Margaret F. Docker

Molecular resolution of the family Dreissenidae (Mollusca: Bivalvia) with emphasis on Ponto-Caspian species, including first report of Mytilopsis leucophaeata in the Black Sea basin.

Considerable uncertainty exists in determination of the phylogeny among extant members of the Dreissenidae, especially those inhabiting the Ponto-Caspian basin, as multiple systematic revisions based on morphological characteristics have failed to resolve relationships within this group of bivalves. In this study we use DNA sequence analyses of two mitochondrial gene fragments, 16S rRNA and cytochrome c oxidase subunit I (COI), to determine phylogenetic relationships among Dreissena rostriformis, D. bugensis, D. polymorpha, D. stankovici, Congeria kusceri, and Mytilopsis leucophaeata. Dreissena stankovici was determined to represent a sister taxa to D. polymorpha and both are more closely related to other extant Dreissena species than Congeria or Mytilopsis. Sequence divergence between D. rostriformis and D. bugensis was relatively low (0.3-0.4%), suggesting that these two taxa constitute a single species. However, environmental differences suggest two races of D. rostriformis, a brackish water race (rostriformis) and a freshwater race (bugensis). Spread of bugensis-type individuals into habitats in the Caspian Sea that are occupied by rostriformis-type individuals may create novel hybridization opportunities. Species-specific molecular markers also were developed in this study since significant intraspecific variation in morphological features complicates dreissenid identification. Using two gene fragments (nuclear 28S and 16S), we identified restriction fragment length polymorphisms (RFLPs) that distinguish among D. rostriformis/bugensis, D. polymorpha, and D. stankovici and revealed the presence of a cryptic invader to the Black Sea basin, Mytilopsis leucophaeata. This is the first report of this North American native in southern Europe.

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within‐region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site–associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and ‘dwarf’ adults (FCT = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow.

Genetic comparison between sympatric anadromous steelhead and freshwater resident rainbow trout in British Columbia, Canada

Sympatrically occurring steelhead and rainbowtrout (n = 100) were collected from fiveriver systems in British Columbia, Canada, and1300 bp from the mitochondrial genome and 270bp of the nuclear growth hormone 2 gene weresequenced to determine if the two forms aregenetically differentiated. ND3 and D-loopsequence differences produced nine haplotypeswhile two length variants of the GH2 intron Dwere present. In one river system, steelheadand rainbow were genetically divergent based onmtDNA data but overall, no consistent geneticdifference between life history types wasfound. Rather, genetic differences wereassociated with geography, suggesting thatsteelhead and rainbow trout are polyphyleticand the result of parallel evolution ratherthan members of two distinct lineages.

Similarities, differences, and unknowns in biology and management of three Parasitic lampreys of North America.

Abstract Sea lampreys, Petromyzon marinus, are invasive to the Laurentian Great Lakes where they have decimated native fishes. Great Lakes sea lampreys have been subjected to control measures for several decades, and the drive to control them has led to major advances in understanding their biology and in informing management. In contrast, anadromous sea and Pacific (Entosphenus tridentatus) lampreys have co-evolved with their oceanic prey. Both of these anadromous lampreys are in decline, and a limited amount of information on their biology has stymied conservation. The tendency has been to make biological inferences about anadromous lampreys based on the Great Lakes sea lamprey without justifiable evidence. We identify areas in which key information is missing for the juvenile (parasitic feeding) phase and adult freshwater spawning migrations, and compare and contrast information for these lampreys. Our comparisons reveal major differences, some intriguing similarities, and key unknowns that will requir...

Hybridization dynamics between sympatric species of trout: loss of reproductive isolation

Although reinforcement should enhance reproductive barriers in sympatric species, sympatric trout species do hybridize. Using mitochondrial and nuclear species markers, we investigated hybridization directionality, hybrid mating biases, and selection against hybrids in 13 sympatric cutthroat and rainbow trout populations on Vancouver Island, Canada. Approximately 50% of the genotyped fish were hybrid (F1 or higher‐order) and populations ranged from very recent (all F1 hybrids) to extremely advanced higher‐order hybridization. Overall, interbreeding was reciprocal, although some populations showed directional hybridization. Pronounced cytonuclear disequilibrium in post‐F1 hybrids indicated a remarkable mating bias not previously reported, which is most likely because of behavioural reproductive preferences. Selection against hybrids was observed in only two populations, indicative of extrinsic selection. Two populations were ‘hybrid swarms’, with a complete loss of reproductive isolation. The complex hybridization dynamics in this system represent a valuable natural experiment of the genetic and evolutionary implications of recent and on‐going interspecific hybridization.

Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey

Most species with lengthy migrations display some degree of natal homing; some (e.g. migratory birds and anadromous salmonids) show spectacular feats of homing. However, studies of the sea lamprey (Petromyzon marinus) indicate that this anadromous species locates spawning habitat based on pheromonal cues from larvae rather than through philopatry. Previous genetic studies in the anadromous Pacific lamprey (Entosphenus tridentatus) have both supported and rejected the hypothesis of natal homing. To resolve this, we used nine microsatellite loci to examine the population structure in 965 Pacific lamprey from 20 locations from central British Columbia to southern California and supplemented this analysis with mitochondrial DNA restriction fragment length polymorphism analysis on a subset of 530 lamprey. Microsatellite analysis revealed (i) relatively low but often statistically significant genetic differentiation among locations (97% pairwise FST values were <0.04 but 73.7% were significant); and (ii) weak but significant isolation by distance (r2 = 0.0565, P = 0.0450) but no geographic clustering of samples. The few moderate FST values involved comparisons with sites that were geographically distant or far upstream. The mtDNA analysis—although providing less resolution among sites (only 4.7%FST values were significant)—was broadly consistent with the microsatellite results: (i) the southernmost site and some sites tributary to the Salish Sea were genetically distinct; and (ii) southern sites showed higher haplotype and private haplotype richness. These results are inconsistent with philopatry, suggesting that anadromous lampreys are unusual among species with long migrations, but suggest that limited dispersal at sea precludes panmixia in this species.

Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey.

Next‐generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high‐throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high‐throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run‐timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species’ range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.

Erosion of interspecific reproductive barriers resulting from hatchery supplementation of rainbow trout sympatric with cutthroat trout

The frequency of hybridization between cutthroat (Onchorhynchus clarki clarki) and rainbow (O. mykiss irideus) trout from coastal habitats in British Columbia, Canada, was examined in seven populations where the two species are sympatric with no history of rainbow trout stocking and compared with areas where native rainbow trout populations have been supplemented with hatchery fish (three populations). Four nuclear markers were used to identify each species and interspecific hybrids and one mitochondrial marker showed the direction of gene exchange between species. The frequency of hybrids was significantly higher (Fisher exact test, P < 0.001) in river systems where hatchery rainbow trout have been introduced (50.6% hybrids) than in populations where the two species naturally co‐occur without supplementation (9.9% hybrids).

Genetic Differentiation among Sympatric Migratory and Resident Life History Forms of Rainbow Trout in British Columbia

Abstract Rainbow trout Oncorhynchus mykiss in coastal areas of North America occur as two divergent migratory types: Steelhead that migrate to salt water and return to their natal river to spawn and resident rainbow trout that either do not migrate or migrate locally within the freshwater system. We extracted DNA from sympatrically occurring steelhead and rainbow trout collected from five major drainages in British Columbia. We used three types of genetic markers to test for differentiation within the sympatric population: Microsatellite DNA markers, gene intron polymorphisms (restriction fragment length polymorphisms [RFLPs] and fragment size polymorphisms), and major histocompatibility complex (MHC) exon polymorphisms (RFLPs). The migratory and resident forms were genetically differentiated in only one sympatric population based on microsatellite data, but no significant differentiation was found using the combined gene locus marker data. Overall, most of the observed allele variation at all marker type...

Redescription of the Presumed-Extinct Miller Lake Lamprey, Lampetra minima

Abstract Lampetra minima, believed eradicated in 1958 and extinct, survives in upper tributaries of the historical Williamson drainage in Klamath and Lake Counties, Oregon. The species, the smallest known parasitic lamprey, was believed to be endemic to Miller Lake. Its current disjunct distribution includes Miller Creek, Jack Creek, and upper sections of the Williamson and Sycan Rivers. We compare new specimens with the type series and other Klamath Basin lampreys and redescribe L. minima. It appears most similar to Lampetra lethophaga but is smaller (72–145 mm vs 115–170 mm TL), has a larger disc length (5.0–8.6% vs 4.2–6.4% TL), larger prebranchial length (11.0–17.0% vs 8.8–13.7% TL), and larger eye (2.1–3.3% vs 1.4–2.3% TL). Klamath Basin Lampetra differ from anadromous Lampetra tridentata in a single transition in cytochrome b, and L. minima have an additional, but not unique, transition. Our data do not support the suggestion that L. minima recently evolved from a L. tridentata–like ancestor; rather we suggest a more ancient separation and a sister relationship with L. lethophaga.