Stable Species Boundaries Despite Ten Million Years of Hybridization in Tropical Eels

Mapping Intimacies ◽

10.1101/635631 ◽

2019 ◽

Author(s):

Julia M. I. Barth ◽

Chrysoula Gubili ◽

Michael Matschiner ◽

Ole K. Tørresen ◽

Shun Watanabe ◽

...

Keyword(s):

Sequence Data ◽

F1 Hybrids ◽

Species Boundaries ◽

Hybrid Breakdown ◽

Genome Wide ◽

Dynamic Scenario ◽

Stable Species ◽

Species Pairs ◽

History Of ◽

Tropical Eels

AbstractGenomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genusAnguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.

Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?

Systematic Biology ◽

10.1093/sysbio/syz072 ◽

2019 ◽

Vol 69 (4) ◽

pp. 708-721 ◽

Cited By ~ 3

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

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.]

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.

Verticillium Systematics and Evolution: How Confusion Impedes Verticillium Wilt Management and How to Resolve It

Phytopathology ◽

10.1094/phyto-11-13-0315-ia ◽

2014 ◽

Vol 104 (6) ◽

pp. 564-574 ◽

Cited By ~ 87

Author(s):

Patrik Inderbitzin ◽

Krishna V. Subbarao

Keyword(s):

Plant Pathogens ◽

Sequence Data ◽

Current System ◽

Species Boundaries ◽

Individual Species ◽

Distribution Data ◽

Dna Sequence Data ◽

Taxonomic History ◽

History Of ◽

Taxonomic Changes

Verticillium wilts are important vascular wilt diseases that affect many crops and ornamentals in different regions of the world. Verticillium wilts are caused by members of the ascomycete genus Verticillium, a small group of 10 species that are related to the agents of anthracnose caused by Colletotrichum species. Verticillium has a long and complicated taxonomic history with controversies about species boundaries and long overlooked cryptic species, which confused and limited our knowledge of the biology of individual species. We first review the taxonomic history of Verticillium, provide an update and explanation of the current system of classification and compile host range and geographic distribution data for individual species from internal transcribed spacer (ITS) GenBank records. Using Verticillium as an example, we show that species names are a poor vehicle for archiving and retrieving information, and that species identifications should always be backed up by DNA sequence data and DNA extracts that are made publicly available. If such a system were made a prerequisite for publication, all species identifications could be evaluated retroactively, and our knowledge of the biology of individual species would be immune from taxonomic changes, controversy and misidentification. Adoption of this system would improve quarantine practices and the management of diseases caused by various plant pathogens.

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

Molecular Ecology ◽

10.1111/mec.12023 ◽

2012 ◽

Vol 22 (3) ◽

pp. 787-798 ◽

Cited By ~ 317

Author(s):

Catherine E. Wagner ◽

Irene Keller ◽

Samuel Wittwer ◽

Oliver M. Selz ◽

Salome Mwaiko ◽

...

Keyword(s):

Adaptive Radiation ◽

Sequence Data ◽

Lake Victoria ◽

Species Boundaries ◽

Genome Wide

Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

Journal of Heredity ◽

10.1093/jhered/esz032 ◽

2019 ◽

Cited By ~ 1

Author(s):

Haige Han ◽

Kenneth Bryan ◽

Wunierfu Shiraigol ◽

Dongyi Bai ◽

Yiping Zhao ◽

...

Keyword(s):

Sequence Data ◽

Genomic Diversity ◽

Data Sets ◽

Domestic Horse ◽

Snp Data ◽

Genome Wide ◽

History Of ◽

Genomic Characterization ◽

Mongolian Horse ◽

Free Ranging

Abstract The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2015.03.027 ◽

2015 ◽

Vol 88 ◽

pp. 55-63 ◽

Cited By ~ 21

Author(s):

Gary Longo ◽

Giacomo Bernardi

Keyword(s):

Evolutionary History ◽

Sequence Data ◽

Genome Wide ◽

History Of

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

10.1101/019745 ◽

2015 ◽

Cited By ~ 3

Author(s):

Santiago Herrera ◽

Timothy M. Shank

Keyword(s):

Species Delimitation ◽

Sequence Data ◽

Conclusive Evidence ◽

Species Boundaries ◽

Effective Population ◽

Dna Sequence Data ◽

Genome Wide ◽

Phylogenetic Resolution ◽

Specific Factors ◽

Morphological Species

Species delimitation is problematic in many taxa due to the difficulty of evaluating predictions from species delimitation hypotheses, which chiefly relay on subjective interpretations of morphological observations and/or DNA sequence data. This problem is exacerbated in recalcitrant taxa for which genetic resources are scarce and inadequate to resolve questions regarding evolutionary relationships and uniqueness. In this case study we demonstrate the empirical utility of restriction site associated DNA sequencing (RAD-seq) by unambiguously resolving phylogenetic relationships among recalcitrant octocoral taxa with divergences greater than 80 million years. We objectively infer robust species boundaries in the genusParagorgia, which contains some of the most important ecosystem engineers in the deep-sea, by testing alternative taxonomy-guided or unguided species delimitation hypotheses using the Bayes factors delimitation method (BFD*) with genome-wide single nucleotide polymorphism data. We present conclusive evidence rejecting the current morphological species delimitation model for the genusParagorgiaand indicating the presence of cryptic species boundaries associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences in divergent taxa cannot be assessed in terms of absolute time, but depend on taxon-specific factors such as mutation rate, generation time and effective population size. We show that classic morphological taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypothesis. Our results pave the way for addressing further questions in biogeography, species ranges, community ecology, population dynamics, conservation, and evolution in octocorals and other marine taxa.

Frequent paternal mitochondrial inheritance and rapid haplotype frequency shifts in copepod hybrids

10.1101/2021.05.10.443310 ◽

2021 ◽

Author(s):

Jeeyun Lee ◽

Christopher S Willett

Keyword(s):

Population Genetics ◽

Mitochondrial Dna ◽

Haplotype Frequency ◽

Total Sample ◽

F1 Hybrids ◽

Hybrid Breakdown ◽

Paternal Leakage ◽

Marine Copepod ◽

Phylogenetic Studies ◽

Genome Wide

Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.