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Data from: The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals

Cite this dataset

Hughes, Jonathan; Lagunas-Robles, German; Campbell, Polly (2024). Data from: The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals [Dataset]. Dryad. https://doi.org/10.5061/dryad.zw3r228gp

Abstract

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.

README: 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

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 (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)
  • 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.
----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)
  • 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 -> 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 -> variant). Rates inferred using the function ratebytree() from the R package phytools. 

Sharing/Access information

Links to other publicly accessible locations of the data:

Additional sources of data:

Funding

National Science Foundation, Award: 2211661, Environmental Biology (DEB)

National Science Foundation, Award: 1326120, Graduate Research Fellowship Program (GRFP)