DOI: 10.5061/dryad.44j0zpcdf
title: Data from: Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria

description: Speciation genes contribute disproportionately to species divergence, but
 few examples exist, especially in vertebrates. In mammals, the Zan gene
 encodes the sperm acrosomal protein zonadhesin that mediates
 species-specific adhesion to the egg’s zona pellucida. Here we identify
 Zan as a speciation gene in placental mammals. Genomic ontogeny revealed
 that Zan arose by repurposing of a stem vertebrate gene that was lost in
 multiple lineages but retained in Eutheria on acquiring a function in egg
 recognition. A 112-species Zan sequence phylogeny, representing 17 of 19
 placental Orders, resolved all species into monophyletic groups
 corresponding to recognized Orders and Suborders, with &lt;5%
 unsupported nodes. Three other rapidly evolving germ cell genes (Adam2,
 Zp2, and Prm1), a paralogous somatic cell gene (TectA), and a
 mitochondrial gene commonly used for phylogenetic analyses (Cytb) all
 yielded trees with poorer resolution than the Zan tree and inferior
 topologies relative to a widely accepted mammalian supertree. Zan
 divergence by intense positive selection and domain duplications and
 accelerated divergence rates in the Myomorpha Suborder of Rodentia
 produced dramatic species differences in the protein’s properties, with
 ordinal divergence rates generally reflecting species-richness of
 placental Orders consistent with expectations for a speciation gene that
 acts across a wide range of taxa. Furthermore, Zan’s combined phylogenetic
 utility and divergence exceeded those of all other genes known to have
 evolved in Eutheria by positive selection, including the only other
 speciation gene, Prdm9. We conclude that species-specific egg recognition
 conferred by Zan’s functional divergence served as a mode of prezygotic
 reproductive isolation that promoted the extraordinary adaptive radiation
 and success of Eutheria.
description: We aligned authentic <em>Zan</em> 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 <em>Zan</em>-like gene from Chinese
 soft-shelled turtle (<em>Pelodiscus</em>
 <em>sinicus</em>) as outgroup in the <em>Zan</em>
 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 100<sup>th</sup> 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. The above methodology was applied to
 analyze an additional 35 rapidly-evolving genes as reported from the
 literature.
description: T-coffee, MEGA X, jModelTest2.1.10, MrBayes 3.2.6, and Microsoft
 Office are all software programs required to open the data files
 uploaded.