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Phylogenomic Analyses of Bat Subordinal Relationships Based on Transcriptome Data

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Phylogenomic Analyses of Bat Subordinal Relationships Based on Transcriptome Data

Ming Lei et al. Sci Rep.

Abstract

Bats, order Chiroptera, are one of the largest monophyletic clades in mammals. Based on morphology and behaviour bats were once differentiated into two suborders Megachiroptera and Microchiroptera Recently, researchers proposed alternative views of chiropteran classification (suborders Yinpterochiroptera and Yangochiroptera) based on morphological, molecular and fossil evidence. Since genome-scale data can significantly increase the number of informative characters for analysis, transcriptome RNA-seq data for 12 bat taxa were generated in an attempt to resolve bat subordinal relationships at the genome level. Phylogenetic reconstructions were conducted using up to 1470 orthologous genes and 634,288 aligned sites. We found strong support for the Yinpterochiroptera-Yangochiroptera classification. Next, we built expression distance matrices for each species and reconstructed gene expression trees. The tree is highly consistent with sequence-based phylogeny. We also examined the influence of taxa sampling on the performance of phylogenetic methods, and found that the topology is robust to sampling. Relaxed molecular clock estimates the divergence between Yinpterochiroptera and Yangochiroptera around 63 million years ago. The most recent common ancestor of Yinpterochiroptera, corresponding to the split between Rhinolophoidea and Pteropodidae (Old World Fruit bats), is estimated to have occurred 60 million years ago. Our work provided a valuable resource to further explore the evolutionary relationship within bats.

Figures

Figure 1
Figure 1. Maximum likelihood phylogenetic tree for nucleotide and amino acid datasets with bootstrap support values (1000 replicates) under partition model.
The asterisks indicate 100/100 bootstrap support for nucleotide and amino acid datasets respectively.
Figure 2
Figure 2. Bat gene expression phylogeny.
Neighbor-joining tree based on pairwise distance matrices for brain transcriptome.
Figure 3
Figure 3. Eight proposed species tree topologies differing in the position of bats within mammals.
Figure 4
Figure 4. Influence of taxon sampling on the performance of phylogenetic trees.
Both concatenated and coalescent analyses yield consistent phylogeny of Yinpterochiroptera-Yangochirptera classification.

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