Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards

Abstract

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference. [Coalescence; concatenation; Cryptoblepharus; exon capture; gene tree; phylogenomics; species tree.].

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

“…While testing Aspect I by interrogating individual nuclear gene trees is unfeasible (i.e. individual gene alignments are too short and too conserved to resolve nuclear gene genealogies with confidence; Barrow et al, 2018;Blom, Bragg, Potter, & Moritz, 2017), our SVDquartets and SNAPP analyses (Figure 2c,d), which take into account coalescent histories inferred from individual alignment sites, appear to provide robust resolution.…”

Leap‐frog dispersal and mitochondrial introgression: Phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea

“…We obtained genomic data for Lesser Sundas Limnonectes using transcriptome-based exon-capture (Bi et al, 2012(Bi et al, , 2013Blom, Bragg, Potter, & Moritz, 2017;Jones & Good, 2016), a recently developed method that allows for the rapid and inexpensive collection of massively multilocus sequence data from non-model organisms. Transcriptome-based exon-capture methods provide datasets ideal for phylogenetic and demographic inference as they can screen hundreds to thousands of independent loci that can be quite long (>1,000 bp) with roughly equal capture efficiency across samples characterized by high levels of nuclear sequence divergence (Bragg, Potter, Bi, & Moritz, 2016;McCartney-Melstad, Mount, & Shaffer, 2016;Portik, Smith, & Bi, 2016).…”

Diversification across biomes in a continental lizard radiation

“…Sequences from G. spheniscus and G. xenopus, AMT rock-dwelling species, were not available; otherwise, sampling of known species and component lineages of the variegata group is complete. The exon capture probes we used targeted four commonly used phylogenetics genes (BDNF, C-mos, PDC, and RAG1) and 1716 other protein coding exon regions developed from G. nana (Bragg et al 2017) and G. oceanica (Tonione et al 2016) transcriptomes. The target regions were identified on the basis of a reciprocal best BLAST (Altschul et al 1990) hit to an exon from the Anolis genome (Alfoldi et al 2011;accessed in Ensembl release 67, Flicek et al 2013), and were >200 bp in length.…”

“…Resolving the diversity and relationships of lineages in the G. variegata group has previously proved intractable, despite the use of karyotypic, allozyme, morphological, mtDNA, and small-scale nuclear datasets (King 1979;Moritz 1986Moritz , 1992Heinicke et al 2011;Sistrom et al 2013;Sistrom et al 2014). As for the AMT nana clade , the much-improved resolution and largely consistent estimates of phylogeny for the AAZ radiation of Gehyra emphasize the value of phylogenomic datasets with comprehensive sampling of taxa for resolving the diversity of radiating taxa (Blom et al 2017).…”