The future of zoological taxonomy is integrative, not minimalist

Systematics and Biodiversity, Journal Year: 2022, Volume and Issue: 20(1), P. 1 - 14

Published: May 19, 2022

Roughly 18,000 species are described annually as new to science, while estimated extinction rates comparable or even exceeding these discoveries. Considering the estimates of up 15 million extant eukaryotic on Earth, which only about 2 have been so far, there has a recent 'boom' potential approaches more quickly discover and describe millions unknown species. This deficit is particularly noted in hyperdiverse taxa, current rate discovery considered too slow. Recently, 'minimalist' alpha taxonomic approach was proposed, relying solely DNA barcoding habitus photograph, claimed effort expedite naming combat so-called impediment. In this paper, we point limitations minimalist taxonomy, present arguments favour integrative approach, finally explore number solutions impediment taxa without sacrificing utility quality for apparent speed quantity.

Language: Английский

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mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(5), P. 2038 - 2053

Published: Jan. 30, 2022

DNA data are increasingly being used for phylogenetic inference, and taxon delimitation identification, but scarcely the formal description of taxa, despite their undisputable merits in taxonomy. The uncertainty regarding robustness diagnoses, however, remains a major impediment to use. We have developed new program, mold, that identifies diagnostic nucleotide combinations (DNCs) sequence alignments selected which can be provide diagnoses these taxa. To test we carry out iterated haplotype subsampling query species published sets varying complexity. quantify reliability diagnosis by diagnosing each subsample then checking if this valid against entire set. demonstrate widely types characters often absent or not sufficiently reliable. thus propose type diagnosis, termed "redundant DNC" (or rDNC), takes into account unsampled genetic diversity, constitutes much more reliable descriptor taxon. mold successfully retrieves rDNCs all two analysed sets, even those comprising hundreds species. shows unparalleled efficiency large is only available software capable compiling suit predefined criteria reliability.

Language: Английский

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A DNA barcode reference library for the native woody seed plants of Japan

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(4), P. 855 - 871

Published: Jan. 24, 2023

DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application barcode-based studies. Here we announce development comprehensive reference library Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, comprising 77.3% 72.2% species in Japan. A total 6216 plant specimens were collected from 223 sites across subtropical, temperate, boreal alpine biomes Japan with most represented by multiple accessions. This utilized three chloroplast regions (rbcL, trnH-psbA matK) consists 14,403 sequences. Individual varied their identification rates, species-level genus-level rates rbcL, matK based on blast being 57.4%/96.2%, 78.5%/99.1% 67.8%/98.1%, respectively. Identification higher using region combinations, two combinations (rbcL & trnH-psbA, rbcL ranging between 90.6% 95.8%, all equal to 98.6%. Genus-level even higher, 99.7% 100% regions. These results indicate that this is an effective resource investigations barcodes provides useful template libraries other components flora.

Language: Английский

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A widespread Ponto-Caspian invader with a mistaken identity: integrative taxonomy elucidates the confusing taxonomy ofTrichogammarus trichiatus(=Echinogammarus) (Crustacea: Amphipoda)

Zoological Journal of the Linnean Society, Journal Year: 2023, Volume and Issue: 198(3), P. 821 - 846

Published: April 15, 2023

Abstract Amphipods have diversified greatly in the Ponto-Caspian region. Although many of these species are prominent invaders their systematics remains unclear. Taking an integrative approach, we investigate taxonomy Trichogammarus trichiatus, a widespread invader European inland waters. It was initially described from north-eastern Black Sea coast as Chaetogammarus trichiatus by Martynov 1932. A similar taxon, tenellus major, Cărăușu western 1943 but later synonymized with C. trichiatus. itself shuffled between and Atlanto-Mediterranean Echinogammarus, currently being assigned to Trichogammarus. Our analyses (six DNA markers, 60 measurements scanning electron microscopic imaging) reveal that T. major distinct species; former is Caucasian endemic, whereas latter invaded Europe. Unexpectedly, incipient molecularly nested ischnus, despite pronounced morphological geographical differentiation. We also recover polyphyletic, yet its member radiation, thus Echinogammarus. Consequently, reassign (Chaetogammarus trichiatus), synonymize place new genus Spirogammarus gen. nov. (Spirogammarus comb. & stat. nov.). necessitates further systematic refinement.

Language: Английский

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Taxonomizing a truly morphologically cryptic complex of dwarf geckos from Madagascar: molecular evidence for new species-level lineages within the Lygodactylus tolampyae complex

Zootaxa, Journal Year: 2024, Volume and Issue: 5468(3), P. 416 - 448

Published: June 13, 2024

The Lygodactylus tolampyae complex includes several deep genetic lineages of small diurnal geckos from the West and North Madagascar whose taxonomy is largely unsolved. We sequenced DNA fragments one mitochondrial four nuclear-encoded genes for up to 70 samples across entire known range these geckos. find as many 11 differentiated by >4% pairwise distances in 16S rRNA gene fragment, with >9% distance majority lineage comparisons. Many were concordantly all without any haplotype sharing, despite syntopic occurrence some them. therefore hypothesize that contains seven candidate species, but a comprehensive taxonomic resolution complicated various hindrances. These include incomplete sampling, two each only single specimen, further no voucher specimens available examination. Further hurdles are probably lost holotype L. its imprecise type locality, well apparent lack morphological differentiation between lineages. Based on survey historical literature travel routes original collector, A. Grandidier, we conclude provenance likely wider Morondava area assign sole species this name. then proceed describe three represent separate markers studied: morii sp. nov., common Ankarafantsika National Park nearby sites West; herilalai occurring close syntopy signal admixture; schwitzeri nov. Sahamalaza Peninsula West. This leaves more name need gather additional samples, Namoroka other confirm be an apparently rare example truly cryptic reptile Madagascar, where even detailed examination does not reveal differences among clearly evolutionarily independent require recognition distinct due their co-occurrence admixture.

Language: Английский

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Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification

Life, Journal Year: 2023, Volume and Issue: 13(2), P. 482 - 482

Published: Feb. 9, 2023

The mitogenome of an endemic catfish Clarias camerunensis was determined from the Cameroon water. This circular 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer a single AT-rich control region. heavy strand accommodates 28 whereas light is constituted by ND6 eight RNA (tRNA) genes. C. mitochondrial genome AT biased (56.89%), as showcased other species. comparative analyses revealed that most species have 6 overlapping 11 intergenic spacer regions. Most PCGs were initiated terminated with ATG start codon TAA stop codon, respectively. tRNAs folded into distinctive cloverleaf secondary structure, except trnS1. placement conserved domains region similar all highly variable nucleotides CSB-I. Both maximum likelihood Bayesian-based matrilineal phylogenies distinctly separated five clades on basis their known distributions (South China, Sundaland, Indochina, India, Africa). TimeTree analysis two major (Indo-Africa Asia) might diverged during Paleogene (≈28.66 MYA). Our findings separation Indian (C. dussumieri) African gariepinus) took place Paleogene, well South Chinese (Clarias fuscus) Sundaland batrachus) splits Indochinese macrocephalus) Neogene through independent colonization. pattern biotic relationships highlights influence topography geological events determining evolutionary history enrichment mitogenomic data multiple nuclear loci native range or type locality will confirm true diversification Asian countries.

Language: Английский

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Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species

Zootaxa, Journal Year: 2024, Volume and Issue: 5397(4), P. 451 - 485

Published: Jan. 7, 2024

The area around the Malagasy village of Andasibe, which includes Analamazaotra-Mantadia National Park as well other protected areas, is characterized by very species-rich and well-studied communities animals plants, but new species are still regularly discovered. Three phytotelmic frogs subgenus Pandanusicola in genus Guibemantis known from this area, G. flavobrunneus, liber, pulcher. Further have been provisionally assigned to bicalcaratus or albolineatus, pending detailed taxonomic review. During preliminary exploration ecology these specialized that live reproduce leaf axils Pandanus screw pines, we noticed syntopic presence two differently colored sized Andasibe could not be unambiguously any species. A genetic screening revealed correspond yet further area. Based on our data, seven occur nearby forests: (1) only non-phytotelmic region; (2) flavobrunneus largest a diagnostic yellowish brown dorsal pattern; (3) pulcher, translucent-green color with purplish spotting observed area; (4) methueni, brownish usually lacking contrasted dorsolateral bands differs emitting characteristic trill-like advertisement call series (rather than clicks chirps) according data widespread along Madagascars east coast; three species: (5) ambakoana sp. nov., species, typically incomplete light single click-like calls; (6) vakoa equally lacks has calls short duration; (7) rianasoa smaller less distinct femoral glands all others, emits soft chirp-like calls. All genetically highly distinct, >5% uncorrected pairwise distances mitochondrial 16S rRNA gene, lack haplotype sharing nuclear-encoded genes. co-occurrence relatively small geographic unprecedented Madagascar for in-depth studies possible differentiation habitat use life history.

Language: Английский

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A description of Aliichlorella ignota gen. et sp. nov. and a comparison of the efficiency of species delimitation methods in the Chlorella‐clade (Trebouxiophyceae, Chlorophyta)

Phycological Research, Journal Year: 2024, Volume and Issue: 72(3), P. 180 - 190

Published: April 15, 2024

Abstract The present study reports a new representative of Chlorella ‐clade that was newly isolated from the Lake Vos'merka (Samara region, Russian Federation). 18S–ITS1–5.8S–ITS2 sequence analyses indicated studied strain ACSSI 368 and related chlorelloides , pulchelloides formed an separate cluster in ‐clade, unrelated to holotype genus – vulgaris. independent place also confirmed by genetic distances. individual species status 368, compared with sister C. morphological differences (cell number per colony, type chloroplast, autospores), distances interspecific level fragment, alone internal transcribed spacer 1 (ITS1) 2 (ITS2) sequences, one complementary base change ITS1, results delimitation using five methods. A description provided as authentic Aliichlorella ignota . Currently, includes comb. nov. In general, six different algorithms were used study. ASAP (i.e. assemble automatic partitioning) LocMin ‘local minimum’ function) showed synchronous results, but their accuracy respect closely somewhat lower. mlPTP algorithm simultaneously aimed combine at same time divide slightly distinguishing strains within into several molecular operational taxonomic units. bPTP separated excessively representatives species. generalized mixed Yule coalescent (GMYC) consistent most modern understanding taxonomy. However, method is time‐consuming because, for its implementation, it necessary carry out long preparatory work. KoT less accurate than GMYC although this because does not require preliminary construction ultrametric trees.

Language: Английский

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A race against extinction: The challenge to overcome the Linnean amphibian shortfall in tropical biodiversity hotspots

Diversity and Distributions, Journal Year: 2024, Volume and Issue: 30(12)

Published: Aug. 22, 2024

Abstract Aim There is an urgent need to explore, characterize, describe and preserve as many species possible prevent their decline. Tropical biodiversity hotspots harbour most of the known land diversity vast amounts undiscovered undescribed species. Here, we quantify taxonomically unassessed amphibian richness in Madagascar, one best‐studied explored tropical worldwide, identify knowledge gaps conservation implications. Location Madagascar. Time Period Present. Major Taxa Studied Amphibians. Methods We used Madagascar fauna a model unveil neglected by analysing 10,873 mitochondrial sequences using delimitation algorithms incorporating all previously published bioacoustics, distributional, morphological nuclear data with integrative approach. Results Besides currently described 413 species, identified 408 divergent lineages. Among this, 310 fit category candidate pending taxonomic assessment, while 98 are considered deep conspecific These figures suggest that could be twice high represented current taxonomy. Geographically, these occur well‐studied areas within island. Main Conclusions Despite being countries worldwide for amphibians, found awaiting assessment Paradoxically, this concentrates on highly regions, emphasizing importance exploring inventorying new areas. Our results highlight magnitude Linnean Wallacean shortfalls, affecting both estimates distribution ranges biogeographic setting fauna. Current efforts should consider novel unexplored they will likely yet discovered. expect similar patterns across less studied realms encourage researchers perform such studies different clades before becomes irremediably lost.

Language: Английский

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Antholoba fabiani sp. nov. (Actiniaria, Metridioidea, Antholobidae fam. nov.), a new species and family of sea anemone of the southwestern Atlantic, Brazil

Marine Biodiversity, Journal Year: 2024, Volume and Issue: 54(3)

Published: April 5, 2024

Language: Английский

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