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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How not to describe a species: lessons from a tangle of anacondas (Boidae: Eunectes Wagler, 1830)

Zoological Journal of the Linnean Society, Год журнала: 2024, Номер 201(4)

Опубликована: Авг. 1, 2024

Abstract A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with description a new species green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies evidence used and errors in nomenclature. We here use case this problematic publication to: (i) highlight common issues affecting delimitations, especially an over-reliance on mitochondrial DNA data, reiterate best practices; (ii) reanalyse data available for establish true current state knowledge lines further research; (iii) analyse nomenclatural history status genus. While our analysis reveals significant morphological variation both yellow anacondas, denser sampling informative nuclear markers are required meaningful delimitation Eunectes. Tracing name-bearing types establishes Trinidad as type locality Boa murina Linnaeus, 1758 allows identification extant lectotype species. Finally, we emphasize responsibility journals authors ensure that published taxonomic work meets burden substantiate descriptions named compliance rules zoological

Язык: Английский

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DNA Barcoding of the Genus Discogobio (Teleostei, Cyprinidae) in China

Fishes, Год журнала: 2025, Номер 10(4), С. 157 - 157

Опубликована: Апрель 3, 2025

Discogobio is a genus of small, economically important freshwater fishes that are widely distributed in Southwestern China. The species the morphologically very similar, which makes their taxonomic identification quite challenging. DNA barcoding technology can identify at molecular level, thus overcoming limitations morphological classification. In this study, we collected 16 from China, analyzed mitochondrial cytochrome oxidase I subunit (COI) gene sequences 206 samples, and applied to species. COI amplicon was 651 bp length, mean base contents were: (T) 28.83%, (C) 27.63%, (A) 25.97%, (G) 17.57%. AT content (54.8%) higher, composition biased. intraspecific differences were not significant, genetic distances all less than 2%. average interspecific (3.94%) about 18.8 times (0.21%), suggesting there barcode gaps among Discogobio. Five different definition methods, Automatic Barcode Gap Discovery (ABGD), Assemble Species by Partitioning (ASAP), Bayesian Poisson Tree Process (bPTP), Generalized Mixed Yule Combination (GMYC), Refined Single Linkage (RESL), used infer operational units (MOTU). number MOTUs ranged 9 18. Phylogenetic analysis based on haplotypes showed most formed well-evolved branches phylogenetic tree, clustering obvious without mixing. results study provide reliable information for within Discogobio, great significance identification.

Язык: Английский

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Molecular phylogeny of the operculated land snail family Pupinidae (Caenogastropoda, Cyclophoroidea) in mainland Southeast Asia

Zoologica Scripta, Год журнала: 2025, Номер unknown

Опубликована: Апрель 7, 2025

Abstract The operculated land snail family Pupinidae from mainland Southeast Asia has been systematically revised based on shell morphology. Despite previous morphological studies, the evolutionary relationships within this remained unclear. This study represents first comprehensive molecular phylogeny of group, utilising two mitochondrial (COI and 16S rRNA) nuclear (5.8S rRNA + ITS2 28S genetic markers. Additionally, we conducted phylogenetic analyses Pupina species 1106 loci generated through double‐digest restriction site‐associated DNA sequencing (ddRADseq). It turned out that Asian Pollicaria emerged as a sister clade to Central American Aperostoma Megalomastomatidae, leading resurrection Pollicariidae. Among remaining pupinid genera, Tortulosa was nested Coptocheilus clade, while Pupinella were not monophyletic. previously recognised arula group found be monophyletic reclassified into Tylotoechus (formerly subgenus), distinctive conchological characters such an extending parietal tooth callus wide, outward‐curving posterior canal. However, some retrieved monophyletic, suggesting presence multiple ‘cryptic species’. Divergence time estimation indicated split could date back Late Triassic Early Cretaceous, with diversification genera occurring during Middle Jurassic Cretaceous. successful reconstruction robust using ddRADseq demonstrates significant potential RADseq techniques in elucidating deeply divergent taxa. Further studies incorporating type destructus keraudrenii are necessary justify usage these genera.

Язык: Английский

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An updated survey of molecular diversity in Madagascar's velvet geckos, genus Blaesodactylus, with description of a new species from the island’s arid West

Zootaxa, Год журнала: 2025, Номер 5620(2), С. 230 - 254

Опубликована: Апрель 8, 2025

Madagascar velvet geckos, genus Blaesodactylus, are classified in six species distributed over low-elevation sites across most of Madagascar. Based on DNA sequences one mitochondrial and two nuclear-encoded gene fragments obtained from numerous newly collected tissue samples, we provide an updated review their molecular variation. Our genetic screening confirms extended distribution B. ambonihazo, so far only known its type locality Ankarafantsika, now reaching northwards to the Sahamalaza Peninsula. Compared previously available data, also verify minor range extensions boivini (southeastwards Bezavona), antongilensis (northwards Marojejy Massif), sakalava complex. Samples assigned according current taxonomy fell into sister lineages differing by about 8.5% pairwise distances 16S rRNA gene, lack haplotype sharing CMOS various subtle but consistent differences body proportions scalation. We conclude that lineage occurring South Madagascar, encompassing locations south Morombe, corresponds sensu stricto based morphological characters name-bearing type; describe West north Morombe as a new species, ganzhorni sp. nov.

Язык: Английский

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Molecular Investigation of the Diversity of Cirratulidae (Annelida) Doubles the Number of Known Species in European Waters

Zoologica Scripta, Год журнала: 2025, Номер unknown

Опубликована: Май 2, 2025

ABSTRACT Cirratulidae is a group of common marine benthic annelids with about 397 nominal species described worldwide, 58 which are reported in European waters. Due to the general morphological homogeneity among from several genera, this considered difficult identify level, has complex taxonomical and nomenclatural history largely understudied. The aim study was assess diversity Available samples ranged Arctic Ocean North Svalbard, along Atlantic coast western Mediterranean Sea, intertidal zone down 2600 m deep, over 400 sampling sites included. We included 2120 partial sequences two mitochondrial (COI 16S rRNA) one nuclear marker (28S 1098 specimens analyses, 65% were newly produced for study. performed relevant distance tree‐based delimitation analyses (ASAP, PTP, mPTP GMYC). As result, 125–129 lineages compatible evolutionary definition identified, out 83 96 represent putative new science. This represents most inclusive phylogenetic date. Multitentaculate retrieved as monophyletic inclusion Chaetocirratulus. genera Cirratulus , Chaetocirratulus Caulleriella Tharyx Raricirrus recovered monophyletic. genus Chaetozone paraphyletic nested within it, status Aphelochaeta Kirkegaardia unresolved.

Язык: Английский

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Mitogenomic resolution of phylogenetic conflicts and adaptive signatures in feliform carnivorans

Heredity, Год журнала: 2025, Номер unknown

Опубликована: Май 28, 2025

Язык: Английский

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A new microendemic gecko from the small forest fragments of south-eastern Madagascar (Squamata, Gekkonidae, Paragehyra)

ZooKeys, Год журнала: 2025, Номер 1240, С. 1 - 38

Опубликована: Июнь 2, 2025

Historically, herpetological research in Madagascar has largely overlooked small forest fragments outside the country protected area network. Despite substantial declines species diversity compared to large continuous forests, these continue sustain diverse communities and frequently harbour microendemic species. We describe a new gecko belonging genus Paragehyra , apparently isolated surrounding Andringitra Massif south-eastern Madagascar. tsaranoro sp. nov. is different from its congeneric based on genetic distances mitochondrial markers (16S COI), phylogenetic position, lack of haplotype sharing at one nuclear locus (POMC). The also distinguishable congeners combination 14 morphological characters. New data are provided for sympatric P. felicitae we propose assessment conservation status within IUCN Red List. mostly found managed by local (community-managed reserves) legally areas. This study highlights importance community-based management herpetofauna, particularly regions heavily impacted anthropogenic pressure unsuitable forest-dwelling findings emphasise conducting fragments, as they essential completing inventory Malagasy herpetofauna.

Язык: Английский

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The biology and toxinology of blunt-nosed vipers

npj Biodiversity, Год журнала: 2025, Номер 4(1)

Опубликована: Июнь 3, 2025

Blunt-nosed vipers (genus Macrovipera) are among the venomous snakes of highest medical relevance in Palearctic region. Extensive research has been conducted on their venoms, covering toxin composition, biochemistry, function, pathology and biodiscovery. However, these studies widely dispersed across scientific literature, almost exclusively focus biochemistry drug discovery aspects, largely neglect zoological systematic context snakes. Here, we provide a comprehensive, transdisciplinary compilation what is known about biology, taxonomy toxinology blunt-nosed vipers. After contextualising three generally recognised Macrovipera species (Macrovipera lebetina, razii schweizeri) within taxonomic framework, compile venom proteomes available literature identify general compositional patterns genus. We then report biological activities venoms discuss clinical pharmacological potential. Furthermore, detail mainly haemorrhagic, coagulopathic cytotoxic pathophysiological effects viper envenoming, recommendations for management bites. Finally, propose future directions, advocating expanded to enhance our understanding drive further innovation both therapeutic applications treatment bites inflicted by remarkable

Язык: Английский

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Four in one: An integrative taxonomic revision of the Microhyla berdmorei complex (Amphibia: Anura: Microhylidae) illustrates the tremendous amphibian diversity of Southeast Asia

Vertebrate Zoology, Год журнала: 2024, Номер 74, С. 595 - 641

Опубликована: Окт. 4, 2024

Abstract Berdmore’s narrow-mouthed frog, Microhyla berdmorei (Blyth, 1856), is the largest member of genus and distributed all over Southeast Asia, from Northeast India southern China to Sumatra Borneo in Indonesia. Here we demonstrate that M. represents a complex four species are morphologically, acoustically, genetically distinct each other, implement taxonomic revisions. Phylogenetic analyses three mitochondrial DNA (hereafter mtDNA, including COI, 12S, 16S rRNA; 3119 bp) one nuclear (BDNF; 716 gene sequences corroborated by phylogenomic 2700 ddRAD-seq loci (387,270 bp). All support complex, which originates early Miocene (ca. 19.7 mya), consists two clades date late 7.5 mya). The first clade, regroups populations large-sized individuals, Indo-Burma includes lineage India, Bangladesh, Myanmar ( sensu stricto) West Malaysia, Thailand, Laos, Cambodia, Vietnam (for propose resurrect malcolmi Cochran, 1927). second small-sized occurs Sundaland also lineages for provide descriptions on rank. new widely Peninsular Malaysia islands (described herein as sundaica sp. nov. ), while restricted Malay Peninsula extreme Thailand adjacent peninsularis ). We further evidence synonymy Callula natatrix Cope, 1867 with stricto, fowleri Taylor, 1934 . Our study illustrates high diversity Asian amphibians, especially , presently totals 54 species.

Язык: Английский

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