reduction in population size must have occurred, if mtDNA is neutral. Such a reduction has not been found for nuclear genomic data.
So, the evidence for population expansion from nuclear DNA is not consistent with mtDNA variation. Nor are estimates taken from microsatellites consistent with those taken from nuclear SNPs. All bottlenecks and expansions are simply not alike. Weaver and Roseman (2005) imply that these different sources of evidence are converging on a single answer. In fact, they are diverging from each other.
Why isn't an expansion just an expansion?
It is important to keep in mind the parameters of the possible models, to understand why evidence for expansions is not all alike. The simplest model of ancient demography is a one-parameter model: a single population size, unchanging over time back to infinity. This is the hypothesis of "no expansion", and it is in fact an assertion: the assertion that a model with more parameters does not explain the data better than the one-parameter model.
The next simplest model of demography is a three-parameter model. The parameters are the population size before a change, the population size after the change (or alternately, the magnitude of the change), and the time that the change happened. (A two-parameter model would include only time and magnitude of change as long as the actual size of the population is important to us we are stuck with the third parameter.) This kind of model is often called a "two-epoch" model, meaning that the population was one size for some period of time, and another size for a second period of time. The only two-epoch demographic models are simple expansions and crashes.
A population crash causes genetic drift to increase -- and genetic drift tends to eliminate rare alleles from the population. So populations that have undergone a crash are expected to show a deficit of rare (low-frequency) alleles, or a surplus of high-frequency alleles. (This, by the way, is also the prediction of balancing selection.)
In contrast, a population expansion reduces the strength of genetic drift, meaning that rare (new) alleles should be more common than expected if population size had been constant. It takes a while for these new alleles to appear, so the strength of evidence depends on the time of the expansion -- that third parameter.
Now, let's stop to notice a couple of things. First of all, microsatellites are different from SNPs in that SNPs are often unique mutations, whereas microsatellite alleles are length polymorphisms that can be arrived at by lots of different mutations. This means that "rare" microsatellite alleles do not provide the same kind of evidence for expansion that rare SNPs do. In practice, estimates of ancient demography from microsatellite data do not depend on rare alleles at all instead, they depend on the pattern of allele size variation among different microsatellite loci. That's one reason why the results of the microsatellite and SNP studies look so different: they are using different, apparently incommensurable, observations of variation.
Second, the consideration of the two-epoch model shows two options: a population crash or a population expansion. But one of these -- the crash -- is extraordinarily unlikely to be true for humans.
For one thing, the human population really did expand in size recently. Not only was there an incredible explosion of populations after the advent of agricultural subsistence, but also there is good archaeological evidence for substantial population expansions in the Late Pleistocene (e.g. Stiner et al. 2000).
For another, the human population is subdivided into many populations -- a structure that itself increases the proportion of rare alleles in the global population (Ptak and Przeworski 2002). So a population crash is essentially not an option. If the data significantly refute the one-parameter model (i.e. constant size), then expansion is the only kind of three-parameter model at play.
In other words, human genetic data are biased. They ought to show evidence of strong population expansion. They ought to be inconsistent with constant population size back to infinity.
So why, in so many cases, aren't they?
No expansion? Are you kidding?
As Weaver and Roseman (2005:681) note, Ptak and Przeworski (2002) reviewed more than 400 genomic regions and found no substantial evidence for expansion. And the "expansion" found by Marth et al. (2004 likewise Marth et al. 2003) is not the manyfold population growth that actually happened: it is an expansion from 10,000 people to 18,000 (at a minimum) or 25,000 (at a maximum) (!). As we have seen, only microsatellite data look remotely like the magnitude of human population growth, but they are completely wrong about the initial size and time of expansion.
There is a simple answer: the proportion of rare alleles is affected by things besides population size. As Ptak and Przeworski (2002), population subdivision is one of these. As Polanski and Kimmel (2003) note, ascertainment bias may be another. And natural selection is very likely to be another influence on the proportion of rare alleles -- even at "neutral" sites, considering the effects of linkage to selected sites (Gillespie 2000).
And as discussed by Marth et al. (2004), nuclear SNP data actually do not fit the three-parameter model. For non-African populations, they fit a five-parameter model: a bottleneck. This model reflects a mix of observations at different sites: there is an excess of low-frequency (rare) alleles, at the same time there is an excess of high-frequency alleles (Sherry 1996), as compared to both the three-parameter and one-parameter models. This excess of common alleles does not greatly reduce the appearance of a slight expansion in the three-parameter model, so it cannot account for the mismatch between genomic variation and archaeological data. But it may also result from the effects of selection, as certain SNPs may have been driven to high frequencies by positive or balancing selection.
Eswaran et al. (2005) suggest another explanation for the signature of a bottleneck in nuclear SNPs. They find that such a pattern is the expected result of the assimilation of archaic human lineages into an expanding modern human population. This pattern contrasts strongly with the expected signature of population expansion under a replacement scenario of modern human origins. They conclude that archaic assimilation is more consistent with the pattern of genomic SNP data than replacement.
As we can see, the explanation of nuclear genomic variation requires the consideration of many complexities that may affect the outcome. These complexities, taken together, mean that nuclear DNA variability bears no simple causal relationship with ancient population sizes. In particular, it cannot replicate the pattern of Upper Paleolithic and Holocene expansions that are reconstructed from archaeological data. Instead, estimates based on genetics (under assumptions of neutrality in up to five-parameter models) are generally more than an order of magnitude different.
It is therefore incorrect to say that nuclear genomic evidence is consistent with mtDNA variation. In fact, it currently appears to be inconsistent, although it is fairer to say that we do not know the relevance (if any) of genomic variation to demographic reconstruction. Strikingly, one of the few ways to make these different sources of data consistent with each other may be to require the survival and proliferation of nuclear gene lineages from archaic humans (Eswaran et al. 2005). Populations did grow, and and this growth may have affected the pattern of mtDNA variation. But the inconsistencies are great enough that they cannot currently be explained by demography alone.
Ancient genes and geography: the data Weaver and Roseman omit
Weaver and Roseman (2005) substantiated their assertion that mtDNA is neutral by using four primary references: Marth et al. (2004), Zhivotovsky et al. (2003), Ptak and Przeworski (2002), and Pritchard et al. (1999). As reviewed above, one of these (Ptak and Przeworski 2002) contradicts their argument, as do two others mentioned more briefly (Pereira et al. 2001 Hammer et al. 2003).
But there are other relevant sources of information not included in the paper. Three of them are absolutely critical, since they bear directly on the hypothesis that genetic material from archaic humans survives in present human populations.
The first category of "missing information" are the many studies of gene-geography relationships by Alan Templeton and colleagues (e.g., Templeton 2002). Based on the examination of the geographic variability of a dozen nuclear genes, these studies have concluded that an Out of Africa replacement of archaic humans cannot explain the pattern of human genetic diversity. Instead, the studies find significant evidence for ancient genetic structure including Europeans and East Asians. Templeton has argued (2002) that the pattern of mtDNA (and Y chromosomal) variation may represent one recent migration among many out of Africa but the data are also consistent with a recent selective sweep. These data conclusively refute the hypothesis that no archaic gene lineages survived into living human populations.
Templeton's studies have been critiqued on the grounds that they may not actually distinguish survival of archaic gene lineages outside Africa from survival of archaic lineages inside Africa. In other words, it has been claimed (Pearson 2003 Eswaran et al. 2005) that ancient population structure within Africa might mimic the survival of gene lineages from outside Africa. Eswaran et al. (2005) show that this scenario is likely not the case, as nuclear genomic data apparently reflect the survival of archaic non-African lineages. But this equivocation bears little importance to the explanation of mtDNA: even the survival of archaic lineages from within Africa challenges the idea that mtDNA variation reflects the expansion of one small African population and the displacement of others. Instead, survival of archaic African lineages suggests that the ancient population size of Africans was effectively much larger (perhaps many orders of magnitude larger) than a neutral mtDNA hypothesis would admit. Together Templeton's work and the analysis of Eswaran et al. (2005) indicate that the majority of genomic loci preserve allelic variation that originally characterized archaic human populations.
The second category of evidence missing from Weaver and Roseman (2005) also bears on this issue of archaic survival. In addition to the genomewide analyses and Templeton's phylogeographic studies, both of which suggest the survival of a large proportion of archaic gene lineages, recent work has uncovered several genes that cannot be accommodated within the framework of a recent mtDNA expansion and replacement of archaic humans. These genes include (but are not limited to) the region around Xp21.1 (Garrigan et al. 2005), the Xp/Yp and 12q telomeric regions (Baird et al. 2000), and an inversion on 17q21.31 (Stefansson et al. 2005). Several other loci were discussed at the 2005 AAPA meetings, and I know of a few more that are in press.
In short, genomic data are not consistent with mtDNA neutrality, and a growing number of detailed studies have documented loci that represent the survival (and proliferation) of archaic human gene lineages. Much of this literature on specific loci has emerged in the last year it is no surprise that it is missing from Weaver and Roseman (2005).
But Templeton's analyses have been well known for years, and they bear directly on the issue. They are mentioned by Weaver and Roseman (2005:677) only as evidence that anthropological geneticists "favor a predominantly extra-European origin for the earliest modern populations in Europe" (. ).
The third category of missing information is the fossil and archaeological record. According to Weaver and Roseman (2005:682):
It is therefore striking that the paper includes no acknowledgement of the fossil and archaeological evidence that supports Neandertal-modern reproductive continuity. This evidence includes (but is not limited to):
- The persistence of Neandertal traits in post-Neandertal populations (Frayer 1993 Duarte et al. 1999 Wolpoff et al. 2001 Trinkaus et al. 2003). Trinkaus (2005:218) concludes that the model of no interbreeding between Neandertals and modern humans is "intellectually dead."
- The intergradation of Neandertal and contemporary populations, illustrated by their substantial morphological overlap in West Asia (Kramer et al. 2001 McCown and Keith 1939).
- Shared directionality of morphological evolution in Neandertals and contemporary populations (Hawks and Wolpoff 2001).
- The cognitive continuity of Neandertals and succeeding populations, evidenced by their substantially shared technical and symbolic ability (d'Errico 2003).
It seems clear that no genetic model that excludes a role for Neandertal genetic persistence can be considered to be "integrated" with these archaeological and fossil observations. Certainly considerable disagreement exists about the level of Neandertal contribution to later Europeans (as well as the level of Upper Paleolithic contribution to the more recent European gene pool). But evidence of intermixture is clear and recognized even by those who suspect that the actual level of such intermixture was low (Bräuer et al. 2004). Together with the full pattern of genomic evidence, it seems clear that such intermixture is a potent explanation for the evolutionary pattern of the early Upper Paleolithic in Europe, as well as other regions during the Late Pleistocene.
The bottom line
The issue here is not whether a population expansion occurred in the Late Pleistocene and Holocene. It certainly did. But does this expansion by itself explain the distinctive pattern of human mtDNA variation? And if so, does the fate of the Neandertals hinge on this demographic hypothesis?
A consideration of a fuller set of genomic data indicates that the answer to both these questions is no.
Human mtDNA has very likely been under positive selection. The evidence for this selection is as strong as for nearly any other selected locus. Although the specific target of the most recent selective sweep has not yet been identified, the same is true of other genes that are believed to have been under selection, such as FoxP2. The pattern of variation cannot be explained by population expansion, because other genomic regions are either inconsistent with mtDNA, inconsistent with each other, or inconsistent with any expansion at all.
Determining whether Neandertals particularly contributed genetic material to the living human population is a challenge. Even if clear evidence of archaic lineages is found, it is difficult to substantiate that these lineages were found in a particular region of Europe over 40,000 years ago.
Yet, substantial evidence of archaic lineages has been found. There is no question that some -- perhaps most -- human genes preserve allelic variation from archaic human populations.
The morphological and archaeological evidence suggest strongly that Neandertal genetic lineages survived into later Upper Paleolithic populations. Ultimately, the genetic test of Neandertal survival may be carried out by finding nuclear DNA sequences from Neandertal fossils themselves. Until that time, we can say only that some Neandertal contribution to the modern human nuclear gene pool is consistent with the known evidence.
Ambrose SH. 1998. Late Pleistocene human population bottlenecks, volcanic winter and differentiation of modern humans. J Hum Evol 34:623-652.
Arnason U, Gullberg A, Janke A, Xu X. 1996. Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J Mol Evol 43:650-661.
Baird DM, Coleman J, Rosser ZH, Royle NJ. 2000. High levels of sequence polymorphism and linkage disequilibrium at the telomere of 12q: Implications for telomere biology and human evolution. Am J Hum Genet 66:235-250.
Bruer G, Collard M, Stringer C. 2004. On the reliability of recent tests of the Out of Africa hypothesis for modern human origins. Anat Rec 279A:701-707.
Caspari R, Lee SH. 2004. Older age becomes common late in human evolution. Proc Natl Acad Sci U S A 101:10,895-10,900.
Currat M, Excoffier L. 2004. Modern humans did not admix with Neanderthals during their range expansion into europe. PLoS Biol 2:e421.
d’Errico F. 2003. The invisible frontier: A multiple species model for the origin of behavioral modernity. Evol Anthropol 12:188-202.
Duarte C, Maurcio J, Pettitt PB, Souto P, Trinkaus E, van der Plicht H, Zilhao J. 1999. The early Upper Paleolithic human skeleton from the Abrigo do Lagar Velho (Portugal) and modern human emergence in Iberia. Proc Natl Acad Sci U S A 96:7604-7609.
Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monasco AP, Pbo S. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-872.
Eswaran V, Harpending H, Rogers AR. 2005. Genomics refutes an exclusively African origin of humans. J Hum Evol 49:1-154.
Fay JC, Wu CI. 1999. A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol Biol Evol 16:1003-1005.
Frayer DW. 1993. Evolution at the European edge: Neanderthal and Upper Paleolithic relationships. Prehistoire Europeenne 2:9-69.
Garrigan D, Mobasher Z, Severson T, Wilder JA, Hammer MF. 2005. Evidence for archaic Asian ancestry on the human X chromosome. Mol Biol Evol 22:189-192.
Gillespie JH. 2000. Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155:909-919.
Hammer MF, Blackmer F, Garrigan D, Nachman MW, Wilder J. 2003. Human population structure and its effects on sampling Y chromosome sequence variation. Genetics 164:1495-1509.
Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST. 1998. Genetic traces of ancient demography. Proc Natl Acad Sci U S A 95:1961-1967.
Harpending HC, Sherry ST, Rogers AR, Stoneking M. 1993. The genetic structure of ancient human populations. Curr Anthropol 34:483-496.
Hawks J, Wolpoff MH. 2001. The accretion model of Neandertal evolution. Evolution 55:1474-1485.
Kimmel M, Chakraborty R, King J, Bamshad M, Watkins W, Jorde LB. 1997. Signatures of population expansion in microsatellite repeat data. Genetics 148:1921-1930.
Klein R, Edgar B. 2002. The dawn of human culture. New York: John Wiley and Sons.
Kramer A, Crummett TL, Wolpoff MH. 2001. Out of Africa and into the Levant: Replacement or admixture in Western Asia. Quaternary International 75:51-63.
Lee SH, Wolpoff MH. 2003. The pattern of evolution in Pleistocene human brain size. Paleobiology 29:186-196.
Leonard WR, Robertson ML. 1996. On diet, energy metabolism and brain size in human evolution. Curr Anthropol 37:125-128.
Leonard WR, Robertson ML. 1997. Rethinking the energetics of bipedality. Curr Anthropol 38:304-309.
Lowell BB, Shulman GI. 2005. Mitochondrial dysfunction and Type 2 diabetes. Science 307:384-397.
Manderscheid EJ, Rogers AR. 1996. Genetic admixture in the Late Pleistocene. Am J Phys Anthropol 100:1-5.
Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, Phan L, Czabarka E, Murvai J, Cutler D, Wooding S, Rogers A, Chakravarti A, Harpending HC, Kwok PY, Sherry ST. 2003. Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci U S A 100:376-381.
Marth GT, Czabarka E, Murvai J, Sherry ST. 2004. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166:351-372.
McCown TD, Keith A. 1939. The stone age man of Mount Carmel: The fossil human remains from the Levalloiso-Mousterian, volume 2. Oxford: Clarendon Press.
Merriwether DA, Clark AG, Ballinger SW, Schurr TG, Soodyall H, Jenkins T, Sherry ST, Wallace DC. 1991. The structure of human mitochondrial DNA variation. J Mol Evol 33:543-55.
Niemi AK, Majamaa K. 2005. Mitochondrial DNA and ACTN3 genotypes in Finnish elite endurance and sprint athletes. Eur J Hum Genet 13:965-969.
Niemi AK, Moilanen JS, Tanaka M, Hervonen A, Hurme M, Lehtimki T, Arai Y, Hirose N, Majamaa K. 2005. A combination of three common inherited mitochondrial DNA polymorphisms promotes longevity in Finnish and Japanese subjects 13:166-170.
Pearson O. 2003. Has the combination of genetic and fossil evidence solved the riddle of modern human origins? Evol Anthropol 13:145-159.
Pereira L, Dupanloup I, Rossser ZH, Jobling MA, Barbujani G. 2001. Y-chromosome mismatch distributions in Europe. Mol Biol Evol 18:1259-1271.
Polanski A, Kimmel M. 2003. New explicit expressions for relative frequencies of single-nucleotide polymorphisms with applications to statistical inference on population growth. Genetics 165:427-436.
Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. 1999. Population growth of human Y chromosomes: A study of Y chromosome microsatellites. Mol Biol Evol 16:1791-1798.
Ptak SE, Przeworski M. 2002. Evidence for population growth in humans is confounded by fine-scale population structure 18:559-563.
Ruff CB, Trinkaus E, Holliday TW. 1997. Body mass and encephalization in Pleistocene Homo. Nature 387:173-176.
Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. 2004. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303:223-226.
Sherry S. 1996. Estimating human effective population sizes with genetic models incorporating demographic fluctuation. Ph.D. thesis, Pennsylvania State University.
Sherry ST, Rogers AR, Harpending H, Soodyall H, Jenkins T, Stoneking M. 1994. Mismatch distribution of mtDNA reveal recent human population expansions. Hum Biol 66:761-775.
Sorensen MV, Leonard WR. 2001. Neandertal energetics and foraging efficiency. J Hum Evol 40:483-495.
Stefansson H, Helgason A, Steinthorsdottir GTV, Masson G, Bernard J, Baker A, Jonasdottir A, Ingason A, Gudnadottir VG, Desnica N, Hicks A, Gylfason A, Gudbjartsson DF, Jonsdittir GM, Sainz J, Agnarsson K, Birgisdottir B, Ghosh S, Olafsdottir A, Cazier JB, Kristjansson K, Frigge ML, Thorgeirsson TE, Gulcher JR, Kong A, Stefansson K. 2005. A common inversion under selection in Europeans. Nature Genet 37:129-137.
Stiner MC, Munro ND, Surovell TA. 2000. The tortoise and the hare: Small-game use, the broad-spectrum revolution, and Paleolithic demography. Curr Anthropol 41:39-73.
Templeton AR. 2002. Out of Africa again and again. Nature 416:45-51.
Trinkaus E. 2005. Early modern humans. Annu Rev Anthropol 34:207-230.
Trinkaus E, Ştephan Milota, Rodrigo R, Mircea G, Moldovan O. 2003. Early modern human cranial remains from the Peştera cu Oase, Romania. J Hum Evol 45:245-253.
Weaver AH. 2005. Reciprocal evolution of the cerebellum and neocortex in fossil humans. Proc Natl Acad Sci U S A 102:3576-3580.
Wise CA, Sraml M, Easteal S. 1998. Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees. Genetics 148:409-421.
Wise CA, Sraml M, Rubinsztein DC, Easteal S. 1997. Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees. Mol Biol Evol 14:707-716.
Wolpoff MH, Hawks J, Frayer DW, Hunley K. 2001. Modern human ancestry at the peripheries: A test of the replacement theory. Science 291:293-297.
Zhivotovsky LA, Bennett L, Bowcock AM, Feldman MW. 2000. Human population expansion and microsatellite variation. Mol Biol Evol 17:757-767.
Zhivotovsky LA, Rosenberg NA, Feldman MW. 2003. Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet 72:1171-1186.
Zhu X, Smith MA, Perry G, Aliev G. 2004. Mitochondrial failures in Alzheimer’s disease. American Journal of Alzheimers Disease and Other Dementias 19:345-352.
Updated: September 5, 2005
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Similarities Between DNA Fingerprinting and DNA Profiling
- These are two molecular methods involved in the identification of individuals depending on their genetic makeup.
- Moreover, they focus on polymorphic regions of the genome that are mainly minisatellites or microsatellites.
- PCR is one of the main techniques used in both methods.
- Both methods can use biological samples such as blood, hair, semen, etc. for the extraction of DNA.
Forensic Science: Real Practice vs. Television Drama
MURRAY: Hi, everyone, and welcome to our chat session! I’m glad you’re here and hoping to answer as many of your questions as possible. I’d like to begin by thanking The Great Courses and its awesome staff for setting up this opportunity for us. Let’s get started!
CONCERNEDINCA: Improved data (facts) is always desirable. What are your views on which has improved more due to recent advances in forensic science, public safety & law enforcement efforts or justice for those falsely accused/convicted of crimes?
MURRAY: I don’t think we’ve managed to improve the data or facts so much as we have found better ways to uncover them and assess them. I would like to hope that advances in forensic science are improving public safety and law enforcement, while at the same time not compromising our rights. However, my personal interest has leaned more toward justice for those falsely convicted of crimes – in fact, my most recent book is about that topic. DNA technology has revolutionized much in the way of forensics!
NORMXXX: How accurate is most of the forensic evidence? There has been much evidence recently that most if not all such evidence is suspect, even techniques in unquestioned use for many decades, e.g. fingerprint ids, bite marks, blood spatter…
MURRAY: Obviously we always hope our evidence is good, but recent investigations into certain techniques – such as bitemarks, as you suggest – have shown them to be problematic. While I can’t agree with the analogy of a Rorschach test, the 2009 National Academy of Science’s Report on the state of forensics has prompted some great inquiry into techniques. I see this as a very positive thing, and look forward to what the future will bring.
Right now the nation’s forensic scientists are working on new standards that will take us forward, and it’s very exciting. Some methods did need analysis, but also some practitioners are not trained as well as they could or should be. These new standards will be about both training and methodology.
BRADLEY STEEG: Gun control is a hot topic. Do you have any recommendations on how we might reduce criminal gun violence through legislation or other methods in the future? I’m trying to decipher which policies have a good chance of working and which ones are less effective.
MURRAY: Wow, that’s a big topic to tackle, and you are right, our country is in the midst of a major epidemic of criminal violence involving guns. People are so tired of the killing, but yet both sides have strong feelings and arguments. I don’t have the answers, and in fact, the issue is so polarizing that it’s difficult to even discuss. For instance, I had talked with my publisher about writing a book for young adults on gun violence, and really had to consider whether I wanted to do that.
For now, the book is on hold. It’s a vastly important topic, but so polarizing. I wish I had the answers, but I don’t.
MIKE GNITECKI: How often do you develop an initial theory based on your first impression, versus how often it comes purely from analyzing evidence deeply?
MURRAY: When I analyze skeletal remains, I always do a thorough “first impression” take first (I guess that’s kind of an oxymoron, but…). I like to use my training and impressions BEFORE I tackle the more analytic aspects. If I did the assessments the other way around (i.e. measure then observe), the analytics could bias my judgment. Does that answer your question?
ALAN ROCKER: “Speculating in the absence of data is a capital mistake.” Sherlock Holmes.
MURRAY: Don’t misunderstand, I do my visual assessments FIRST to try and avoid bias (and sometimes my visual assessments are more accurate than the measurements particularly if remains are not stereotypical). I fear if the metric analyses are done first, they would potentially cloud my judgment. So these are not “speculations” so much as subjective methods that I confirm (or refute) with analytical methods subsequently.
PROTRAINER: What is the minimum education required to be able to become a Forensic Investigator?
MURRAY: That depends on what type of forensic investigator. There are so many different fields within the overall umbrella of forensics. Some law enforcement officers and death investigators are doing forensic investigations with a bachelor or even associate’s degree. However, more specialized fields require more training. Forensic pathologists, for example, go through medical school, a fellowship, and beyond. I have a bachelor’s, master’s, and a PhD.
At present, you must have a PhD to be a board-certified forensic anthropologist. Different fields have different requirements, and interestingly, some don’t have any official “schools” for them (like handwriting analysis), but are more “on the job” training and/or residencies/apprenticeships. I talk a lot about the preparation for various fields in my first series for The Great Courses.
ROY B: Do you have any favorite fiction/crime writers that really do a good job getting the forensics right?
MURRAY: I used to read a lot of Patricia Cornwell, and of course my friend and colleague, Kathy Reichs is a great author. Both are experienced practitioners, so very true-to-life. I had a great experience speaking for a mystery writer’s conference, and there seem to be a lot of up-and-coming authors. But my go-to books are often true-crime stories, not novels. Anything about past forensic mysteries and investigations.
MATT REDLE: In your opinion, what is the most important effort, currently underway, to improve the quality of forensic science?
MURRAY: Subsequent to the previously-mentioned 2009 report on the state of forensic science, the National Institute of Standards and Technology has organized working groups to develop standards to ensure that what we do is impeccably valid work. This is a huge effort and involves many different practitioners and disciplines. Exciting times in forensics!
JAMES M TEMPLE: How do you feel about the CSI shows on TV. I Laugh when I see a civilian CSI tech conduct investigations, question witnesses and suspects then turn to a sworn officer or turn to a police officer and tell them to lock that person up?
MURRAY: Well, I think they want us to follow a cast of characters more so than the science in those shows. It’s ludicrous when they have the lab people questioning witnesses, talking to family members, carrying a gun and badge, and so forth. Some of the shows are definitely better than others. I have to say that most of the professionals do not watch them though.
PROTRAINER: You agree with Ms. Cornwell on the identity of Jack the Ripper?
MURRAY: A lot of people have a lot of Ripper theories – to each his own. That is one COLD case, and I don’t think we will ever resolve it. I do have to say that the bogus claim last year really had some people excited. Big splash in the news. But when it was revealed that they had read the DNA wrong, that part didn’t make the big splash it should have.
HEATHER: In your opinion, if the fingerprints of all Americans were on file for use by law enforcement, would it be a boon to crime solving? What about privacy issues?
MURRAY: I think taking each person’s DNA would be more useful, but I don’t think people would find that comforting. While either might boost crime resolutions, if we hold to “innocent until proven guilty” using our jury system, well, we can’t go there. I do support taking the DNA and prints of those who are convicted, though – it has helped resolve additional offenses.
THOMAS PAWLICK: Forensics is a science, which automatically means it should be constantly re-examined by other scientists to verify its accuracy. That’s how it should be. That said, however, I might add that it is also a wonderful profession and can sometimes be a lot of fun. I have been an investigative journalist for 45 years and both my police friends and I think there is no profession better.
MURRAY: Agreed! It has been a wonderful career, and combined with teaching, I could not have asked for more.
MAUREEN: I teach high school science and some of my students have expressed interest in pursuing a career in forensic science. How would you advise them to proceed?
MURRAY: I emphasize that “forensic” is the adjective, but “science” is the noun. They need to focus on science (all types) and math, and work to be diligent in their observational skills. Communication skills are also very important – both oral and written. It’s not for everyone, but I love that students are taking more of an interest in science due to the forensic applications. And I salute all you high school teachers out there!
ALAN ROCKER: A lot of people don’t seem to realize that “forensic” means “legal” or “related to lawyers”.
MURRAY: Actually, “forensics” has come to mean “legal,” but it emerges from the Latin word for “public” or “in the public eye” (i.e. from “forum”). Some would translate as “open to public debate” (in fact, some may recall the “forensic team” was the “debate team” in schools of the past). You are correct, Alan, that many people do not know its origin many I ask seem to think it means “dead” or “crime”.
BLAINE: Do you feel a need to “decompress” after an investigation – I imagine you get used to adopting a dispassionate attitude when looking at certain evidence, but I would imagine it’d wear on a person.
MURRAY: Of course the worst part of the job is seeing what people can and will do to each other. It can be terrible, and cases involving children are the worst, by far. I think you just have to keep a clear head and recognize that your emotions can cloud your judgment. When that happens, you can’t do your best work. But yes, sometimes it is very difficult.
BLAINE: Thank you for the reply. I’m looking at these slides of Laos, Guatemala, and I think it must be staggering. The one in Guatemala with the onlookers was especially poignant.
MURRAY: Yes, I have worked many crime scenes in my years, but none where the family sat alongside the grave, singing, talking, and observing. Puts a different feeling to it, and it actually felt better to me, more so than worse — though these people were REQUESTING their loved ones be exhumed to document the war crimes involved in their deaths.
CODY: One of my colleagues thinks handwriting analysis is bogus, and compared it to palmistry. But I find handwriting psychology analysis works well with other types of psychology training. What say you?
MURRAY: Depends on what type of handwriting analysis you’re talking about. The idea that you can tell someone’s sex, mood, or the like is bogus (in my opinion and training) — but handwriting comparison is common and valuable in the hands of a trained practitioner.
RICHARD: What organizations set the standards for forensic evidence?
MURRAY: The premier organization in the US — and really the world — is the American Academy of Forensic Sciences. I am proud to be a fellow in that organization. Each February some 6000 of us come together and meet and share new research. Many of our accrediting groups also convene at the same time. Board exams are held, students are encouraged, and just general “hob-nobbing with our fellow wizards!”
Professor Murray with a slow loris in Laos, 2000
LESTAHL: Did the detectives in the O J Simpson case do a thorough enough job? What evidence did they miss in your opinion?
MURRAY: I don’t think I’m going too far out on a limb to say that I am convinced that OJ did kill his wife and her friend. However, with that said, there were mistakes made in evidence collection and possibly analysis. We hold that all that needs to be present is “reasonable doubt,” and clearly if there was tainted evidence, that’s enough for a not guilty verdict.
Do I think he is a danger to society? Not so much as a danger to those closest to him. I honestly think the greater good was done to set him free because of the reasonable doubt and the tensions involved in that case.
JAMES M TEMPLE: Is there one unsolved case within the last 50 years that you were never involved with that you would like to look into to see if you can come up with more evidence?
MURRAY: Well, I have so many cold cases in my care through the National Missing and Unidentified Persons System. I wish I had more evidence in all of them. Sadly, some have been cremated, records destroyed and the like. Some will never be resolved.
I think I originally missed the part of your question in that you weren’t referring to my own cases. A case that is completely intriguing to me is that of the Tylenol Murders of 1982. Perhaps because I so vividly recall the nightly news in that regard (and though had taken two years of HS chemistry, and two years of college chemistry at that point, was not yet involved in forensics).
But anthropology took me in another direction, and the Tylenol case doesn’t involve bones, so I would not have been involved. Nonetheless, I am really surprised that one has not been solved. I do like (spoiler alert…) James Lewis for it, though (as the prime suspect), as I discuss in “Forensic History”.
GORDYSOCCERUK: Has DNA ever been used to frame somebody? #ForensicChat
MURRAY: I don’t know of a specific case, but I can imagine that’s possible. It’s an interesting thought. And please, as they say, “Do not try this at home!”
BRADLEY STEEG: Google and others are making rapid advances in image recognition thanks to machine learning algorithms. And we all post photos to Facebook. I’m thinking of the Boston Bombers. If I take a photo with my smart phone the image is automatically uploaded (backed up) to my Google account over wireless within minutes, sometimes seconds. Consequently, an event like the Boston Marathon will have enormous amounts of visual data collection stored on various social media services. But, I might die in the blast and I won’t be able to authorize the FBI to use my image data taken during the event. What *legal* efforts are underway by the FBI to utilize distributed smart phone data collection stored on social media servers? Are we looking forward to an ‘opt-out’ selection on our social media privacy agreements?
MURRAY: Interesting (again, Bradley). I believe with probable cause, important evidence — including digital evidence — can be obtained for use in a criminal investigation. This happens all the time. Our privacy only goes so far when criminal matters are in issue.
HUGH: This country must spend 100s of billions of dollars on criminal justice. Are there any priority paid to do R&D on reliable determination of what people state are true or false?
MURRAY: I think you are talking about lie detection methods? If so, I think we have to consider that there are some people who do not show the tell-tale signs of lying (if there are tell-tale signs). Psychopaths and sociopaths will always allude these tests, I bet. And they are the most frightening characters of all for that and other reasons. Also, memory is not accurate, so people may not realize they are not “telling the truth.” Memory is complex. So is truth.
MELNUCLEAR: What are some of the most interesting type of cases you have worked on? I don’t want to sound corny, but my only real exposure to a forensic anthropologist is my favorite character Dr. Temperance Brennan. It sounds like very important and interesting work.
MURRAY: It is important and interesting work, for sure. And because the Tempe character is written by and based on a real forensic anthropologist, there’s a strong element of reality in some of the casework examples, I think. The most interesting cases to me are those involving identification. I wrote a book (for young adults) on all facets of ID — from skin, to bones and medical devices, to molecular means (such as DNA).
Now people may think that DNA renders anthropology obsolete — or will do so in the future. Perhaps if everybody gets their DNA taken at birth and put into a database, that could happen. But until then, the anthropologist comes in first to develop a biological profile (age, sex, stature, etc.) and then the DNA or the dentist gets the credit. (I am being facetious about the “credit” part.)
ALAN ROCKER: “Data science” has become a hot topic recently. Is there anything in the way of data storage, processing, or computing, that could be of real benefit in your work?
MURRAY: Your question immediately makes me think of all my cold cases. The problem with so much of our past casework was we had no way to store all that bulky data (x-rays, photos, etc.). Computers and their data storage have revolutionized what we do these days. I only wish that we could retrieve all the lost data from the past! I don’t know where that will take us in the future, but it sure would have benefited us in the past. Microfilm is a poor substitute for a storage drive!
Professor Murray on a dig in Laos, 2000
KAREN ROWE: How does new information and processes get disseminated to forensics practitioners especially in small towns?
MURRAY: All practitioners are required to have continuing education, regardless of big or small towns. Research is conducted all over the world, and through publication and presentation at national meetings, it becomes accepted. With the internet, there is so much sharing of information. And believe it or not, I just got a call the other day from a friend who is a magistrate here in town, and he was doing continuing education and they were using my Teaching Company material!
How awesome is that? Anyway, there are mandatory trainings for officers, coroners, anthropologists and the like. Just as for other practitioners, like nurses and others.
BLAINE: What did your anthropology training give you over and above what you learned in your biology training? At my university they had internships for undergraduates at the coroner’s office, and they accepted both anthropology majors and biology majors. Of course many who went were double-majors, but I always wondered if those who hadn’t experienced both had different experiences because of what they learned.
MURRAY: My anthropology master’s experience was the “four field” approach (physical, linguistic, archaeology, and cultural), and that was great. However, my bachelor’s in biology, with 2.5 years of chemistry, was really a superb preparation for physical — and specifically — forensic anthropology, which is a sub-discipline in physical, as you know.
I still think that the other parts of anthropology are crucial, but where forensics is concerned, I think more science is important.
PARTINGTON: What advances have been made in analyzing cremated remains?
MURRAY: Interesting you should ask — I was part of the first group to look into this from a forensic perspective. It was after the Noble, GA crematorium scandal. The question was, how do you analyze bone ash — particularly given it’s already burned. Many analytical methods — like GC mass spec — use burning to assess the components in a mixture. But you can’t do that with cremains. At UT Chattanooga and at my own university, we worked on other methods to analyze cremains.
The question there (in the crematory scandal) was whether the cremains were adulterated (i.e. watered down) and if so, with what? It was a very interesting matter. At present, I am no longer working on that issue, but it was critical in that situation.
GENE HULL: Do all major cities have the same forensic labs available to police, etc?
MURRAY: Well, yes and no. Smaller jurisdictions typically send evidence to larger regional crime labs. Some states have a lab that is open to any jurisdiction in the state, free of charge. There are also national labs (FBI and U of North TX) that can be called on for “big jobs”. So, the problem becomes collection and proper transfer. There should never be a reason for not being able to analyze evidence (at least I hope!).
NINAMAE: Can a person with a health care background (such as Nursing) transition into a Forensics career? If so, what degree would they need to attain?
MURRAY: Have you heard of forensic nursing? Some coroner and ME offices are using forensic nurses to analyze deaths — particularly hospital deaths. I think if you do some research, you can find more about that. Some are SANE nurses (sexual assault nurse examiners) and take rape kits and such in emergency departments. The problem is, I don’t know how well that is catching on, or what agencies use forensic nurses.
MELANIE: Legally can the forensic team or the specific doctors be held accountable for not doing their jobs adequately?
MURRAY: I definitely think so — anyone can be charged with malpractice, and some forensic practitioners have been. Joyce Gilchrist is one heinous example. I also talk about “dirty cops” in some of my Teaching Company presentations. We had a local sheriff who was dealt with after aiding the disposal of a body. Yes, yes, yes — bad apples need to be weeded out! And the good news is there are always ways of doing so.
DENNIS TOMLINSON: What do you think of the Missing 411 books by David Paulides? Are the cases in the books part of the National Missing and Unidentified Persons System?
MURRAY: Well, his works are non-fiction, so I imagine some could be in NamUs, but without having the lists of his books’ cases in front of me, I wouldn’t know for sure. NamUs is a service that is open to the public, so if you are interested, you could go on the site and do a search by name for some of Paulides’ cases. Some of my students browse NamUs on a regular basis because the missing person stories are so fascinating. Unfortunately, some are also very sad.
ALAN ROCKER: Not all areas of science can be considered equally certain. Do you have a spectrum of topics ranging from “Easy to be absolutely sure” to “on a balance of probabilities, maybe”, or the equivalent, and if so, what would they be?
MURRAY: Yes, some methods are fairly cut-and-dried with regard to their accuracy. If a good sample, DNA and fingerprints are extremely reliable, since they are individuating evidence (i.e. unique). Bitemarks, hair microscopy, and arson investigation have been really called into question of late (pursuant to the 2009 National Academy of Science report). However, it’s sometimes difficult to separate whether its the method or an improperly-trained practitioner that’s at fault.
There are too many poorly-trained investigators out there, owing, perhaps, to the rapid growth and popularity of the field of forensics (growing faster than the training programs can keep up). Hair analysis, though, has been essentially thrown out by the FBI based on their retrospective analyses (I talk about that in my course and my “Overturning Wrongful Convictions” book).
As an anthropologist, our certainty often depends on how stereotypical skeletal remains are, for example, in the expression of traits related to sex, age or ancestry. It doesn’t mean the methods are unreliable if we can’t give a good assessment, it usually means the remains are atypical or show a mixture of traits. Also, time since death has so many variables, it’s a difficult area to assess. These more subjective areas are where we need help — and that help is coming in the form… We now have software into which we can input measurements and get a more objective profile of a decedent.
CODY: Mind you, I’m still waiting to buy “forensic history”, but in your opinion who was the most likely suspect for Jack the Ripper?
MURRAY: In “Forensic History,” I more so discuss the relationships of the cases and the forensic evidence in them than I do the “suspects.” Mainly because we have facts about the evidence, but only theories about the killer (and far too many of them, at that). As I say in the lecture, a whole series could be done about the Ripper murders and the various suspects. Having read many theories, I honestly don’t find any that are so compelling to me as to be definitive. I could spend the next few years reading Ripper books — there are that many out there. In fact, a new theory just came up in the week of this chat (that poet Francis Thompson was the killer). If forced to choose, I guess I’ll go with Kozminski as my prime suspect, but we will never know.
MEL: Have you done a lot of criminal forensics in your career?
MURRAY: I’m not sure what you mean by “criminal forensics” — I am a forensic anthropologist and have participated in many hundreds of forensic investigations over the past 30 years. Most have involved skeletal remains, but others have been dismemberment cases, child abuse deaths, fire deaths, etc. Forensic anthropologists frequently get involved where bone trauma is an issue (i.e. child abuse) or when there is not enough of a body remaining to do a traditional autopsy.
ERIC: Where are Psychiatric – Psychological Forensics taught? Also what about profiling of international leaders? Is this only the work of the CIA?
MURRAY: I don’t know specific schools, but I recommend visiting the website of the American Academy of Forensic Sciences at aafs.org where you can find a list of accredited forensic programs. I also don’t know who profiles international leaders, but I imagine there are multiple levels of governmental agencies involved.
RON C: How accurate is the TV series “Bones” regarding forensics?
MURRAY: I honestly don’t watch much TV, so I couldn’t tell you. I do know, though, that the Producer is forensic anthropologist Dr. Kathy Reichs, who also writes many episodes, so I imagine the science is as good as she can make it, given it’s a fictional drama.
LESTAHL: Do you feel that TV programs that solve unbelievably difficult cases in an hour give the public a false sense of the real ability to solve such cases?
MURRAY: Yes, but I also think we’re capable of recognizing that “it’s a show” and in that regard has different goals than real casework. At least I hope that’s the case! Some of the “true crime” shows seem worse at that — these real investigators who come to a town and delve into a cold case and settle it in an hour, even though it was an open case for years. With that said, I support anything that will help close a case. Have you heard of the CSI effect with regard to juries? It’s interesting to think that people know more about forensics (or think they do) from fictional shows than most ever learned about science in school — but I think we’re even educating the perpetrators. In 2015 I wrote a chapter called “Postmortem Trauma and the ‘CSI Effect’: Is TV Making Smarter Criminals?” in the edited volume “Skeletal Trauma Analysis: Case Studies in Context.” As I say repeatedly in the “Trails of Evidence” Great Courses series, I think we are making smarter criminals!
GINA: Care to comment on the Fox Lake situation?
MURRAY: I posted about that case to my professional Facebook page just this week what a sad, sad situation — what a waste of resources in investigating it (and the pathologist was originally apparently not believed by his own superiors when he suspected suicide). It sounds like the amount of money the officer embezzled was only about $50,000 — was his life worth only that? Or maybe his ego?
As if the good guys didn’t have enough bad PR these days, Gliniewicz goes and does this — and the more that comes out about the case, the worse things seem to get. Threatening the life of another official and now having his mistress marry his own son, who is in the military to get cash from military benefits! It’s sickening. Here’s a link to the latest… http://abc7chicago.com/news/gliniewicz-may-have-arranged-sham-marriage-between-son-mistress-report-says/1071246/
ALAN ROCKER: Do you think that handwriting analysis is any more accurate than, say, astrology?
MURRAY: As I replied to another chat participant, that depends on whether you are talking about graphology (the “assessment” of personality or mood from handwriting — which is bogus) or you are talking about forensic document examination in which signatures are being compared for authenticity (which does have some scientific bases).
GINA: IF Finger print ID is suspect, is it because of technique or the actual ID?
MURRAY: I’m not sure I understand the question — but if you’re asking if fingerprints are unique — they are. So if there is sufficient detail and enough of a print surface present, there should be no issue with a fingerprint identification. Even identical twins don’t have identical prints. Partial prints, though, can be problematic.
GENE: Are DNA results regarded as empirical evidence?
MURRAY: Yes, particularly if a full nuclear genetic profile is obtained. Only identical twins would have the same nuclear DNA. Mitochondrial DNA, however, is passed from a mother to all of her offspring (we do not get mitochondrial DNA from our father), so everyone in a female’s line will share that. Keep in mind that DNA is often just one piece of evidence in a case — one would hope that a case had multiple lines of evidence leading to the same conclusion.
KMBURLEY: How accurately can forensics determine time of death?
MURRAY: Due to the large numbers of variables involved, assessments of the postmortem interval can be complex. The accuracy depends — in my opinion — on two things: How long the individual has been deceased, and how much is known about the environmental conditions where the death/decomposition occurred. In general, the closer to the time of death, the more accurate we can be conversely, the longer since death, the less confident we can be.
JACK HAUTALUOMA: What are the most useful kinds of evidence that the layman would be least aware of? What kinds of evidence are most useful to you in criminal cases?
MURRAY: This is a good question and it would depend a lot on the type of case, but I guess it also depends on how “educated” the layman is (whether professionally educated or “educated” from television shows). I think most people know that our prime sources of evidence are DNA (from a variety of biological sources), fingerprints, blood spatter, fibers, broken glass, etc. — but what always amazes me are the minute bits of evidence that can reveal so much — like pollen… or cut marks on bone (which — in the right hands — can indicate how many teeth-per-inch a saw blade had). I’d have to say the minute details are what impress me most.
BOB SMITH: I am interested in learning more about emerging technologies in forensic science Nanotechnologies and the like. What does the future hold?
MURRAY: They are working now on nanoparticles present in fingerprints that could tell more about a person (like drug use — and I don’t mean the presence of cocaine on the finger, but its — or its metabolites’ — presence in the body). Also I’ve heard talk of being able to tell how old a blood sample is by the nano-features (if that’s a word) of its surface, using atomic force microscopy. These aren’t areas with which I’m familiar, but it is really interesting.
Isotopes in bone and tooth are being compared to what is known about worldwide groundwater isotopes, in an effort to tell a person’s geographic origin. Cool stuff!
THOMAS PAWLICK: For most ballistics testing, a slug or part of one is needed. What other ways can help trace a weapon or ammunition if all that’s present are some bits or pieces of a slug, minus the rifling markings?
MURRAY: I don’t know the answer to this — just saw my former student the other day, who is now our local firearms and toolmark expert — so I wish I could have asked him this question for you. There are so many fields in forensics — I am expert on but a few — and while I do teach the basics (including in “Trails of Evidence”), it’s difficult to stay up on the latest technologies in all of them.
LASLOO: Are there any examples in cases you have been apart of… that were really amazing? That is, with what would seem little to go on… new/advanced forensic science was able to be used to really deduce a whole load of new facts and/or solve a case that really seemed unsolvable otherwise?
MURRAY: Another good question. I have to say that even though forensic anthropology is “all about bones,” there’s so much variation in the casework, it can amaze me, even after 30 years. A few specific “amazing” cases come to mind — I examined the remains of three women, each case about a month apart, and began to suspect a serial killer was involved (and reported that to the coroner of the county).
After a thorough exam of the bones of one of the victims, whose skeletonized remains had been found in the woods, I saw one tiny, near-microscopic, nick on just one of the vertebrae of the neck. I said that I thought her throat had been slashed. The perpetrator had been burning all his victims, and these remains also showed evidence of burning — but even the pathologist questioned why I thought that one tiny nick (among many surface anomalies on the bones) was evidence of a knife wound.
When the perpetrator was caught and he talked about the killings, he said — of the four related cases — in that one case, he slit the victim’s throat. (He was caught in the killing of the fourth, so I didn’t examine her she was within a few hours since death when he was caught.) Another amazing case for me was one where we got a woman identified nearly 40 years after she went missing — that one is covered in the “Forensic Art” section of “Trails of Evidence”.
PROTRAINER: Minimum education to do your work?
MURRAY: My work as a board-certified forensic anthropologist currently requires a PhD. One needs the PhD before sitting for the American Board of Forensic Anthropology’s board exam. There are people practicing forensic anthropology at the Master’s level — and probably some out there practicing with a Bachelor’s Degree.
The National Institute of Standards and Technology has created the Organization of Scientific Area Committees (OSAC) that are currently developing subcommittees to create both methodology and training standards for all of the forensic sciences. Most people would be surprised that doesn’t already exist, but forensic science grew in popularity and use so quickly in the past 30 years that it has resulted in a real hodge-podge of qualifications and methods that need to be standardized.
MATT REDLE: What improvements would you like to see in the pattern evidence fields?
MURRAY: I think the biggest improvements are the ongoing use of lasers and computers in assessing, preserving, and analyzing patterns. I don’t know what is on the horizon, though. Also, the ability to use 3-D printing to preserve evidence allows it to be shared and analyzed by multiple investigators at the same time. Interesting stuff!
JAMES MEYER: How do investigators avoid cognitive biases such as confirmation bias, anchoring or recency bias in their pursuit of the truth?
MURRAY: Because we are human (as investigators, victims, and witnesses), I don’t think anyone can completely disengage from their biases. With regard to investigations, we must try to blind ourselves to our preconceived notions (confirmation bias), as difficult as that can be. (I am reminded of the defense’s closing argument in the Grisham novel/movie “A Time to Kill”.) In some regard, I guess the CSI Effect I’ve written about in this chat is a form of anchoring bias, would you agree? I guess the exclusion of mention of past crimes in a trial is an attempt to thwart recency bias. I will say that forensic investigators aren’t necessarily trained in avoiding bias. I try to avoid it by asking anyone who brings a case to me NOT to tell me “what they think happened” or “who the victim probably is”, so that my assessments can be as independent as possible, but I don’t know if that’s the case with all investigators (nor do I know that it avoids bias!).
JUDY: In a recent crime show, lab testers of a splinter stated that they can determine the species of the tree and the exact tree the splinter came from. Is this possible?
MURRAY: We have a wood expert at our local crime lab, and he’s quite good. I believe a splinter would have to be analyzed beyond microscopy (i.e. chemical/physical/molecular methods) in order to speciate. Here’s an NPR story about wood analysis from splinters interesting! As for which tree, I say no way! http://www.npr.org/2015/06/28/417164514/wildlife-forensics-lab-uses-tech-to-sniff-identify-illegal-wood
LAWRENCE WEBB: How does forensics play into the rash of shootings and murders by police who shoot to kill as their first step rather than as the last resort? Is there adequate evidence to support proper action against these crimes by law enforcement officers?
MURRAY: I think/hope the key here is unbiased and neutral investigations of these incidents. I am of the opinion that the tensions are so high on both sides in these recent rash of incidents — on the part of both the police and the victims (especially minority victims) that neither side is acting in a conscientious manner at this point. Both sides in these conflicts are so highly charged that they are not acting rationally fear runs high and it can cloud judgment.
I do think the body cameras are key components in these cases, as they hopefully provide an accurate account that neither party can taint in its favor (which I’m sure happened often in the past).
LEA: Do you think ‘shows’ such as CSI help the public view of forensic science or hurt.
MURRAY: That’s a mixed bag, for sure. There is actually a term “CSI Effect” that refers to how members of the public (especially jurors) have such an “awareness” of forensics now that they have higher expectations of evidence (when on juries) than is warranted. They expect each side to use certain techniques (that may or may not be possible) and are dissatisfied when certain evidence is not present or utilized.
On the positive side, it has increased an interest in science and math in younger students, and that can never be a bad thing!
CAROLYN CARRUTH: Does this type of showings increase the criminal mind’s way of covering up evidence possibilities?
MURRAY: I’m not sure I understand your question. If you mean are the TV shows making smarter criminals, I wrote a book chapter this year indicating that is my belief. Some people who saw “Trails of Evidence” (my first Great Courses series) were critical of my reoccurring saying, “Here I go, making smarter criminals again” as I explained a variety of crime-solving methods — but I do think it’s really true, and my book chapter “Postmortem Trauma and the ‘CSI Effect& Is TV Making Smarter Criminals?” in the edited volume “Skeletal Trauma Analysis: Case Studies in Context” documents one case where the perpetrators referred repeatedly to TV forensics when they were trying to rid themselves of a body!
Professor Murray on a Dig in Guatemala, 2004
BOB: Outside of DNA have there been any improvements in the way way we can evaluate evidence?
MURRAY: Yes, lots — so many that I can’t begin to address them here. My final lecture in “Forensic History” references advances in fingerprints, and how computerization has really revolutionized so much of what we do in forensics (as in other facets of our lives).
ERIC: Why are lie detectors still used in many venues?
MURRAY: Lie detectors aren’t accepted in most courts (unless both parties agree to it), but they are still used — in my opinion — to “trick” or “coerce” people who are being questioned about an issue/event. I wish that wasn’t allowed, but you may be surprised at what is allowed during police questioning of suspects. I have a couple of lectures about that in “Forensic History” and also talk about that in my book “Overturning Wrongful Convictions.”
ANNE: Is DNA always infallible proof of guilt or innocence?
MURRAY: DNA doesn’t “prove” guilt or innocence so much as indicate the source of evidence. There are lots of ways someone’s DNA can get somewhere — without that person even actually ever being present! Such as transfer of hairs by an intermediate vector (person or other animal). DNA, like other evidence should be part of a big picture of evidence that tells a story sufficient to convince a jury of the merits of the case.
TERRENCE LENAHAN: Your view of the program CSI Miami.
MURRAY: Sorry, never seen it!
MROBINSP: At any time in her career did Dr. Murray encounter the work of Sir Bernard Spillsbury a great British ME in the early to mid 1900s…if so was there any case that made her say “Wow. ” M.P. Robinson
MURRAY: I’m getting old, but I’m not that old! (Ha!) Oh, you mean in my work, have I seen HIS work? It’s actually been more through my teaching that I have read about Spillsbury — he is an icon, and always seemed to be willing to go out on a limb. But there have been criticisms of him in terms of his independence, showmanship, and unwillingness to share with others (wouldn’t train students).
Still, he set the stage for thinking outside the box with regard to forensic pathology, and such thinking is necessary to advance the field.
WHERE CAN I GET THAT PHOTO…: Where can I get the photo processing software they use on NCIS? If only Photoshop was that Good!
MURRAY: Don’t know, and don’t even know if it’s a real software or just a TV fantasy! Sorry. When you see some of these things on television, it doesn’t even mean they are real or existing technology. Are they pointing to the future, a la Jules Verne? I don’t know, but it’s interesting.
BRADLEY STEEG: RE: Lecture 24 “The Past, Present, and Future of Forensics” The United States and Europe are currently funding human brain research (US Brain Initiative, EU Brain Project). In a broad sense, we may be able to ‘read’ minds fairly soon through brain imaging, meaning we will have highly accurate polygraph testing. It looks like they will be able to distinguish between a reliable memory and a fabricated memory where the brain fills in the blanks. In fact, DARPA is even working on projects to restore lost memories. Is it too early — or too expensive — for forensic science to take live brain imaging projects seriously yet?
MURRAY: Wow, cool and scary at the same time! I think the biggest hurdle here would be how creepy many people would find this concept with regard to their rights.
ALAN ROCKER: I take it you know Kathy Reichs? Forensic pathology seems to attract female practitioners don’t you find it gross?
MURRAY: Yes, Kathy and I are friends — she’s a wonderful anthropologist, writer, and person! You are correct there are a lot of female forensic anthropologists, and it’s interesting. Many of us have discussed that phenomenon. As for it being gross, it definitely can be gross. However (not to be sexist), I could argue that females have been the ones in society throughout much of history who handle a lot of the “gross and messy stuff” — from birth and baby diapers, to sick people and the care of the dead. Many ladies seem to have a pretty good constitution for handling things that are unpleasant. I also teach gross anatomy, and I find that the females are just as capable of handling that unsettling setting as the males. There are also more females going into the funerary sciences these days, too, and many in forensic pathology. Interesting.