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Data from: Bayesian analysis of a single gamete recognition gene yields a robust Eutherian phylogeny at all taxonomic levels

Citation

Roberts, Emma (2021), Data from: Bayesian analysis of a single gamete recognition gene yields a robust Eutherian phylogeny at all taxonomic levels, Dryad, Dataset, https://doi.org/10.5061/dryad.44j0zpcdf

Abstract

The extraordinary morphological diversity among extant mammals poses a challenge for studies of speciation, adaptation, molecular evolution, and reproductive isolation.  Despite the recent wealth of molecular studies on mammalian phylogenetics, remaining uncertainties surrounding both ancestral and more recent divergence events have proven difficult to resolve.  Multi-gene datasets often provide increased support for higher-level affinities within Mammalia, but such analyses require vast amounts of information (genomic-level sequence data) and computational effort (high-performance computing).  This study presents a phylogenetic solution based on a single reproductive molecular marker, Zan, a candidate “speciation gene” encoding the sperm protein zonadhesin that mediates species-specific adhesion to the egg and thereby promotes reproductive isolation.  Topological comparison of Zan Bayesian phylogenies to a widely cited supertree showed that Zan sequences were phylogenetically informative and provided stronger support for resolution at both deeper and more terminal nodes in the placental mammalian phylogeny.  This single gene marker provides a similar but more robustly supported topology than a supertree generated using DNA sequences from 66 genes, and thus provides unique new insight into the divergence of both early and recent mammalian radiations.

Methods

We aligned authentic Zan nucleotide sequences encoding the zonadhesin protein's von Willebrand D0, D1, D2, D3, and approximately the first 25% of D4 domains (range: 330-1560 nts each) using T-coffee software in Meta-coffee mode. To confirm correct reading frames and detect premature stop codons, we translated the aligned sequences in MEGA X. We examined 88 maximum likelihood models with the hierarchical likelihood ratio tests with Akaike Information Criterion-correction in jModelTest2.1.10 to detect the best-fit model of nucleotide substitution, and identified GTR+G+I as the most appropriate model. We selected a Zan-like gene from Chinese soft-shelled turtle (Pelodiscus sinicus) as outgroup in the Zan alignment. To perform likelihood analysis under a Bayesian inference model, we used MrBayes 3.2.6 with the following options: 2 independent runs with four chains, one cold and three heated (Metropolis-coupled Markov chain Monte Carlo numerical method), 10 million generations, and sample frequency every 100th generation from the last 750,000 generated, then constructed a consensus tree (50% majority rule) from the remaining trees and plotted posterior probability values on the topology in FigTree 1.4.4.

Funding

American Society of Mammalogists

Southwestern Association of Naturalists

Texas Academy of Science

Texas Tech University