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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 draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. We used our assembly to localize microsatellite markers previously used to demarcate evolutionary significant units (ESU), quantified genomic divergence and transposable element profiles between species, and compared C. tularosa genomic diversity related species. Our de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08 Gb draft genome with a contig N50 of 1.4 Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterygii conserved complete single-copy orthologues. Many of the C. tularosa microsatellite markers used for conservation assessments fell within, or near, genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Nuclear alignments between these two species revealed 193 genes contained in rapidly diverging tracts; transposable element profiles were largely concordant and suggest a shared, rapid expansion of LINE and Gypsy elements. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from other related species, probably because of smaller long-term effective population sizes constrained by their isolated and limited habitat. Overall, these inferences provide new insights into C. tularosa that should help inform future management efforts., (© 2021 John Wiley & Sons Ltd.)

The name killifish refers to the oviparous secondary freshwater fishes in the order Cyprinodontiformes. Killifishes are abundant in Mexico and are represented by four extant families, Rivulidae, Profundulidae, Fundulidae and Cyprinodontidae, comprising > 50 species in a wide variety of habitats. This paper reviews the current classification of the killifishes of Mexico, as well as aspects of their distribution, biology, ecology and current population conservation status., (© 2016 The Fisheries Society of the British Isles.)

The secondary freshwater fish fauna of the western-Iberian Peninsula basin is primarily restricted to local coastal streams, and man-made salt evaporation ponds, etc., which are susceptible to periodical flood and drought events. Despite its uniqueness in ecological adaptation to high saltwater tolerance, very little is known about this fauna's population dynamics and evolutionary history. The killifish, Aphanius baeticus (Cyprinodontidae) is an endemic species restricted to river basins on Spain's southern Atlantic coastline, considered as "Endangered." In this study, the genetic structure, diversity and historical demography of A. baeticus were analyzed using mitochondrial (cytochrome b, N=131) and nuclear (4 out of 19 microsatellites tested, N=288) markers across its distribution range. The phylogenetic and networking reconstruction revealed subtle phylogeographic structuring. A scattered expansion at the beginning of the interglacial periods, coupled with posterior events of extinction and colonization caused by periodical cycles of flooding, could explain the absence of well-defined phylogenetic relationships among populations. Moreover, very low genetic diversity values and a weak population differentiation were detected. We proposed that dispersals allowed by periodic floods connecting river drainages may have promoted a wide genetic exchange among populations and could have contributed to the current genetic relatedness of these populations., (© The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

A comparison of allozyme and mtDNA frequencies was used for insight into a situation in the Pecos River, Texas where contact between the endemic pupfish (Cyprinodon pecosensis) and an introduced congener (C. variegatus) has resulted in rapid, geographically extensive genetic introgression. Temporal changes in mean frequencies of diagnostic allozyme markers indicate that the clinal pattern of introduced genetic material (Echelle and Connor 1989) is slowly decreasing in amplitude. Significant rank concordance in diagnostic allele frequencies among sites and across sampling years indicates directional influences upon temporal allele frequency change. These observations are consistent with the theory of gene flow in neutral clines. Levels of introgression indicated by each of four allozyme loci and mtDNA were roughly equivalent. The early history of the hybrid swarm is explained by genetic swamping, possibly mediated by selection for C. variegatus or C. variegatus × C. pecosensis, at a time when the normally abundant endemic species had been catastrophically depleted. High frequencies of an introduced GPI-A allele in all samples of intergrades suggests that the introduced genome originated with a single founding event., (© 1996 The Society for the Study of Evolution.)

A phylogenetic analysis of mitochondrial DNA (mtDNA) restriction sites was used to examine the geographic history of the Cyprinodon nevadensis complex of pupfishes, a group of four species (seven extant subspp.) in two endorheic (closed) basins of the Death Valley System in California and Nevada (Owens River Valley and Ash Meadows-Death Valley). The mtDNA results suggest that the group contains mtDNAs from two divergent clades. One such clade is represented by the mtDNAs of the Owens Valley pupfish (C. radiosus) and the existing species in the Colorado River (C. macularius), while the other includes the mtDNAs of the Ash Meadows-Death Valley species (C. nevadensis, C. salinus, and C. diabolis) and a species located much farther to the east (C. fontinalis from the Guzman Basin, Chihuahua, Mexico). These results, together with evidence from other studies, suggest two separate invasions of the Death Valley System by pupfishes carrying phylogenetically divergent mtDNAs. The C. nevadensis complex apparently is either an artificial group or else it is monophyletic and its genetic history includes loss of the original mtDNA in either Owens Valley or Ash Meadows-Death Valley following genetic introgression after an invasion by a pupfish carrying a divergent mtDNA., (© 1992 The Society for the Study of Evolution.)