Comparative species delimitation of a biological conservation icon

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Highlights•The first legal test of the US Endangered Species Act concerned Snail Darter•The Darter is not a species but subpopulation Stargazing Darter•A reference-based approach can be used in delimiting any taxonomic group•Such comparative frameworks for taxa better guide conservation decisionsSummaryThe United States (ESA) 1973 set precedent biodiversity across globe.1 A key requirement protections afforded by ESA accurate delimitation imperiled species. We present to that integrates genomic and morphological data objectively assessing distinctiveness targeted protection governmental agencies. apply this protocol (Percina tanasi), freshwater fish from Tennessee River was discovered declared an endangered under 1975.2 Concurrently, Darter's habitat slated destroyed through construction Tellico Dam Valley Authority (TVA),3,4 inspiring nationwide protests advocating suspension federal project. This David versus Goliath struggle between supporters 3-inch TVA culminated major conflict over ESA, Supreme Court case Hill v. TVA, 437 U.S. 153 (1978), with 6 3 ruling favor protecting interrupting completion Dam. Here, we integrate multiple lines evidence framework demonstrate despite its legacy, distinct population uranidea) described 1887. These results illustrate how dramatically aids proper direction efforts toward biodiversity.

Language: Английский

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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

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A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 37(4), P. 1211 - 1223

Published: Dec. 6, 2019

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer events and estimate the timing intensity of introgression, providing an important means advance our understanding role speciation. Here, we implement multispecies-coalescent-with-introgression model, extension multispecies-coalescent model incorporate Bayesian Markov chain Monte Carlo program Bpp. The accommodates deep coalescence (or incomplete lineage sorting) provides a natural framework for inference using genomic data. Computer simulation confirms good statistical properties method, although hundreds thousands loci are typically needed probabilities reliably. Reanalysis sets from purple cone spruce hypothesis homoploid hybrid We estimated probability six mosquito Anopheles gambiae complex, which varies considerably across genome, likely driven by differential selection against introgressed alleles.

Language: Английский

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A demonstration of unsupervised machine learning in species delimitation

Molecular Phylogenetics and Evolution, Journal Year: 2019, Volume and Issue: 139, P. 106562 - 106562

Published: July 16, 2019

Language: Английский

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Fungal species boundaries in the genomics era

Fungal Genetics and Biology, Journal Year: 2019, Volume and Issue: 131, P. 103249 - 103249

Published: July 4, 2019

Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used be based on phenotypes, molecular frequently revealed that morphological traits are insufficient describe biodiversity. Genomics holds promise revealing even more genetic discontinuities, but parameters species from genomic remain unclear. Fungi have been a successful case in which use markers uncovered existence boundaries where no crosses possible. In this minireview, we highlight recent advances, propose set standards sequences uncover boundaries, point out potential pitfalls, present possible future research directions.

Language: Английский

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Incorporating the speciation process into species delimitation

PLoS Computational Biology, Journal Year: 2021, Volume and Issue: 17(5), P. e1008924 - e1008924

Published: May 13, 2021

The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus of populations within species. Consequently, as both the and spatial resolution data increases, a proliferation artifactual results within-species population lineages, detected due to restrictions in gene flow, are identified distinct toll this extends beyond systematic studies, getting magnified across disciplines rely upon an accurate framework Here we present first new class addresses issue by incorporating extended speciation process for delimitation. We formation lineages their subsequent development into independent separate processes provide way incorporate current understanding boundaries system through specification identities subset lineages. As result, can be discriminated entire system, assigned remaining unknown affinities quantified probabilities. In addition identification units nature, primary goal delimitation, incorporation also allows us insights links species-level processes. By explicitly accounting flow only between, but within, species, address limits delimiting Specifically, while alone sufficient when considered conjunction other information able learn about boundaries, tempo itself.

Language: Английский

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Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

Systematics and Biodiversity, Journal Year: 2020, Volume and Issue: 18(3), P. 269 - 280

Published: April 2, 2020

Species are a fundamental unit of biodiversity that delimited via genetic data and coalescent-based methods with increasing frequency. Despite the widespread use species delimitation, we do not fully understand sensitivity these to potential sources bias violations their underlying assumptions. One implicit assumption delimitation is geographic sampling adequate representative variation among populations within lineage interest. Yet exhaustive logistically difficult, if impossible, for many taxa span large expanses or occupy remote regions. Here, examine impact on output Bayes-factor SNAPP, popular pipeline. First, demonstrate problematic nature sparse isolation by distance using simulated sets connected different levels gene flow. We then whether similar trends present in an empirical dataset Andesiops mayflies (Ephemeroptera: Baetidae) from high elevation transect Ecuadorian Andes. In both analyses, systematically exclude geographically intermediate sites quantify delimitation. find removing genetically admixed individuals incorrectly favors multi-species scenarios. Oversplitting especially pronounced when strong, but exists even flow neighboring relatively high. These findings highlight importance urge caution interpreting such species' distributions sparsely sampled systems characterized strong patterns distance.

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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Empirical and philosophical problems with the subspecies rank

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(7)

Published: July 1, 2022

Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed are independent given a particular methodology ontology, which relates metaphysical concept to what "kind" thing is in reality. Often, fail link epistemology back ontology. This lack coherence part responsible for persistence subspecies rank, modern usage often functions as placeholder between events divergence or collapse incipient species. Thus, prospective like merging diverging require information unknowable future information. also conditioned on evidence lineage already has detectably distinct history. Ranking these can seem attractive many do not exhibit intrinsic reproductive isolation. We argue using indefensible philosophical grounds. Ontologically, rank either identical undefined context representing spatiotemporally defined individuals. Some more inclined consider subspecies, Biological Species Concept, disconnected ontology genealogy. Even ignored, methods addressing isolation indirect capture range scenarios linking gene flow identity over space time. The use reliance basis an operational conflict with ethical issues governing protection provide way forward recognizing naming links theoretical regardless magnitude

Language: Английский

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: June 6, 2022

Abstract Informed management and conservation efforts are vital to sustainable recreational fishing biodiversity conservation. Because the taxonomic rank of species is important in strategies, success these depends on accurate delimitation. The Black Basses ( Micropterus ) an iconic lineage freshwater fishes that include some world’s most popular for world's invasive species. Despite their popularity, previous studies delimit lineages suffer from insufficient geographic coverage uninformative molecular markers. Our phylogenomic analyses ddRAD data result delimitation 19 , which includes 14 described species, undescribed but well-known Altamaha, Bartram’s, Choctaw basses, two additional currently classified as Smallmouth Bass M. dolomieu ). We provide a revised Largemouth complex necessitates change scientific nomenclature: salmoides retained Florida nigricans elevated synonymy Bass. new understanding diversity, distribution, systematics will serve basis this charismatic economically clade fishes.

Language: Английский

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