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1,492 results for “species delimitation”
Data from: A demonstration of unsupervised machine learning in species delimitation
One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. Here we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.
Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen
The breve species group includes closely related Bembidion Latreille ground beetles commonly found at high elevation in the mountains of western North America. For several decades, the group has been considered to consist of two species. Here, we present evidence from morphological, molecular and geographic data that the group contains nine species: Bembidion ampliatum, B. breve, B. geopearlis, B. laxatum, B. lividulum, B. oromaia, B. saturatum, B. testatum and B. vulcanix. We describe three species (B. geopearlis, B. oromaia and B. vulcanix) as new and resurrect four previously synonymized names (B. ampliatum, B. lividulum, B. saturatum and B. testatum). Species diversity is highest throughout the Cascades in Oregon and Washington, and Sierra Nevada of California, where up to seven species can occur in sympatry. We resolved challenging nomenclatural issues through analysis of sequences obtained from century-old type specimens by using a novel application of rDNA copy number analysis – an approach that may prove useful for other historical specimens.
Data from: Species delimitation in Tetraploid, Apomictic Amelanchier (Rosaceae)
Diversification in Amelanchier tetraploid apomicts differs from that of diploid sexuals and produces groups that are taxonomically difficult. Apomixis facilitates expansion of ecologically successful genotypes into numerous, narrowly distributed, and often minimally distinct microspecies. Residual sexuality in tetraploids creates hybrid swarms and intergradation of taxa. This gene flow is evident in DNA sequences from nuclear and chloroplast regions that record mostly allotetraploid, convoluted histories. Ongoing apomixis in successful tetraploid genotypes fosters their expansion into geographically widespread phenotypic clusters. We delimit such clusters as species and deny species status to microspecies. We demonstrate polyploid complexity and our approach to species delimitation in three taxa of Amelanchier. The tetraploid microspecies A. "rubra" of southeastern Maine, while morphologically distinct, hybridizes with sympatric congeners. Eastern North American A. bartramiana contains diploids and polyploids (tetraploids and a few triploids) that are sometimes morphologically semi-cryptic. We group all ploidy levels in the A. bartramiana agamic complex and recognize as a species the diploid (A. bartramiana). The tetraploid is not given species status because it intergrades extensively with tetraploid congeners, as exemplified by the nothospecies named here, A. × neglecta . Western North American A. cusickii is tetraploid, mostly distinct morphologically and ecologically, distinct genetically, and merits species status.
Species delimitation with limited sampling: an example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)
<p>The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed, and subjective decision-making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit the methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus <em>Cyclocosmia</em> Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over-splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within North American <em>Cyclocosmia</em>, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over-splitting.</p>
Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)
<p>Mangrove pit vipers of the <em>Trimeresurus</em> <em>purpureomaculatus</em>-<em>erythrurus</em> complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiated the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/ differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.</p>
Data from: Population structure and species delimitation in the Wehrle's salamander complex
<p>Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Here we report on a molecular systematic investigation of woodland salamanders in the <em>Plethodon wehrlei</em> group, which has recently been split from two species into five. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data using anchored hybrid enrichment, which resulted in 319 loci averaging 1300 base pairs in length. Biallelic single nucleotide polymorphisms (SNPs) were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure using PCA, DAPC, FEEMS, and STRUCTURE, and found that all of the recognized species formed genetic clusters; however, <em>P. wehrlei</em> and <em>P. punctatus</em> were relatively weakly differentiated, and STRUCTURE identified three separate clusters within <em>P. jacksoni.</em> Species trees inferred using wASTRAL, BPP, and TreeMix all recovered the same topology, with <em>P. dixi </em>sister to the other taxa, which included a northern clade (<em>P. wehrlei, P. punctatus, P. pauleyi</em>) and a southern clade (<em>P. jacksoni, </em>with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species using BPP and the genealogical divergence index (<em>gdi</em>). While BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the <em>gdi</em> only strongly supported <em>P. dixi </em>and <em>P. pauleyi</em>, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research with the aim of better testing and diagnosing the species diversity within the <em>P. wehrlei</em> group.</p>
Data from: High species diversity of Phintella and Phintella-like spiders (Araneae: Salticidae) in Vietnam revealed by DNA-based species delimitation analyses
<p>Salticidae (jumping spiders) usually exhibit pronounced sexual dimorphism in adult morphology, particularly body coloration and size and shape of the first legs. Consequently, the male and female from the same species might be erroneously assigned to different species or even different genera, which could generate synonymies in classification if only morphological data were used. <em>Phintella </em>is a species-rich genus of Salticidae, which currently exhibits 76 named species. However, the male–female counterpart is unknown for nearly half of the species. In this study, we used a molecular approach to delineate the species boundaries for <em>Phintella </em>and <em>Phintella</em>-like specimens collected in Vietnam, using morphological information as supporting data. We used three gene fragments (mitochondrial COI, 16S-ND1, and nuclear 28S) and biogeographical consideration for species delimitation. A total of 22 putative species were recognized: 18 species of the genus <em>Phintella</em>, one species of the genus <em>Lechia </em>(<em>L. squamata</em>), and three species of the genus <em>Phinteloides</em>. Eleven undescribed species were discovered, of which seven have a male–female combination, two species have only males, and two species have only females. The crown age of <em>Phintella </em>was estimated at the Serravallian stage of the Miocene after the increase of species number around 16 MYA. The crown ages of most putative species recognized in this study were estimated in Pleistocene, and the divergence among sister species likely occurred from the mid-Miocene to the Pliocene. Our ancestral range reconstruction results showed that the diversification of our ingroup was governed by progressive dispersal events, i.e., <em>Phintella </em>and their related species in Vietnam diversified while expanding their range on the continent. Our results provide fundamental biodiversity data for a high-diversity genus in Vietnamese <em>Phintella </em>spiders.</p>
F I G U R E 4 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation
F I G U R E 4 Legend on next page.
F I G U R E 2 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation
F I G U R E 2 Histogram of HKY pairwise distance with bars increasing by 0.25 pairwise distance.
Figure 1 in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data
Figure 1. Guidelines for studies of cetacean taxonomy based on genetic data.
Data from: Species Delimitation of Endemic Atlantic Forest Inga subnuda (Leguminosae, Caesalpinioideae, mimosoid clade) Subspecies Based on Morphological, Ecological and Palaeoecological Data
<p><i>Inga subnuda</i> Salzm. ex Benth. are one of 31 endemic species in the Brazilian Atlantic Forest. Intermixed leaf and floral traits have made morphological distinctiveness difficult, and its current taxonomic treatment considers <i>I. subnuda</i> as one species with two subspecies. We aim to explore different lines of evidence to disentangle and clarify species boundaries in these two subspecies. Morphological variation and bioclimatic data of the two subspecies of the complex were assessed by using multivariate morphometric analyses and ecological niche modeling. Morphological quantitative characters allowed the recognition of different groups. The climatic space was similar but not identical, and the recent climatic cycles that could have shaped the current distribution are discussed. The results of our integrative study suggest regard both subspecies as two different species. Moreover, we propose a change in status of <i>I. subnuda subsp. luschnathiana</i> to the rank of species. The new up-ranked taxon is described and illustrated.</p>
Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding i) species-level diversity, ii) hybridization and admixture, and iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation. --
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
<p>Cold-water corals build up reef structures or coral gardens and play an important role for many organisms in the deep sea. Climate change, deep-sea mining, and bottom trawling are severely compromising these ecosystems, making it all the more important to document the diversity, distribution, and impacts on corals. This goes hand in hand with species identification, which is morphologically and genetically challenging for Hexa- and Octocorallia. Morphological variation and slowly evolving molecular markers both contribute to the difficulty of species identification. In this study, a fast and cheap species delimitation tool for Octocorallia and Scleractinia of the Northeast Atlantic was tested based on 49 specimens. Two nuclear markers (ITS2 and 28S rDNA) and two mitochondrial markers (COI and mtMutS) were sequenced. The sequences formed the basis of a reference library for comparison to the results of species delimitation based on proteomic analysis using the MALDI-TOF MS method. The genetic methods were able to distinguish 17 of 18 presumed species. The MALDI-TOF MS method was able to distinguish 7 species. Species that could not be distinguished from one another still achieved good signals but were not represented by enough specimens for comparison. Therefore, it is predicted that with an extensive reference library of proteome spectra for Scleractinia and Octocorallia, MALDI-TOF MS may provide a rapid and cost-effective alternative for species discrimination in corals.</p>
Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: A case study on Cylindera pseudocylindriformis complex (Coleoptera, Cicindelidae)
<p>Alpha taxonomy is fundamental for many biological fields. Delineation of species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary, and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the <em>Cylindera</em> <em>pseudocylindriformis</em> complex. We discuss the association between genetic divergence and microhabitat specialization, and we further corroborated that <em>C</em>. <em>subtilis</em> sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can form at a small geographic scale, even in a winged insect-like tiger beetle. Our results also indicated that there may still be undocumented species diversity of Taiwanese <em>Cylindera</em> remaining to be discovered.</p>
Fig. 1 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Fig. 1. Sample sites location in the Paraná and Tietê rivers, state of São Paulo, Brazil.
Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow
Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.
Data from: Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation
Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snappers). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species (L. campechanus). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favor the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. While we find evidence of introgression in geographically neighboring populations in northern South America, the genetic differences strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.
FIGURE 27 in Torrenticola trimaculata n. sp. (Parasitengona: Torrenticolidae), a three-spotted water mite from eastern North America: taxonomic history, species delimitation, and survey of external morphology
FIGURE 27: Torrenticola trimaculata n. sp. commensals (LT-SEM): A – diatoms (Cocconeis placentula Ehrenberg, 1838) covering dorsum; B – close-up of C. placentula covering T. trimaculata dorsum; C – bacteria covering body, especially within depressions.
FIGURE 23 in Torrenticola trimaculata n. sp. (Parasitengona: Torrenticolidae), a three-spotted water mite from eastern North America: taxonomic history, species delimitation, and survey of external morphology
FIGURE 23: Torrenticola trimaculata n. sp. venter (LT-SEM; female depicted): coxal glandularia (Cxgl); excretory pore (ep); ventral glandularia (Vgl): and area of primary (1°) and secondary (2°) sclerotization.
FIGURE 24 in Torrenticola trimaculata n. sp. (Parasitengona: Torrenticolidae), a three-spotted water mite from eastern North America: taxonomic history, species delimitation, and survey of external morphology
FIGURE 24: Torrenticola trimaculata n. sp. ventral posterior (LT-SEM): A – posterior area of secondary sclerotization (2°) depicting vestigial ventral glandularium 1 (Vgl-1), ventral glandularia 2 (Vgl-2), and excretory pore (ep); B – close-up of excretory pore; C – genital plates, note rim of setae surrounding each plate.
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