The Endangered White Sands pupfish (Cyprinodon tularosa) genome reveals
low diversity and heterogenous patterns of differentiation
The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in
Southwestern North America, is of conservation concern due in part to
invasive species, chemical pollution, and groundwater withdrawal.
Herein, we developed a high quality draft reference genome and use it to
provide biological insights into the evolution and conservation of C.
tularosa. Specifically, we localized microsatellite markers previously
used to demarcate Evolutionary Significant Units, evaluated the
possibility of introgression into the C. tularosa genome, and compared
genomic diversity among related species. The de novo assembly of PacBio
Sequel II error-corrected reads resulted in a 1.08Gb draft genome with a
contig N50 of 1.4Mb and 25,260 annotated protein coding genes, including
95% of the expected Actinopterigii conserved orthologs. Many of the
previously described C. tularosa microsatellite markers fell within or
near genes and exhibited a pattern of increased heterozygosity near
genic areas compared to those in intergenic regions. Genetic distances
between C. tularosa and the widespread invasive species C. variegatus,
which diverged ~1.6-4.7 MYA, were 0.027 (nuclear) and
0.022 (mitochondrial). Nuclear alignments revealed putative tracts of
introgression that merit further investigation. Genome-wide
heterozygosity was markedly lower in C. tularosa compared to estimates
from related species, likely because of smaller long-term effective
population sizes constrained by their isolated and limited habitat.
These population inferences, generated from our new genome assembly,
provide insights into the long term and contemporary White Sands pupfish
populations that are integral to future management efforts.