Genomics clarifies taxonomic boundaries in a difficult species complex.

Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors

Diversification, speciation, and phylogeography of freshwater sculpins (Cottus, Cottopsis) in California

Freshwater systems across North America and Eurasia are home to inconspicuous species of fish known as sculpins (genus Cottus). As generally small, benthic species, sculpins have largely been ignored by humans. One lineage in particular, Cottopsis, is endemic to the west coast of North America and inhabits diverse geographic areas and ecological conditions. Such complexity is the perfect setting for understanding issues related to speciation, divergence, population structure, gene flow, and phylogeography of freshwater fishes. Comprehensive phylogenetic work using multiple nuclear and mitochondrial markers generated species trees and delimitations which varied slightly by technique and statistical approach, but which revealed a number of cryptic lineages and relationships within the clade. Three species groups in particular showed remarkable variation in California, riffle (C. gulosus) and Pit (C. pitensis) sculpin, and prickly sculpin (C. asper). Following an extensive distributional sampling, a number of phylogeographic breaks, cryptic lineages, and speciation mechanisms were discovered. Within C. gulosus and C. pitensis, the Sacramento River proved to be distinctive showing potential historical hybridization, complete C. pitensis mitochondrial introgression, and restricted contemporary population structure. Consistent with other studies, a phylogeographic break along the Sacramento/San Joaquin River Delta led to the prospective divergence of C. pitensis into the Sacramento/Pit River basin and C. gulosus into the San Joaquin River basin; with different measures of isolation by distance and intra-population structure. A similar break and population structure was seen in inland C. asper populations. Estimated to have diverged from amphidromous coastal populations 110,000 years ago, inland C. asper represent incipient speciation, as evident by poor phylogenetic distinctiveness. Low measures of gene flow and hybridization in the narrow connective corridor between coastal and inland populations, along with no sign of physical barriers suggest inland C. asper are diverging by way of parapatric speciation. A novel lineage of C. asper in Clear Lake is also well-supported, originating from coastal, not inland populations. Overall, results clearly signify sculpin are a complex species group, with structure reflective of their historical hydrology, and worthy of intensive conservation and management strategies

A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex

Baumsteiger, Jason, Moyle, Peter B. (2019): A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex. Zootaxa 4543 (2): 221-240, DOI: https://doi.org/10.11646/zootaxa.4543.2.

Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated

Data from: Novel concordance between geographic, environmental and genetic structure in the ecological generalist prickly sculpin (Cottus asper) in California

Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41–191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California’s historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments

Comprehensive microsatellite allele table for 11 loci

Microsatellite alleles used in study for each sampled site. Some individuals were less successful and may have been removed before final analysis. Location information can be found in the main paper (GPS, etc.)

Data from: Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus).

Species ranges which span different geographic landscapes frequently contain cryptic species or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (C. pitensis), display ranges based on morphological identifications which do not coincide with these breaks. Using a comprehensive sampling and nuclear, mitochondrial, and microsatellite markers, we hypothesized proposed species ranges are erroneous based on potential hybridization/gene flow between species. Results identified a phylogeographic signature consistent with this hypothesis, with breaks at the Coast Range Mountains and Sacramento/San Joaquin River confluence. Coastal locations of C. gulosus represent a unique lineage and “true” C. gulosus were limited to the San Joaquin basin, both regions under strong anthropogenic influence and potential conservation targets. C. pitensis limits extended historically throughout the Sacramento/Pit River basin but currently are restricted to the Pit River. Interestingly, locations in the Sacramento River contained low levels of ancestral hybridization and gene flow from C. gulosus but now appear to be a distinct population. The remaining population structure was strongly correlated with Sierra Nevada presence (high) or absence (low). This study stresses the importance of testing phylogeographic breaks across multiple taxa/habitats before conservation decisions are made, but also the potential impact of different geographic landscapes on evolutionary diversification

Nuclear_517_sequence_alignment

Aligned nuclear marker 517 sequences for all location

Data from: Rangewide landscape genetics of an endemic Pacific northwestern salamander

A species' genetic structure often varies in response to ecological and landscape processes that differ throughout the species' geographic range, yet landscape genetics studies are rarely spatially replicated. The Cope's giant salamander (Dicamptodon copei) is a neotenic, dispersal-limited amphibian with a restricted geographic range in the Pacific northwestern USA. We investigated which landscape factors affect D. copei gene flow in three regions spanning the species' range, which vary in climate, landcover and degree of anthropogenic disturbance. Least cost paths and Circuitscape resistance analyses revealed that gene flow patterns vary across the species' range, with unique combinations of landscape variables affecting gene flow in different regions. Populations in the northern coastal portions of the range had relatively high gene flow, largely facilitated by stream and river networks. Near the southeastern edge of the species' range, gene flow was more restricted overall, with relatively less facilitation by streams and more limitation by heat load index and fragmented forest cover. These results suggested that the landscape is more difficult for individuals to disperse through at the southeastern edge of the species' range, with terrestrial habitat desiccation factors becoming more limiting to gene flow. We suggest that caution be used when attempting to extrapolate landscape genetic models and conservation measures from one portion of a species' range to another