Low genetic diversity and small long-term population sizes in the spring endemic watercress darter, Etheostoma nuchale

On the brink of extinction: a new freshwater amphipod Jesogammarusacalceolus (Anisogammaridae) from Japan

Freshwater habitats, especially cold springs, are environments in which the risk of extinction faced by organisms remains high due to human activities. To conserve endangered species, it is important to describe and name them. Here, a new, endangered freshwater anisogammarid amphipod species, Jesogammarus (Jesogammarus) acalceolussp. nov., found in a spring in Aomori Prefecture, Japan, is described which is potentially the sole remaining habitat of this species. Both morphological and molecular phylogenetic results strongly support the nesting of the new species within Jesogammarus. Jesogammarus (J.) acalceolussp. nov. is the first species of genus Jesogammarus that was found to lack a calceolus, a sensory organ located on male antenna 2. Thus, the diagnostic criteria for this genus required amendment. A reconstruction of ancestral calceoli, based on a molecular phylogenetic tree, revealed that the common ancestor of Jesogammarus possessed calceoli, which were secondarily lost in J. (J.) acalceolussp. nov. Our results indicate that this new species, which is key to clarifying the evolution of the calceolus, is of high conservation significance.

Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)

Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD-seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream-biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.

Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China

In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise F_ST, gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.

Population Structure and Habitat Use of the Endangered Watercress Darter

Despite Alabama's exceptionally diverse freshwater fish fauna, many of its fish species face extinction. Some of the state's most imperiled species dwell within coldwater springs, but a deficit of knowledge about their ecology hampers protection efforts. The watercress darter Etheostoma nuchale is a species confined to five springs in the greater Birmingham metropolitan area. Roebuck Spring likely harbors the largest population. Its pool has been surveyed occasionally, but there had been no survey of its run, a shallow stream flowing from the pool. We investigated the darter's use of the run, its habitat preferences, and characteristics of the habitats where it is most abundant. We quantified the abundance of stream microhabitats, then estimated darter density in the stream's five most common habitats using a throw trap, a high-walled metal frame dropped in the habitat. We found darters at densities vastly exceeding typical estimates derived using seine nets. We estimated the run harbored 116,932 (79,358–155,965) darters, two-thirds of which were juveniles. The most preferred habitat was coontail Ceratophyllum demersum, a submergent plant not previously known to provide darter habitat. Coontail grew prolifically in swift currents, which was surprising given that darter habitats described previously had little to no current. Coontail provided a more structurally complex habitat than the plants of the other microhabitats studied. Our results suggest that spring runs can support substantial densities of the watercress darter if dense submergent vegetation is present.

The influence of life-history strategy on genetic differentiation and lineage divergence in darters (Percidae: Etheostomatinae)

Recent studies determined that darters with specialized breeding strategies can exhibit deep lineage divergence over fine geographic scales without apparent physical barriers to gene flow. However, the extent to which intrinsic characteristics interact with extrinsic factors to influence population divergence and lineage diversification in darters is not well understood. This study employed comparative phylogeographic and population genetic methods to investigate the influence of life history on gene flow, dispersal ability, and lineage divergence in two sympatric sister darters with differing breeding strategies. Our results revealed highly disparate phylogeographic histories, patterns of genetic structure, and dispersal abilities between the two species suggesting that life history may contribute to lineage diversification in darters, especially by limiting dispersal among large river courses. Both species also showed striking differences in demographic history, indicating that extrinsic factors differentially affected each species during the Pleistocene. Collectively, our results indicate that intrinsic and extrinsic factors have influenced levels of gene flow among populations within both species examined. However, we suggest that life-history strategy may play a more important role in lineage diversification in darters than previously appreciated, a finding that has potentially important implications for understanding diversification of the rich North American freshwater fish fauna.

Genetic evaluation of remnant and translocated shiners, Notropis heterodon and Notropis heterolepis

Population and conservation genetics of two freshwater fish species, Notropis heterodon and Notropis heterolepis, were evaluated in north-eastern Illinois, U.S.A., where both species have severely declined. Fishes were sampled from two remnant populations occurring in small glacial lakes (source samples) and from two man-made ponds that had been stocked with fishes from those same lakes (sanctuary samples). The goal was to obtain information that would help inform conservation programme planning to reintroduce sanctuary fishes to areas where both species are extirpated. Microsatellite data showed that the two species were genetically quite distinct and there was no evidence of hybridization in either source or sanctuary samples. Within each species, source and sanctuary samples had moderate levels of heterozygosity and were not significantly different from each other. Many alleles observed in the source samples, however, were not detected in the sanctuary samples, indicating that translocation had resulted in reduced allelic diversity of the sanctuary samples. Sibship analysis indicated that full and half sibs occurred within source-lake samples, thus reducing the effective population size of the reintroduced stock. Taken together, these results suggest that source-lake stocks rather than sanctuary stocks are more appropriate for future reintroductions of both species in their native range, unless sanctuary populations can be established with hundreds of fishes. Also, fishes should be harvested from multiple locations in source lakes to avoid over-representation of family groups.