scholarly journals Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3724 ◽  
Author(s):  
Ana C. Afonso Silva ◽  
Natali Santos ◽  
Huw A. Ogilvie ◽  
Craig Moritz
Keyword(s):  
Species Delimitation ◽  
A Priori ◽  
Integrated Approach ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Gene Trees ◽  
Separate Species ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Alternative Species

While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species ofCarliaskinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia,Carlia johnstoneiandC. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genusCarlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identifiedCarlialineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not requirea prioriresolved species or gene trees. Compared to the situation inC. triacantha, morphological divergence was greater between the two lineages within Kimberley endemicC. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species withinC. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespreadC. triacantha. With this work, we describe two new species,Carlia insularissp. nov andCarlia isostriacanthasp. nov. in the northwest of Australia. This contributes to increasing recognition that this region of tropical Australia has a rich and unique fauna.

scholarly journals Species delimitation and phylogeny estimation under the multispecies coalescent

2014 ◽  
Author(s):  
Graham R Jones
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
A Priori ◽  
Simulated Data ◽  
Species Trees ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Multiple Loci ◽  
Population Sizes ◽  
Phylogeny Estimation

This article describes a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using DNA sequences from multiple loci. The focus here is on species delimitation with no a priori assignment of individuals to species, and no guide tree. The method uses a new model for the population sizes along the branches of the species tree, and three new operators for sampling from the posterior using the Markov chain Monte Carlo (MCMC) algorithm. The correctness of the moves is demonstrated both by proofs and by tests of the implementation. Current practice, using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al, 2014). The same simulated data set is used to demonstrate the accuracy and efficiency of the present method. The method is implemented in a package called STACEY for BEAST2.

Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

2021 ◽  
Author(s):  
Zaynab Shaik ◽  
Nicola Georgina Bergh ◽  
Bengt Oxelman ◽  
Anthony George Verboom
Keyword(s):  
Species Delimitation ◽  
Bayes Factor ◽  
Cape Floristic Region ◽  
Parametric Models ◽  
Western Cape ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Separate Species ◽  
Multiple Sequence ◽  
Data Set

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

scholarly journals Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Nannie L Persson ◽  
Ingrid Toresen ◽  
Heidi Lie Andersen ◽  
Jenny E E Smedmark ◽  
Torsten Eriksson
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Nuclear Markers ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Single Marker ◽  
Named Groups

Abstract The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

Species delimitation and nematode biodiversity: phylogenies rule

Nematology ◽  
2002 ◽  
Vol 4 (5) ◽  
pp. 615-625 ◽  
Author(s):  
Steven Nadler
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Gene Trees ◽  
California Sea Lions ◽  
Separate Species ◽  
Nucleotide Sequence Data ◽  
Sea Lions ◽  
Multiple Loci ◽  
Fur Seals

AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.

scholarly journals The Genealogical Divergence Index Across a Speciation Continuum in Hercules Beetles

2021 ◽  
Vol 5 (6) ◽  
Author(s):  
Jen-Pan Huang
Keyword(s):  
Species Delimitation ◽  
Integrative Taxonomy ◽  
Biological Species ◽  
Multispecies Coalescent ◽  
Genetic Groups ◽  
Allopatric Species ◽  
Geographic Populations ◽  
Speciation Continuum ◽  
Meta Analyses ◽  
Genetic Structures

Abstract The genealogical divergence index (gdi) was developed to aid in molecular species delimitation under the multispecies coalescent model, which has been shown to delimit genetic structures but not necessarily species. Although previous studies have used meta-analyses to show that gdi could be informative for distinguishing taxonomically good species, the biological and evolutionary implications of divergences showing different gdi values have yet to be studied. I showed that an increase in gdi value was correlated with later stages of divergence further along a speciation continuum in an Amazonian Hercules beetle system. Specifically, a gdi value of 0.7 or higher was associated with diverge between biological species that can coexist in geographic proximity while maintaining their evolutionary independence. Divergences between allopatric species that were conventionally given subspecific status, such as geographic taxa that may or may not be morphologically divergent, had gdi values that fell within the species delimitation ambiguous zone (0.2 < gdi < 0.7). However, the results could be drastically affected by the sampling design, i.e., the choice of different geographic populations and the lumping of distinct genetic groups when running the analyses. Different gdi values may prove to be biologically and evolutionarily informative should additional speciation continua from different empirical systems be investigated, and the results obtained may help with objectively delimiting species in the era of integrative taxonomy.

scholarly journals Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

2020 ◽  
Author(s):  
Claudia Isabel Navarro-Rodríguez ◽  
Alejandro Valdez-Mondragón
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Species Delimitation ◽  
Sister Group ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Taxonomic Approach ◽  
Morphological Differences ◽  
Unique Species ◽  
A New Species

Based on an integrative taxonomic approach, a new species of the genus Loxosceles Heineken & Lowe, 1832, is described from the state of Hidalgo, Mexico. Loxosceles tolantongo sp. nov. is described based on DNA barcoding using cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2), and morphology. For species delimitation, four molecular methods were implemented: 1) corrected p-distances under neighbor joining (NJ); 2) automatic barcode gap discovery (ABGD); 3) general mixed yule coalescent model (GMYC) and 4) Bayesian Poisson tree processes (bPTP). The new species morphologically resembles L. jaca, another species from Hidalgo, but there are morphological differences mainly in the tibiae of the male palp, the seminal receptacles of the females and also the high genetic p-distances. CO1 was more informative than ITS2 for the genetic separation; however, both concatenated genes (CO1 + ITS2) present robust evidence for species delimitation. Loxosceles tolantongo sp. nov. is considered a unique species for four reasons: 1) it can be diagnosed and distinguished by morphological characters (of the male palps mainly, but also of the seminal receptacles of the females); 2) the genetic p-distances with CO1 were high (>10%); 3) the molecular species delimitation methods were congruent under CO1 and CO1 + ITS2; and 4) under CO1 and CO1 + ITS2, the new species is a putative sister group of L. jaca + L. tenango.

scholarly journals Inferring Species Trees Using Integrative Models of Species Evolution

2018 ◽  
Author(s):  
Huw A. Ogilvie ◽  
Timothy G. Vaughan ◽  
Nicholas J. Matzke ◽  
Graham J. Slater ◽  
Tanja Stadler ◽  
...  
Keyword(s):  
Gene Evolution ◽  
Sequence Data ◽  
A Priori ◽  
Morphological Characters ◽  
Mirror Image ◽  
Integrative Model ◽  
Species Trees ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Molecular Sequence

AbstractBayesian methods can be used to accurately estimate species tree topologies, times and other parameters, but only when the models of evolution which are available and utilized sufficiently account for the underlying evolutionary processes. Multispecies coalescent (MSC) models have been shown to accurately account for the evolution of genes within species in the absence of strong gene flow between lineages, and fossilized birth-death (FBD) models have been shown to estimate divergence times from fossil data in good agreement with expert opinion. Until now dating analyses using the MSC have been based on a fixed clock or informally derived node priors instead of the FBD. On the other hand, dating analyses using an FBD process have concatenated all gene sequences and ignored coalescence processes. To address these mirror-image deficiencies in evolutionary models, we have developed an integrative model of evolution which combines both the FBD and MSC models. By applying concatenation and the MSC (without employing the FBD process) to an exemplar data set consisting of molecular sequence data and morphological characters from the dog and fox subfamily Caninae, we show that concatenation causes predictable biases in estimated branch lengths. We then applied concatenation using the FBD process and the combined FBD-MSC model to show that the same biases are still observed when the FBD process is employed. These biases can be avoided by using the FBD-MSC model, which coherently models fossilization and gene evolution, and does not require an a priori substitution rate estimate to calibrate the molecular clock. We have implemented the FBD-MSC in a new version of StarBEAST2, a package developed for the BEAST2 phylogenetic software.

scholarly journals Snails in depth: integrative taxonomy of Famelica, Glaciotomella and Rimosodaphnella (Conoidea: Raphitomidae) from the deep sea of temperate Australia

2021 ◽  
Author(s):  
Francesco Criscione ◽  
Anders Hallan ◽  
Nicolas Puillandre ◽  
Alexander Fedosov
Keyword(s):  
Deep Sea ◽  
Species Delimitation ◽  
New Genus ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
New Genera ◽  
Undescribed Species ◽  
Suitable Material ◽  
Eastern Australia ◽  
The Family

The deep sea of temperate south-eastern Australia appears to be a ‘hotspot’ for diversity and endemism of conoidean neogastropods of the family Raphitomidae. Following a series of expeditions in the region, a considerable amount of relevant DNA-suitable material has become available. A molecular phylogeny based on this material has facilitated the identification of diagnostic morphological characters, allowing the circumscription of monophyletic genera and the introduction of several new genus-level taxa. Both named and new genera are presently being investigated through integrative taxonomy, with the discovery of a significant number of undescribed species. As part of this ongoing investigation, our study focuses on the genera Famelica Bouchet & Warén, 1980, Glaciotomella Criscione, Hallan, Fedosov & Puillandre, 2020 and Rimosodaphnella Cossmann, 1914. We subjected a comprehensive mitochondrial DNA dataset of representative deep-sea raphitomids to the species delimitation methods ABGD and ASAP that recognised 18 and 15 primary species hypotheses (PSHs) respectively. Following additional evaluation of shell and radular features, and examination of geographic and bathymetric ranges, nine of these PSHs were converted to secondary species hypotheses (SSHs). Four SSHs (two in Famelica and two in Rimosodaphnella) were recognised as new, and formal descriptions are provided herein.

The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

2019 ◽  
Vol 69 (1) ◽  
pp. 184-193 ◽  
Author(s):  
E Anne Chambers ◽  
David M Hillis
Keyword(s):  
Species Delimitation ◽  
Isolation By Distance ◽  
A Priori ◽  
Genetic Data ◽  
Species Group ◽  
Recent Analysis ◽  
Multispecies Coalescent ◽  
Species Complexes ◽  
Taxonomic Changes ◽  
Recent Species

AbstractMany recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic–nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.

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