DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams

Abstract

There is growing interest in broad-scale biodiversity assessments that can serve as benchmarks for identifying ecological change. Genetic tools have been used for such assessments for decades, but spatial sampling considerations have largely been ignored. Here, we demonstrate how intensive sampling efforts across a large geographical scale can influence identification of taxonomic units. We used sequences of mtDNA cytochrome c oxidase subunit 1 and cytochrome b, analysed with maximum parsimony networks, maximum-likelihood trees and genetic distance thresholds, as indicators of biodiversity and species identity among the taxonomically challenging fishes of the genus Cottus in the northern Rocky Mountains, USA. Analyses of concatenated sequences from fish collected in all major watersheds of this area revealed eight groups with species-level differences that were also geographically circumscribed. Only two of these groups, however, were assigned to recognized species, and these two assignments resulted in intraspecific genetic variation (>2.0%) regarded as atypical for individual species. An incomplete inventory of individuals from throughout the geographical ranges of many species represented in public databases, as well as sample misidentification and a poorly developed taxonomy, may have hampered species assignment and discovery. We suspect that genetic assessments based on spatially robust sampling designs will reveal previously unrecognized biodiversity in many other taxa.

Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana)

“…For example, a recent paper looking at marine crustaceans noted that of the 17,635 morphologically described Decapoda species (e.g., crayfish, crabs, and lobsters) only 5.4% were represented by cytochrome C oxidase subunit I (COI) sequences [15], despite the fact that this genomic region is the target of a global effort to catalog all taxa [16]. Furthermore, consensus between taxonomies described by morphological versus genetic information may be low [17, 18], and many morphologically described species are indistinguishable using short regions of the mitochondrial genome [19, 20]. Finally, many species groups lack a comprehensive tissue archive suitable for DNA analysis.…”

Slow climate velocities of mountain streams portend their role as refugia for cold-water biodiversity

“…Many thousands of kilometers of habitat remain uninventoried even for the most charismatic species like salmonid fishes in a well-studied region such as the northwestern United States (19). Moreover, new cold-water species have recently been described in that region (45), which is indicative of the broader appreciation of cryptic biodiversity that is emerging for mountain streams (46,47). Extensive spatial surveys and geodatabases of occurrence locations for all species will be needed to complement traditional information about habitat quality and population dynamics for a few species if future conservation efforts are to be comprehensive.…”

“…We considered seven species: (i) three native species of conservation concern (bull trout = 1,100 sites; cutthroat trout = 927 sites; Rocky Mountain tailed frogs = 953 sites); (ii) three trout species that have been broadly introduced in the region Table 2. Summary conditions associated with six climate velocity scenarios calculated for streams and rivers in the northwestern United States and are regarded as threats to the native taxa [brown trout = 722 sites, a species of conservation concern in the southern portion of its native range in Europe (14); rainbow trout = 1,332 sites, native to the western two-thirds of the study area; and brook trout = 3,061 sites, a species of conservation concern in its native range of eastern North America (18)]; and (iii) the native slimy sculpin (Cottus cognatus = 458 sites), a glacial relic species for which the taxonomy is uncertain in western North America (46). Thermal conditions at species locations were summarized in scatterplots and cumulative distribution curves.…”

Mitochondrial COI Gene Sequence Analyses of Puntius ticto and Compared with Seven Species of Genus Puntius of Family Cyprinidae: A Finding for Phylogenetic Positioning and DNA Barcoding as Model Study for Cryptic Species

“…Complementing taxonomic descriptions with the knowledge from molecular tools such as mitochondrial DNA sequences [1][2][3] is now considered relevant to understand the phylogenetic relationships and the precise systematic of taxons and description of biodiversity [4][5][6]. Assessing biodiversity depends not only on the organization of organisms into taxonomic units, but also on understanding the phylogenetic relatedness of these taxonomic units [7].…”