Next‐generation species delimitation and taxonomy: Implications for biogeography

Journal of Biogeography, Год журнала: 2024, Номер 51(9), С. 1709 - 1722

Опубликована: Фев. 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.

Язык: Английский

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DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy

Methods in molecular biology, Год журнала: 2024, Номер unknown, С. 77 - 104

Опубликована: Янв. 1, 2024

Язык: Английский

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Concatenator, a user-friendly program to concatenate DNA sequences, implementing graphical user interfaces for MAFFT and FastTree

Bioinformatics Advances, Год журнала: 2022, Номер 2(1)

Опубликована: Янв. 1, 2022

Phylogenetic and phylogenomic analyses require multi-gene input files in different formats, but there are few user-friendly programs facilitating the workflow of combining, concatenating or separating, aligning exploring datasets.

Язык: Английский

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Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice

PLoS Biology, Год журнала: 2023, Номер 21(8), С. e3002251 - e3002251

Опубликована: Авг. 22, 2023

Modern advances in DNA sequencing hold the promise of facilitating descriptions new organisms at ever finer precision but have come with challenges as major Codes bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, diagnoses), which is particularly problematic DNA-based taxonomy. We, commissioners International Commission on Zoological Nomenclature, advocate a tightening definition "species diagnosis" future editions bionomenclature, example, through introduction specific information character states differentiating traits comparison similar species. Such provisions would enhance taxonomic standards ensure that all diagnoses, including ones, adequate context. Our recommendations are intended to spur discussion among biologists, broad community consensus critical ahead implementation Code Nomenclature other bionomenclature.

Язык: Английский

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Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex

Biology, Год журнала: 2023, Номер 12(3), С. 418 - 418

Опубликована: Март 9, 2023

Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with morphological patterns. In such TCGs, mosaic-like character combinations conflicts data molecular phylogenies present major problem for classification. Here, we used the large polyploid apomictic European Ranunculus auricomus to study relationships among five diploid sexual progenitor 75 derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal stem leaves, receptacles), genomic (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed clusters correspond groupings basal leaves concatenated traits, were best resolved data; (2) described taxa usually overlap within trait morphospace except those at space edges; (3) phenotypes are highly influenced by parental subgenome composition lesser extent climatic factors; (4) allopolyploid compared their progenitor, resemble mosaic ecological intermediate transgressive biotypes. The joint evaluation phylogenomic, phenotypic, reproductive, supports revision purely descriptive, subjective traditional classifications.

Язык: Английский

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Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(3), С. 1822 - 1822

Опубликована: Фев. 2, 2024

The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure and variations Cephalopholis species along with their phylogenetic relationships, focusing specifically taeniops from Eastern Atlantic Ocean. generated mitogenome spans 16,572 base pairs exhibits a gene order analogous to that ancestral teleost’s, featuring 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer (tRNAs), an AT-rich control region. C. displays AT bias (54.99%), aligning related species. majority PCGs initiate start codon ATG, exceptions being COI (GTG) atp6 (TTG). relative synonymous usage analysis revealed maximum abundance leucine, proline, serine, threonine. nonsynonymous/synonymous ratios were <1, which indicates strong negative selection among all In taeniops, prevalent RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), lacks dihydrouracil (DHU) stem. A comparative examination conserved domains sequence blocks across various noteworthy length nucleotide diversity. Maximum likelihood, neighbor-joining, Bayesian analyses, employing concatenated combination + rRNAs, distinctly separate species, including taeniops. Overall, these findings deepen our understanding relationships serranid emphasizing significance structural considerations mitogenomic analyses.

Язык: Английский

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Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction and haploweb calculation

Bioinformatics Advances, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 1, 2024

Abstract Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still importance, especially in species diagnosis and delimitation, where limited amount sequence usually available sufficient, along with other datasets the framework integrative taxonomy. In diploid organisms, this often requires separating (phasing) sequences heterozygotic positions, typically separate programs required for phasing, reformatting input files, haplotype network construction. We therefore developed Hapsolutely, user-friendly program an ergonomic graphical user interface that integrates phasing from five approaches network/genealogy reconstruction. Results Among novel options implemented, Hapsolutely reconstruction steps networks, supports partition common SPART SPART-XML formats, calculates visualizes haplowebs fields recombination, thus allowing comparison allele distribution sharing subsets purpose delimitation. The new tool has been specifically focus on workflow alpha-taxonomy, exploring recombination across alternative partitions may help Availability implementation written Python, code Phase, SeqPHASE, PopART C++ Haxe. Compiled stand-alone executables MS Windows Mac OS detailed manual can be downloaded https://www.itaxotools.org; source openly GitHub (https://github.com/iTaxoTools/Hapsolutely).

Язык: Английский

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“Dark taxonomy”: A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment

Cladistics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 16, 2025

Abstract We are entering the sixth mass extinction with little data for “dark taxa”, although they comprise most species. Much of neglect is due to fact that conventional taxonomic methods struggle handling thousands specimens belonging hundreds thus here propose a new strategy we call taxonomy”. It addresses (i) impediments, (ii) lack biodiversity baselines and (iii) low impact revisionary research. Taxonomic impediments reduced by carrying out revisions at small geographic scales keep number low. The risk error delimiting species based on two types data. furthermore show dark taxonomy can yield important baseline using samples obtained biomonitoring traps. Lastly, argue research be improved publishing papers addressing different readerships. principles illustrated our treatment Singapore's fungus gnats (Mycetophilidae) only Malaise trap samples. first batch ( N = 1454) contains 120 species, which 115 science, reducing increasing described Oriental 25%. Species delimitation started DNA barcodes estimate Molecular Operational Units (MOTUs) before “LIT” (Large‐scale Integrative Taxonomy) was used obtain boundaries integrating morphological molecular To test completeness revision, next analysed second 1493 found >97% belonged delimited batch. Indeed, contained 18 rare MOTUs, i.e. study suggests single revision simultaneously names all relevant Overall, believe taxonomy” quickly ready large unknown taxon biomonitoring.

Язык: Английский

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Mitogenomic Characterization and Phylogenetic Insights of the Ornamental Sail-Fin Molly (Poecilia velifera) in Non-Native Indonesian Waters

Biochemical Genetics, Год журнала: 2025, Номер unknown

Опубликована: Апрель 4, 2025

Язык: Английский

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A DNA barcode reference library for endemic Ponto-Caspian amphipods

Scientific Reports, Год журнала: 2022, Номер 12(1)

Опубликована: Июль 5, 2022

Abstract The Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species severely threatened in their native range, while at same time they invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna paramount for its conservation within and monitoring outside it. Here, we assemble a DNA barcode reference library nearly 60% all amphipod species. We use methods to define molecular operational units (MOTUs), based on two mitochondrial markers (COI 16S), assess congruence current species-level taxonomy morphology. Depending method, find 54–69% had congruent morpho-molecular boundaries. cases incongruence resulted from lumping distinct morphospecies into single MOTU (7–27%), splitting MOTUs (4–28%), or both (4–11%). defined by distance-based without priori divergence thresholds showed highest morphological taxonomy. results indicate barcoding valuable clarifying diversity amphipods, but reveals extensive work needed resolve uncertainties. Our study advances aquatic biota, paving way towards improved enhance efforts.

Язык: Английский

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