Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizardXantusia vigilisspecies complex (Squamata: Xantusiidae)

Abstract A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]

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Early history of Neanderthals and Denisovans

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1706426114 ◽

2017 ◽

Vol 114 (37) ◽

pp. 9859-9863 ◽

Cited By ~ 41

Author(s):

Alan R. Rogers ◽

Ryan J. Bohlender ◽

Chad D. Huff

Keyword(s):

Gene Flow ◽

Dna Sequence ◽

Evolutionary History ◽

Sequence Data ◽

Early History ◽

Middle Pleistocene ◽

Dna Sequence Data ◽

The Past ◽

History Of

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

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Range-wide population structure and history of the northern quahog (Merceneria merceneria) inferred from mitochondrial DNA sequence data

ICES Journal of Marine Science ◽

10.1093/icesjms/fsn007 ◽

2008 ◽

Vol 65 (2) ◽

pp. 155-163 ◽

Cited By ~ 23

Author(s):

P. Baker ◽

J. D. Austin ◽

B. W. Bowen ◽

S. M. Baker

Keyword(s):

Mitochondrial Dna ◽

Population Structure ◽

Dna Sequence ◽

Sequence Data ◽

Dna Sequence Data ◽

Mitochondrial Dna Sequence ◽

History Of ◽

Wide Population

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The Age of a Unique Event Polymorphism

Genetics ◽

10.1093/genetics/156.1.401 ◽

2000 ◽

Vol 156 (1) ◽

pp. 401-409

Author(s):

Lada Markovtsova ◽

Paul Marjoram ◽

Simon Tavaré

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Hypervariable Region ◽

Data Set ◽

Dna Sequence Data ◽

Unique Event ◽

Mitochondrial Data ◽

Region I ◽

History Of ◽

Hypervariable Region I

Abstract We develop a Markov chain Monte Carlo approach for estimating the distribution of the age of a mutation that is assumed to have arisen just once in the history of the population of interest. We assume that in addition to the presence or absence of this mutation in a sample of chromosomes, we have DNA sequence data from a region completely linked to the mutant site. We apply our method to a mitochondrial data set in which the DNA sequence data come from hypervariable region I and the mutation of interest is the 9-bp region V deletion.

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Model-based species delimitation: are coalescent species reproductively isolated?

10.1101/764092 ◽

2019 ◽

Author(s):

Luke C. Campillo ◽

Anthony J. Barley ◽

Robert C. Thomson

Keyword(s):

Reproductive Isolation ◽

Dna Sequence ◽

Sequence Data ◽

Species Recognition ◽

Species Boundaries ◽

Simultaneous Estimation ◽

Dna Sequence Data ◽

Multispecies Coalescent ◽

Species Pairs ◽

History Of

ABSTRACTA large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

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