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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Erosion of heterogeneous rock drives diversification of Appalachian fishes

Science, Journal Year: 2023, Volume and Issue: 380(6647), P. 855 - 859

Published: May 25, 2023

The high levels of biodiversity supported by mountains suggest a possible link between geologic processes and biological evolution. Freshwater is not only in tectonically active settings but also quiescent montane regions such as the Appalachian Mountains. We show that erosion through different rock types drove allopatric divergence lineages Greenfin Darter (Nothonotus chlorobranchius), fish species endemic to rivers draining metamorphic rocks Tennessee River basin United States. In past, preferred N. chlorobranchius was more widespread, exposed other types, this were progressively isolated tributaries farther upstream, where remained. Our results mechanism for initiating diversification long after tectonic activity ceases.

Language: Английский

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Hierarchical Heuristic Species Delimitation under the Multispecies Coalescent Model with Migration

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(6), P. 1015 - 1037

Published: Aug. 20, 2024

Abstract The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer history divergence gene flow. Given set populations, hypotheses delimitation (and phylogeny) may be formulated as instances MSC models (e.g., 1 versus 2 species) compared using Bayesian selection. This approach, implemented in program bpp, has been found prone over-splitting. Alternatively, heuristic criteria based on population parameters (such split times, sizes, migration rates) estimated used delimit species. Here, we develop hierarchical merge algorithms index (gdi) implement them Python pipeline called hhsd. We characterize behavior gdi under few simple scenarios apply new approaches dataset simulated isolation by distance well 3 empirical datasets. Our tests suggest that produced sensible results were less oversplitting. discuss possible strategies accommodating paraphyletic algorithm, challenges criteria.

Language: Английский

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Inconsistent estimates of hybridization frequency in newts revealed by SNPs and microsatellites

Conservation Genetics, Journal Year: 2023, Volume and Issue: 25(1), P. 215 - 225

Published: Sept. 7, 2023

Abstract Hybridization between the European smooth and palmate newts has recurrently been mentioned in literature. The only two studies that attempted to quantify frequency of hybridization gene admixture these species came strikingly opposite conclusions. According Arntzen et al. (1998, 42 allozymes), hybrids are rare nature introgression negligible, while according Johanet (2011, 6 microsatellites), introgressive is significant widespread across shared distribution range. To clarify this question, we implemented high-throughput SNP genotyping with diagnostic biallelic SNPs on 965 specimens sampled Europe. Our results line al., since F1 were identified distinct French localities, no further hybrid generations or backcrosses. Moreover, reanalysis 78 samples previously studied by (2011) using our panel could not reproduce their results, suggesting microsatellite-based inference overestimated species. Since did detect methodological issues analyses suggest approaches outperform assessments frequency, conclusions published topic a small number microsatellite loci should be taken caution, ideally repeated an increased genomic coverage.

Language: Английский

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Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)

Systematic Biology, Journal Year: 2022, Volume and Issue: 72(1), P. 179 - 197

Published: Sept. 28, 2022

Abstract Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis phylogeography taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters genome-scale data as strong initial evidence speciation most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We now hypotheses linking trait differentiation to specific mechanisms divergence with increasingly large sets. Integrative can, therefore, reflect understanding how each axis variation relates underlying processes, nomenclature for lineages. illustrate this approach here Seal Salamanders (Desmognathus monticola) introduce new unsupervised machine-learning delimitation. Plethodontid salamanders are renowned their morphological conservatism despite extensive phylogeographic divergence. discover 2 geographic genetic clusters, which demographic spatial ecology gene flow provide robust support ecogeographic limited phenotypic These integrated (e.g., spatially localized reduced migration) reflected emergent properties expected reinforcement ethological isolation selection against hybrids). Their prima facie species-level distinctiveness, supported by along axes such behavior, geography, climate suggest ecological basis subsequent through prezygotic isolation. As sets grow more comprehensive, species-delimitation tested, rejected, or corroborated hypotheses, providing reciprocal illumination processes integrative taxonomies. [Desmognathus; taxonomy; machine learning; delimitation.]

Language: Английский

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Phylogenomic species delimitation of studfishes (Fundulidae: Fundulus): evidence for cryptic species in agreement with the central highlands vicariance hypothesis

Zootaxa, Journal Year: 2025, Volume and Issue: 5604(3), P. 309 - 328

Published: March 13, 2025

The Central Highlands ecoregion of the eastern United States represents a hotspot freshwater biodiversity, with replicated patterns vicariant speciation east and west Mississippi River. Previous phylogeographic investigation studfishes (Fundulus subgenus Fundulus) revealed evidence for in Highlands, but data were limited to small number gene sequences generated Sanger sequencing. We used double digest restriction-site associated DNA sequencing (ddRADseq) improve resolution better characterize population genetic variation. Our sample design included individuals from Fundulus catenatus species group (F. catenatus, F. bifax, stellifer) two outgroup taxa julisia rathbuni). Phylogenetic analyses support monophyletic complex sister relationship Mobile Basin bifax stellifer). Population genomics delimitation tests provide three species-level subdivisions catenatus. describe as Tennessee River its drainages, caddo sp. nov., Ouachita cryptocatenatus occupying remainder range. Modally, was characterized by fewer left pectoral rays (16 vs. 17). nov. had modally anal (15 16) lateral scale rows (13 14). higher dorsal 14) caudal geographic distribution is likely result multiple pre-Pleistocene vicariance events congruent Vicariance Hypothesis well separate, possibly subsequent, dispersal events. Overall, results this study corroborate previous biogeographic history endemic rivers ecoregion. improved genomic variation among studfish populations will guide future studies morphological conservation plans rare biodiversity hotspot.

Language: Английский

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Phylogeny, biology, and evolution of acanthopterygian fish clades

Reviews in Fish Biology and Fisheries, Journal Year: 2025, Volume and Issue: unknown

Published: March 13, 2025

Language: Английский

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Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 168, P. 107400 - 107400

Published: Jan. 11, 2022

Language: Английский

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Biogeography of the Macrhybopsis aestivalis complex (Teleostei: Cyprinidae): emphasis on speciation and ancient heterospecific mitochondrial transfer

Environmental Biology of Fishes, Journal Year: 2022, Volume and Issue: 105(2), P. 261 - 287

Published: Feb. 1, 2022

Language: Английский

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Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma)

Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 178, P. 107645 - 107645

Published: Oct. 15, 2022

Language: Английский

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