Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae)

Abstract

Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between individual gene trees, both of which are common in groups that diverged recently and/or rapidly, make it impossible to infer a species tree using methods that are designed to estimate gene trees. Therefore, in this study, we estimate relationships between members of the lecontei species group using four approaches that are intended to estimate species, not gene, trees: (1) minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian estimation of species trees (BEST), and (4) a novel approach that combines concatenation with monophyly constraints (CMC). Multiple populations are sampled for most species and all four methods incorporate this intraspecific variation into estimates of interspecific relationships. We investigate the sensitivity of each method to taxonomic sampling, and, for the BEST method, we assess the impact of prior choice on species-tree inference. We also compare species-tree estimates to one another and to a morphologically based hypothesis to identify clades that are supported by multiple analyses and lines of evidence. We find that both taxonomic sampling and method choice impact species-tree estimates and that, for these data, the BEST method is strongly influenced by Theta and branch-length priors. We also find that the CMC method is the least sensitive to taxonomic sampling. Finally, although interspecific genetic variation is low due to the recent divergence of the lecontei group, our results to date suggest that incomplete lineage sorting and interspecific gene flow are the main factors complicating species-tree inference in Neodiprion. Based on these analyses, we propose a phylogenetic hypothesis for the lecontei group. Finally, our results suggest that, even for very challenging groups like Neodiprion, an underlying species-tree signal can be extracted from multi-locus data as long as intraspecific variation is adequately sampled and methods that focus on the estimation of species trees are used.

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

“…Genomic processes that do not track evolutionary history at the organismal level might therefore cause it to yield misleading inferences of species phylogeny (Doolittle, 1999;Zhang and Hewitt, 2003;Ballard and Whitlock, 2004;Spinks and Shaffer, 2009). Explicit methods for deducing species phylogenies from gene trees exist (Lerat et al, 2003;Maddison and Knowles, 2006;Liu et al, 2007;Linnen and Farrell, 2008;Edwards, 2009) but these necessarily rest upon data from entire genomes (Lerat et al, 2003), parts of multiple genomes (e.g. Carstens and Knowles, 2007;Liu et al, 2008;Spinks and Shaffer, 2009) or simulations (e.g.…”

A test of the sympatric host race formation hypothesis in Neodiprion (Hymenoptera: Diprionidae)

“…(b) Phylogenetic and dating analyses For comparative tests of speciation mode, we used the 'best estimate' of the Neodiprion (lecontei group) species tree described in Linnen & Farrell (2008a; figure 1). Many nodes in this tree had high (more than 95%) posterior probabilities, were robust to taxonomic sampling and species-tree method, and were supported by independent morphological evidence (Linnen & Farrell 2008a).…”

Estimating the species tree for Hawaiian Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution

“…Species tree approaches that simultaneously consider each gene tree have the potential to provide a useful integration of population genetics and phylogenetics, particularly where conditions of high gene tree discordance due to incomplete lineage sorting are to be expected, such as those encountered in recent, rapid radiations (Edwards et al, 2007). However, their implementation can be challenging, and few empirical studies have used species-tree methods for large numbers of samples (Linnen and Farrell, 2008).…”

“…Further, ours is among the largest data set analyzed to date using the BEST method. To our knowledge, only Linnen and Farrell (2008) analyzed more samples. Although we had to use a uniform clock prior in BEST in order to achieve convergence, the results appear to be stable based on multiple runs.…”

“…This program applies a coalescent framework to estimate the posterior distribution of a species tree jointly with those of the gene trees for each locus, and has been successfully applied to several phylogenetic studies (Belfiore et : prior ages at 7.3, 4.7, and 3.7 (Fig. 6) or at 4.7 and 3.7 ( Linnen and Farrell, 2008;Spinks and Shaffer, 2009), although lack of convergence has been reported (Wares et al, 2009). This version of MB-BEST uses a uniform prior for the species tree and accounts for multiple accessions per species.…”