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Restoration of access to lost habitat for threatened and endangered fishes above currently impassable dams represents a major undertaking. Biological monitoring is critical to understand the dynamics and success of anadromous recolonization as, in the case of Oncorhynchus mykiss, anadromous steelhead populations are reconnected with their conspecific resident rainbow trout counterparts. We evaluate three river systems in the Lower Columbia River basin: the White Salmon, Sandy, and Lewis rivers that are in the process of removing and/or providing passage around existing human-made barriers in O. mykiss riverine habitat. In these instances, now isolated resident rainbow trout populations will be exposed to competition and/or genetic introgression with steelhead and vice versa. Our genetic analyses of 2,158 fish using 13 DNA microsatellite (mSAT) loci indicated that within each basin anadromous O. mykiss were genetically distinct from and significantly more diverse than their resident above-dam trout counterparts. Above long-standing natural impassable barriers, each of these watersheds also harbors unique rainbow trout gene pools with reduced levels of genetic diversity. Despite frequent releases of non-native steelhead and rainbow trout in each river, hatchery releases do not appear to have had a significant genetic effect on the population structure of O. mykiss in any of these watersheds. Simulation results suggest there is a high likelihood of identifying anadromous x resident individuals in the Lewis and White Salmon rivers, and slightly less so in the Sandy River. These genetic data are a prerequisite for informed monitoring, managing, and conserving the different life history forms during upstream recolonization when sympatry of life history forms of O. mykiss is restored.

The Yazoo Darter Etheostoma raneyi is a small imperiled snubnose darter endemic to Upper Gulf Coastal Plain streams in north-central Mississippi. Installation of rip-rap and wood is being considered in an effort to increase suitable habitat and spawning substrate for the species. In common with other snubnose darters, Yazoo Darters attach their eggs to appropriate spawning substrate. However, it is not known if Yazoo Darters, or other imperiled Coastal Plain snubnose darters, will use rock substrate for spawning given it is almost entirely absent from streams of occurrence. If Yazoo Darters show no preference between wood and rock (rip-rap) for spawning, management would have greater flexibility when designing stream habitat installations for imperiled Coastal Plain snubnose darters, because the installation of rip-rap is much less expensive and time consuming than installation of wood. We used a randomized block experiment in an outdoor mesocosm facility to test for spawning substrate preferences. We counted >7600 eggs and Yazoo Darters used both substrates but used wood more than twice as often as rip-rap. Though we cannot recommend habitat installations using only rip-rap, any installation using a mix of wood and rip-rap will enhance spawning habitat for the Yazoo Darter and at least four other imperiled Coastal Plain snubnose darters.

The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b ( cytb ) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.

Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri , the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.

Headwater fishes in the southeastern United States make up much of the fish biodiversity of the region yet many are imperiled. Despite this, the specific habitat requirements of imperiled headwater fishes in lowland Coastal Plain streams have rarely been quantified. Using data collected over three years of seasonal sampling we provide estimates of the microhabitat requirements of the imperiled Yazoo darter ( Etheostoma raneyi Suttkus and Bart), a small benthic insectivore. Our results indicate that the species is a microhabitat specialist and that optimum microhabitat within degraded contemporary streams consists of a narrow range of water depths (about 20–30 cm), current velocity ≥ 0.25 m·s −1 , complex stable debris piles, rooted macrophytes, and likely coarse substrate. No pronounced or generalized seasonal shifts in microhabitat use occurs, and no evidence exists for intraspecific partitioning of microhabitat. Though stable and complex instream cover is one of the most important variables explaining variation in microhabitat use by Yazoo darters, such cover is rare in the degraded streams within the range of the species. Current conservation classifications of the Yazoo darter by governmental agencies and nongovernmental organizations as well as associated management plans that are based on the assumption that Yazoo darters are habitat generalists should be reviewed in recognition of the increased risk of decline because Yazoo darters are microhabitat specialists. These considerations should also be extended to other closely related imperiled species of snubnose darters.

The use of genetic methods to quantify the effects of anthropogenic habitat fragmentation on population structure has become increasingly common. However, in today’s highly fragmented habitats, researchers have sometimes concluded that populations are currently genetically isolated due to habitat fragmentation without testing the possibility that populations were genetically isolated before European settlement. Etheostoma raneyi is a benthic headwater fish restricted to river drainages in northern Mississippi, USA, that has a suite of adaptive traits that correlate with poor dispersal ability. Aquatic habitat within this area has been extensively modified, primarily by flood-control projects, and populations in headwater streams have possibly become genetically isolated from one another. We used microsatellite markers to quantify genetic structure as well as contemporary and historical gene flow across the range of the species. Results indicated that genetically distinct populations exist in each headwater stream analyzed, current gene flow rates are lower than historical rates, most genetic variation is partitioned among populations, and populations in the Yocona River drainage show lower levels of genetic diversity than populations in the Tallahatchie River drainage and other Etheostoma species. All populations have negative F IS scores, of which roughly half are significant relative to Hardy–Weinberg expectations, perhaps due to small population sizes. We conclude that anthropogenic habitat alteration and fragmentation has had a profoundly negative impact on the species by isolating E. raneyi within headwater stream reaches. Further research is needed to inform conservation strategies, but populations in the Yocona River drainage are in dire need of management action. Carefully planned human-mediated dispersal and habitat restoration should be explored as management options across the range of the species.

The Yazoo Darter, Etheostoma raneyi (Percidae: subgenus Ulocentra), is a narrowly restricted endemic occurring in small tributaries in the Loessial Hills of the upper Yazoo River basin in northern Mississippi. The range of the species is shared between the Little Tallahatchie and adjacent upper Yocona rivers, but populations in the two rivers are separated by unsuitable habitat in the Mississippi Alluvial Plain. The Chickasaw Darter, Etheostoma cervus, and Firebelly Darter, E. pyrrhogaster, show analogous distributions in the Forked Deer and Obion rivers, respectively, of western Tennessee and Kentucky. Phylogenetic analyses of cyt b and control region mtDNA (1497 sites) data from E. raneyi (n  =  12), E. cervus (n  =  4), and E. pyrrhogaster (n  =  5) recovered two clades of E. raneyi with high bootstrap and decay support that are congruent with localities of specimens from the Little Tallahatchie and Yocona drainages, respectively. Divergence between the clades of E. raneyi was 1.3% (SE  =  0.3%). Within drainage divergence was 0.3% (SE  =  0.1%) for the Little Tallahatchie clade and 0.1% (SE < 0.1%) for the Yocona clade. Etheostoma cervus and E. pyrrhogaster showed interspecific divergence of 1.3% (SE  =  0.2%) and intraspecific divergence of 0.7% (SE  =  0.2%) and 0.8% (SE  =  0.2%), respectively. These results suggest isolation by vicariance as a mode of speciation in fishes restricted to the Upper Coastal Plain. Conservation action may be in order for E. raneyi as populations from the Little Tallahatchie and Yocona rivers should be treated as separate management units with the latter known from only five small streams, some of which are threatened by encroaching development.