The Effects of Inference Method, Population Sampling, and Gene Sampling on Species Tree Inferences: An Empirical Study in Slender Salamanders (Plethodontidae: Batrachoseps)

Abstract

Species tree methods are now widely used to infer the relationships among species from multilocus data sets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a data set including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this data set, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest leverage in these different methods, showing that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. This leverage is inherent to the mtDNA locus and results from its high variation and lower assumed ploidy. This mtDNA leverage may be problematic when mtDNA has undergone introgression, as is likely in this data set. By contrast, the leverage of RAG1 in STEM analyses does not reflect properties inherent to the locus, but rather results from a gene tree that is strongly discordant with all others, and is best explained by introgression between distantly related species. Within-species sampling was also important, especially in *BEAST analyses, as shown by differences in tree topology across 100 subsampled data sets. Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved for Batrachoseps.

Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics

“…However, substantial variation of delimitation results can be induced when modifying ploidy settings. In line with [93–95] we argue that using the same ploidy settings for all loci represents a more robust approach to estimate species or minimal cluster trees by equally weighting variability in each locus. Our results strongly support promoting STACEY as the method of choice for integrative taxonomy, at least in caddisflies.…”

“…We used equal ploidy settings, following results and arguments presented in [93–95]. We chose this approach to avoid disproportionate influence from mitochondrial partial sequence data and, consequently, treat each gene tree as likely as any other to diverge from the species tree.…”

Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

“…5, population 11). A similar pattern has been found among species of slender salamander where Batrachoseps gavilanensis, found in the Gabilan Mountains, is more closely related to Batrachoseps major major in southern California than to Batrachoseps nigriventis in the central coast of California [62].…”

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

“…A burn-in period of 10% of the total running time was specified after trace inspection, and a Maximum Clade Credibility consensus tree was constructed with the program TreeAnnotator, which is distributed as part of the BEAST package. A similar analysis, but excluding the mtDNA partition was also run to test for the effect of mtDNA on the species tree (see for instance Jockusch et al, 2015).…”