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1,492 results for “species delimitation”
Data from: Species Delimitation of Endemic Atlantic Forest Inga subnuda (Leguminosae, Caesalpinioideae, mimosoid clade) Subspecies Based on Morphological, Ecological and Palaeoecological Data
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Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan
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FIGURES 14–20 in COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico
FIGURES 14–20. Ixchela zapatai sp. nov. Male: 14–15, Habitus, lateral and dorsal views, respectively. 16, Carapace and chelicerae, frontal view. 17, Chelicerae, frontal view. 18, Chelicerae, lateral view. 19–20, Left palp, prolateral and retrolateral views, respectively. FAC, frontal apophysis of chelicerae, PAB: prolateroventral apophysis of bulb, VPP, ventrobasal protuberance of procursus. Scale bars: 0.5 mm (Fig. 17, 18), 1 mm (Figs 16, 19, 20), 2 mm (Figs 14, 15).
FIGURES 25–30. 25–28 in COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico
FIGURES 25–30. 25–28, Living specimens (females) of Ixchela zapatai sp. nov. from type locality. 29–30, Temperate pine-oak forest at 2399 m.a.s.l. at the type locality (red arrow indicates the microhabitat where the specimens of I. zapatai sp. nov were collected).
FIGURES 3–9 in COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico
FIGURES 3–9. Ixchela panchovillai sp. nov. Male: 3–4, Habitus, lateral and dorsal views, respectively. 5, Carapace and chelicerae, frontal view. 6, Chelicerae, frontal view. 7, Chelicerae, lateral view. 8–9, Left palp, prolateral and retrolateral views, respectively. PAB: prolateroventral apophysis of bulb, SAC: sclerotized apophysis of chelicerae, VAF: ventrodistal apophysis of femur, VPP, ventrobasal protuberance of procursus. Scale bars: 0.5 mm (Figs 6, 7), 1 mm (Figs 5, 8, 9), 2 mm (Figs 3, 4).
Data from: Taxonomic delimitation of species complexes: a challenge for conservation, first steps with Abarema cochliacarpos complex
Taxonomic and ecological knowledge of plant species complexes informs their conservation status. Poorly delimited species boundaries can lead to incorrect assessments of biodiversity, and a rare species might have its distribution range overestimated if considering other closely related taxa as the same one. The present study investigates the level of morphometric variation within the Abarema cochliacarpos complex, throughout its entire distribution range in Brazilian Atlantic Forest and Caatinga vegetation, and considers the drivers of this variation. A morphometric study using cluster, PERMANOVA, and NMDS analyses was conducted. We analyzed patterns of trait variation among and within populations, and their relationship with environmental factors along with their geographical gradient. From the four morphotypes previous cited for the complex, the analyses delimited three morphological groups. Their morphological characteristics differed in response to environmental drivers. We identified morphological characters that differentiated the groups within the complex. The development of conservation strategies and actions to fully protect a species complex requires the understanding of the morphological variation within the complex. In the Abarema cochliacarpos complex different threats and challenges are associated with the conservation of each morphotype. We highlight the importance of conserving the various morphotypes of a species complex which has a large distribution range as evolutionary significant units, something that is frequently neglected in the published literature.
Phylogenomics and species delimitation for effective conservation of manta and devil rays
<p>Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation, and law enforcement strategies.</p>
Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
<p>The genetic variation of the COI gene has a great effect on the final results of the species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for comprehensively appraising the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis based on different thresholds were compared among 4,288 genera (35,068 species). Besides, we also compared the match ratios obtained from two species delimitation methods: the clustering analysis (distance-based method) and the bPTP analysis (tree-based method). Furthermore, the effectiveness of two different results of the bPTP analysis: bPTP_h and bPTP_ml was also tested. Approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (> 3%), and a conservative estimate of this value is 12.05-22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of species diversity. In metabarcoding studies, a threshold of 3% can only be used to estimate the insect diversity roughly. As for the clustering analysis, the "threshOpt" or "localMinima" algorithms can provide a priori value for the researcher. Nevertheless, if the minimum interspecific genetic distance of congeneric species was greater than or equal to 2%, it is possible to avoid overestimating the species diversity based on the empirical thresholds. Besides, the match ratios of the bPTP_ml results were higher than those of the bPTP_h results. As for the bPTP analysis, the bPTP_ml results were recommended. If a proper threshold was selected, the clustering analysis may outperform the bPTP analysis.</p>
Species delimitation, classical taxonomy, and genome skimming: a review of the ground beetle genus Lionepha (Coleoptera: Carabidae)
<p>The western North American genus <i>Lionepha</i> is shown to contain at least 11 species through a combination of eight-gene species delimitation analyses and morphological study. In order to confirm the names of several species, we sequence DNA of primary types of several names, including a LeConte lectotype collected in the 1850s, using next-generation sequencing. We examine chromosomes of eight species, and show that all have 12 pairs of autosomes and an X0/XX sex-chromosome system. The following species are described as new: <i>Lionepha australerasa</i>, <i>L. kavanaughi</i>, <i>L. lindrothi</i>, and <i>L. tuulukwa</i>. The name <i>Lionepha erasa</i> is shown to belong to a relatively rare, western species ranging from Oregon through Alaska; the common, widespread species previously known as <i>Lionepha erasa</i> now takes the name <i>L. probata</i>. <i>Bembidion lindrothellus</i>, <i>B. chintimini</i>, and <i>B. lummi </i>are synonymized with<i> L. erasa.</i> We provide tools to identify specimens to species, including illustrations and diagnoses.</p>
The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)
<p>Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (<i>Terrapene</i> spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.</p>
Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance
<p>The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g. cryptic species), differences in criteria of species concepts, and discordance between gene topologies (e.g. mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offer the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that proper taxonomy has over conservation related actions.</p>
FIGURE 1 in Discovery of a new species of Trieces (Hymenoptera: Ichneumonidae: Metopiinae) questioning the traditional delimitation between Trieces and Chorinaeus
FIGURE 1. Morphology of Trieces confusus sp. nov., female: A—habitus, lateral view (holotype); B—head, front view (holotype); C—head, dorsal view (holotype); D –metasoma, dorsal view (paratype); E—mesosoma and head, dorsal view, paratype; F—metasoma, lateral view (holotype), G—mesosoma and head, lateral view (paratype).
FIGURE 3 in Discovery of a new species of Trieces (Hymenoptera: Ichneumonidae: Metopiinae) questioning the traditional delimitation between Trieces and Chorinaeus
FIGURE 3. Morphology of Trieces confusus sp. nov., male, paratype: A—habitus, lateral view; B—head, front view; C—head, dorsal view; D—metasoma, dorsal view; E—mesosoma and head, dorsal view; F—metasoma, lateral view; G—mesosoma and head, lateral view.
FIGURE 2 in Discovery of a new species of Trieces (Hymenoptera: Ichneumonidae: Metopiinae) questioning the traditional delimitation between Trieces and Chorinaeus
FIGURE 2. Morphology of Trieces confusus sp. nov. (SEM), female, holotype: A—tergites I–III, lateral view; B—mesosoma, lateral view; C—tergites I–III, dorsal view; D—anterior part of mesosoma, lateral view; E—metapleuron; F—head, dorsolateral view.
Data from: In the shadows: phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)
The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.
Data from: Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
Data from: 'Fix me another marguerite!': species delimitation in a group of intensively hybridising lineages of ox-eye daisies (Leucanthemum Mill., Compositae-Anthemideae)
Delineating species boundaries in the framework of the multi-species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. The present study evaluates the robustness of currently available species delimitation methods implemented in BEAST (BFD, BFD, and DISSECT) in the closely-knit ox-eye daisy group around Leucanthemum ageratifolium Pau. Comprising five taxa being allopatrically distributed between northern Spain and southern Italy this study group shows signs of hybridisation with the widespread and co-distributed species Leucanthemum vulgare (Vaill.) Lam. to various extent. As expected, our empirical analyses based on both AFLP fingerprinting and sequence data demonstrate that the robustness of species delimitation results is considerably influenced by the intensity of hybridisation among species and the number of hybrid individuals included. Therefore, we set up a methodological pipeline with a first step of identification and subsequent removal of individuals showing admixed genetic patterns caused by actual interbreeding using AFLP-fingerprint and morphometric data, followed by application of different Bayesian MSC species delimitation methods based on the remnant individuals using both AFLP-fingerprint and sequence data (four nuclear markers, five concatenated intergenic spacer regions of the plastid genome). The results argue for acknowledgement of Leucanthemum laciniatum, L. legraeanum, and L. ligusticum as independent species, show the close relationship of L. ageratifolium, L. monspeliense, and L. vulgare, and give rise to the description of three nothospecies new to science.
Data from: Molecular species-delimitation methods recover most song-delimited cicada species in the European Cicadetta montana complex
Molecular species delimitation is increasingly being used to discover and inform illuminate species level diversity and a number of methods have been developed. Here we compare the ability of two molecular species delimitation methods to recover song-delimited species in the Cicadetta montana cryptic species complex throughout Europe. Recent bioacoustics studies of male calling songs (pre-mating reproductive barriers) have revealed cryptic species diversity in this complex. Maximum likelihood and Bayesian phylogenetic analyses were used to analyze the mitochondrial genes COI and COII and the nuclear genes EF1α and period for thirteen European Cicadetta species as well as the closely related monotypic genus Euboeana. Two molecular species delimitation methods, general mixed Yule-coalescent (GMYC) and Bayesian Phylogenetics and Phylogeography (BPP), identified the majority of song-delimited species and were largely congruent with each other. None of the molecular delimitation methods were able to fully recover a recent radiation of four Greek species.
Data from: Intragenomic ITS2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis
A recent DNA barcoding study of Australian microgastrines (Hymenoptera: Braconidae) sought to use next generation sequencing of the cytochrome c oxidase subunit 1 (COI) barcoding gene region, the wingless (WG) gene and the internal transcribed spacer 2 (ITS2) to delimit molecular species in a highly diverse group of parasitic wasps. Large intragenomic distances between ITS2 variants, often larger than the average interspecific variation, caused difficulties in using ITS2 for species delimitation in both threshold and tree‐based approaches, and the gene was not included in the reported results of the previous DNA barcoding study. We here report on the intragenomic, and the intra‐ and interspecies, variation in ITS2 in the microgastrine genus Diolcogaster to further investigate the value of ITS2 as a marker for species delimitation and phylogenetics of the Microgastrinae. Distinctive intragenomic variant patterns were found in different species of Diolcogaster, with some species possessing a single major variant, and others possessing many divergent variants. Characterising intragenomic variation of ITS2 is critical as it is a widely used marker in hymenopteran phylogenetics and species delimitation, and large intragenomic distances such as those found in this study may obscure phylogenetic signal.
Data from: Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea)
Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the harvestmen genus Sclerobunus found throughout the mountainous regions of western North America. Based on our analyses, we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus with Sclerobunus including transfer of S. cavicolens comb. nov. and elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis stat. nov. Additionally, five new species of Sclerobunus are described from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp. nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni sp. nov. Several of the newly described species are single-cave endemics, and our findings suggest that further exploration of western North American cave habitats will likely yield additional new species.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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