Dataset Information

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios.

ABSTRACT: Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.

SUBMITTER: Luo A

PROVIDER: S-EPMC6101526 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios.

Luo Arong A Ling Cheng C Ho Simon Y W SYW Zhu Chao-Dong CD

Systematic biology 20180901 5

Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Baye ...[more]

PMID: 29462495

Similar Datasets

Project description:The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.

Project description:Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence C tax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index R tax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist approaches). Quantifying excessive splitting is more difficult than quantifying excessive lumping, suggesting a priority for conservative taxonomies in which errors are more liable to be detected and corrected by subsequent studies.

Dataset Information

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios.

Publications

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets