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37 results for “coalescent species delimitation”
Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
<p>The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g., MSC for one species versus MSC for two species) and compared using Bayesian model selection. This approach, implemented in the program bpp, has been found to be prone to over-splitting. Alternatively, heuristic criteria based on population parameters under the MSC model (such as population/species divergence times, population sizes, and migration rates) estimated from genomic sequence data may be used to delimit species. Here we extend the approach of species delimitation using the genealogical divergence index (𝑔𝑑𝑖) to develop hierarchical merge and split algorithms for heuristic species delimitation and implement them in a python pipeline called hhsd. Applied to data simulated under a model of isolation by distance, the approach was able to recover the correct species delimitation, whereas model comparison by bpp failed. Analyses of empirical datasets suggest that the procedure may be less prone to over-splitting. We discuss possible strategies for accommodating paraphyletic species in the procedure, as well as the challenges of species delimitation based on heuristic criteria.</p>
Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
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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: 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: 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: 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: 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.
Figure 2. Coalescent species trees with 13 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches
Figure 2. Coalescent species trees with 13 (A) and 14 (B) assumed species based on 18S rRNA gene, ITS1-5.8S-ITS2 region and 28S rRNA gene sequences. Posterior probabilities of clades are provided along internal branches and posterior probabilities for the presence of individual species are provided behind the terminal branches. Scale bars denote the fraction of substitutions per site.
Figure 11 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 11. Dugesia hoidi: A, holotype RMNH.VER.21056.1, photomicrograph showing the penial fold (pf) in sagiưal section; B, paratype RMNH.VER.21056.2, photomicrograph showing the penis papilla (pp) and the penial fold (pf) in transverse section.
Figure 10. Dugesia hoidi. Holotype RMNH.VER.21056.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 10. Dugesia hoidi. Holotype RMNH.VER.21056.1: A, sagiưal reconstruction of the male copulatory apparatus (anterior to the right); B, sagiưal reconstruction of the penial fold and female copulatory apparatus; C, photomicrograph of sagiưal section, showing penis bulb (pb) with the seminal vesicle (sv), right (rvd) and the less (lvd) vas deferens, penis papilla (pp) with the pointed diaphragm (d), and the ejaculatory duct (ed).
Figure 7. Dugesia benazzii s.s., CGAS Pla 25.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 7. Dugesia benazzii s.s., CGAS Pla 25.1: A, sagiưal reconstruction of the male copulatory apparatus (anterior to the right); B, sagiưal reconstruction of the fold and female copulatory apparatus; C, photomicrograph of sagiưal section, showing the penis bulb (pb), penis papilla (pp) with conical, pointed diaphragm (d), ejaculatory duct (ed), penial fold (pf), and 'angled' bursal canal (abc).
Figure 6 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 6. Karyogram of (A) Dugesia benazzii s.s. from Su Rizzolu River (Oưi, loc. 13) and (B) Dugesia hoidi.
Figure 1. A in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 1. A, sampling localities of the present study. Numbers correspond to population codes listed in Appendix, Table A1 and coincide with those in Dols-Serrate et al. (2020). Red circles indicate populations used for morphological analyses. B, rectangular inset: enlargement of the Bunnari–Mascari confluence area. Ŋe map was created using Q-GIS v.3.2.2 (hưps://qgis.org/es/site/ last accessed September 2023) and edited in ILLUSTÞTOR CC v.22.0.1 (hưps://www.adobe.com/products/illustrator.html last accessed September 2023).
Figure 14 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 14. Dugesia mariae: A, CGAS Pla 27. 1, photomicrograph showing the penis bulb with the seminal vesicle (sv), less (lvd) and right (rvd) vas deferens, the penial papilla (pp) and the two atrial folds (af) in horizontal section; B, CGAS Pla 27. 4, photomicrograph showing the penis papilla (pp) and the penial fold (pf) in transverse section.
Figure 9. Dugesia benazzii s.s in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 9. Dugesia benazzii s.s.: A, CGAS Pla 25. 6, photomicrograph showing the penial fold (pf) and the two atrial folds (af) in sagiưal section; B, CGAS Pla 25. 4, photomicrograph showing the penis papilla (pp) and the penial fold (pf) in transverse section.
Figure 3 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 3. mtDNA (dataset I) phylogenetic tree and species discovery delimitation schemes for ABGD, GMYC, and mPTP, as well as PSHs and PSCs. Ultrametric tree from BEAST is shown only for visual purposes; posterior probabilities (pp) and bootstrap support values (bs) relate to MrBayes and ÞxML analyses, respectively; pp and bs node support values represented by squares and circles, filled with white (unsupported), grey (supported), and black (maximum support), respectively.
Figure 8. Dugesia benazzii s.s., CGAS Pla 25.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 8. Dugesia benazzii s.s., CGAS Pla 25.1. Photomicrograph of the copulatory bursa with a ciliate parasite (cp) and a spermatophore (sp) in a sagiưal section.
Figure 5 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 5. BFD results for the array of models tested (1–6), with different a priori species-delimitation hypotheses tested on three datasets (I, IV, and V). Each column represents a model with a unique combination of lineages (rows). Star symbol indicates reassignment of PSC4. Marginal-likelihood estimates (MLE) and Bayes' factors comparison results (2lnBf) from the combined analyses of five independent runs with PS (path-sampling) and SS (stepping stone) are represented with circles and a grey-scale scheme. 2lnBf comparison support indicates differences from the best model: non-significant indicates no difference in support for the two models; positively supported and decisively-supported indicate clear support in favour of the best-fiưing model over its alternative.
Figure 4 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 4. Schematic representation of BPP results on multi-locus data for two topologies. Colour scheme and squares represent posterior probability (pp) for each node under four different prior combinations, using two algorithms (A0 and A1) and three datasets (I, IV, and V). *Unsupported node with a pp of 0.94.
Figure 2 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 2. Simplified Bayesian (A–E1) and ML dendrograms (E2). A, dataset I: COI–NADH4–tRNAW–COII; B, dataset II: Dunuc10; C, dataset III: Dunuc12; D, dataset IV: Dunuc10 * 12; E, dataset V: mtDNA * nDNA. Posterior probabilities (pp) are indicated by filled squares and bootstrap support values (bs) with filled circles. Full trees are represented in Figure 3 (dataset I) and Supporting Information, Figure S1 (datasets I–V).
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