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89 results for “integrated species delimitation”
From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals
<p>With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus <em>Pocillopora</em>, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve <em>Pocillopora</em> phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine <em>Pocillopora</em> species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus <em>Pocillopora</em>. These results give new insights into the usefulness of multiple criteria for resolving <em>Pocillopora</em>, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.</p> <p> </p> <p>This deposit contains the data related to Oury N, Noël C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific <em>Pocillopora </em>corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803</p> <p>See 0_README.txt for more content details.</p>
Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon
<p>This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus <em>Calandrella</em>, with the description of a range-restricted African relic taxon" by Stervander <em>et al</em>. </p> <p>For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript. </p> <p><strong>Phylogenetic analyses</strong></p> <ol> <li>Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa</li> <li>BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml</li> <li>BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log</li> <li>BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees</li> <li>TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk</li> </ol> <p><strong>Species delimitation</strong></p> <ol> <li>Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk</li> <li>mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt</li> <li>mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt</li> <li>mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg</li> </ol>
Data from: Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae)
<p>Species delimitation is fundamental to deciphering the mechanisms that generate and maintain biodiversity. Alpha taxonomy historically relied on expert knowledge to describe new species using phenotypic and biogeographic evidence, which has the appearance of investigator subjectivity. In contrast, DNA‐based methods using the multispecies coalescent model (MSC) promise a more objective approach to describing biodiversity. However, recent criticisms suggest that under some conditions the MSC may over‐split lineages, identifying species that do not reflect biological reality. Here, we reconcile these approaches using empirical data for the Greenthroat Darter complex (<em>Etheostoma lepidum</em>), a small freshwater fish species with a disjunct distribution in Texas and New Mexico, USA. We demonstrate that MSC methods recognizes all nine sampled populations as distinct species, sometimes splitting specimens from a single locality into multiple species. However, environmental, phenotypic and biogeographic evidence do not corroborate the nine species supported by the MSC. Instead, collective evidence indicates that <em>E. lepidum</em> is comprised of just three species that are consistent with the molecular phylogeny: <em>Etheostoma lepidum</em> (Greenthroat Darter) in rivers draining the eastern Edwards Plateau, <em>Etheostoma</em> cf. <em>lepidum</em> (Texas Darter) in the Concho and San Saba rivers and <em>Etheostoma</em> cf. <em>lepidum</em> (Pecos Darter) in the Pecos River. The Pecos Darter is likely highly imperiled due to its localized distribution and reliance on vanishing spring‐fed stream habitats. The impending biodiversity crisis makes integrative and swift species delimitation more necessary than ever. Our study exemplifies how classic taxonomic expertise combined with molecular phylogenetics can produce a more robust description of threatened biodiversity.</p>
Data from: Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae)
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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>
Integrating host use and dispersal ability with species delimitation to unravel a cryptic radiation of photosynthetic sea slugs
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‘Picking up signals’ in male genital morphospace and integrating phylogenomics to delimit Neotropical Nylanderia Emery species (Hymenoptera: Formicidae)
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Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: A case study on Cylindera pseudocylindriformis complex (Coleoptera, Cicindelidae)
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Data and code from: Integrating genomics, collections, and community science to delimit species clarifies the taxonomy of a variable monitor lizard (<em>Varanus tristis</em>)
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Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan
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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.
Data from: Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)
In species differentiation, characters do not usually diverge synchronously and there are also processes that effectively shuffle character states present in lineages descendant from a common ancestor. Species are thus expected to show some degree of incongruence among characters, and we argue that taxonomic delimitation actually benefits from integrative approaches and objective strategies dealing with character conflict. We illustrate the potential of exploiting conflict for species delimitation in a study-case of ground beetles of the subgenus Carabus (Mesocarabus), where traditional taxonomy fails to accurately delimit species. The molecular phylogenies of four mitochondrial and three nuclear genes, cladistic analysis of the aedeagus, ecological niche divergence, and morphometry of pronotal shape in altogether more than 500 specimens of Mesocarabus, show that none of these character sets are fully congruent with each other. For these data, a three-steps operational strategy is proposed for species delimitation by (1) delineating candidate species based on the integration of incongruence among conclusive lines of evidence, (2) corroborating candidate species with inconclusive lines of evidence, and (3) refining a final species proposal based on an integrated characterization of candidate species based on the evolutionary analysis of incongruence. This procedure provided a general understanding of the reticulate process of hybridization and introgression acting on Mesocarabus and generated the hypothesis of seven Mesocarabus species, including two putative hybrid lineages. Our work emphasizes the importance of incorporating critical analyses of character and phylogenetic conflict to infer both the evolutionary history and species boundaries through an integrative taxonomic approach.
Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Systematics at the species level is still marked by theoretical and empirical tensions amongst the desires to identify geographical lineages, delimit species, and estimate their relationships. These goals are often confounded because each relies, at least to some extent, on the others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us to generate large-scale molecular data sets to examine variation within species at a fine scale. Finally, a renaissance in morphological species validation allows us to integrate historical species definitions with coalescent models for species delimitation. Here, we investigate the applicability of these methods in an empirical case, in the Nearctic snake genus Storeria. Integrating trait data into species delimitation reduces the number of species delimited from molecular data alone. Whereas molecular data support eight distinct species-level lineages, including morphological data reduces this to four. The taxa Storeria dekayi, Storeria occipitomaculata, Storeria storerioides, and Storeria victa are considered distinct, monotypic species, with no subspecies recognized. We highlight the need for careful assessment of species delimitation, combining both computational genetic methods as well as traditional character-based descriptions. It is now possible to identify phylogeographical lineages, delimit species using molecular and morphological data, and estimate their relationships in a single coherent set of analyses. Moving forward, this will allow for more rapid and objective assessments of cryptic diversity at the species level.
FIGURE 7 in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 7. Ventral color variation in the type series for both Varanus dalubhasa sp. nov. (top) and V. bangonorum sp. nov. (bottom). Scale = 50mm.
FIGURE 8 in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 8. Photos in life of Varanus dalubhasa sp. nov. (A; KU 306601) and V. bangonorum sp. nov. (B; KU 335742).
FIGURE 6 in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 6. Dorsal color variation in the type series for both Varanus dalubhasa sp. nov. (top) and V. bangonorum sp. nov. (bottom). Scale = 50mm.
FIGURE 5 in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 5. Holotype of Varanus dalubhasa sp. nov. (PNM 9796), with body shown in dorsal and ventral aspects; and head shown in dorsal, ventral, and profile aspects. Scale = 50 mm.
FIGURE 3 in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 3. Comparison of gular coloration and patterning among Varanus dalubhasa sp. nov. (Bicol, Polillo, Catanduanes), V. bangonorum sp. nov. (Mindoro, Semirara), V. marmoratus, V. nuchalis, and V. palawanensis. Scale = 50mm.
FIGURE 4. Principal Components Analyses for A in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 4. Principal Components Analyses for A) mensural, and B) meristic characters for Varanus nuchalis, V. marmoratus, V. palawanensis, V. dalubhasa sp. nov., and V. bangonorum sp. nov..
FIGURE 1 in Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species
FIGURE 1. The distribution of the Varanus salvator Complex water monitor species. Pleistocene Aggregate Island Complex (PAIC) faunal regions in the Philippines (indicated by island group color differences) are delineated by the 120m underwater contour (Voris 2000; Brown & Diesmos 2009). Both V. togianus and V. s. macromaculatus are reported to occur on Sulawesi Island (Koch et al. 2010a). The distribution of V. rasmusseni is denoted with an asterisk, "*", while the distributions of the two newly identified evolutionary lineages (Welton et al. 2013a,b) are denoted by question marks (?); see Figure 2.
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