Mariah H. Meek

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.

Migration‐related phenotypic divergence is associated with epigenetic modifications in rainbow trout

Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological and behavioural transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable and displays intra‐ and interpopulation variation in migration propensity. Migratory individuals can produce nonmigratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration‐related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome‐scale DNA methylation in fin tissue using reduced representation bisulphite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (nonmigratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were high in magnitude, with up to 62% differential methylation between life history types, and over half of the gene‐associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration‐related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with migration‐related traits in any species.

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq

Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon.

Ecological insights into the polyp stage of non-native hydrozoans in the San Francisco Estuary

The populations of several invasive jellyfish appear to be increasing around the globe. While data on non-native hydromedusae in the San Francisco Estuary have been accumulating in recent years, little is known regarding their polyp phase. The goal of this study was to gather the first field-derived ecological data for polyp stages of Blackfordia virginica, Moerisia sp., and Cordylophora caspia in the estuary. Monthly fouling plates were deployed at five sites during 2007 and 2008. Settlement data indicate a seasonal presence of B. virginica and Moerisia sp., with both distribution and abundance correlated with a combination of water quality and physical parameters. Cordylophora caspia appeared to be present beyond the time period sampled and may be active in the system year-round. The ability of polyps to persist month to month was low, likely due to predation by other non-native species and competition for space.

Trophic ecology of two non-native hydrozoan medusae in the upper San Francisco Estuary

Blooms of some gelatinous zooplankton are increasing worldwide, often disrupting foodwebs. Invasions of non-native jellyfish are a growing problem in many estuaries, including the San Francisco Estuary, where at least two species of Ponto-Caspian hydrozoans, Maeotias marginata Modeer, 1791 and Moerisia sp., are abundant. The present study investigated their trophic ecology, testing the following hypotheses: (1) diets over the bloom and at the diel scale are comprised of a variety of prey items; (2) hydrozoans are generalist feeders; (3) hydrozoans feed on the larvae of declining fish species; and (4) the potential for prey competition exists between the hydrozoans and two declining planktivorous fishes, striped bass (Morone saxatilis) and threadfin shad (Dorosoma petenense). Both hydrozoans ate a variety of crustaceans, most notably calanoid copepods, which were found in greater proportion in the guts than in the environment. The only fish larvae consumed were gobies. Density of Moerisia sp., was negatively correlated with gut fullness for both fishes, and diet overlap was high between shad and hydrozoans, but low for bass. Because of strong spatial and temporal overlap between hydrozoans and shad, competition for zooplankton may be occurring. These hydrozoans have invaded other systems, and should be monitored to assess potential ecological interactions in these locations.

Climate Change Likely to Facilitate the Invasion of the Non-Native Hydroid, Cordylophora caspia, in the San Francisco Estuary

Climate change and invasive species can both have negative impacts on native species diversity. Additionally, climate change has the potential to favor invasive species over natives, dealing a double blow to native biodiversity. It is, therefore, vital to determine how changing climate conditions are directly linked to demographic rates and population growth of non-native species so we can quantitatively evaluate how invasive populations may be affected by changing conditions and, in turn, impact native species. Cordylophora caspia, a hydrozoan from the Ponto-Caspian region, has become established in the brackish water habitats of the San Francisco Estuary (SFE). We conducted laboratory experiments to study how temperature and salinity affect C. caspia population growth rates, in order to predict possible responses to climate change. C. Caspia population growth increased nonlinearly with temperature and leveled off at a maximum growth rate near the annual maximum temperature predicted under a conservative climate change scenario. Increasing salinity, however, did not influence growth rates. Our results indicate that C. caspia populations in the SFE will benefit from predicted regional warming trends and be little affected by changes in salinity. The population of C. caspia in the SFE has the potential to thrive under future climate conditions and may subsequently increase its negative impact on the food web.

Using Next‐Generation Sequencing to Assist a Conservation Hatchery: a Single‐Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

AbstractThe Delta Smelt Hypomesus transpacificus, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive populations overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) grea...

Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon

Abstract Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large‐scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single‐nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well‐chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site‐associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.

Genomic Analysis Reveals Genetic Distinctiveness of the Paiute Cutthroat Trout Oncorhynchus clarkii seleniris

AbstractThe Paiute Cutthroat Trout (PCT) Oncorhynchus clarkii seleniris is classified as a subspecies within the greater Cutthroat Trout O. clarkii ssp. complex and is federally listed as threatened under the Endangered Species Act. However, genetic studies to date have revealed very little genetic differentiation between the PCT and its closest relative, the Lahontan Cutthroat Trout (LCT) O. clarkii henshawi. These results casted doubt on whether the PCT is a genetically distinct subspecies or merely a phenotypic variant of the LCT. Here, we present a genomic analysis of Cutthroat Trout subspecies and populations to resolve the genetic and phylogenetic relationship between PCT and LCT. Our results demonstrate substantial genetic structure and differentiation between PCT and LCT populations. In contrast to current thinking, our phylogenetic reconstructions show the PCT to be a distinct evolutionary lineage that diverged from LCT before the LCT differentiated into its current populations (i.e., rather than...

Genetic characterization of California's Central Valley chinook salmon

This data set includes genotypes for 5000 chinook salmon individuals collected from throughout Californias Central Valley between 1998 and 2013. We genotyped these samples using a panel of 96 single nucleotide polymorphism (SNP) markers. This is the most comprehensive genetic characterization published to date, covering all of the California Central Valley Evolutionary Significant Units (ESUs) and including all major river drainages within each ESU (total of 17 rivers and 5 hatchery populations). These populations are the foci of considerable basic and applied scientific research given the ecological, economic, and cultural importance of salmonid species. Moreover, all Central Valley ESUs are listed as federally threatened, endangered, or species of concern. This data set improves our ability to study basic ecological questions about salmonid biology, including testing hypotheses about population structure, genetic diversity, introgression between ESUs, and levels of gene flow among populations. Addition...