Phylogeography
From ISOGG Wiki
Phylogeography is a field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species.[1] Phylogeography is a subdiscipline of biogeography. It is "inherently interdisciplinary, with input from, for example, molecular genetics, population genetics, phylogenetics, demography, climatology, ecology, and historical geography — plus archaeology, anthropology, and linguistics, in the case of humans, and ethology and palaeontology in the case of other species".[2]
In the field of population genetics phylogeography refers to the joint phylogenetic (genealogical) relationships and geographic distributions of genetic lineages. It is a method of mapping the DNA sequence variants to their geography to show the present-day distribution of genetic lineages. Phylogeography is most often applied to mitochondrial DNA and Y chromosome lineages. Phylogeography is a scientifically legitimate term. One can talk of – for example – high or low phylogeographic structure; with the former, closely related lineages are also found to be geographically clustered, with the latter there is little correlation between the relatedness of lineages and their geographic distribution. There is also no doubt that the phylogeographic structure of a genetic locus (a piece of DNA that is inherited as a chunk, and so has a single phylogenetic tree / genealogy associated with it) contains information on the ancestry of a population, or even an individual (although the amount of information contained can be surprisingly small). The main issue is how do we extract that information to make reliable inferences about the ancestry of a population or even an individual?
Contents
Systematic and interpretative phylogeography
While phylogeography in itself is perfectly valid as a description of the spatial distribution of observed lineages, issues arise when it comes to making inferences about the geographic location of unobserved lineages, such as those in the past, and the population history that shaped the phylogeography. Approaches to this can be broadly lumped into two categories: systematic and interpretative.
A systematic approach is one that can be formalised in an algorithm and automated (usually using a computer programme). This means that given the same phylogeographic data, it should give the same answer every time. The attraction of making an inference approach systematic is that it can be tested explicitly to see if it works (by simulating data under a known history and seeing if the approach recovers that history). The first major systematic phylogeographic inference approach was designed by Alan Templeton and was called Nested Clade Phylogeographic Analysis (NCPA).[3] NCPA has been tested and explicitly shown not to work (see Nielsen and Beaumont 2009, and references therein).[4][5] Other systematic approaches have also been developed and hold out some promise.[6]
The more widely-used approach to inferring the geographic location of unobserved lineages, and the population history that shaped the phylogeography, is known as interpretative phylogeography. It is the interpretative aspect that is questioned by the majority of population geneticists. Interpretative approaches are, by definition, not formalised in an algorithm, and so not testable. The analysis is usually performed by interpreting phylogeographic patterns as indicating a particular population history, rather than by systematically exploring a range of population histories to test which best explain a particular phylogeographic pattern (using, for example, computer simulations). What is more, such approaches are easily steered by subjective biases, which may help to explain their popularity among some ancestry ‘testing’ companies.
Interpretative phylogeography has been criticised by population geneticists because of its lack of scientific and statistical rigour, and has been described by many scientists as storytelling.[7][8][9][10][11]
The scientific approach is to construct explicit models of population histories – incorporating what we know about the inheritance process (population genetics) – to make predictions about those relationships and geographic distributions in the past, and then see which of those models best explain the genetic data.[12] This follows the standard hypothesis testing / hypothesis comparison paradigm that is the cornerstone of modern science. However, a number of people short cut this hypothesis testing / hypothesis comparison step and merely interpret phylogeography post hoc. The problems with this approach to inferring ancestry are numerous. Many of the problems are somewhat obvious, such as it is easy for interpretations to be steered by subjective biases. For example, some genetic ancestry testing companies will try and claim an association with a haplogroup and a historical personality.[13][14] More worryingly, some researchers will attempt to mould a population's history to some nationalist or political agenda.[15][16] Other problems are somewhat more subtle, such as the failure to take into account the intrinsically noisy nature of genetic inheritance; any phylogeographic pattern could be explained by a very wide range of often very different population histories / ancestries.
Interpretative phylogeography is best viewed "as a means of generating hypotheses (storytelling), whereas explicit models permit those hypotheses (or stories) to be tested".[9]
Despite the criticisms, many researchers have published papers in peer-reviewed scientific journals in the last 25 years using the technique of interpretative phylogeography. Their presence in the scientific literature has been considerable, but is now on the decline, though the debate continues.
Martin Richards and Vincent Macaulay published a defence of the interpretative approach in an article in The Guardian newspaper in 2013.[17] A rebuttal was posted on the UCL website by Mark Thomas.[18]
Scientific papers
- Schlebusch C, Loog L, Groucutt HS et al (2021). Human origins in Southern African palaeo-wetlands? Strong claims from weak evidence. Journal of Archaeological Science 130: 105374. Provides a useful overview of the pitfalls of making strong claims about human origins based on weakly informative single locus data (eg Y-DNA and mtDNA).
- Chikhi L (2010). Update to Chikhi et al.'s "Clinal Variation in the Nuclear DNA of Europeans” (1998): Genetic Data and Storytelling - From Archaeogenetics to Astrologenetics?". Human Biology 81(5/6): 639-643.
- Balloux F (2009). The worm in the fruit of the mitochondrial DNA tree. Heredity 104: 419-420.
- Nielsen R, Beaumount MA (2009). Statistical inferences in phylogeography Molecular Ecology 18: 1034–1047.
- Emerson BC, Hewitt GM (2010). Phylogeography. Current Biology 15 (10). A useful primer on the subject.
- Beaumont MA, Nielsen R, Robert C et al (2010). In defence of model-based inference in phylogeography. Molecular Ecology 19: 436–446.
Videos
The limitations of interpretative phylogeography are discussed in a presentation given by Professor Mark Thomas of University College London at Who Do You Think You Are? Live in April 2015.
Further reading
- Sense about genetic ancestry testing. A briefing from Sense About Science, 7 March 2013.
- Wikipedia article on phylogeography
See also
References
- ↑ Avise, JC. Phylogeography: The History and Formation of Species''. Harvard University Press, 2000.
- ↑ Richards M. The Neolithic invasion of Europe. Annual Review of Anthropology 2003. 32:135–62
- ↑ Templeton AR (1988). Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7(4): 381-397.
- ↑ Nielsen R, Beaumount MA (2009). Statistical inferences in phylogeography Molecular Ecology 18: 1034–1047.
- ↑ Panchal M, Beaumont MA (2007). The automation and evaluation of nested clade phylogeographic analysis. Evolution 61-6: 1466–1480.
- ↑ Lemey, P; Rambaut, A; Drummond, AJ et al (2000). Bayesian phylogeography finds its roots. Plos Computational Biology 5(9): e1000520.
- ↑ Chikhi L (2010). Update to Chikhi et al.'s "Clinal Variation in the Nuclear DNA of Europeans” (1998): Genetic Data and Storytelling - From Archaeogenetics to Astrologenetics?". Human Biology 81(5/6): 639-643.
- ↑ Nielsen R, Beaumount MA (2009). Statistical inferences in phylogeography Molecular Ecology 18: 1034–1047.
- ↑ 9.0 9.1 Gerbault P, Allaby RG, Boivinc N et al (2014). Storytelling and story testing in domestication. Proceedings of the National Academy of Sciences USA 111 (17) 6139-6146.
- ↑ Goldstein DB, Chikhi L (2002). Human migrations and population structure: what we know and why it matters. Annual Review of Genomics and Human Genetics 3: 129-152.
- ↑ Stoneking M, Krause J (2011). Learning about human population history from ancient and modern genomes. Nature Reviews Genetics 12: 603.
- ↑ Servedio MR, Brandvain Y, Dhole S et al (2014). Not just a theory—the utility of mathematical models in evolutionary biology. PLOS Biology, published online 9 December 2014.
- ↑ Mckie R. DNA project reveals Tom Conti's Napoleonic blood and rich roots of Scotland's genetic legacy. The Guardian, 14 April 2012.
- ↑ Moffat A. Interview with James Naughtie. BBC Radio 4 Today programme. 13 February 2013.
- ↑ Rubin R. "Jews a race" genetic theory comes under fierce attack by a DNA expert. Forward website, 7 May 2013.
- ↑ Yanover Y. No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews. The Jewish Press, 23 February 2014.
- ↑ Richards M, Macaulay V. It is unfair to compare genetic ancestry testing to astrology. The Guardian, 8 April 2013.
- ↑ Thomas M. Rebuttal of Richards and Macaulay's post. UCL Molecular and Cultural Evolution Lab website.