Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multi-locus studies and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence 1088 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades were largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in a large, economically important groups of coral reef fishes. More broadly, we demonstrate how accounting for sources of biological variability from incomplete lineage sorting and exploring systematic error at conflicting nodes can aid in evaluating alternative phylogenetic hypotheses. [coral reefs; divergence time estimation; exon-capture; fossil calibration; incomplete lineage sorting.]
Recent phylogenetic analyses differ in their interpretations of the origin and interrelationships of snakes, resulting in polarized views of snake ecology, habit and acquisition of features associated with wide-gaped feeding (macrostomy). Here, we report a new specimen of the Late Cretaceous nest predator Sanajeh indicus that helps to resolve the origin of macrostomy. The new specimen preserves an ossified upper temporal bar and a posteriorly expanded otooccipital region that lacks a free-ending supratemporal bone and retains a lizard-like palatomaxillary arch that allows limited movements during swallowing. Phylogenetic analyses of a large-scale total evidence dataset resolve Sanajeh near the base of Pan-Serpentes, as the sister group of Najash, Dinilysia and crown-group Serpentes. The Cretaceous Tetrapodophis and Coniophis represent the earliest-diverging members of Pan-Serpentes. The Cretaceous hindlimbed pachyophiids and Cenozoic Australian ‘madtsoiids’ are inside crown Alethinophidia, whereas mosasaurs are recovered invariably within anguimorphs. Our results suggest that the wide-gape condition in mosasaurs and snakes might have evolved independently, as functionally distinct mechanisms of prey ingestion. The intermediate morphology preserved in Sanajeh indicates that ingestion of large prey items (macrophagy) preceded wide-gaped, unilateral feeding (macrostomy), which appeared 35 Myr later, in the common ancestor of pachyophiids, Cenozoic Australian ‘madtsoiids’ and alethinophidians.
more » « less- Award ID(s):
- 1736606
- NSF-PAR ID:
- 10413063
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Zoological Journal of the Linnean Society
- Volume:
- 197
- Issue:
- 3
- ISSN:
- 0024-4082
- Page Range / eLocation ID:
- p. 656-697
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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