dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Methods in Ecology and Evolution, Год журнала: 2022, Номер 13(10), С. 2150 - 2158

Опубликована: Июнь 11, 2022

Abstract Innumerable approaches to analyse genetic data are now available guide conservation, ecological and agricultural projects. However, streamlined accessible tools needed bring these within the reach of a broader user base. dartR was released in 2018 lessen intrinsic complexity analysing single nucleotide polymorphisms (SNPs) dominant markers (presence/absence amplified sequence tags) by providing user‐friendly quality control marker selection functions. users have grown steadily since its release provided valuable feedback on their interaction with package allowing us enhance capabilities. Here, we present Version 2 . In this version, substantially increased number functions from 45 144. addition improved functionality, focused enhancing experience extending plot customisation, function standardisation, increasing support speed. provides for various stages data, manipulation reporting. many importing, exporting linking other packages, provide an easy‐to‐navigate conduit between generation analysis options already via packages. We also implemented simulation whose results can be analysed seamlessly several As more methods mature inform envision that platforms will play crucial role translating science into practice.

Язык: Английский

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Acknowledging more biodiversity without more species

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(40)

Опубликована: Сен. 25, 2023

Delimiting and naming biodiversity is a vital step toward wildlife conservation research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can spent effectively objectively. To date, newly discovered lineages typically are either left undescribed thus remain unprotected or being erroneously proposed as new despite mixed evidence completed speciation, in turn contributing to emerging problem of taxonomic inflation. Inspired by recent conceptual methodological progress, we propose standardized workflow combines phylogenetic hybrid zone analyses genomic datasets (“genomic taxonomy”), which phylogeographic do not freely admix ranked species, while those have remained fully genetically compatible subspecies. In both cases, encourage their formal naming, diagnosis, description promote social awareness biodiversity. The use loci throughout genome overcomes unreliability widely used barcoding genes when patterns complex, evaluation divergence reproductive isolation unifies long-opposed concepts lineage biological species. We suggest shift assessments from single level (species) two-level hierarchy (species subspecies) will lead more balanced perception intraspecific interspecific diversity valued adequately protected.

Язык: Английский

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The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

Systematic Biology, Год журнала: 2019, Номер 69(1), С. 184 - 193

Опубликована: Июнь 5, 2019

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these often are regarded as conclusive support for taxonomic changes. However, most MSC-based methods have well-known unmet assumptions. Uncritical application genetic-based approaches (without due consideration sampling design, effects a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, population structure) can lead to over-splitting species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding limitations, especially cases well-studied, geographically variable, parapatrically distributed complexes. We consider points with respect historically controversial group, American milksnakes (Lampropeltis triangulum complex), using analysis (Ruane et al. 2014). show over-reliance program Bayesian Phylogenetics Phylogeography, without adequate its assumptions resulted this study. Several hypothesized instead appear represent arbitrary slices continuous geographic clines. conclude best available evidence supports three, rather than seven, within complex. More generally, recommend coalescent-based incorporate thorough variation carefully examine putative contact zones among delimited before making

Язык: Английский

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Genetic evidence supports three previously described species of greater glider, Petauroides volans, P. minor, and P. armillatus

Scientific Reports, Год журнала: 2020, Номер 10(1)

Опубликована: Ноя. 6, 2020

Abstract The identification and classification of species are essential for effective conservation management. This year, Australia experienced a bushfire season unprecedented severity, resulting in widespread habitat loss mortality. As result, there has been an increased focus on understanding genetic diversity structure across the range individual to protect resilience face climate change. greater glider ( Petauroides volans ) is large, gliding eucalypt folivore. nocturnal arboreal marsupial wide distribution eastern considered sole extant member genus . Differences morphology have led suggestions that one accepted actually three. would substantial impacts management, particularly given recent history declining populations, coupled with extensive wildfires. Until now, evidence support multiple lacking. For first time, we used DArT sequencing tissue samples from regions found three operational taxonomic units (OTUs) representing northern, central southern groups. OTUs were also supported by our morphological data. These findings important implications management highlight role genetics helping assess status.

Язык: Английский

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Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species

Ichthyology & Herpetology, Год журнала: 2021, Номер 109(3)

Опубликована: Сен. 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.

Язык: 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, Год журнала: 2019, Номер 19(6), С. 1578 - 1592

Опубликована: Сен. 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.

Язык: Английский

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How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake

Molecular Phylogenetics and Evolution, Год журнала: 2021, Номер 162, С. 107194 - 107194

Опубликована: Май 1, 2021

Язык: Английский

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Evidence of fine-scale genetic structure for reef manta rays Mobula alfredi in New Caledonia

Endangered Species Research, Год журнала: 2022, Номер 47, С. 249 - 264

Опубликована: Янв. 5, 2022

Our understanding of the genetic connectivity manta ray populations and drivers that shape population structure is still limited. This information crucial to identify spatial boundaries discrete guide decisions on units conserve. In this study, we used genome-wide single nucleotide polymorphisms (SNPs) assess diversity reef rays Mobula alfredi at a local scale within New Caledonia regionally in western Pacific Ocean. We provide first evidence fine-scale differentiation M. , found between 3 cleaning station aggregation sites (n = 65 samples, N 2676 SNPs, F ST 0.01, p < 0.0001). Furthermore, was evident regional individuals from 73) East Australia 19) basis statistics (3619 0.096, 0.0001) clustering algorithms, with unidirectional gene flow detected east (New Caledonia) west (Australia). These results reveal can form genetically distinct groups relatively small geographic range highlights need consider when designating management for conservation action planning.

Язык: Английский

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The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation

Systematic Biology, Год журнала: 2022, Номер 72(2), С. 357 - 371

Опубликована: Авг. 22, 2022

Abstract With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability draw accurate boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa determine if assortative mating or selection against hybrids exists (supporting the presence two distinct species), alternatively is random among genotypes admixture adjacent populations gradual continuous species). Here, we test alternative hypotheses for pairs named at American milksnake (Lampropeltis triangulum) complex. A prior morphological found areas intergradation taxa, concluded represented geographical races polytypic species. In contrast, subsequent gene sequence data, but with near zones, hypothesized boundaries zones. At zone proposed L. triangulum Lampropeltis gentilis, examined $\sim$700 km-wide transect across states Kansas Missouri, reduced-representation genomic-level sequencing, opposing taxonomic hypotheses. Our analyses included examinations population structure, fixed differences, cline-fitting, an index analysis. These all supported cline broad intergrade forms triangulum, thus providing strong support in this region (and no recognition gentilis as second elapsoides (but variously treated subspecies by different researchers) Kentucky Tennessee, re-evaluated data. case, indicated sympatry reproductive isolation strongly conclude detailed studies based on either genetic are essential distinguishing intraspecific case widely continuously distributed taxa. [Contact zones; speciation; concepts; delimitation; taxonomy.]

Язык: Английский

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Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays

Systematic Biology, Год журнала: 2022, Номер 71(6), С. 1453 - 1470

Опубликована: Май 9, 2022

Abstract Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships species limits. In North America, cases complex speciation are common, due at least in part to the cyclical Pleistocene glacial history continent. Scrub-Jays genus Aphelocoma provide a useful case study because their range throughout America is structured by phylogeographic barriers with secondary contact between divergent lineages. Here, we show that comprehensive approach genomic reconstruction evolutionary history, i.e., synthesizing results from delimitation, tree reconstruction, demographic model testing, tests for capable clarifying despite speciation. We find concordant evidence across all statistical approaches distinctiveness an endemic southern Mexico lineage (A. w. sumichrasti), culminating support status this under any commonly applied concept. also novel Texas A. texana, which equivocal delimitation were clarified modeling spatially explicit models flow. Finally, signatures both ancient modern flow non-sister California Scrub-Jay (Aphelocoma californica) Woodhouse’s woodhouseii) result discordant trees species’ genomes clear overall isolation status. sum, multi-faceted analysis increase our understanding histories, even well-studied groups. Given emerging recognition relatively commonplace, framework demonstrate interrogation limits using data necessary roadmap disentangling impacts incomplete sorting (ILS) better understand systematics other groups similarly histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; delimitation; trees; systematics.]

Язык: Английский

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