Genealogies from Time-Stamped Sequence Data

Drummond, Alexei J.; Nicholls, Geoff K.; Rodrigo, Allen G.; Solomon, Wiremu

doi:10.1007/978-1-4471-0231-1_7

Cited by 13 publications

(10 citation statements)

References 29 publications

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“…Second, to further test whether haplotype divergence times date to the Pleistocene, we used the program beast (Drummond & Rambaut 2003), which also uses an MCMC approach (Drummond et al . 2002), to estimate the time to the most recent ancestor ( T mrca ) for all black‐throated blue warbler haplotypes included in our study.…”

Section: Methodsmentioning

confidence: 99%

Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation

et al. 2006

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Like many other migratory birds, the black-throated blue warbler (Dendroica caerulescens) shows pronounced differences in migratory behaviour and other traits between populations: birds in the southern part of the breeding range have darker plumage and migrate to the eastern Caribbean during the winter, whereas those in the north have lighter plumage and migrate to the western Caribbean. We examined the phylogeography of this species, using samples collected from northern and southern populations, to determine whether differentiation between these populations dates to the Pleistocene or earlier, or whether differences in plumage and migratory behaviour have arisen more recently. We analysed variation at 369 bp of the mitochondrial control region domain I and also at seven nuclear microsatellites. Analyses revealed considerable genetic variation, but the vast majority of this variation was found within rather than between populations, and there was little differentiation between northern and southern populations. Phylogeographic analyses revealed a very shallow phylogenetic tree, a star-like haplotype network, and a unimodal mismatch distribution, all indicative of a recent range expansion from a single refugium. Coalescent modelling approaches also indicated a recent common ancestor for the entire group of birds analysed, no split between northern and southern populations, and high levels of gene flow. These results show that Pleistocene or earlier events have played little role in creating differences between northern and southern populations, suggesting that migratory and other differences between populations have arisen very recently. The implications of these results for the evolution of migration and defining taxonomic groups for conservation efforts are discussed.

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Section: Methodsmentioning

confidence: 99%

Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation

et al. 2006

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“…Although there are proof-ofconcept examples in several application areas in Buck et al (1996) and others have also published examples (Orton, 2000;Millard, 2002;Millard and Gowland, 2002;Byers and Roberts, 2003;Millard, 2004Millard, , 2005Finke et al, 2008;van Leusen et al, 2009;Fernandes et al, 2014), there is really only one application area where Bayesian methods can be said to be routine: absolute, scientific-dating-based chronology construction. There is one other application area with close connections to archaeology, that of phylogeny (both genetic and linguistic), where use of Bayesian methods is also increasingly routine (Drummond et al, 2004;Edwards et al, 2007;Kitchen et al, 2009;Drummond et al, 2012;Bouckaert et al, 2014). Here, however, methodological development was driven largely by the genetics and linguistic research communities.…”

Section: Bayesian Archaeologymentioning

confidence: 99%

On being agoodBayesian

Buck

Meson

2015

World Archaeology

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Bayesianism is fast becoming the dominant paradigm in archaeological chronology construction. This paradigm shift has been brought about in large part by widespread access to tailored computer software which provides users with powerful tools for complex statistical inference with little need to learn about statistical modelling or computer programming. As a result, we run the risk that such software will be reduced to the status of black-boxes. This would be a dangerous position for our community since good, principled, use of Bayesian methods requires mindfulness when selecting the initial model, defining prior information, checking the reliability and sensitivity of the software runs and interpreting the results obtained. In this paper, we provide users with a brief review of the nature of the care required and offer some comments and suggestions to help ensure that our community continues to be respected for its philosophically rigorous scientific approach.

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“…In turn, the shape of the genealogy depends on the population size through time and on the sample size and is affected by factors such as selection and (in subdivided populations) gene flow (30). Serial coalescence, in particular, allows one to consider both ancient and modern samples within the same genealogy (31) and test hypotheses regarding their demographic history. Here we used a serial coalescent program, SERIAL SIMCOAL (5), an extension of SIMCOAL (32), to simulate the evolution of the population of Tuscany.…”

Section: An Etruscan Social Elite?mentioning

confidence: 99%

Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans

Belle

Ramakrishnan

Mountain

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The Etruscans, the only preclassical European population that has been genetically characterized so far, share only two haplotypes with their modern geographic counterparts, the Tuscans, who, nonetheless, appear to be their closest relatives. We modeled 10 demographic scenarios spanning the last 2,500 years and tested by serial coalescent simulation whether any are consistent with the patterns of genetic diversity observed within and between the Etruscan and the modern Tuscan populations. Models in which the Etruscans are the direct ancestors of modern Tuscans appear compatible with the observed data only when they also include a very high mutation rate and an ancient founder effect. A better fit was obtained when the ancient and the modern samples were extracted from two independently evolving populations, connected by little migration. Simulated and observed parameters were also similar for a scenario in which the ancient samples came from a subset, e.g., a social elite, genetically differentiated from the bulk of the Etruscan population. In principle, these results may be biased by factors such as gross and systematic errors in the ancient DNA sequences and failure to sample suitable modern individuals. If neither proves to be the case, this study strongly suggests that either the mitochondrial mutation rate is much higher than currently believed or the Etruscans left very few modern mitochondrial descendants.ancient DNA ͉ mtDNA ͉ population genetics

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Genealogies from Time-Stamped Sequence Data

Cited by 13 publications

References 29 publications

Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation

Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation

On being agoodBayesian

Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans

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