Genomic Signatures of Local Adaptation in Clam Shrimp (Eulimnadia texana) from Natural Vernal Pools.

Genome Biology and Evolution
James G Baldwin-Brown, Anthony D Long

Abstract

Vernal pools are unique in their isolation and the strong selection acting on their resident species. Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, small genomes, and obligate desiccated diapaused eggs. Clam shrimp are also androdioecious (sexes include males and hermaphrodites), and here we use population-scaled recombination rates to support the hypothesis that the heterogametic sex is recombination free in these shrimp. We collected short-read sequence data from pooled samples from different vernal pools to gain insights into local adaptation. We identify genomic regions in which some populations have allele frequencies that differ significantly from the metapopulation. BayPass (Gautier M. 2015. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201(4):1555-1579.) detected 19 such genomic regions showing an excess of population subdivision. These regions on average are 550 bp in size and had 2.5 genes within 5 kb of them. Genes located near these regions are involved in Malpighian tubule function and osmoregulation, an essential function in vernal pools. It is likely that salinity profiles vary between poo...Continue Reading

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Methods Mentioned

BETA
Poolseq
Illumina sequencing
genotyping
chips
PCR

Software Mentioned

Poolseq
BayEnv
RepeatMasker
tools
npstat
BWA
Treemix
texana
mpileup
BLAST

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