Accuracy and Precision of Species Trees: Effects of Locus, Individual, and Base Pair Sampling on Inference of Species Trees in Lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae)

Abstract

Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consists of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy substantially decreased only when using only one individual per species or 25% of the full sequence length (∼ 147 bp). In addition, locus "informativeness" was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with the previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed toward further assessment of other factors that can impact performance of species trees, including gene flow, locus "informativeness," tree shape, missing data, and errors in species delimitation.

How Do You Solve a Problem like Letharia? A New Look at Cryptic Species in Lichen-Forming Fungi Using Bayesian Clustering and SNPs from Multilocus Sequence Data

“…[66], [67]). A number recently developed coalescent-based species tree methods may accurately reconstruct relatively shallow divergence histories from multilocus sequence data, even with moderate levels of recombination [68], [69]. However, most of these methods require that species/population assignments are made a priori [10], [55], [70], [71].…”

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

“…Information on multiple lineages of the same species can have a significant effect on the performance of species tree inference methods, and many methods can use information on coalescences within and between species as part of the inference process (e.g., [19-21,23,25-27,88-90]). Therefore, it is important to keep in mind that we have used one of a number of potential schemes for sampling individuals within our data, as sampling scheme can have an impact on the efficacy of species tree estimators [15,20,36,91,92]. …”

Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in theLiolaemus montanusgroup (Squamata: Liolaemidae)

“…To further resolve the relationships of the northernmost species of the L. montanus group, we sampled other species assigned to this species group (L. andinus Koslowsky, 1895, L. dorbignyi Koslowsky, 1898, L. famatinae Cei, 1980), the rothi complex (L. rothi Koslowsky, 1898), and the fitzingeri group (L. melanops Burmeister, 1888; Olave et al, 2014b). We used L. ornatus, a species belonging to the darwini group (Camargo et al, 2012) as the outgroup. …”