Machine learning approaches delimit cryptic taxa in a previously intractable species complex

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 195, С. 108061 - 108061

Опубликована: Март 12, 2024

Язык: Английский

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Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)

Systematic Biology, Год журнала: 2022, Номер 72(1), С. 179 - 197

Опубликована: Сен. 28, 2022

Abstract Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis phylogeography taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters genome-scale data as strong initial evidence speciation most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We now hypotheses linking trait differentiation to specific mechanisms divergence with increasingly large sets. Integrative can, therefore, reflect understanding how each axis variation relates underlying processes, nomenclature for lineages. illustrate this approach here Seal Salamanders (Desmognathus monticola) introduce new unsupervised machine-learning delimitation. Plethodontid salamanders are renowned their morphological conservatism despite extensive phylogeographic divergence. discover 2 geographic genetic clusters, which demographic spatial ecology gene flow provide robust support ecogeographic limited phenotypic These integrated (e.g., spatially localized reduced migration) reflected emergent properties expected reinforcement ethological isolation selection against hybrids). Their prima facie species-level distinctiveness, supported by along axes such behavior, geography, climate suggest ecological basis subsequent through prezygotic isolation. As sets grow more comprehensive, species-delimitation tested, rejected, or corroborated hypotheses, providing reciprocal illumination processes integrative taxonomies. [Desmognathus; taxonomy; machine learning; delimitation.]

Язык: Английский

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Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Molecular Ecology, Год журнала: 2023, Номер 32(17), С. 4844 - 4862

Опубликована: Июль 29, 2023

Abstract Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately may have unique even conflicting evolutionary histories. Phylogenetic reconstructions from these can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance discordant histories between the mitochondrial genomes) has been widely documented, but its causes often considered idiosyncratic inscrutable. We show that case in Todiramphus kingfishers be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely result explosive diversification history this genus. For kingfishers, quartet frequencies reveal genome is dominated topologies, with none internal branches our consensus tree recovered >50% gene trees. Meanwhile, lack inter‐species shared ancestry, non‐significant pairwise tests for flow, little evidence meaningful migration edges species, leads to conclusion flow cannot explain we observe. This combined discordance, hallmark ILS, us conclude observe results specifically deep coalescence genome. Based on study, hypothesize similar demographic other ‘great speciator’ taxa across Indo‐Pacific predispose groups high levels ILS likelihoods

Язык: Английский

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Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds

Molecular Phylogenetics and Evolution, Год журнала: 2022, Номер 179, С. 107671 - 107671

Опубликована: Ноя. 25, 2022

Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite nature speciation process, implementation conservation policies relies on delimitation species significant units (ESUs). Puffinus shearwaters are globally distributed threatened pelagic seabirds. Due to remarkable morphological status group has been under intense taxonomic debate for past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) genotype subspecies North Atlantic Mediterranean across their entire geographical range. We assess phylogenetic relationships population structure among within group, evaluate boundaries, characterise genomic landscape divergence. find that current taxonomies not supported data propose more accurate taxonomy integrating information with other sources evidence. Our results show several taxon pairs at different stages continuum. study emphasises potential resolve uncertainties, which can help focus management actions relevant taxa, even if they do necessarily coincide rank species.

Язык: Английский

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Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 189, С. 107939 - 107939

Опубликована: Окт. 5, 2023

Язык: Английский

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triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones

Heredity, Год журнала: 2025, Номер unknown

Опубликована: Апрель 12, 2025

Abstract Hybridization provides a window into the speciation process and reshuffles parental alleles to produce novel recombinant genotypes. Presence or absence of specific hybrid classes across zone can provide support for various modes reproductive isolation. Early generation be distinguished by their combination index interclass heterozygosity, which estimated with molecular data. Hybrid heterozygosity are routinely calculated studies zones, but available resources next-generation sequencing datasets computationally demanding tools visualizing triangle plots lacking. Here, we resource identifying ancestry-informative markers (AIMs) from single nucleotide polymorphism (SNP) datasets, calculating relationship as plot. Our methods implemented in R package triangulaR . We validate our on an empirical dataset simulations genetic data between two groups at low, medium, high levels divergence. accurate precise estimates sample sizes low five individuals per group, similar error another program estimation, bgchm explore allele frequency difference thresholds AIM identification, how this threshold influences accuracy precision estimates. contextualize interpretation describing theoretical expectations under Hardy-Weinberg Equilibrium recommendations best practices AIMs building plots.

Язык: Английский

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Spatiotemporal Dynamics of Non‐Ecological Speciation in Rubyspot Damselflies (Hetaerina spp.)

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Май 15, 2025

ABSTRACT Non‐ecological speciation is a common mode of speciation, which occurs when allopatric lineages diverge in the absence pronounced ecological differences. Yet, relative to other mechanisms, non‐ecological remains understudied. Numerous damselfly clades are characterised as non‐adaptive radiations (the result several rounds without subsequent divergence), but there few for we have detailed understanding spatiotemporal dynamics divergence. Recent phylogeographic analyses demonstrate that American rubyspot damselflies ( Hetaerina americana sensu lato) actually comprise at least two cryptic coexist sympatrically across most Mexico. To broaden our diversification lineages, investigated history smoky titia ) using genomic data collected Central and North America. Unexpectedly, found evidence reproductive isolation between highly genetically differentiated Pacific Atlantic H. narrow secondary contact zone on Isthmus Tehuantepec, We then fit models historical demography both lato place these comparisons temporal context. Our findings indicate split more recently than broadly sympatric within lato, supporting key assumptions model demonstrating pairs sister different stages cycle.

Язык: Английский

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Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum inPipilotowhees

Evolution, Год журнала: 2022, Номер 77(3), С. 852 - 869

Опубликована: Дек. 28, 2022

Abstract Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid also spatially complex, shift time, and even lead to the formation lineages with right combination dispersal vicariance. We reassessed Sibley’s (1950) gradient between Collared Towhee (Pipilo ocai) Spotted maculatus) in Central Mexico test whether it conformed typical tension-zone cline model. By comparing historical modern data, we found that centers for genetic phenotypic traits have not shifted course 70 years. This equilibrium suggests secondary contact these species, which originally diverged 2 million years ago, likely dates Pleistocene. Given amount mtDNA divergence, parental ends very low autosomal nuclear differentiation (FST = 0.12). Dramatic coincident shifts throat color suggest possibility sexual selection as factor differential introgression, while contrasting green back hints at role natural selection. Supporting idea continuum clinal lineage formation, towhee analyzed one population under isolation-by-distance, two-population cline, three experiencing divergence gene flow. In middle gradient, has become partly isolated, due forested habitat shrinking fragmenting moved upslope after last glacial maximum stark environmental transition. system offers window into potential outcomes hybridization across dynamic landscape including creation novel genomic combinations incipient lineages.

Язык: Английский

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Multiple contact zones and karyotypic evolution in a neotropical frog species complex

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Янв. 11, 2024

Abstract Previous studies of DNA sequence and karyotypic data have revealed high genetic diversity in the Physalaemus cuvieri – ephippifer species complex—a group small leptodactylid frogs South America. To date, seven major lineages been recognized this group, with delimitation tests supporting four to them as valid species. Among these, only P. shows heteromorphic sex chromosomes, but implications cytogenetic divergence for evolution are unknown. We analyzed karyotypic, mitochondrial DNA, 3RAD genomic characterize a putative contact zone between Lineage 1, finding evidence admixture evolution. also describe preliminary two other members complex—Lineage 1 3 . Our study sheds new light on evolutionary relationships complex, suggesting an important role its history underscoring importance hybridization mechanism chromosome amphibians.

Язык: Английский

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Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators

Evolution Letters, Год журнала: 2024, Номер 8(6), С. 813 - 827

Опубликована: Июль 26, 2024

Abstract The paradox of the great speciators describes a contradictory biogeographic pattern exhibited by numerous avian lineages in Oceania. Specifically, these display broad geographic distributions across region, implying strong over-water dispersal capabilities; yet, they also repeated genetic and phenotypic divergence—even between geographically proximate islands—implying poor inter-island capabilities. One group originally cited as evidence for this is dwarf kingfishers genus Ceyx. Here, using genomic sequencing comprehensive sampling monophyletic Ceyx radiation from northern Melanesia, we find repeated, deep divergence no gene flow found on islands, providing an exceptionally clear example speciators. A dated phylogenetic reconstruction suggests significant burst diversification occurred rapidly after reaching 3.9 2.9 MYA. This supports shift net rate, concordant with expectations “colonization cycle” hypothesis, which implies historical dispersiveness among speciator during evolutionary past. present formalized framework that explains how founder effects shifting selection pressures highly dispersive genotypes are only ultimate causes needed to generate Within framework, emphasize lineage-specific traits island-specific abiotic factors will result varying levels pressure against dispersiveness, caused eco-evolutionary mechanisms. Overall, highlight understanding patterns helped us cohesive provides rigorous mechanistic explanation emergence radiations island archipelagoes globe.

Язык: Английский

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