Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(24), P. 5195 - 5213

Published: Nov. 7, 2018

Abstract Understanding the evolutionary history of diversifying lineages and delineation evolutionarily significant units species remains major challenges for biology. Low‐cost representational sampling genome single nucleotide polymorphisms shows great potential at temporal scales that are typically focus delimitation phylogeography. We apply these markers to a case study freshwater turtle, Emydura macquarii , whose systematics has so far defied resolution, bring light dynamic system substantive allopatric diverging on independent trajectories, but held back in process speciation by low level episodic exchange alleles across drainage divides various timescales. In context low‐level gene flow, is often reticulate, rather than bifurcating process. argue needs take into account pattern ancestry descent allopatry together with recent contemporary processes dispersal flow retard obscure divergence. Underpinned strong lineage diagnosability, this combined approach provides means addressing incompletely isolated populations uncommon, recurrent studies delimitation, situation likely be frequently encountered. Taxonomic decisions cases require subjective judgements. Our strategy, which adds an additional objectivity before subjectivity applied, reduces risk taxonomic inflation can accompany approaches delimitation.

Language: Английский

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Two new species of treefrog (Pelodrydidae: Litoria) from southern New Guinea elucidated by DNA barcoding

Zootaxa, Journal Year: 2019, Volume and Issue: 4609(3)

Published: May 24, 2019

New Guinea is home to the world’s most diverse insular frog biota, but only a small number of taxa have been included in genetically informed assessments species diversity. Here we describe two new treefrog genus Litoria that were first flagged during genetic diversity (DNA barcoding) and are currently known from holotypes. pterodactyla sp. nov. large green graminea complex hill forests Western Province, Papua third member this group south Central Cordillera. vivissimia small, spike-nosed mid-montane on It morphologically very similar pronimia, occurs nearly 1000 m higher than any locality for species. More extensive assessment frogs seems certain reveal many more as-yet-unrecognised complexes

Language: Английский

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Multilevel fine-scale diversity challenges the ‘cryptic species’ concept

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: May 1, 2019

'Cryptic' species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic definition was suggested for those which manifest low morphological, but considerable genetic, disparity. As case study we unique material from charismatic group of nudibranch molluscs genus Trinchesia European waters to reveal three new and demonstrate they show dual nature: on one hand, can be considered 'cryptic' complex due their overall similarity, other stable morphological differences as well molecular demonstrated every complex. Thus, this equally named 'cryptic', 'pseudocryptic' or 'non-cryptic'. We also evidence extremely rapid speciation rate link with epigenetics. Available metazoan-wide data, study, unsuitability concept because degree crypticity represents continuum when finer multilevel scale applied uncover more narrowly defined making addition 'species' redundant. Morphological methods should concordance form fine-scale taxonomic framework, not necessarily implying only posteriori transformation exclusively molecular-based into morphologically-defined ones. Implications have importance many fields, including conservation biology biodiversity assessments.

Language: Английский

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Estimating Global Biodiversity: The Role of Cryptic Insect Species

Systematic Biology, Journal Year: 2022, Volume and Issue: 72(2), P. 391 - 403

Published: Oct. 27, 2022

Abstract How many species are there on Earth and to what groups do these belong? These fundamental questions span systematics, ecology, evolutionary biology. Yet, recent estimates of overall global biodiversity have ranged wildly, from the low millions trillions. Insects a pivotal group for estimates. make up roughly half currently described extant (across all groups), with ~1 million species. Insect diversity is also crucial because other taxa that may be unique each insect host species, including bacteria, apicomplexan protists, microsporidian fungi, nematodes, mites. Several projections total (described undescribed) converged ~6 However, not incorporated morphologically cryptic revealed by molecular data. Here, we estimate extent diversity. We perform systematic review studies used explicit species-delimitation methods multilocus morphology-based contains (on average) 3.1 then use project number their distribution among major groups. Our suggest range 563 2.2 billion [Biodiversity; species; insects; delimitation; richness.]

Language: Английский

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Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(1), P. 40 - 57

Published: May 6, 2021

Abstract In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden species diversity. Typically, phylogenetic and distance-based approaches are used demonstrate the distinctness clades justify recognition new species. However, this approach does not account for gene flow, spatial, environmental processes that can obfuscate inference bias delimitation. As case study, we sequenced genome-wide exons introns evince underlie diversification Philippine Puddle Frogs—a group widespread, phenotypically conserved, exhibits geographically based structure. We showed widely adopted tree- inferred up 20 species, compared genomic analyses an optimal number five distinct groups. Using suite clustering, admixture, network analyses, extensive admixture among groups elucidate two specific ways in which flow cause overestimations diversity: 1) admixed populations be as lineages characterized by long branches phylograms; 2) appear genetically divergent, even from their parental when simple measures distance used. relationship between mitochondrial nuclear $p$-distances decoupled clades, leading erroneous estimates distances and, consequently, Additionally, was also biased spatial processes. Overall, diversity Frogs predominantly comprise metapopulation arose through complex patterns isolation-by-distance, isolation-by-environment opposed divergence. Our findings suggest speciation may major process underlying observed many taxonomic methods overestimate presence flow. [Cryptic species; flow; introgression; isolation-by-distance; isolation-by-environment; network; delimitation.]

Language: Английский

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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Animals, Journal Year: 2023, Volume and Issue: 13(3), P. 471 - 471

Published: Jan. 29, 2023

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles—lizards and snakes—recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity phenotypic genomic traits, resources in non-avian have accumulated more slowly than they mammals birds, remaining amniotes. Here we review remarkable natural history reptiles, focus on physical characteristics, sequence compositional patterns that key axes variation across We argue high evolutionary can fuel new generation whole-genome phylogenomic analyses. A survey phylogenetic investigations shows capture-based approaches are commonly used, studies markers known ultraconserved elements (UCEs) especially well represented. However, many other types exist increasingly being mined from genome assemblies silico, including some greater information potential UCEs for certain investigations. discuss importance high-quality methods bioinformatically extracting range marker sets assemblies. Finally, encourage herpetologists working genomics, genetics, biology, fields to work collectively towards building squamates, rival those already place birds. Overall, development this cross-amniote tree life will contribute illuminate interesting dimensions biodiversity broader

Language: Английский

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An overview of speciation and species limits in birds

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: April 6, 2021

Abstract Accurately determining avian species limits has been a challenge and work in progress for most of century. It is fascinating but difficult problem. Under the biological concept, only lineages that remain essentially independent when they are sympatry clearly species. Otherwise, there no clear line yet found marks pair diverging (e.g., allopatry) become different enough to warrant full status. Also, with more data, often require reevaluation. The process divergence speciation itself very complex focus intense research. Translating what we understand into taxonomic names can be challenging. A series issues important. Single-locus criteria unlikely convincing. Genetic independence not requirement, degree (gene flow) needs considered opportunity gene flow complete. Time-based (limits determined by time separation) unsatisfactory, though integrating effectively our datasets warranted. We need disentangle data signal due neutral processes vs. selection prioritize latter as main driver speciation. Assortative mating also likely an adequate criterion limits. Hybridization important than ever, condition being treated evenly taxonomy: evolutionary trysts 2 or stuck together through just short over long periods. Comparative methods use occurs between good contact infer among allopatric forms gold standard, inaccurate controversial. Species-level taxonomy birds unsettled some time. While study never exciting dynamic, silver bullet delimitation, nor it will ever one. Careful using integrative comparative framework promising way forward.

Language: Английский

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A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest‐species group

Insect Science, Journal Year: 2024, Volume and Issue: unknown

Published: April 1, 2024

Abstract Identifying cryptic species poses a substantial challenge to both biologists and naturalists due morphological similarities. Bemisia tabaci is complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting delimiting evolution this has proved problematic. To develop comprehensive framework for delimitation identification, we evaluated performance distinct data sources individually in combination numerous samples B. acquired worldwide. Distinct datasets include full mitogenomes, single‐copy nuclear genes, restriction site‐associated DNA sequencing, geographic range, host speciation, reproductive compatibility datasets. Phylogenetically, our well‐supported topologies generated from three dense molecular markers highlighted evolutionary divergence suggested that serve as accurate representation diversity. Reproductive facilitated identification at least 17 different within samples. Native range information provides complementary assessment recognition, while provide low rate resolution. We further summarized performances classification when compared with compatibility, indicating mtCOI divergence, markers, recognition. Finally, represent model understanding untangling complexes based on evidence study previously published articles.

Language: Английский

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Delimitation of cryptic species drastically reduces the geographical ranges of marine interstitial ghost-worms (Stygocapitella; Annelida, Sedentaria)

Molecular Phylogenetics and Evolution, Journal Year: 2019, Volume and Issue: 143, P. 106663 - 106663

Published: Oct. 25, 2019

Language: Английский

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Conservation status of the world's skinks (Scincidae): Taxonomic and geographic patterns in extinction risk

Biological Conservation, Journal Year: 2021, Volume and Issue: 257, P. 109101 - 109101

Published: April 20, 2021

Language: Английский

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