Bernie May

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.

Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis)

Mammal species characterized by highly fluctuating populations often maintain genetic diversity in response to frequent demographic bottlenecks, suggesting the ameliorating influence of life history and behavioral factors. Immigration in particular is expected to promote genetic recovery and is hypothesized to be the most likely process maintaining genetic diversity in fluctuating mammal populations. Most demographic bottlenecks have been inferred retrospectively, and direct analysis of a natural population before, during, and after a bottleneck is rare. Using a continuous 10-year dataset detailing the complete demographic and genetic history of a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis), we analyzed the genetic consequences of a 4-year demographic bottleneck that reduced the population to seven adult squirrels, and we evaluated the potential “rescue effect” of immigration. Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase. In addition, we found no evidence for inbreeding depression during or after the bottleneck. By identifying immigrants and analyzing their demographic and genetic contributions, we found that immigration promoted demographic recovery and countered the genetic effects of the bottleneck, especially the loss of allelic richness. Within 3xa0years both population size and genetic variation had recovered to pre-bottleneck levels, supporting the role of immigration in maintaining genetic variation during bottleneck events in fluctuating populations. Our analyses revealed considerable variation among analytical techniques in their ability to detect genetic bottlenecks, suggesting that caution is warranted when evaluating bottleneck events based on one technique.

Evaluating the Performance of Captive Breeding Techniques for Conservation Hatcheries: A Case Study of the Delta Smelt Captive Breeding Program

The delta smelt, an endangered fish species endemic to the San Francisco Bay-Delta, California, United States, was recently brought into captivity for species preservation. This study retrospectively evaluates the implementation of a genetic management plan for the captive delta smelt population. The captive genetic management plan entails tagging fish, molecular data collection, pedigree reconstruction, relatedness estimation, and recommending fish crosses annually in an effort to minimize the average coancestry in the population and limit inbreeding. We employed 12 microsatellite DNA markers to examine temporal genetic diversity in consecutive, discrete generations to determine the effects of intensive genetic management on the population and to quantify the amount of wild genetic diversity present within each captive generation. Wild fish are incorporated into the captive population each generation to minimize genetic drift, and 91% of the original founders are still represented in the F(3) generation. The average mean kinship in the third generation in captivity was 0.0035. There was no evidence of significant genetic divergence of the captive population from the wild population. The results of this study yield management insights into the practical application of genetic management plans for captive populations and conservation hatcheries, in an attempt to preserve the genetic integrity of endangered species.

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.

Introgressive Hybridization of Redband Trout in the Upper McCloud River Watershed

Abstract Introgressive hybridization is an obstacle to the conservation of many species and subspecies. Diagnostic genetic markers or markers with high allele frequency differentials, such as single-nucleotide polymorphisms (SNPs), are becoming increasingly useful for detecting introgression between species or subspecies, such as subspecies of rainbow trout Oncorhynchus mykiss known as redband trout in the upper McCloud River watershed. Using a diagnostic mitochondrial SNP as well as nine nuclear SNPs, we quantified introgression levels between native redband trout and nonnative rainbow trout at 14 locations in the upper McCloud watershed and two locations in the lower McCloud region. Our analyses suggest that Sheepheaven, Edson, Moosehead, and Swamp creeks contain a large portion of the nonintrogressed redband trout individuals remaining in the upper McCloud watershed, implying a dramatic loss of populations free from introgressive hybridization. The results of this study have key management implications...

Detection of Threatened Delta Smelt in the Gut Contents of the Invasive Mississippi Silverside in the San Francisco Estuary Using TaqMan Assays

Abstract In the San Francisco Estuary, predation of the threatened delta smelt Hypomesus transpacificus by the invasive Mississippi silverside Menidia audens has been hypothesized but unconfirmed in the wild due to difficulties in reliably identifying egg or larval fish remains in gut contents. This study describes the use of TaqMan assays to examine the gut contents of wild Mississippi silversides for the presence of delta smelt DNA. The species-specific delta smelt assay was found to be highly sensitive and, in feeding trial experiments, capable of detecting delta smelt DNA in Mississippi silverside gut contents up to 36xa0h postingestion for some individuals. A substantial percentage (41%) of the 37 Mississippi silversides caught in the wild with midchannel trawling were positive for delta smelt DNA in their gut contents. Conversely, none of the 614 Mississippi silversides caught in the wild in nearshore beach seining contained delta smelt DNA in their gut contents. Received May 25, 2012; accepted July 2...

Meiotic instability of chicken ultra-long telomeres and mapping of a 2.8 megabase array to the W-sex chromosome

The objective of this research was to study the meiotic stability of a subset of chicken telomere arrays, which are the largest reported for any vertebrate species. Inheritance of these ultra-long telomere arrays (200xa0kb to 3xa0mb) was studied in a highly homozygous inbred line, UCD 003 (F ≥ 99.9). Analysis of array transmission in four families indicated unexpected heterogeneity and non-Mendelian segregation including high-frequency-generation of novel arrays. Additionally, the largest array detected (2.8xa0Mb) was female-specific and correlated to the most intense telomeric DNA signal on the W-sex chromosome by fluorescence in situ hybridization (FISH). These results are discussed in regard to the potential functions of the ultra-long telomere arrays in the chicken genome including generation of genetic variation through enhanced recombination, protection against erosion by providing a buffer for gene-dense regions, and sex-chromosome organization.

Conserving the endangered Mexican fishing bat (Myotis vivesi): genetic variation indicates extensive gene flow among islands in the Gulf of California

The endangered Mexican fishing bat, Myotis vivesi, appears to have suffered widespread extinction and population decline on islands throughout the Gulf of California, largely due to predation by introduced cats and rats. To restore populations of fishing bats and other native species, conservation efforts have focused on eradicating introduced vertebrates from several Gulf islands. These efforts assume that individuals from existing populations will recolonize islands and that continued dispersal will help sustain vulnerable populations thereafter. However, the extent of inter-island dispersal in fishing bats is unknown. In this study we analyzed patterns of genetic variation to gauge the extent of gene flow and, thus, potential dispersal among islands. DNA was sampled from 257 fishing bats on 11 Gulf islands (separated by ca. 6–685xa0km of open water), and individuals were genotyped at six microsatellite loci and haplotyped at a 282xa0bp fragment of the mtDNA control region. With microsatellites, we found weak population genetic structure and a pattern of isolation by distance, while with mtDNA we found strong structure but no isolation by distance. Our results indicate that island subpopulations separated by large expanses of open water are nonetheless capable of maintaining high genetic diversity and high rates of gene flow. Unfortunately, little is known about the spatial patterns of dispersal or mating system of fishing bats, and these behavioral factors, in particular female philopatry, might reduce the probability of the species recolonizing Gulf islands.

Introgression Between Lahontan and Endangered Owens Tui Uhubs, and Apparent Discovery of a New Tui Chub in the Owens Valley, California

Owens tui chubs (Siphateles bicolor snyderi [Miller]) have become extirpated throughout most of their range by introgression with introduced Lahontan tui chubs. The remaining non-introgressed Owens tui chub populations persist in a small number of fragmented habitats. These survivors are listed as “endangered” under both the state and federal endangered species acts. This study employs six microsatellite DNA loci to assess degrees of genetic difference within and among populations of Owens and Lahontan tui chubs and their putative hybrids. It reveals four distinct groups of tui chubs: Owens, Lahontan, hybrid Owens × Lahontan, and Cabin Bar. Patterns of microsatellite DNA variation confirm that tui chubs in the Owens River and its tributaries, and Mono Lake tributaries comprise a hybrid swarm. The overall degree of introgression between Lahontan and Owens tui chubs is approximately 40%, while the remaining 60% derives from Owens tui chub’s original genetic composition. Unexpectedly, Owens tui chubs are more genetically similar to Lahontan tui chubs than to Cabin Bar tui chubs, although they share the same river basin with the latter. Cabin Bar tui chubs possess a 3xa0bp deletion in the flanking region of microsatellite locus Gbi-G79. We give the Cabin Bar tui chub a common name “toikona tui chub” to distinguish it from the Owens tui chub, and recommend independent protection and recovery efforts. Management practices should prevent any future genetic mixing of non-introgressed Owens, toikona, or Lahontan tui chubs with each other, or with the hybrid swarm. Habitats of Owens and toikona tui chubs should remain isolated from the Owens River. Toikona tui chubs should be established in multiple sites.

Ten real‐time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta

The effect of predation on native fish by introduced species in the San Francisco Estuary–Delta (SFE) has not been thoroughly studied despite its potential to impact species abundances. Species‐specific quantitative PCR (qPCR) is an accurate method for identifying species from exogenous DNA samples. Quantitative PCR assays can be used for detecting prey in gut contents or faeces, discriminating between cryptic species, or detecting rare aquatic species. We designed ten TaqMan qPCR assays for fish species from the SFE watershed most likely to be affected by non‐native piscivores. The assays designed are highly specific, producing no signal from co‐occurring or related species, and sensitive, with a limit of detection between 3.2 and 0.013 pg/μL of target DNA. These assays will be used in conjunction with a high‐throughput qPCR platform to compare predation rates between native and non‐native piscivores and assess the impacts of predation in the system.