ASAP: assemble species by automatic partitioning

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(2), P. 609 - 620

Published: Oct. 15, 2020

Abstract Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough split sets as large 10 4 sequences into putative in several minutes. Although grounded evolutionary theory, the implementation of hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding computational burden phylogenetic reconstruction. Importantly, proposes ranked scoring system no biological prior insight intraspecific diversity. stand‐alone program can be used either through graphical web‐interface or downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP GMYC) on real COI representing various degrees challenge (from small easy cases complicated also Monte‐Carlo simulations multispecies coalescent framework assess strengths weaknesses other programs. Through these analyses, demonstrate has potential become major tool taxonomists it rapidly full exploratory interface relevant hypothesis first step integrative taxonomy process.

Language: Английский

---

Finding Evolutionary Processes Hidden in Cryptic Species

Trends in Ecology & Evolution, Journal Year: 2017, Volume and Issue: 33(3), P. 153 - 163

Published: Dec. 11, 2017

Language: Английский

---

Guidelines for DNA taxonomy, with a focus on the meiofauna

Marine Biodiversity, Journal Year: 2015, Volume and Issue: 45(3), P. 433 - 451

Published: Feb. 27, 2015

Language: Английский

---

Next‐generation species delimitation and taxonomy: Implications for biogeography

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 51(9), P. 1709 - 1722

Published: Feb. 13, 2024

Abstract An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, data are of importance species delimitation. We here review recent developments future perspectives direct relevance biogeographers. The understanding that independently evolving segments population‐level lineages, the rise integrative approaches to delimit such advent high‐throughput sequencing have considerably renewed discipline taxonomy. Using genome‐scale molecular datasets, extent admixture across hybrid zones can now be effectively assessed evolutionary independence lineages inferred, leading more reliable comparable delimitation criteria. Substantially divergent but admixing phylogeographical conveniently named as subspecies, thus avoiding taxonomic oversplitting inflation. At same time, comprehensive DNA barcoding metabarcoding efforts uncovering an enormous proportion undiscovered biotic diversity, we encourage development bioinformatic pipelines combine discovery with diagnosis scientific naming, approach a inventory globe without abandoning established Linnaean system.

Language: Английский

---

DNA BARCODING: FOUNDATIONS AND APPLICATIONS FOR SOUTHEAST ASIAN FRESHWATER FISHES

TREUBIA, Journal Year: 2025, Volume and Issue: 43, P. 1 - 16

Published: March 7, 2025

Identifying and delineating species are the primary tasks of taxonomy. Owing to decreasing interest nations for taxonomy inventory living beings, funds have been drastically during last two decades taxonomic studies. As a consequence, worldwide pool taxonomists has dramatically decreased. DNA barcoding, as an automated tool delineation identification, proved rejuvenate field open new perspectives in ecology conservation. In present review, we will discuss how barcoding established paradigm recently integrated We further detail potential applications identifications may positively impact conservation particularly biodiversity hotspots. emphasise benefit Southeast Asian freshwater fishes.

Language: Английский

---

Navigating the pitfalls and promise of landscape genetics

Molecular Ecology, Journal Year: 2016, Volume and Issue: 25(4), P. 849 - 863

Published: Jan. 12, 2016

The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms appear like clockwork with each new journal issue. developments are an encouraging, at times bewildering, sign progress exciting study. However, we suggest that rapid expansion belied important flaws development field, add air caution to this breakneck pace expansion. Specifically, genetic studies often lose sight fundamental principles complex consequences gene flow, instead favouring simplistic interpretations broad inferences not necessarily warranted by data. Here, describe common pitfalls characterize such studies, provide practical guidance improve investigation, careful consideration inferential limits, scale, replication, ecological evolutionary context spatial patterns. Ultimately, utility will depend on translating relationship between flow features into understanding long-term population outcomes. We hope perspective presented here steer down a more scientifically sound productive path, garnering is as informative future it popular now.

Language: Английский

---

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

Systematic Biology, Journal Year: 2019, Volume and Issue: 69(1), P. 184 - 193

Published: June 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

Language: Английский

---

Incomplete estimates of genetic diversity within species: Implications for DNA barcoding

Ecology and Evolution, Journal Year: 2019, Volume and Issue: 9(5), P. 2996 - 3010

Published: Feb. 16, 2019

Abstract DNA barcoding has greatly accelerated the pace of specimen identification to species level, as well delineation. Whereas application matching unknown specimens known is straightforward, its use for delimitation more controversial, discovery hinges critically on present levels haplotype diversity, patterning standing genetic variation that exists within and between species. Typical sample sizes molecular biodiversity assessment using barcodes range from 5 10 individuals per However, required are necessary fully gauge at level presumed be strongly taxon‐specific. Importantly, little attention been paid determining appropriate reveal majority intraspecific any one In this paper, we a brief outline current literature methods size estimation COI barcode sampling completeness. The importance adequate studies stressed, with variety metazoan taxa, through reviewing foundational statistical population models, specific ray‐finned fishes (Chordata: Actinopterygii). Finally, promising avenues further research in area highlighted.

Language: Английский

---

Invertebrate population genetics across Earth's largest habitat: The deep‐sea floor

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(19), P. 4872 - 4896

Published: Aug. 22, 2017

Abstract Despite the deep sea being largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non‐chemosynthetic ecosystems deep‐sea floor (below 200 m depth). We review and synthesize results these papers. Studies reveal levels diversity comparable to shallow‐water species. Generally, populations at similar depths were well connected over 100s–1,000s km, but that sampled across depth ranges structure much smaller scales (100s–1,000s m) consistent with isolation by adaptation environmental gradients, or existence physical barriers connectivity depth. Few ocean‐wide (under 4%), 48% Atlantic‐focused. There is strong emphasis megafauna commercial species research into meiofauna, “ecosystem engineers” other ecologically important lacking. Only nine papers account for ~50% planet's surface (depths below 3,500 m). Just two studied 5,000 m, a quarter Earth's seafloor. Most used single‐locus mitochondrial genes revealing common pattern non‐neutrality, demographic instability selective sweeps; hydrothermal vent fauna. The absence clear difference between non‐vent could signify in sea, sweeps render demographically uninformative. number genetics date miniscule relation size sea. paucity constrains meta‐analyses where broad inferences about ecology be made.

Language: Английский

---

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

---