Inferring the History of Speciation from Multilocus DNA Sequence Data: The Case of Drosophila pseudoobscura and Close Relatives

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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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)

Molecular Ecology ◽

10.1111/j.1365-294x.2007.03496.x ◽

2007 ◽

Vol 16 (21) ◽

pp. 4455-4481 ◽

Cited By ~ 29

Author(s):

DEAN H. LEAVITT ◽

ROBERT L. BEZY ◽

KEITH A. CRANDALL ◽

JACK W. SITES JR

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Dna Sequence Data ◽

History Of

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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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Gene Flow and Natural Selection in the Origin of Drosophila pseudoobscura and Close Relatives

Genetics ◽

10.1093/genetics/147.3.1091 ◽

1997 ◽

Vol 147 (3) ◽

pp. 1091-1106 ◽

Cited By ~ 5

Author(s):

Rong Lin Wang ◽

John Wakeley ◽

Jody Hey

Keyword(s):

Gene Flow ◽

Natural Selection ◽

Sequence Data ◽

Sexual Isolation ◽

Secondary Contact ◽

Drosophila Pseudoobscura ◽

Dna Sequence Data ◽

Principal Finding ◽

Close Relatives ◽

Parapatric Speciation

The divergence of Drosophila pseudoobscura and close relatives D. persimilis and D. pseudoobscura bogotana has been studied using comparative DNA sequence data from multiple nuclear loci. New data from the Hsp82 and Adh regions, in conjunction with existing data from Adh and the Period locus, are examined in the light of various models of speciation. The principal finding is that the three loci present very different histories, with Adh indicating large amounts of recent gene flow among the taxa, while little or no gene flow is apparent in the data from the other loci. The data were compared with predictions from several isolation models of divergence. These models include no gene flow, and they were found to be incompatible with the data. Instead the DNA data, taken together with other evidence, seem consistent with divergence models in which natural selection acts against gene flow at some loci more than at others. This family of models includes some sympatric and parapatric speciation models, as well as models of secondary contact and subsequent reinforcement of sexual isolation.

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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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