DOI: 10.5061/dryad.4g6q63g
title: Data from: Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae)

description: Population extirpations are often precursors to species extinctions.
 Anthropogenic activities often lead to smaller populations that are more
 prone to extirpations and advocates for active conservation management
 have recently called for the preservation and monitoring of genetic
 diversity, particularly with regard to the adaptive potential of
 vulnerable populations. We used genomics and curated arrays of molecular
 markers, including those expected to impact key fitness traits, to
 quantify evidence of genomic erosion in core and peripheral populations of
 a gallinaceous bird. The Montezuma quail (Cyrtonyx montezumae) is a game
 species considered vulnerable to extirpation in Texas, but core
 populations in Arizona and New Mexico are robust and have the potential to
 serve as genetic reservoirs. We sequenced the Montezuma quail genome then
 developed a single nucleotide polymorphism (SNP) assay to quantify genetic
 variation, effective population sizes, signatures of natural selection,
 and population structure. We genotyped SNPs from gene deserts and from
 genes associated with fitness traits and found the isolated Texas
 population exhibits an extremely small effective population size, is
 genetically distinct from our Arizona and New Mexico samples, and has
 reduced heterozygosity at the fitness-related markers. Thus, our samples
 from Texas exhibit symptoms of genetic erosion that could exacerbate
 future risk of local extirpation. Management agencies must decide if
 active conservation efforts such as assisted gene flow or genetic rescue
 are now warranted. This decision may not be straightforward because the
 current conservation status of the Texas population reflects its isolated
 geographic locale on the periphery of the species’ range.
description: Cyrtonyx montezumae SNP
 genotypes186 Montezuma quail
 samples (AZ=165, TX=16, NM=5) were genotyped at 169 loci containing 87
 non-neutral, 80 neutral, and 2 mitochondrial markers. Missing data is
 shown as N:NMQU_SNP_genotypes.xlsxCyrtonyx montezumae genome annotation17,573 genes were annotated in the Cyrtonyx montezumae genome. This is the .gff file associated with the annotations.genome.all.gffCyrtonyx montezumae mitochondrial genome assemblyThe C. montezumae mitochondrial genome was assembled using MITObim vs. 1.6. The genome assembly is 16,977 bp long and contained 13 protein coding genes, 2 ribosomal subunit genes, and 33 tRNA genesMQU_female_mito.fastaCyrtonyx montezumae genome annotation - protein sequences17,573 genes were annotated in the Cyrtonyx montezumae genome. This is the .fasta file with predicted protein sequences.AbySS_min5000_MQU_male_proteins.fastaCyrtonyx montezumae (Female) genome assembly scaffoldsThe Cyrtonyx montezumae draft genome was generated from paired-end and mate-paired reads using ABySS vs. 1.5.2 using k=60. These are the sequences for the female individual.MQU_female_k60_SE-scaffolds.fastaCyrtonyx montezumae (Male) genome assembly scaffoldsThe Cyrtonyx montezumae draft genome was generated from paired-end and mate-paired reads using ABySS vs. 1.5.2 using k=60. These are the sequences for the male individual.MQU_male_k60_SE-scaffolds.fasta