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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Cryptic speciation in arid mountains: An integrative revision of the Pristurus rupestris species complex (Squamata, Sphaerodactylidae) from Arabia based on morphological, genetic and genomic data, with the description of four new species

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(2), P. e0315000 - e0315000

Published: Feb. 24, 2025

In the arid landscapes of Arabian Peninsula, high levels cryptic diversity among reptiles, and especially in geckos, have recently been revealed. Mountain ranges within peninsula were shown to contain highest richness reptile endemicity, serving as refugia species less adapted hyper-arid conditions lowlands. With up 19 endemic species, Hajar Mountains southeastern Arabia are a clear example this pattern. Owing its old geological history, complex topography geographic isolation from rest peninsula, mountain range rises hotspot biodiversity endemicity Arabia, provides perfect scenario study processes evolution diversification reptiles ranges. present we investigate systematics Pristurus rupestris complex, group geckos exhibiting morphological traits along with remarkably deep evolutionary history. Initially considered single distributed throughout coastal some scattered populations at Horn Africa, several recent studies that actually comprises restricted Arabia. Here, utilize an integrative approach assembling morphological, genetic, genomic, ecological datasets resolve long-standing systematic challenge. Results support existence four new three Oman endemics. While no unique diagnostic characters identified, slight differences occur between high-elevation relative rest. Despite lack differentiation, extreme genetic variation found distances 24% 12S mitochondrial marker, resulting divergence times 10 mya. Moreover, all sympatry least another representative without any signs apparent ongoing gene flow them. These findings yield profound implications for conservation efforts, one these newly described presents extremely distribution (only known locality individuals), requiring immediate attention protection. Overall, sheds light on hidden P . emphasizing importance preserving face environmental changes, while highlighting, once again, cradle biodiversity.

Language: Английский

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Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data

Frontiers in Zoology, Journal Year: 2022, Volume and Issue: 19(1)

Published: Feb. 22, 2022

The diversity of biological and ecological characteristics organisms, the underlying genetic patterns processes speciation, makes development universally applicable species delimitation methods challenging. Many approaches, like those incorporating multispecies coalescent, sometimes delimit populations overestimate numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, cryptic resulting from nonecological speciation. These present a conundrum when delimiting species: analyses rely heavily, if not entirely, on data which over split species, while other lines evidence lump. We showcase this harvester Theromaster brunneus, taxon wide geographic distribution potential for species. Integrating morphology, mitochondrial, sub-genomic (double-digest RADSeq ultraconserved elements) data, we find discordance across types number inferred further that coalescent approaches split. demonstrate power supervised machine learning approach effectively by creating "custom" training set derived well-studied lineage similar as Theromaster. novel uses known particular inform unknown characteristics, using modern computational tools ideally suited delimitation. also considers natural history organisms make more biologically informed decisions, principle broadly tree life.

Language: Английский

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

Systematic Biology, Journal Year: 2022, Volume and Issue: 72(2), P. 357 - 371

Published: Aug. 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.]

Language: Английский

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Species boundaries to the limit: Integrating species delimitation methods is critical to avoid taxonomic inflation in the case of the Hajar banded ground gecko (Trachydactylus hajarensis)

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 186, P. 107834 - 107834

Published: May 30, 2023

Language: Английский

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Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 14(1)

Published: Nov. 22, 2021

The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models quantify the impacts of paleoclimate change, geographic features, habitat heterogeneity on spatial patterns genetic diversity. In this study, we combine thousands genotyping-by-sequencing (GBS) loci mtDNA sequences (ND1) from Texas horned lizard (Phrynosoma cornutum) relative support for different catalysts Phylogenetic clustering analyses GBS indicate at least three primary populations. distribution populations appears concordant type, desert in AZ NM showing largest divergence remaining also a divergent population, but other relationships differ suggest introgression. Genotype-environment association bioclimatic variables supports along precipitation gradients more than temperature gradients. Demographic complex history, introgression gene flow playing important role during Bayesian multispecies coalescent (MSci) that occurred between Paleo-species two southern refugia geographically correspond contemporary lineages. We find times are underestimated population sizes overestimated when is ignored analyses, furthermore, inference ancient events demographic history sensitive inclusion single recently admixed sample. Our cannot refute riverine barrier or glacial hypotheses. Results continuing diverge Finally, strong evidence admixture, flow, among suggests P. cornutum should considered widespread species under General Lineage Species Concept.

Language: Английский

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The origin of a mountain biota: hyper-aridity shaped reptile diversity in an Arabian biodiversity hotspot

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 8, 2023

Abstract Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive formation biotas. These include from broad biogeographic patterns, to population dynamics adaptations these environments. However, significant challenges remain integrating large-scale fine-scale findings develop a comprehensive biodiversity. One challenge is lack genomic data, particularly historically understudied arid regions where reptiles are diverse vertebrate group. We generated de novo genome-wide SNP data for more than 600 specimens integrated state-of-the-art analyses at community, species level. We, thus, provide first time, holistic integration how whole endemic reptile community has originated, diversified dispersed through range. Our results show independently colonized Hajar Mountains eastern Arabia 11 times. After colonization, delimitation methods suggest high levels within-mountain diversification, supporting up 49 putative species. This diversity strongly structured following local topography, with highest peaks acting as barrier gene flow among entire community. Surprisingly, orogenic events do not seem rise key drivers history this system. paleoclimate seems had major role assemblage. observe an increase vicariant Late Pliocene onwards, coinciding unstable climatic period rapid shifts between hyper-arid semiarid conditions led ongoing desertification Arabia. conclude paleoclimate, extreme aridification, acted main driver diversification systems which tangled generation highly adapted endemicity. study provides valuable contribution evolution biodiversity environmental factors shaping distribution regions.

Language: Английский

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Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: July 1, 2024

Abstract Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive formation biotas. These span from broad biogeographic patterns to population dynamics adaptations these environments. However, significant challenges remain integrating large-scale fine-scale findings develop a comprehensive biodiversity. One challenge is lack genomic data, especially historically understudied arid regions where reptiles are particularly diverse vertebrate group. In present study, we assembled de novo genome-wide SNP dataset for complete endemic reptile fauna range (19 described species with more than 600 specimens sequenced), integrated state-of-the-art analyses at population, species, community level. Thus, provide holistic integration how whole has originated, diversified dispersed through system. Our results show independently colonized Hajar Mountains southeastern Arabia 11 times. After colonization, delimitation methods suggest high levels within-mountain diversification, supporting up 49 deep lineages. This diversity strongly structured following local topography, highest peaks acting as barrier gene flow among entire community. Interestingly, orogenic events do not seem key drivers history this Instead, past climatic had major role assemblage. We observe an increase vicariant Late Pliocene onwards, coinciding unstable period rapid shifts between hyper-arid semiarid conditions led ongoing desertification Arabia. conclude paleoclimate, extreme aridification, acted main driver diversification systems which tangled generation highly adapted endemicity. Overall, study does only valuable contribution evolution but also offers flexible scalable approach can be reproduced any taxonomic group discrete environment.

Language: Английский

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Establishing species boundaries in Bornean geckos

Biology Letters, Journal Year: 2024, Volume and Issue: 20(8)

Published: Aug. 1, 2024

Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering delimiting species. However, species with a single locus (e.g. barcoding) is biased towards overestimating diversity. The highly diverse gecko genus Cyrtodactylus one such group where mtDNA the paradigm. In this study, we use genomic data to test putative boundaries established within three recognized of on island Borneo. We predict that multi-locus will estimate fewer than mtDNA, which could have ramifications diversity genus. aim (i) investigate correspondence between delimitations data, (ii) infer trees each target species, (iii) quantify gene flow identify migration patterns assess population connectivity. find overestimated differ nuclear data. This underscores value reassess mtDNA-based taxa lacking clear boundaries. expect number continue increasing, but, when possible, should be included inform more accurate

Language: Английский

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Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 16, 2024

Abstract Galapagos giant tortoises are endemic to the Archipelago, where they found in isolated populations. While these populations widely considered distinguishable morphology, behavior, and genetics, recent divergence of taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for delimitation whole-genome resequencing data from 38 across all 13 extant assess support delimiting species. In contrast previous studies based solely on time, find strong evidence reject hypothesis that belong a single Instead, conservative interpretation model-based divergence-based results indicates form complex consisting minimum 9 species, with most analyses supporting There is mixed living same island, some suggesting multiple per island. These make clear tortoise represent different stages process speciation, further along evolutionary than others. Our study provides insight into speciation islands, which urgently needed given threatened island around world.

Language: Английский

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