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1,492 results for “species delimitation”
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: Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae)
Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.
Data from: Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation.
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct computer simulations to explore the effects of violating this assumption in the form of species-specific positive selection when estimating species trees, species delimitations, and coalescent parameters under the model. We simulated datasets under an array of evolutionary scenarios that differ in both speciation parameters (i.e., divergence times, strength of selection) and experimental design (i.e., number of loci sampled) and incorporated species-specific positive selection occurring within branches of a species tree to identify the effects of selection on multispecies coalescent inferences. Our results highlight particular evolutionary scenarios and parameter combinations in which inferences may be more, or less, susceptible to the effects of positive selection. In some extreme cases, selection can decrease error in species delimitation and increase error in species tree estimation, yet these inferences appear to be largely robust to the effects of positive selection under many conditions likely to be encountered in empirical datasets.
Data from: Comparing and co-analysing microsatellite and morphological data for species delimitation in the New Zealand native Myosotis pygmaea species group (Boraginaceae)
Delimiting species boundaries in recent plant radiations can be challenging. The New Zealand native Myosotis pygmaea (Boraginaceae) species group is a case in point. This species complex is of interest as it includes threatened species as well as possibly threatened unnamed putative taxa. Integrative taxonomic approaches using multiple lines of evidence are frequently used to overcome the difficulties of identifying lineages resulting from recent radiations. Here we analyse genotypic data from nearly 500 Myosotis individuals using microsatellite markers, and compare and co-analyse this dataset with previously published morphological data. Within the M. pygmaea group, several genetic clusters can be identified, none of which align exactly with the current taxonomy and morphological variation previously identified. When co-analysing the molecular and morphological data, M. brevis can be distinguished from the remainder of the M. pygmaea species group, but no other species or previously recognised morphological groups are supported. Other groupings within the molecular dataset appear to reflect geographic structure. Within the M. pygmaea species group, the resulting pattern of low within, and high between, population genetic variation is consistent with self-fertilization and low levels of seed dispersal.
Data from: Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs
Cherax is a genus of 58 species of decapod crustaceans that are widespread across Australia and New Guinea. We use single-nucleotide polymorphisms (SNPs) to examine phylogeographic patterns in the most widespread species of Cherax, namely, C. destructor, and test the distinctiveness of one undescribed species, two C. destructor subspecies, previously proposed evolutionarily significant units, and management units. Both the phylogenetic analyses and the analysis of fixed allelic differences between populations support the current species-level taxonomy of C. setosus, C. depressus, C. dispar and C. destructor, the distinctiveness of C. destructor albidus and C. d. destructor and the existence of one undescribed species. The two populations of C. d. albidus from the Glenelg and Wimmera rivers were significantly distinct, with eight diagnostic differences (<1% fixed differences, null expectation is four fixed differences), but this low level of divergence is interpreted as within the range that might be expected of management units, that is, among allopatric populations of a single species or subspecies. A southern clade of C. d. destructor comprising the Murray River and its tributaries upstream from its confluence with the Darling River is genetically distinct from a northern clade comprising populations from the Lake Eyre Basin, the northern half of the Murray–Darling Basin (Darling River catchment) and the Lower Murray River below the Darling confluence.
Data from: Species delimitation and phylogeny in the genus Nasutitermes (Termitidae: Nasutitermitinae) in French Guiana
Species delimitation and identification can be arduous for taxa whose morphologic characters are easily confused, which can hamper global biodiversity assessments and pest species management. Exploratory methods of species delimitation that use DNA sequence as their primary information source to establish group membership and estimate putative species boundaries are useful approaches, complementary to traditional taxonomy. Termites of the genus Nasutitermes make interesting models for the application of such methods. They are dominant in Neotropical primary forests but also represent major agricultural and structural pests. Despite the prevalence, pivotal ecological role and economical impact of this group, the taxonomy of Nasutitermes species mainly depends on unreliable characters of soldier external morphology. Here, we generated robust species hypotheses for 79 Nasutitermes colonies sampled throughout French Guiana without any a priori knowledge of species affiliation. Sequence analysis of the mitochondrial cytochrome oxidase II gene was coupled with exploratory species-delimitation tools, using the automatic barcode gap discovery method (ABGD) and a generalized mixed Yule-coalescent model (GMYC) to propose primary species hypotheses (PSHs). PSHs were revaluated using phylogenetic analyses of two more loci (mitochondrial 16S rDNA and nuclear internal transcribed spacer 2) leading to 16 retained secondary species hypotheses (RSSH). Seven RSSHs, represented by 44/79 of the sampled colonies, were morphologically affiliated to species recognized as pests in the Neotropics, where they represent a real invasive pest potential in the context of growing ecosystem anthropization. Multigenic phylogenies based on combined alignments (1426–1784 bp) were also reconstructed to identify ancestral ecological niches and major-pest lineages, revealing that Guyanese pest species do not form monophyletic groups.
Data from: The challenge of species delimitation at the extremes: diversification without morphological change in Philippine sun skinks
Species represent one of the fundamental units of the evolutionary process, and an accurate understanding of species diversity is essential to studies across a wide range of biological subdisciplines. However, delimiting species remains challenging in evolutionary radiations where morphological diversification is rapid and accompanied by little genetic differentiation or when genetic lineage divergence is not accompanied by morphological change. We investigate the utility of a variety of recently developed approaches to examine genetic and morphological diversity, and delimit species in a morphologically conserved group of Southeast Asian lizards. We find that species diversity is vastly underestimated in this unique evolutionary radiation, and find an extreme case where extensive genetic divergence among lineages has been accompanied by little to no differentiation in external morphology. Although we note that different conclusions can be drawn when species are delimited using molecular phylogenetics, coalescent-based methods, or morphological data, it is clear that the use of a pluralistic approach leads to a more comprehensive appraisal of biodiversity, and greater appreciation for processes of diversification in this biologically important geographic region. Similarly, our approach demonstrates how recently developed methodologies can be utilized to obtain robust estimates of species limits in "non-adaptive" or "cryptic" evolutionary radiations.
Data from: Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data
BACKGROUND: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). RESULTS: We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but more of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. CONCLUSIONS: Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.
Data from: Congruent species delimitation of two controversial gold-thread nanmu tree species based on morphological and restriction site-associated DNA sequencing data
Species delimitation is fundamental to conservation and sustainable use of economically important forest tree species. However, the delimitation of two highly valued gold-thread nanmu species (Phoebe bournei and P. zhennan) has been confusing and debated. To address this problem, we integrated morphology and restriction site-associated DNA sequencing (RADseq) to define their species boundaries. We obtained highly consistent results from both data sets, supporting two distinct lineages corresponding to P. bournei and P. zhennan. In Phoebe bournei, higher order leaf venation is more prominent, petioles are thicker and leaf apex angle is narrower, compared to P. zhennan. Both data sets also showed that putative P. bournei localities from north-eastern Guizhou were P. zhennan. The two species have different distributions and only overlap in the Wuling Mountains. Phoebe bournei occurs mainly in Central Fujian, southern Jiangxi, the Nanling Mountains and the Wuling Mountains, whereas P. zhennan is found in the adjoining eastern regions of the Qionglai Mountains, the Southern Sichuan Hills and the Wuling Mountains. The improved delimitation of P. bournei and P. zhennan and clarification of their ranges provide a better guidance for conservation and sustainable utilization of these tree species.
Data from: The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly
The Palearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that likely remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise FST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, issue likely of relevance to a significant proportion of global biodiversity.
Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.
Data from: Species delimitation and phylogeny of Epithelantha (Cactaceae)
The genus Epithelantha (Cactaceae, Cactoideae, Cacteae) is native to Mexico and the southern USA and includes several uncertain species and ambiguous phylogenetic relationships. We applied multivariate analysis to a set of nine quantitative characters and six qualitative characters and we used Bayesian inference and maximum likelihood to reconstruct the phylogeny of Epithelantha using molecular data from four chloroplast regions (petL-psbE, psbA-trnH, trnL-F, and trnQ-rps16). Eleven taxa were collected in 39 localities where digital images of five individuals were taken. A correlation analysis allowed us to eliminate correlated characters. A discriminant canonical analysis (DCA) for quantitative characters and principal components analyses with mixed data (PCA mix) for quantitative and qualitative characters, identified the length of the flower, number of spines, areole length/width ratio, the expansion of the hilar region of the seed, multicellular sculpture and the relief of the periclinal wall as the most variable characters. The partial least squares-discriminant analysis (PLS-DA) allowed us to recognize nine of eleven taxa. As a complement, the molecular data matrix included 68 substitutions and 12 indels between the four markers. The 39 terminals analyzed were recovered in nine strongly supported clades, confirming the results of multivariate analyses. Epithelantha was recovered as a monophyletic group strongly supported by four substitutions and an indel, with Turbinicarpus being the sister group. Based on our results, we include a taxonomic synthesis of Epithelantha where we recognize ten species, propose two new combinations, designate seven lectotypes, and provide a key for species.
Data from: Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity
The increasing availability of DNA sequence data enables exciting new opportunities for fungal ecology. However, it amplifies the challenge of how to objectively classify the diversity of fungal sequences into meaningful units, often in the absence of morphological characters. Here, we test the utility of modern multilocus Bayesian coalescent-based methods for delimiting cryptic fungal diversity in the orchid mycorrhiza morphospecies Serendipita vermifera. We obtained 147 fungal isolates from Caladenia, a speciose clade of Australian orchids known to associate with Serendipita fungi. DNA sequence data for 7 nuclear and mtDNA loci were used to erect competing species hypotheses by clustering isolates based on: (a) ITS sequence divergence, (b) Bayesian admixture analysis, and (c) mtDNA variation. We implemented two coalescent-based Bayesian methods to determine which species hypothesis best fitted our data. Both methods found strong support for eight species of Serendipita among our isolates, supporting species boundaries reflected in ITS divergence. Patterns of host plant association showed evidence for both generalist and specialist associations within the host genus Caladenia. Our findings demonstrate the utility of Bayesian species delimitation methods and suggest that wider application of these techniques will readily uncover new species in other cryptic fungal lineages.
Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of species-level polyphyly. Bayes factor comparisons of species delimitation models accounting for incomplete lineage sorting under the multispecies coalescent decisively supported the recognition of two distinct species within Amatitlania corresponding to Amatitlania nigrofasciata and A. kanna lineages. The only clearly genetically and morphologically diagnosable species was A. kanna. These results strongly suggest that incomplete lineage sorting provides the best explanation for the polyphyly of A. kanna, whereas the polyphyly of A. siquia is likely a result of an imperfect taxonomy. Additional insights from coalescent-dating, network, and historical demographic analyses suggested that the two species of Amatitlania diversified only since the early Pleistocene, and that A. nigrofasciata experienced population expansions from approximately 200 000 years ago in the mid-late Pleistocene onward. We discuss implications of our results for the taxonomy and evolutionary history of Amatitlania and, more broadly, of Central American freshwater fishes.
Data from: What have been and what can be delimited as species using molecular data under the multi-species coalescent model? A case study using Hercules beetles (Dynastes; Dynastidae)
Molecular species delimitation using the multi-species coalescent model has become common for statistically and objectively determining species limits. Empirical examples of how consistently different molecular data sets delimit the same level of divergence as species using coalescent-based methods are still lacking. I applied the method of molecular species delimitation in the Bayesian Phylogenetics and Phylogeography (BPP) program to study species delimitation in the divergence between populations and between putative species across four species of Hercules beetles. The quantity and variability of the molecular data affected species delimitation. A divergence that represented a late stage along the speciation continuum, e.g. between sympatric biological species, could be delimited by BPP by fewer and less variable loci than a recent divergence, e.g. between geographic populations. My results further indicated that the use of genomic data could even over-split geographically continuously distributed populations into species. I compared my results with those from other empirical studies and argue for the need of a thorough review of the kind of evolutionary entities, e.g. geographic populations versus morphologically distinct taxa, that have been designated as species and whether such designations are consistent among studies.
Data from: Marginal likelihood estimate comparisons to obtain optimal species delimitations in Silene sect. Cryptoneurae (Caryophyllaceae)
Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be applied to optimise model of species classification. In a Bayesian framework, Bayes factors (BF), based on marginal likelihood estimates, can be used to test a range of possible classifications for the group under study. Here, we explore BF and the Akaike Information Criterion (AIC) to discriminate between different species classifications in the flowering plant lineage Silene sect. Cryptoneurae (Caryophyllaceae). We estimated marginal likelihoods for different species classification models via the Path Sampling (PS), Stepping Stone sampling (SS), and Harmonic Mean Estimator (HME) methods implemented in BEAST. To select among alternative species classification models a posterior simulation-based analog of the AIC through Markov chain Monte Carlo analysis (AICM) was also performed. The results are compared to outcomes from the software BP&P. Our results agree with another recent study that marginal likelihood estimates from PS and SS methods are useful for comparing different species classifications, and strongly support the recognition of the newly described species S. ertekinii.
Data from: High stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas
A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is "high stakes" - it is imperative that species hypotheses are data-rich, objective, and robust. This paper focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial, and nuclear DNA sequence data evidence, analyzed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni, and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era.
Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs
Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each new species description, enthusiasm has been tempered with scientific scepticism. Here, we present a statistically justified and unbiased Bayesian approach towards mouse lemur species delimitation. We perform validation tests using multilocus sequence data and two methodologies: (i) reverse-jump Markov chain Monte Carlo sampling to assess the likelihood of different models defined a priori by a guide tree, and (ii) a Bayes factor delimitation test that compares different species-tree models without a guide tree. We assess the sensitivity of these methods using randomized individual assignments, which has been used in bpp studies, but not with Bayes factor delimitation tests. Our results validate previously diagnosed taxa, as well as new species hypotheses, resulting in support for three new mouse lemur species. As the challenge of multiple researchers using differing criteria to describe diversity is not unique to Microcebus, the methods used here have significant potential for clarifying diversity in other taxonomic groups. We echo previous studies in advocating that multiple lines of evidence, including use of the coalescent model, should be trusted to delimit new species.
Data from: A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets
Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases.
Data from: Model-based species delimitation: are coalescent species reproductively isolated?
A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.