A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics

Systematic Biology, Journal Year: 2018, Volume and Issue: 67(6), P. 1061 - 1075

Published: April 3, 2018

As we collect range-wide genetic data for morphologically-defined species, increasingly unearth evidence cryptic diversity. Delimiting this diversity is challenging, both because the divergences span a continuum and lack of overt morphological differentiation suggests divergence has proceeded heterogeneously. Herein, address these challenges as diagnose describe species in three co-occurring groups Australian lizards. By integrating genomic with on hybridization introgression from contact zones, explore several approaches-and their relative benefits weaknesses-for testing validity lineages. More generally, advocate that delimitations must consider whether lineages are likely to be durable persistent through evolutionary time.

Language: Английский

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A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 162, P. 107204 - 107204

Published: May 18, 2021

There are particular challenges in defining the taxonomic status of recently radiated groups due to low level phylogenetic signal. Members Salmo trutta species-complex, which mostly evolved during and following Pleistocene, show high morphological ecological diversity that, along with their very wide geographic distribution, have led description 47 extant nominal species. However, many these species not been supported by previous studies, could be partly lack significant genetic differences among them, limited resolution offered molecular methods previously used, as well often local scale studies. The development next-generation sequencing (NGS) related analytical tools enhanced our ability address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) 15,169 filtered SNPs mitochondrial DNA (mtDNA) D-loop sequences were combined assess relationships 166 brown trouts representing 21 described three undescribed collected from 84 localities throughout natural distribution Europe, west Asia, North Africa. data analysed using different clustering algorithms (admixture analysis discriminant principal components-DAPC), a Bayes Factor Delimitation (BFD) test, tree reconstruction, gene flow tests (three- four-population tests), Rogue taxa identification tests. Genomic contributions Atlantic lineage trout found all major sea basins excluding African Aral Sea basins, suggesting introgressive hybridization native driven stocking strains lineage. After removing noise caused trout, admixture clusters DAPC based on GBS data, respectively, resolved 11 13 species, also BFD test results. Our results suggest that between lineages has probably played an important role origin several putative including S. marmoratus, carpio, farioides, pellegrini, caspius (in Kura River drainage) sp. Danube basin. Overall, support multi-species taxonomy for trouts. They resolve some Adriatic-Mediterranean Black drainages members closely genomic may need revision. any final conclusions pertaining complex should integrative approach combining genomic, morphological, data. To avoid conservation complexes like trouts, it is suggested describe populations instead describing only morphologically differentiated single type populations.

Language: Английский

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DArTseq-based analysis of genomic relationships among species of tribe Triticeae

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: Oct. 31, 2018

Abstract Precise utilization of wild genetic resources to improve the resistance their cultivated relatives environmental growth limiting factors, such as salinity stress and diseases, requires a clear understanding genomic relationships. Although seriously criticized, analyzing these relationships in tribe Triticeae has largely been based on meiotic chromosome pairing hybrids wide crosses, specialized labourious strategy. In this study, DArTseq, an efficient genotyping-by-sequencing platform, was applied analyze genomes 34 species. We reconstructed phylogenetic among diploid polyploid Aegilops Triticum species, including hexaploid wheat. Tentatively, we have identified that are likely involved evolution five species , which remained unresolved for decades. Explanations cast light progenitor A complex status B/G Emmer Timopheevi lineages wheat also provided. This study has, therefore, demonstrated DArTseq genotyping can be effectively plants, especially where genome sequence information not available.

Language: Английский

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Restore and Renew: a genomics‐era framework for species provenance delimitation

Restoration Ecology, Journal Year: 2018, Volume and Issue: 27(3), P. 538 - 548

Published: Oct. 10, 2018

Here we present “Restore and Renew,” a replicable framework for gathering interpreting evolutionary, ecological, genomic data in support of restoration practices. In an era rapid climatic change continuous widespread clearing, revegetation projects need to focus on producing resilient long‐term self‐sustaining populations. Restore Renew expands current knowledge genetic provenance via genome‐scan data, environmental niche modeling (ENM), site‐specific climate information. The sampling strategy is obtain leaf tissue representing the distributions over 100 species commonly used restoration. We apply generalized dissimilarity genome‐wide single nucleotide polymorphism datasets from hundreds samples. Species‐specific local provenances are obtained using model that represents observed patterns variation across landscape. Climate implemented interpret boundaries context future conditions at specified site. Results presented easy‐to‐use webtool ( www.restore‐and‐renew.org.au ), where user simply selects their site interest target size distribution provenance. Although not prescriptive, it allows practitioners make informed decisions source material from, fulfill scenario choice. Two examples, Westringia fruticosa Acacia suaveolens , demonstrate how analytical pipeline responds different ecological evolutionary patterns. has multiple applications biodiversity management will continue evolve with new analytical/interpretative outputs.

Language: Английский

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Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species

Ichthyology & Herpetology, Journal Year: 2021, Volume and Issue: 109(3)

Published: Sept. 28, 2021

Species delimitation is a first step for realizing the extent of biodiversity and relevant all downstream applications in biology. The production large genome-scale datasets non-model organisms combined with development methodological tools have allowed researchers to examine fine-scale processes speciation such as timing origin, degree migration, population-size changes, selection, drift, recombination. Studies using reptiles amphibians have, part, paved way use methods exploring delimitation. While these methodologies improved our understanding diversification, are far from agreeing upon set criteria delimit species. In cases where genetic lineages discovered that unique geographic areas, usually agree two entities exist. Disagreement about taxonomic status often centers on reproductive isolation between taxa probability remaining distinct. However, frequently inferred without examining gene flow, nature hybrid zones, or determining amount type introgression. Here, we review some vexing problems delimiting amphibians, which include by distance, flow differential allelic introgression, zone dynamics, genomic islands divergence. We also respond recent literature criticizing model-based species North American snakes context advancements address how scientists can move forward studies speciation.

Language: Английский

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Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

Molecular Ecology Resources, Journal Year: 2019, Volume and Issue: 19(6), P. 1578 - 1592

Published: Sept. 4, 2019

Natural history museums harbour a plethora of biological specimens which are potential use in population and conservation genetic studies. Although technical advancements museum genomics have enabled genome-wide markers to be generated from aged specimens, the suitability these data for robust inference is not well characterized. The aim this study was test utility by assessing validity single nucleotide polymorphism (SNP) derived such samples. To achieve this, we thousands SNPs 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional samples (i.e. that were collected with primary intent DNA analysis) 113 fresh tissue (cryopreserved liver/muscle) using restriction site-associated marker approach (DArTseq™ ). Thousands successfully most (with mean age 44 years, ranging 5 123 years), although 38% did provide useful data. These exhibited higher error rates contained significantly more missing compared samples, likely due considerable fragmentation. However, based on simulation results, level genotyping had negligible effect structure species. We identify bias towards low diversity older appears compromise temporal inferences diversity. This demonstrates RADseq-based method produce reliable SNP specimens.

Language: Английский

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Exaiptasia diaphana from the great barrier reef: a valuable resource for coral symbiosis research

Symbiosis, Journal Year: 2020, Volume and Issue: 80(2), P. 195 - 206

Published: Feb. 6, 2020

Language: Английский

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Wildlife forensics: A boon for species identification and conservation implications

Forensic Science International, Journal Year: 2020, Volume and Issue: 317, P. 110530 - 110530

Published: Oct. 3, 2020

Language: Английский

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Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid‐zone mammals with high dispersal capacity

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(5)

Published: May 1, 2023

Abstract Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial‐genetic structure. This particularly pertinent research in arid‐zone mammals due to challenges associated unique life history traits, such as boom‐bust population dynamics and long‐distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites testing three explicit landscape genetic hypotheses (isolation‐by‐distance, isolation‐by‐barrier, isolation‐by‐resistance) suite small, the Pilbara region Western Australia. Using clustering algorithms, Mantel tests, linear mixed effects models, compare functional connectivity between marker types across species, including one marsupial, Ningaui timealeyi , two native rodents, Pseudomys chapmani P. hermannsburgensis . resolved subtle structuring not detected by N. where clusters were identified. Furthermore, stronger signatures isolation‐by‐distance isolation‐by‐resistance when using SNPs, model selection based on tended identify more complex resistance surfaces (i.e., composite multiple environmental layers) best‐performing models. While found limited evidence physical barriers all that topography, substrate, soil moisture main drivers shaping connectivity. Our demonstrates new analytical tools can novel ecological insights into arid landscapes, potential application conservation management through identifying corridors mediate impacts ongoing habitat fragmentation region.

Language: Английский

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Systematics of the Little Red Tree Frog, Litoria rubella (Anura: Pelodryadidae), with the description of two new species from eastern Australia and arid Western Australia

Zootaxa, Journal Year: 2025, Volume and Issue: 5594(2), P. 269 - 315

Published: Feb. 27, 2025

The Litoria rubella species complex (L. capitula and L. rubella) is distributed across much of continental Australia, southern New Guinea, the Tanimbar Islands Indonesia, in habitats ranging from deserts to tropical forests. We carried out an appraisal molecular genetics, advertisement calls, morphological variation complex. Analyses thousands nuclear gene SNPs nucleotide sequences mitochondrial ND4 identified four reciprocally monophyletic lineages both marker types, two exclusively one Australia/New Guinea Islands. calls three on Australia have overlapping but significant differences number pulses notes, dominant frequency, call duration, particularly where come into contact. lineage genetically morphologically distinct represents capitula. Molecular data together support recognition Australia: a widespread central arid northern tropics lineage, western zone eastern mesic lineage. sensu stricto Kimberley Top End regions, zone, Murray Darling Basin, making it extreme climate-generalist. SNP indicates that has flow north Lake Eyre Basin not south, possible ring species. does differ appearance or geographically disjunct phylogenetically distinct. primarily east Great Dividing Range Cape York Queensland. redescribe stricto, describe as new species, pyrina sp. nov. larisonans respectively. Although are similar, they do overlap distribution, identification non-problematic. can be distinguished at contact zones by having with higher frequency. investigated history morphology type for mystacina designate nomen dubium. Australian likely conservation status Least Concern abundant, no threats. Little known about outside few existing museum specimens.

Language: Английский

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