A hierarchical analysis of historical processes and phylogeographic patterns in Salvelinus (Pisces: Salmonidae)

Hybrid zones have been studied extensively over the last two decades, but relatively little attention has focused on the historical processes generating hybrid zones. Phylogeography, a subdiscipline of biogeography, evaluates patterns of genetic variation to infer the processes that have shaped the geographic and demographic histories of species and can provide insight into the historical contingencies that facilitated hybridization. Phylogenetic relationships of char (Pisces: Salvelinus) have suggested that hybridization has been a recurring theme throughout their evolutionary history. In this thesis, I used sequence variation in the mitochondrial DNA (mtDNA) control region to perform a hierarchical phylogeographic study that examined intraspecific, interspecific, and trans-species polymorphisms in Salvelinus. I developed a diagnostic assay that identifies bull trout (S. confluentus) mtDNA clades and revealed the presence of both lineages in two coastal watersheds in British Columbia. Headwater stream capture following the last glaciation is suspected to have facilitated this "double invasion". A nested clade analysis (NCA) was performed to evaluate if a widespread hybrid zone between Dolly Varden (S. malma) and bull trout in northwestern North America resulted from two processes: secondary contact of previously isolated lineages and continuous contact resulting from historical introgression in a shared refuge. Despite ambiguity in the statistical parsimony network, NCA provided evidence of secondary contact between Beringian Dolly Varden and bull trout and introgressed (with bull trout mtDNA) Dolly Varden. In addition, I found a degree of phylogeographic substructure amongst bull trout and introgressed Dolly Varden in the Chehalis Refuge, which suggests that introgression has been geographically localized. In a species-level phylogenetic analysis, the "approximately-unbiased test" was used to compare alternate tree topologies and I found that Arctic char lineages were not monophyletic in relation to Beringian Dolly Varden and bull trout. The consensus parsimony tree and the phylogeographic distribution of lineages suggested that both bull trout and Dolly Varden may have experienced historical contact with different Arctic char lineages. I suggest that hybridization has played a significant evolutionary role in the diversification of char. This work presents the most extensive phylogeographic analysis of Salvelinus to date and provides a comparative framework for both small scale and regional studies in northwestern North America.Science, Faculty ofZoology, Department ofGraduat

INmorph

List of extractions and morphological sampling results. Columns: Extraction, Shop name (anonymized to protect proprietor), Region, State, Advertised species, Extraction, Unadvertised species

SummarizeBlasteDNAEnvironmentSepASVs

Perl script summarizes blast results. For each sequence it makes a string containing all the species hits that had the lowest e value for that query. Script removes hits with % identity of query cover < 90. Script also prints if an ASV had no BLAST results or if all e values were equal to the minimum. Returns a table with columns: Sample, Species (String of lowest e value hits), N ASVs, N reads, Proportion of reads, Sequence name (from sample results file)

MorphVeDNASummarizeErrMoreCons

Script compares morphological results to eDNA results. Removes ASVs < than the max error calculated from positive controls. Requires eDNA results input, SppStatus.txt, and INMorph.txt

Primer trimming script

Perl script trims primers and removes sequences with spacer primers that are incorrect (likely index hops). Script cycles through results folders, and puts results in a separate folder for DADA2 merging

Data from: Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: differentiation of fronts, introgression, and eDNA metabarcode detection

The invasive silver carp Hypophthalmichthys molitrix escaped from southern U.S. aquaculture during the 1970s to spread throughout the Mississippi River basin and steadily moved northward, now reaching the threshold of the Laurentian Great Lakes. The silver carp is native to eastern Asia and is a large, prolific filter-feeder that decreases food availability for fisheries. The present study evaluates its population genetic variability and differentiation across the introduced range using 10 nuclear DNA microsatellite loci, sequences of two mitochondrial genes (cytochrome b and cytochrome c oxidase subunit 1), and a nuclear gene (ribosomal protein S7 gene intron 1). Populations are analyzed from two invasion fronts threatening the Great Lakes (the Illinois River outside Lake Michigan and the Wabash River, leading into the Maumee River and western Lake Erie), established areas in the southern and central Mississippi River, and a later Missouri River colonization. Results discern considerable genetic diversity and some significant population differentiation, with greater mtDNA haplotype diversity and unique microsatellite alleles characterizing the southern populations. Invasion fronts significantly differ, diverging from the southern Mississippi River population. About 3% of individuals contain a unique and very divergent mtDNA haplotype (primarily the southerly populations and the Wabash River), which may stem from historic introgression in Asia with female largescale silver carp H. harmandi. Nuclear microsatellites and S7 sequences of the introgressed individuals do not significantly differ from silver carp. MtDNA variation is used in a high-throughput sequence assay that identifies and distinguishes invasive carp species and their population haplotypes (including H. molitrix and H. harmandi) at all life stages, in application to environmental (e)DNA water and plankton samples. We discerned silver and bighead carp eDNA from 10 bait shops in the Great Lakes watershed, indicating that release from retailers comprises another likely vector. Our findings provide key baseline population genetic data for understanding and tracing the invasion’s progression, facilitating detection, and evaluating future trajectory and adaptive success

Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection.

In the 1970s, the introduced silver carp Hypophthalmichthys molitrix (which is indigenous to eastern Asia) escaped from southern U.S. aquaculture to spread throughout the Mississippi River basin, and since has steadily moved northward. This large, prolific filter-feeder reduces food availability for other fishes. It now has reached the threshold of the Laurentian Great Lakes, where it likely will significantly impact food chains and fisheries. Our study evaluates population genetic variability and differentiation of the silver carp using 10 nuclear DNA microsatellite loci, and sequences of two mitochondrial genes-cytochrome b and cytochrome c oxidase subunit 1, along with the nuclear ribosomal protein S7 gene intron 1. We analyze population samples from: two primary Great Lakes' invasion fronts (at the Illinois River outside of Chicago, IL in Lake Michigan and in the Wabash River, which leads into the Maumee River and western Lake Erie), the original establishment "core" in the Lower Mississippi River, and expansion areas in the Upper Mississippi and Missouri rivers. We analyze and compare our results with bighead and other invasive carps, and cyprinid relatives. Results reveal that the silver carp invasion possesses moderate levels of genetic diversity, with more mtDNA haplotypes and unique microsatellite alleles in the "core" Lower Mississippi River population, which also diverges the most. The two invasion fronts also significantly genetically differ. About 3% of individuals (including all populations except the Illinois River) contain a unique and very divergent mtDNA haplotype, which likely stems from historic introgression in Asia with female largescale silver carp H. harmandi. The nuclear microsatellites and S7 sequences of the introgressed individuals do not differ from silver carp and are very distant from bighead carp. These sequence variation data are employed to design and evaluate a targeted high-throughput metabarcoding sequence assay that identifies and distinguishes among species of invasive carps (i.e., silver, bighead, grass, black, and common carps, along with goldfish), as well as native cyprinids, using cytochrome b. Our assay further differentiates among selected silver carp haplotypes (including between H. molitrix and H. harmandi), for use in population genetics and future analyses of spread pathways. We test and evaluate this assay on environmental (e)DNA water samples from 48 bait shops in the Great Lakes' region (along the Lake Erie, Lake St. Clair, and Wabash River watersheds), using positive and negative controls and custom bioinformatic processing. Test results discern silver carp eDNA in four of the shops-three in Lake Erie and one in the Wabash River watershed-and bighead carp from one of the same Lake Erie venues, suggesting that retailers (who often source from established southerly populations) comprise another introduction vector. Our overall findings thus provide key population genetic and phylogenetic data for understanding and tracing introductions, vectors, and spread pathways for silver carp, their variants, and their relatives

Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral <i>Swiftia simplex</i> (Nutting 1909) on the West Coast of the United States

<div><p>Deep-sea corals are a critical component of habitat in the deep-sea, existing as regional hotspots for biodiversity, and are associated with increased assemblages of fish, including commercially important species. Because sampling these species is so difficult, little is known about the connectivity and life history of deep-sea octocoral populations. This study evaluates the genetic connectivity among 23 individuals of the deep-sea octocoral <i>Swiftia simplex</i> collected from Eastern Pacific waters along the west coast of the United States. We utilized high-throughput restriction-site associated DNA (RAD)-tag sequencing to develop the first molecular genetic resource for the deep-sea octocoral, <i>Swiftia simplex</i>. Using this technique we discovered thousands of putative genome-wide SNPs in this species, and after quality control, successfully genotyped 1,145 SNPs across individuals sampled from California to Washington. These SNPs were used to assess putative population structure across the region. A STRUCTURE analysis as well as a principal coordinates analysis both failed to detect any population differentiation across all geographic areas in these collections. Additionally, after assigning individuals to putative population groups geographically, no significant F_ST values could be detected (F_ST for the full data set 0.0056), and no significant isolation by distance could be detected (p = 0.999). Taken together, these results indicate a high degree of connectivity and potential panmixia in <i>S</i>. <i>simplex</i> along this portion of the continental shelf.</p></div