Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

Abstract

The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents

“… Time-calibrated phylogeny of sampled murine species generated in MCMCtree, with a consistent topology estimated in both IQ-TREE and SVDquartets. All phylogenetic analyses were based on a subset of 1,360 loci ( Roycroft et al 2020a ). Nodes with <100% support using more than one branch support approach are indicated with an asterisk.…”

“…We processed raw sequence data using ECPP v1.1.0, largely following the workflow described in Roycroft et al (2020a) , but with some modifications. Briefly, raw reads were deduplicated using FastUniq v1.1 ( Xu et al 2012 ) and quality trimmed using Trimmomatic ( Bolger et al 2014 ).…”

“…To screen for lineage-specific paralogs that were not detected in initial filtering, we calculated average heterozygosity for each sample in each alignment. Alignments with two or more samples with > 3% average heterozygosity ( Teasdale et al 2016 ; Roycroft et al 2020a ) were excluded, as these may represent loci with pervasive paralogy. We assumed that cases where only one sample had >3% average heterozygosity represented lineage-specific duplications and removed only that sample from the alignment.…”

Population genomics and conservation management of a declining tropical rodent

“…Australia contains a diverse array of native rodents in the subfamily Murinae (Aplin 2006;Breed and Ford 2007), with 67 species of rodents in 34 genera thought to be extant prior to colonisation by Europeans (Roycroft et al 2020). The genus Conilurus is one of the so-called 'old endemic' rodents that colonised continental Australia from New Guinea between 6 and 9 million years ago, with three species of Conilurus historically present in Australia.…”

Environment predicts repeated body size shifts in a recent radiation of Australian mammals*

“…; Smissen and Rowe ; Roycroft et al. ). Species in the Pseudomys Division are distributed across all biomes in Australia except the tropical rainforest, and appear to be exceptionally flexible with respect to their habitat association.…”