DOI: 10.5061/dryad.zw3r228gp
title: Data from: The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals

description: The XX/XY sex chromosome system is deeply conserved in therian mammals, as
 is the role of Sry in testis determination, giving the impression
 of stasis relative to other taxa. However, the long tradition of
 cytogenetic studies in mammals documents sex chromosome karyotypes that
 break this norm in myriad ways, ranging from fusions between sex
 chromosomes and autosomes to Y chromosome loss. Evolutionary conflict, in
 the form of sexual antagonism or meiotic drive, is the primary predicted
 driver of sex chromosome transformation and turnover. Yet conflict-based
 hypotheses are less considered in mammals, perhaps because of the
 perceived stability of the sex chromosome system. To address this gap, we
 catalogue and characterize all described sex chromosome variants in
 mammals, test for family-specific rates of accumulation, and consider the
 role of conflict between the sexes or within the genome in the evolution
 of these systems. We identify 152 species with sex chromosomes that differ
 from the ancestral state and find evidence for different rates of
 ancestral to derived transitions among families. Sex chromosome-autosome
 fusions account for 80% of all variants whereas documented sex chromosome
 fissions are limited to three species. We propose that meiotic drive and
 drive suppression provide viable explanations for the evolution of many of
 these variant systems, particularly those involving autosomal fusions. We
 highlight taxa particularly worthy of further study and provide
 experimental predictions for testing the role of conflict and its
 alternatives in generating observed sex chromosome diversity.
description: # Data from: The role of conflict in the formation and maintenance of
 variant sex chromosome systems in mammals
 [https://doi.org/10.5061/dryad.zw3r228gp](https://doi.org/10.5061/dryad.zw3r228gp) A zip folder containing all raw data and R code used for analyses and for figure production.  ## Usage note #### The R scripts herein require three additional files to be downloaded from S8 Data at [https://datadryad.org/stash/dataset/doi:10.5061/dryad.tb03d03](https://datadryad.org/stash/dataset/doi:10.5061/dryad.tb03d03) (Upham et al. 2019). All three are used unedited from the original repository and should be placed in the "rate\_estimation" subfolder. * ##### DR-SUMMARY\_MamPhy\_BDvr\_Completed\_5911sp\_topoCons\_NDexp\_all10k\_v2\_expanded.txt * ##### MamPhy\_5911sp\_tipGenFamOrdCladeGenesSampPC\_NDexp\_DRstats\_DRtreeLABELS.csv * ##### MamPhy\_fullPosterior\_BDvr\_Completed\_5911sp\_topoCons\_NDexp\_MCC\_v2\_target.tre ## Contents of zip folder ##### --File: **families\_of\_interest.csv** #### Input file for mammal\_plot\_v2.R listing orders and families of mammals that contain species with variant sex chromosomes. Monotremes are labelled as "null" on account of having an independently derived sex chromosome system to therian mammals.  * *order*: Orders of mammals with variant sex chromosomes * *family*: Scientific family names * *family_common*: Common names for families (e.g. Soricidae = shrews) * *species*: Representative species of mammals with variant sex chromosomes. One species was selected to represent a given family to enable easy subsetting and plotting of a family-level phylogeny.  * *species_common*: The common name of the species found in the* species* column.  * *has_**atypicalsexchromosomes*: "y" or "n" indicating presence or absence of species with variant sex chromosome systems in a given family. All families in this file have "y" except for monotremes, who are additionally labelled "null" on account of having independently derived sex chromosomes from other mammals.  * *variant_form*: Column indicating the type(s) of variant sex chromosome systems that are found in a given family.  * *number_variant*: Number of species with variant sex chromosomes in a given family.  * *total_species*: Total number of species in a given family based on the Mammal Diversity Database v 1.11 (available here: [https://zenodo.org/records/10595931](https://zenodo.org/records/10595931)) * *fraction_variant*: The percentage of species with a variant sex chromosomes in a given family ##### --File: **family\_tree\_data.csv** #### Input file for mammal\_plot\_v2.R also includes information about the number and type of variant sex chromosome systems in all mammal families * *order*: Orders of mammals with variant sex chromosomes * *family*: Scientific family names * *family_common*: Common names for families (e.g. Soricidae = shrews) * *species*: Representative species of mammals with variant sex chromosomes. One species was selected to represent a given family to enable easy subsetting and plotting of a family-level phylogeny.  * *species_common*: The common name of the species found in the* species* column.  * *has_atypicalsexchromosomes*: "y" or "n" indicating presence or absence of species with variant sex chromosome systems in a given family, or "null" in the case of monotremes. * *variant_form*: Column indicating the type(s) of variant sex chromosome systems that are found in a given family, or "XY" if the family only contains species with ancestral XY chromosomes. * *number_variant*: Number of species with variant sex chromosomes in a given family.  * *fraction_variant*: The percentage of species with a variant sex chromosomes in a given family ##### --File: **mammal\_plot\_v2.R** #### Code for plotting Figure 1 from the manuscript. Will also output several alternative versions that were not used. ###### Takes as input:  * family_tree_data.csv * families_of_interest.csv * rate_estimation/MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre ### **--Subfolder**: rate\_estimation ##### ----File: **upham\_credible\_trees.nex** #### Set of 100 credible mammal trees from Upham et al 2019. * Subset from original dataset of 10,000 trees downloaded from [https://data.vertlife.org/](https://data.vertlife.org/) ##### ----File: **conflict\_family\_subsets\_v3.R** #### R code for rate analysis on single tree. Outputs raw data for Supp Table 1. ###### Takes as input: * MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre * MamPhy_5911sp_tipGenFamOrdCladeGenesSampPC_NDexp_DRstats_DRtreeLABELS.csv ##### ----File: **conflict\_family\_subsets\_multirate\_V2.R** #### R code for multirate analysis across 100 trees. Outputs a table of rates for use with conflict\_rate\_figure.R ###### Takes as input: * MamPhy_5911sp_tipGenFamOrdCladeGenesSampPC_NDexp_DRstats_DRtreeLABELS.csv * upham_credible_trees.nex ###### Outputs: * rates_100trees_udmodel_v2.csv ##### ----File: **conflict\_known\_subsets.R** #### R code for rate analysis on single tree for three families of mammals, subset to only include species with known and published karyotypes. Outputs raw data for Supp Table 2. ###### Takes as input: * MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre * upham_credible_trees.nex * family_level_known_karyotypes.csv ##### ----File: **conflict\_multirate\_known.R** #### R code for multirate analysis across 100 trees. Outputs a table of rates for use with conflict\_rate\_figure.R ###### Takes as input: * MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre * upham_credible_trees.nex * family_level_known_karyotypes.csv ###### Outputs: * known_family_rates_100trees_udmodel.csv ##### ----File: **conflict\_rate\_figure.R** #### R code for producing Figure 2 and Supplementary Figure 1. ###### Takes as input: * rates_100trees_udmodel_v2.csv * known_family_rates_100trees_udmodel.csv ##### ----File: **family\_level\_known\_karyotypes.csv** #### Input data file for conflict\_known\_subsets.R and conflict\_multirate\_known.R describing sex chromosome karyotype in three families of mammal (Herpestidae, Atelidae, and Bovidae) * *order*: Orders of mammals with variant sex chromosomes * *family*: Scientific family names * *upham_species*: Scientific species name as in **upham_credible_trees.nex** * *mdd_species*: Scientific species name as in the Mammal Diversity Database v 1.11 (available here: [https://zenodo.org/records/10595931](https://zenodo.org/records/10595931)) * *mcc_tree_name*: Tip label of species as written in **MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre ** * *sex_chr*: Indicates whether a species has a published sex chromosome karyotype. "1" = variant sex chromosomes. "0" = ancestral XY chromosomes, respectively. NA = No published karyotype could be found.   * *citation*: Citations of published karyotypes. The full citations can be found in file: **complete_karyotype_citations.csv** ##### ----File: **complete\_family\_karyotype\_citations.txt** #### Citations for family\_level\_known\_karyotypes.csv ##### ----File: **rates\_100trees\_udmodel\_v2.csv** #### Output file from conflict\_family\_subsets\_multirate\_v2.R. Used as input for conflict\_rate\_figure.R to produce Figure 2 * *Order*: Orders of mammals with variant sex chromosomes * *Family*: Scientific family names * *run1 - run100*: Each column starting with "run" represents one of the 100 trees in **upham_credible_trees.nex.** Values indicate the estimated transition rate from XY to a variant sex chromosome system in a given mammal family. Transitions are modelled as unidirectional (i.e. only XY -&gt; variant). Rates inferred using the function ratebytree() from the R package phytools.  ##### ----File: **known\_family\_rates\_100trees\_udmodel.csv** #### Output file from conflict\_multirate\_known.R. Used as input for conflict\_rate\_figure.R to produce Supp Figure 1 * *Order*: Orders of mammals with variant sex chromosomes * *Family*: Scientific family names * *run1 - run100*: Each column starting with "run" represents one of the 100 trees in **upham_credible_trees.nex.** Values indicate the estimated transition rate from XY to a variant sex chromosome system in a given mammal family. Transitions are modelled as unidirectional (i.e. only XY -&gt; variant). Rates inferred using the function ratebytree() from the R package phytools.  ## Sharing/Access information Links to other publicly accessible locations of the data: * [https://github.com/jjh359/2023_conflict_review](http://...) Additional sources of data: * Phylogenetic information was sourced from: Upham NS, Esselstyn JA, Jetz W (2019) Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology 17(12): e3000494. [https://doi.org/10.1371/journal.pbio.3000494](https://doi.org/10.1371/journal.pbio.3000494) * Downloaded from: [https://datadryad.org/stash/dataset/doi:10.5061/dryad.tb03d03](https://datadryad.org/stash/dataset/doi:10.5061/dryad.tb03d03) * Set of 100 credible trees is taken from: [https://data.vertlife.org/](https://data.vertlife.org/)