Megan V. McPhee

A centralized model for creating shared, standardized, microsatellite data that simplifies inter-laboratory collaboration

We demonstrate an efficient model for standardizing microsatellite DNA data among laboratories studying Oncorhynchus mykiss. Eight laboratories standardized 13 microsatellite loci following allele nomenclature of a central laboratory (average inter-laboratory genotyping concordance >98%). Following this central model, we have currently standardized 298 alleles from throughout the species native range. Although we focus here on O. mykiss, our experiences and recommendation apply equally to other broadly distributed species that may benefit from multi-laboratory collaborative data collection.

Strontium isotopes delineate fine-scale natal origins and migration histories of Pacific salmon

Strontium isotopes simultaneously delineate fine-scale natal habitats and migrations of Pacific salmon harvested during a coastal commercial fishery. Highly migratory organisms present major challenges to conservation efforts. This is especially true for exploited anadromous fish species, which exhibit long-range dispersals from natal sites, complex population structures, and extensive mixing of distinct populations during exploitation. By tracing the migratory histories of individual Chinook salmon caught in fisheries using strontium isotopes, we determined the relative production of natal habitats at fine spatial scales and different life histories. Although strontium isotopes have been widely used in provenance research, we present a new robust framework to simultaneously assess natal sources and migrations of individuals within fishery harvests through time. Our results pave the way for investigating how fine-scale habitat production and life histories of salmon respond to perturbations—providing crucial insights for conservation.

AGE, GROWTH, AND LIFE HISTORY COMPARISONS BETWEEN THE INVASIVE WHITE SUCKER (CATOSTOMUS COMMERSONI) AND NATIVE RIO GRANDE SUCKER (C. PLEBEIUS)

Abstract I compared the life histories of the invading Catostomus commersoni and the declining native C. plebeius in the upper Rio Grande of northern New Mexico to illuminate the mechanisms by which C. commersoni attains higher abundance than C. plebeius. In the first year of life, the 2 species did not differ in length, but C. plebeius reached greater individual mass. Catostomus plebeius achieved a higher intrinsic reproductive rate by maturing earlier, but C. commersoni attained approximately twice the net reproductive output by living longer, growing larger, and attaining 15-fold higher fecundity. While other factors undoubtedly facilitate the invasion of C. commersoni, I suggest that the high fecundity achieved by large C. commersoni contributes to its dominance in the upper Rio Grande system.

The effects of riverine physical complexity on anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss around the Pacific Rim.

This study explored the relationship between riverine physical complexity, as determined from remotely sensed metrics, and anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss. The proportion of anadromy (estimated fraction of individuals within a drainage that are anadromous) was correlated with riverine complexity, but this correlation appeared to be driven largely by a confounding negative relationship between drainage area and the proportion of anadromy. Genetic diversity decreased with latitude, was lower in rivers with only non-anadromous individuals and also decreased with an increasing ratio of floodplain area to total drainage area. Anadromy may be less frequent in larger drainages due to the higher cost of migration associated with reaches farther from the ocean, and the negative relationship between genetic diversity and floodplain area may be due to lower effective population size resulting from greater population fluctuations associated with higher rates of habitat turnover. Ultimately, the relationships between riverine physical complexity and migratory life history or genetic diversity probably depend on the spatial scale of analysis.

Genetic Diversity, Population Structure, and Demographic History of The Rio Grande Sucker, Catostomus (Pantosteus) Plebeius, in New Mexico

Abstract We used 991 bp of mtDNA (D-loop/ND4L/ND4) and eight microsatellite loci to examine population structure and genetic diversity of Catostomus plebeius from nine localities across the northern part of its range in New Mexico. Two phylogeographic regions (Mimbres and Rio Grande) were defined by phylogenetically distinct collections of mtDNA haplotypes. Mismatch distribution analysis and relatively deep coalescence of haplotypes within the upper Rio Grande suggested rapid population expansion of Rio Grande populations following putative colonization from the ancestral Cabeza de Vaca lake system during the Miocene. Mitochondrial haplotypes indicated that individuals from Palomas Creek (near present-day Elephant Butte Reservoir) shared most recent common ancestry with the Rio Grande phylogeographic region. Microsatellite diversity and allele identity supported the hypothesis of native status of C. plebeius from Sapillo Creek in the Gila River drainage. Analysis of molecular variance within and among samples from the upper Rio Grande suggested low levels of historic gene flow across that basin, with ΦST  =  0.19 and FST  =  0.14 for mtDNA and microsatellites, respectively. Utilizamos marcadores mitocondriales (991 bp) y ocho microsatélites (DNA) para examinar la diversidad y la estructura genética de poblaciones de Catostomus plebeius en nueve localidades en Nuevo México. Se identificaron dos regiones filogeográficas distintas: el Mimbres (Río Mimbres y Sapillo Creek) y el Río Grande (Palomas Creek y localidades a lo largo del Río Grande). El análisis demográfico mitocondrial permitió discernir una estabilidad histórica en la población del Río Mimbres, así como una expansión de poblaciones en el Río Grande después de la colonización del lago Cabeza de Vaca a partir del Plioceno Tardío. Datos genéticos sugieron que la población en Palomas Creek (cercano Elephant Butte Reservoir) es relacionado a las poblaciones in el Río Grande. Un alto número alelos únicos en los microsatélites encontrados en Sapillo Creek (un tributario del Río Gila), sugiere que la población es nativa y que pudo haber colonizado el área durante un proceso de captura de un tributario del Río Mimbres. Encontramos una estructura genética de moderada a fuerte en el mitocondrial y microsatélite DNA entre los tributarios superiores del Río Grande, con ΦST  =  0.19 y FST  =  0.14, respectivamente.

High and dry: intermittent watersheds provide a test case for genetic response of desert fishes to climate change

In desert streams, fishes and other organisms that depend on surface water are predicted to inhabit smaller and more isolated wetted reaches, while the frequency and severity of disturbance is expected to increase under most climate change models. Together, these factors should reduce population genetic diversity and persistence probabilities. In this study, our goal was to understand genetic responses of stream fish populations to disturbance in an intermittent stream network. This network is occupied by Rio Grande sucker (Pantosteus plebeius) that is native to highland desert streams in North America. Sample localities in upland perennial reaches were connected by moderate to high levels of gene flow even when separated by up to a 30-km intermittent reach. However, drier and lower-elevation reaches were significant barriers to gene flow. Effects of genetic drift (lower allelic diversity and higher levels of inbreeding) were more pronounced in the watershed with fewest wetted reaches. Temporal analysis of genetic diversity indicated that streams with several spatially distinct wetted reaches were more genetically resistant to wildfire-induced demographic bottlenecks than a stream with only one wetted reach. Maintenance of multiple wetted reaches within streams and facilitated gene flow among watersheds could slow losses of genetic diversity in upland desert stream fishes, and will be important strategies for conserving stream biodiversity in the face of habitat fragmentation and disturbance related to climate change.

GENEALOGICAL DIVERSITY SUGGESTS MULTIPLE INTRODUCTIONS OF WHITE SUCKERS (CATOSTOMUS COMMERSONII) INTO THE RIO GRANDE

Abstract We used two mitochondrial and eight nuclear microsatellite gene loci to compare genetic diversity and genetic affinities of white suckers (Catostomus commersonii) introduced into the Rio Grande of northern New Mexico to putative source populations in the Pecos and Canadian rivers of northeastern New Mexico. Estimates of genetic diversity based on allelic identity were similar among localities from all three drainages, whereas samples of non-native white suckers from the Rio Grande exhibited greater genealogical diversity. We attributed increased genetic diversity in the Rio Grande to separate introductions from ≥2 genetically distinct source populations, only one of which appeared to be from either the Pecos River or the Canadian River. There also was a divergent haplotype in the Pecos River, consistent with the introduction of a non-native lineage into this native population.

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

Summary Genetic tools are commonly used for conservation and management of at-risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. We previously reported a signature of positive selection in the mitochondrial-encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co-evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5-based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. We used RAD-based next-generation sequencing and identified a nuclear-encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it.

Humpback whales feed on hatchery-released juvenile salmon

Humpback whales are remarkable for the behavioural plasticity of their feeding tactics and the diversity of their diets. Within the last decade at hatchery release sites in Southeast Alaska, humpback whales have begun exploiting juvenile salmon, a previously undocumented prey. The anthropogenic source of these salmon and their important contribution to local fisheries makes the emergence of humpback whale predation a concern for the Southeast Alaska economy. Here, we describe the frequency of observing humpback whales, examine the role of temporal and spatial variables affecting the probability of sighting humpback whales and describe prey capture behaviours at five hatchery release sites. We coordinated twice-daily 15 min observations during the spring release seasons 2010–2015. Using logistic regression, we determined that the probability of occurrence of humpback whales increased after releases began and decreased after releases concluded. The probability of whale occurrence varied among release sites but did not increase significantly over the 6 year study period. Whales were reported to be feeding on juvenile chum, Chinook and coho salmon, with photographic and video records of whales feeding on coho salmon. The ability to adapt to new prey sources may be key to sustaining their population in a changing ocean.

Evidence that Marine Temperatures Influence Growth and Maturation of Western Alaskan Chinook Salmon

AbstractChinook Salmon Oncorhynchus tshawytscha from western Alaska have experienced recent declines in abundance, size, and age at maturity. Declines have led to hardships for the region’s subsistence and commercial salmon harvesters, prompting calls to better understand factors affecting the life history of these populations. Western Alaskan Chinook Salmon are thought to spend their entire marine residency in the Bering Sea. The Bering Sea ecosystem demonstrates high interannual variability that is largely driven by the annual extent of sea ice. However, warming is expected to supersede interannual variability in the next several decades as a consequence of climate change. We investigated the influence of sea surface temperatures (SSTs) on the life history of western Alaskan Chinook Salmon by using information from two regional populations subject to long-term monitoring. We found strong correlations between early marine growth and SSTs. Warmer SSTs appeared to lead to a younger age at maturity, largely...