Molecular systematics and historical biogeography of the Nocomis biguttatus species group (Teleostei: Cyprinidae): Nuclear and mitochondrial introgression and a cryptic Ozark species

Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments

Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region, there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.

Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)

Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between non-sister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.

Fish faunal provinces of the conterminous United States of America reflect historical geography and familial composition

Although the conterminous USA has a long history of ichthyological exploration, the description of biogeographical provinces has been ad hoc. In this study we quantitatively determined fish faunal provinces and interpreted them in the context of the geological history of North America. We also evaluated influences of major river basin occupancy and contemporary environmental factors on provincial patterns. Our data set comprised 794 native fishes, which we used to generate a presence and absence matrix for U.S. Geological Survey (USGS) four-digit hydrologic units. Three nested data sets were analysed separately: primary freshwater families, continental freshwater families (including primary and secondary families) and all freshwater families (including primary, secondary and peripheral families). We used clustering analysis to delimit faunal breaks and one-way analysis of similarity (ANOSIM) to determine significance among clusters (i.e. provinces). We used an indicator-species analysis to identify species that contributed most to province delineations and a similarity-percentage (SIMPER) analysis to describe the relative influence of representatives from each category (i.e. primary, secondary, peripheral) on provincial boundaries. Lastly, we used a parsimony redundancy analysis to determine the roles of historical (i.e. major river basin) and contemporary environmental factors in shaping provinces. Analysis of the nested data sets revealed lessening provincial structure with inclusion of more families. There were 10 primary freshwater provinces, 9 continental freshwater provinces and 7 all freshwater provinces. Major basin occupancy, but not contemporary environmental factors, explained substantial variance in faunal similarities among provinces. However, provincial boundaries did not conform strictly to modern river basins, but reflected river-drainage connections of the Quaternary. Provinces represent broad-scale patterns of endemism and provide a starting point for future studies. Relative malleability of province boundaries in the continental interior highlights this region as biogeographically diverse and dynamic. Interior-core provinces of this region (Central Gulf Coastal Plains, Northern Interior) have not been recognized previously and warrant further study.