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The expression of anadromy in partially migratory salmonid populations is influenced by sex-specific interactions among an individual’s genotype, condition, and environment, but genotype–phenotype relationships prior to the expression of migratory type are poorly understood. We examined whether juvenile growth and condition differed with respect to sex and a migration-associated genomic region (Omy05) in a coastal California population of steelhead and rainbow trout (Oncorhynchus mykiss). Sex and Omy05 genotype had additive effects on annual growth from age 0+ to age 1+ (∼6–18 months old), with higher growth in males and individuals with copies of the rearranged–resident haplotype. Condition at age 1+ increased with the number of copies of the rearranged–resident haplotype, with similar support for additive or interactive effects with sex; additive effects suggested that genotype differences occurred in both sexes and also that condition was slightly higher in males, while interactive effects suggested that the genotype differences occurred only in males. Our results indicate that phenotypic differences related to sex and Omy05 genotype occur well in advance of anadromous migration or freshwater maturation in this southern O. mykiss population.

Unexpectedly simple Chinook salmon are known to return to spawn at two distinct times of the year: spring and fall. Individuals that return during these times have generally been referred to as parts of distinct groups, or ecotypes, with traits specific to their timing and presumed divergence being caused by the lack of interbreeding. By looking at genomes across fish from both runs, Thompson et al. found that a single genomic region of interest was nearly perfectly associated with run timing but not with other traits such as maturity and fat reserves (see the Perspective by McKinney). Further, they conclude that the region operates as a Mendelian trait, with assortment dictating run timing and associated phenotypes being caused by the migration environment rather than genetics. Science , this issue p. 609 ; see also p. 526

Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.

Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10–15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific “dangerous duplicates”, that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns.

The construction of dams and water diversions has severely limited access to spawning habitat for anadromous fishes. To mitigate for these impacts, hatchery programs rear and release millions of juvenile salmonids, including steelhead, the anadromous ecotype of the species Oncorhynchus mykiss. These programs sometimes use nonindigenous broodstock sources that may have negative effects on wild populations. In California, however, only one anadromous fish hatchery program currently uses nonnative broodstock: the steelhead program at Nimbus Fish Hatchery on the American River, a tributary of the Sacramento River in the California Central Valley. The goal of this study was to determine if potentially appropriate sources to replace the broodstock for the Nimbus Hatchery steelhead program exist in the Upper American River, above Nimbus and Folsom dams. We show that all Upper American River O. mykiss sampled share ancestry with other populations in the Central Valley steelhead distinct population segment, with limited introgression from out-of-basin sources in some areas. Furthermore, some Upper American River populations retain adaptive genomic variation associated with a migratory life history, supporting the hypothesis that these populations display adfluvial migratory behavior. Together, these results provide insights into the evolution of trout populations above barrier dams. We conclude that some Upper American River O. mykiss populations represent genetically appropriate sources from which fisheries managers could potentially develop a new broodstock for the Nimbus Hatchery steelhead program to reestablish a native anadromous population in the Lower American River and contribute to recovery of the threatened Central Valley steelhead distinct population segment.

The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California’s equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.

Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and nonparallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while 3 of the 4 populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these 2 inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.

Human-driven evolution can impact the ecological role and conservation value of impacted populations. Most evolutionary restoration approaches focus on manipulating gene flow, but an alternative approach is to manipulate the selection regime to restore historic or desired trait values. Here we examined the potential utility of this approach to restore anadromous migratory behavior in coastal California steelhead trout (Oncorhynchus mykiss) populations. We evaluated the effects of natural and anthropogenic environmental variables on the observed frequency of alleles at a genomic marker tightly associated with migratory behavior across 39 steelhead populations from across California, USA. We then modeled the potential for evolutionary restoration at sites that have been impacted by anthropogenic barriers. We found that complete barriers such as dams are associated with major reductions in the frequency of anadromy-associated alleles. The removal of dams is therefore expected to restore anadromy significantly. Interestingly, accumulations of large numbers of partial barriers (passable under at least some flow conditions) were also associated with significant reductions in migratory allele frequencies. Restoration involving the removal of partial barriers could be evaluated alongside dam removal and fishway construction as a cost-effective tool to restore anadromous fish migrations. Results encourage broader consideration of in situ evolution during the development of habitat restoration projects. This article is protected by copyright. All rights reserved.

As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.

Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwater resident form of the species O. mykiss, is one factor threatening the long-term persistence of native steelhead and other trout populations. To identify where native fish of coastal steelhead lineage remained, we performed a population genetic analysis of microsatellite and SNP genotypes from O. mykiss populations at the extreme southern end of their range in Southern California, USA and Baja California, Mexico. In the northern part of this region, nearly all populations appeared to be primarily descendants of native coastal steelhead. However, in the southern, more urbanized part of this region, the majority of the sampled populations were derived primarily from hatchery trout, indicating either complete replacement of native fish or a strong signal of introgression overlaying native ancestry. Nevertheless, these genetically introgressed populations represent potentially critical genetic resources for the continued persistence of viable networks of O. mykiss populations, given the limited native ancestry uncovered in this region and the importance of genetic variation in adaptation. This study elucidates the geographic distribution of native trout populations in this region, and serves as a baseline for evaluating the impacts of hatchery trout on native O. mykiss populations and the success of steelhead conservation and recovery efforts.

Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

Parallel adaptive divergence of migratory and reproductive behavior can occur in multiple populations when similar selection is acting on these traits. Timing of migration, sexual maturity, and reproduction can have major impacts on the dynamics and viability of a population. Life-history variation in steelhead, Oncorhynchus mykiss, including variation in anadromous run timing, reproductive maturity, and spawn timing, represents an important aspect of their biology and adaptation to local habitats. Here we present a genetic analysis of naturally spawning steelhead to evaluate the genetic relationships and ancestry of summer- and winter-run reproductive ecotypes from multiple river basins in Oregon and Northern California. We infer the phylogeographic relationships among populations of both summer- and winter-run steelhead ecotypes using 12 microsatellite loci and 90 single nucleotide polymorphisms. Phylogenetic trees and analysis of molecular genetic variance revealed that pairs of phenotypically and genetically distinct reproductive ecotypes within rivers were each other’s closest relatives. Isolation by distance was also observed, confirming that genetic relatedness was strongly associated with geographic distance, and indicating limited gene flow among river basins. These patterns support the hypothesis that the summer-run steelhead ecotype has repeatedly evolved through parallel evolution in multiple river basins. Our results, together with further investigations of the underlying molecular basis for the divergence of winter- and summer-run steelhead life-history traits, inform management efforts for these ecotypes and improve our understanding of the role of adaptive genetic variation in conservation.

Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss), SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD) libraries, reduced representation libraries (RRL) and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway) that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU) and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1) which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs) and multi-sequence variants (MSVs). Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25). The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and heterozygosity within each population. We also provide functional annotation based on the genome position of each SNP and evaluate the use of clonal lines for filtering of PSVs and MSVs. These SNPs form a new database, which provides an important resource for a new high density SNP array design and for other SNP genotyping platforms used for genetic and genomics studies of this iconic salmonid fish species.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

From 2002 to 2010, the jumbo squid (Dosidicus gigas) has been regularly encountered in large numbers throughout the California Current System (CCS). This species, usually found in subtropical waters, could affect coastal pelagic ecosystems and fisheries as both predator and prey. Neither the abundance of jumbo squid nor the optimal ocean conditions in which they flourish are well known. To understand better the potential impacts of this species on both commercial fisheries and on food-web structure we collected nearly 900 specimens from waters of the CCS, covering over 201 of latitude, over ar ange of depths and seasons. We used demographic information (size, sex, and maturity state) and analyzed stomach contents using morphological and molecular methods to best understand the foraging ecology of this species in different habitats of the CCS. Squid were found to consume a broad array of prey. Prey in offshore waters generally reflected the forage base reported in previous studies (mainly mesopelagic fishes and squids), whereas in more coastal waters (shelf, shelf break and slope habitats) squid foraged on a much broader mix that included substantial numbers of coastal pelagic fishes (Pacific herring and northern anchovy, as well as osmerids and salmonids in northern waters) and groundfish (Pacific hake, several species of rockfish and flatfish). We propose a seasonal movement pattern, based on size and maturity distributions along with qualitative patterns of presence or absence, and discuss the relevance of both the movement and distribution of jumbo squid over space and time. We find that jumbo squid are a generalist predator, which feeds primarily on small, pelagic or mesopelagic micronekton but also on larger fishes when they are available. We also conclude that interactions with and potential impacts on ecosystems likely vary over space and time, in response to both seasonal movement patterns and highly variable year-to-year abundance of the squid themselves. Published by Elsevier Ltd.

International audience; The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life-history traits in O. mykiss shows substantial evolutionary differences between fish above and below dams. These findings support continued habitat restoration and protection of San Francisco Bay Area O. mykiss populations and demonstrate that ecological conditions in novel habitats above barriers to anadromy influence life-history evolution. We highlight the importance of considering the adaptive landscape in conservation and restoration programs for species living in highly modified habitats, particularly with respect to key life-history traits.

We investigated the interaction among genetically identified origin, behavioral tendency to emigrate, and Na+, K+-ATPase enzyme activity in recently diverged subpopulations of resident (above-barrier) rainbow trout Oncorhynchus mykiss and steelhead (anadromous rainbow trout) in Scott Creek, California. Genetic assignment tests found that the frequency of resident and anadromous origin fish varied by sampling location within the watershed. Individuals immediately below barriers assigned to both above-barrier (37%) and anadromous (63%) subpopulations, and distinct differences in size and age were observed. However, the majority of downstream migration behavior occurred in fish of anadromous ancestry, which represented 97% of the fish sampled as outmigrating smolts. Nonmigratory fish of both life history types and origins typically had low Na+, K+-ATPase activity levels throughout most of the year, but significantly elevated levels were observed in individuals from both groups during the spring smol...

– Differential rates of anadromy between males and females are common in partially migratory salmonid populations, but this pattern is not fully clear for Oncorhynchus mykiss (rainbow trout/steelhead) from the limited but mixed data available. In particular, there are very few data on sex ratios of juvenile and nonanadromous (resident) fish to help assess sex composition of various life stages and life-history types. We used a recently developed Y-chromosome genetic marker to assess sex ratio of stream-dwelling (i.e., juvenile and nonanadromous) O. mykiss in a small coastal basin in central California, USA. We analysed 384 samples collected from three contiguous study reaches over 3 years. Sex ratio was 1:1 among juvenile-sized O. mykiss (

Freshwater-resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River–Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompasses the upper Klamath River and Upper Klamath Lake) and associated tributaries, the construction of Copco Dam in 1918 and Iron Gate Dam in 1962 stopped all upstream migration of fish past these barriers. In the Upper Klamath Lake basin, native Upper Klamath Lake redband trout O. mykiss newberrii are found along with coastal rainbow trout that were trapped above the dams or stocked from hatchery sources. However, relatively little is known about the genetic relationships among the O. mykiss populations within the Upper Klamath Basin. A population genetic analysis based on data from 17 variable microsatellite loci was conducted for samples collected in th...

Novel genetic resources now make it possible to directly assess the effects of natural selection on specific regions of the salmonid genome. Natural selection on specific genetic loci will also affect the variation in linked flanking regions through “hitchhiking” effects, causing greater differentiation between populations than would be expected from purely neutral processes. Here we identify candidate genomic regions for the effects of differential natural selection in two closely related populations of steelhead–rainbow trout Oncorhynchus mykiss separated for the last century following anthropogenic introduction above a barrier waterfall in a coastal California stream. A set of 110 expressed sequence tag (EST)-linked and 188 anonymous microsatellite loci, most of which are mapped, were chosen to provide distributed coverage of all linkage groups in the O. mykiss genome. A genome screen was then performed to identify genomic regions under divergent selection. Multiple complementary statistical m...

*NOAA Southwest Fisheries Science Center, National MarineFisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060,USA, †Department of Ecology and Evolutionary Biology,University of California, Santa Cruz, CA, USA, ‡Department ofApplied Math and Statistics, University of California, SantaCruz, CA, USAReceived 11 March 2009; revision received 30 April 2009;accepted 5 May 2009The effective size, N

Molecular genetic analysis has long been used to identify species or populations that otherwise may be difficult to distinguish. More than 100 species of rockfish (genus Sebastes) occur worldwide, and more than 50 species may be found in relatively small regions, such as the Monterey Bay or Channel Islands in central and southern California. Many species are morphologically similar, particularly during the early larval stages, and identification to the species level is time-consuming and problematic for some groups. We describe a simple genetic method for the rapid identification of rockfish species by means of multilocus nuclear genotypes from a panel of six microsatellite loci. Application to a set of known rockfish tissue samples, including fish collected in different parts of their geographic ranges and species not represented in the reference data set, resulted in high assignment accuracy for the represented species and exclusion of the nonrepresented species. Members of the subgenus Pteropo...

Author(s): Pearse, Devon E.; Garza, John Carlos | Abstract: Steelhead/rainbow trout (Oncorhynchus mykiss) are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California’s Central Valley and enter the ocean through San Francisco Bay and the Golden Gate. This river system is heavily affected by water development, agriculture, and invasive species, and salmon and trout hatchery propagation has been occurring for over 100 years. We collected genotype data for 18 highly variable microsatellite loci and 95 single nucleotide polymorphisms (SNPs) from more than 1,900 fish from Central Valley drainages to analyze genetic diversity, population structure, differentiation between populations above and below dams, and the relationship of Central Valley O. mykiss populations to coastal California steelhead. In addition, we evaluate introgression by both hatchery rainbow trout strains, which have primarily native Central Valley ancestry, and imported coastal steelhead stocks. In contrast to patterns typical of coastal steelhead, Central Valley O. mykiss above and below dams within the same tributary were not found to be each others’ closest relatives, and we found no relationship between genetic and geographic distance among below-barrier populations. While introgression by hatchery rainbow trout strains does not appear to be widespread among above-barrier populations, steelhead in the American River and some neighboring tributaries have been introgressed by coastal steelhead. Together, these results demonstrate that the ancestral population genetic structure that existed among Central Valley tributaries has been significantly altered in contemporary populations. Future conservation, restoration, and mitigation efforts should take this into account when working to meet recovery planning goals.

International audience; Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g., size-at-age) or the state (e.g., size threshold) at which an individual switches between alternative tactics. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier waterfall in 1910, we evaluate how the conditional strategy to migrate evolves in response to selection against migration. We created 9 families and 917 offspring from 14 parents collected from the above- and below-barrier populations. After 1 year of common garden-rearing above-barrier offspring were 11% smaller and 32% lighter than below-barrier offspring. Using a novel analytical approach, we estimate that the mean size at which above-barrier fish switch between the resident and migrant tactic is 43% larger than below-barrier fish. As a result, above-barrier fish were 26% less likely to express the migratory tactic. Our results demonstrate how rapid and opposing changes in size-at-age and threshold size contribute to the contemporary evolution of a conditional strategy and indicate that migratory barriers may elicit rapid evolution toward the resident life history on timescales relevant for conservation and management of conditionally migratory species.

We used genetic data from 7 microsatellite loci to determine the frequency of multiple paternity in clutches of giant Amazon river turtles, Podocnemis expansa, from the Orinoco River in Venezuela. Among hatchlings sampled from 32 clutches, paternity analysis found that a minimum of 10.3% could conclusively be shown to have been sired by more than one male. We contrast this result with those from another population of this species, as well as other species of turtles, and discuss the importance of documenting patterns of paternity in different populations of a given species and considering the effects of ecological differences among populations on female mating behavior.

An analysis of population structure and genetic diversity was conducted on samples of Oncorhynchus mykiss (steelhead/rainbow trout) from 33 sites in the Klamath–Trinity River basin. Genotype data from 16 microsatellite loci in almost 1,700 fish revealed genetic differentiation between most sampled locations. Two pairs of samples from the same sites in different years were not significantly different, indicating stability of population structure, at least on a short time scale. Most sampling sites were genetically distinct from all other sampling sites, and there was an evidence of geographic structure within the Klamath–Trinity River basin, although populations from tributaries within the watershed (e.g. Salmon River, Scott River, Clear Creek) did not always constitute distinct genetic lineages. Population structure was evident using phylogeographic trees, isolation by distance analyses and individual assignment tests, which all found a relationship between geographic and genetic distance. Populations in the lower Klamath region, below the confluence with the Trinity River, consistently clustered together in phylogeographic analyses and had patterns of genetic diversity that suggest reduced gene flow between these sites and sites above the confluence. Finally, in an analysis that included data from other coastal California rivers, the populations closest to the mouth of the Klamath River appeared intermediate between populations from adjacent watersheds and the lineage formed by the other populations in the Klamath–Trinity basin.

Harbour seals sometimes breed along inland travel corridors where females become clustered in space and time and males establish underwater acoustic display territories similar to terrestrial arenas known as resource-based leks. Under these conditions, we predicted that higher levels of polygyny would be observed than has been previously reported for this species mating in open coast environments without travel corridors. Reproductive success (RS) of 70 males was measured using 20 microsatellite DNA loci and likelihood-based paternity analysis of 136 offspring collected over 3 years. Most males were assigned either zero or one paternity with 80% confidence. The greatest number of pups assigned to one male in a season was two. Variance in RS was higher for males than females (which are biologically limited to one offspring per year) indicating low to mild polygyny. In addition, distributions of relatedness values among pups within year classes did not differ significantly from a simulated distribution with R = 0, indicating that half-siblings were uncommon. Overall, polygyny levels were low relative to terrestrial pinniped mating systems and similar to observations from a harbour seal population along an open coast. Due to large confidence intervals associated with our results, we cannot rule out the hypothesis that a travel corridor might increase the degree of polygyny skew relative to that observed in open coast environments. Habitat appeared to influence male strategies as the most successful males in open coast environments patrolled offshore, while the most successful male in this study defended a territory along the travel corridor.

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.

Mating systems within the genus Peromyscus have traditionally been inferred from field observations of spatial relationships of males and females and from laboratory behavioral studies. The majority of species within Peromyscus are assumed to be promiscuous, but rarely have these conclusions been verified with molecular data. Genotypes constructed from 4 microsatellite loci were used to determine paternity in 10 litters of the canyon mouse (Peromyscus crinitus). We applied 3 criteria for paternity assignment: direct observation of paternal alleles, correlation of sampled male and offspring genotypes (mothers known) including spatial relationship data, and application of a likelihood estimator. Multiple paternity occurred in a minimum of 20% of the litters, yet we found no evidence that would indicate that any putative father sired 2 or more litters. Dispersal of males between the time of copulation and parturition was minimal (7.5‐70 m) in most cases, but 1 male was captured in a rock outcropping separate from that of his sired litter (174 m). Our use of 3 different criteria allowed a greater number of male paternity assignments to be inferred than would have been possible when using software program CERVUS alone, and increased confidence in these results.

Both the ability to generate DNA data and the variety of analytical methods for conservation genetics are expanding at an ever-increasing pace. Analytical approaches are now possible that were unthinkable even five years ago due to limitations in computational power or the availability of DNA data, and this has vastly expanded the accuracy and types of information that may be gained from population genetic data. Here we provide a guide to recently developed methods for population genetic analysis, including identification of population structure, quantification of gene flow, and inference of demographic history. We cover both allele-frequency and sequence-based approaches, with a special focus on methods relevant to conservation genetic applications. Although classical population genetic approaches such as Fst (and its derivatives) have carried the field thus far, newer, more powerful, methods can infer much more from the data, rely on fewer assumptions, and are appropriate for conservation genetic management when precise estimates are needed.

When females receive no direct benefits from multiple matings, concurrent multiple paternity is often explained by indirect genetic benefits to offspring. To examine such possibilities, we analyzed genetic paternity for 1,272 hatchlings, representing 227 clutches, from a nesting population of painted turtles (Chrysemys picta) on the Mississippi River. Goals were to quantify the incidence and distribution of concurrent multiple paternity across clutches, examine temporal patterns of sperm storage by females, and deduce the extent to which indirect benefits result from polyandrous female behaviors. Blood samples from adult males also allowed us to genetically identify the sires of surveyed clutches and to assess phenotypic variation associated with male fitness. From the genetic data, female and male reproductive success were deduced and then interpreted together with field data to evaluate possible effects of female mating behaviors and sire identity on offspring fitness. We document that more than 30% of the clutches were likely fathered by multiple males, and that presence of multiple paternity was positively correlated with clutch size. Furthermore, the data indicate that the second male to mate typically had high paternity precedence over the first.

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss . Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

Molecular polymorphisms have been used in a variety of ways to estimate both effective and local census population sizes in nature. A related approach for estimating the current size of a breeding population, explored here for the first time, is the use of genetic 'marks' reconstructed for otherwise unknown parents in paternity or maternity analyses of progeny arrays. This method provides interesting similarities and contrasts to traditional mark-recapture methods based on physical tags. To illustrate, this genetic method is applied to a population of painted turtles on the Mississippi River to estimate the number of successfully breeding males. Non-genetic mark-recapture approaches were also applied to animals trapped at this location. Results demonstrate that such genetic data on parentage can be helpful not only in estimating contemporary population sizes, but also in providing additional information, not present in customary mark-recapture data, about possible extended movements of breeding individuals and the size of the pool of mates which they encounter.

This study examines the effects of general-protein-9 ( Gp-9 ) genotype on the body mass of polygyne (multiple-queens per nest) Solenopsis invicta Buren workers and males. We found that Gp-9 genotype was significantly associated with variation in worker mass in field but not laboratory colonies. Moreover, triploid workers with 2 distinguishable genotypes ( Gp-9BBb and Gp-9Bbb ) weighed significantly more than diploid workers with the heterozygous genotype ( Gp-9Bb ). Our results, combined with those obtained from previous studies, indicate that Gp-9 genotype, ploidy, social form, and colony queen number affect mass of S. invicta workers. We also discovered that Gp-9 genotype significantly influenced the mass of haploid males reared in both field and laboratory environments. As a group, polygyne males were significantly lighter than monogyne males, even when Gp-9 genotype was taken into account, indicating that social environment interacts with Gp-9 genotype to influence male mass. Given that diploid males previously have been shown to be lighter than haploid males, 3 factors ( Gp-9 genotype, social form, and ploidy) are now known to affect the mass of male fire ants.

Sixty-six haplotypes at a locus containing a simple dinucleotide (CA) n microsatellite repeat were isolated by PCR–single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus . These haplotypes were sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) were identified in a region 570 bp long that included the microsatellite motif. In the repeat region itself, CA-number varied in integer values from 5 to 11 across alleles, except that a (CA) 8 class was not observed. Differences among alleles were due also to polymorphisms at 22 sites in regions immediately flanking the microsatellite repeats. Nucleotide substitutions in these regions were used to estimate phylogenetic relationships among alleles, and the gene phylogeny was used to trace the evolution of length variation and CA repeat numbers. A low correlation between size variation and genealogical relationships among alleles suggests that absolute fragment size (as normally scored in microsatellite assays) is an unreliable indicator of historical affinities among alleles. This finding on the molecular fine structure of microsatellite variation suggests the need for caution in the use of repeat counts at microsatellite loci as secure indicators of allelic relationships.

Adaptation to novel habitats and phenotypic plasticity can be counteracting forces in evolution, but both are key characteristics of the life history of steelhead/rainbow trout (Oncorhynchus mykiss). Anadromous steelhead reproduce in freshwater river systems and small coastal streams but grow and mature in the ocean. Resident rainbow trout, either sympatric with steelhead or isolated above barrier dams or waterfalls, represent an alternative life-history form that lives entirely in freshwater. We analyzed population genetic data from 1486 anadromous and resident O. mykiss from a small stream in coastal California with multiple barrier waterfalls. Based on data from 18 highly variable microsatellite loci (He = 0.68), we conclude that the resident population above one barrier, Big Creek Falls, is the result of a recent anthropogenic introduction from the anadromous population of O. mykiss below the falls. Furthermore, fish from this above-barrier population occasionally descend over the falls and have established a genetically differentiated below-barrier subpopulation at the base of the falls, which appears to remain reproductively isolated from their now-sympatric anadromous ancestors. These results support a hypothesis of rapid evolution of a purely resident life history in the above-barrier population in response to strong selection against downstream movement.

Most studies of genetic parentage in natural populations have been limited to a single breeding season or reproductive episode and, thus, provide only a snapshot of individuals' mating behaviours. Female turtles can store viable sperm in their reproductive tracts for as long as several years, but the extent to which this capacity is utilized in nature has remained unknown. Here, we employ microsatellite markers to assess genetic paternity in successive clutches of individually marked, free-ranging female painted turtles (Chrysemys picta) over a four year period. The genetic data from 113 clutches from this natural population demonstrate that most females (80.5%) remated each year and that each female generally used a single male's sperm to fertilize all clutches laid within a year. However, sperm usage among females varied considerably, and some females apparently used sperm that had been stored for up to three years to fertilize some or all eggs laid in consecutive nesting seasons. Thus, remating by females is not necessary for continued offspring production from a given sire. Furthermore, 13.2% of all clutches examined showed evidence of multiple paternity, and the genetic paternity patterns across years suggest a 'last in, first out' operation of the females' sperm storage tubules.

As evidenced by the articles in this volume, a recent increase in interest in the mating systems of poikilothermic vertebrates has focused primarily on fishes, a few amphibians, and squamate reptiles. Turtles by contrast have received relatively little attention, yet they display a wide variety of mating behaviors and life-history characteristics that make them excellent candidates for addressing several aspects of genetic parentage that should contribute to a broader understanding of animal reproductive strategies. Here we focus on genetic studies of the mating systems and reproductive patterns of turtles, specifically with respect to multiple paternity and long-term sperm storage. These phenomena highlight the importance of a temporally extended perspective on patterns of individual reproductive success.

The phylogenetic relationships among populations of the fossorial California legless lizard, Anniella pulchra, were examined by sequencing a 990-bp region of the mitochondrial cytochrome b gene. The mitochondrial DNA gene tree was then compared with the geographic distributions of two currently recognized subspecies: A. p. nigra, a melanic form restricted to two disjunct coastal populations, and A. p. pulchra, a more widely distributed, silvery form. We tested the null hypothesis that all A. p. nigra form a clade that is monophyletic with respect to A. p. pulchra. Our results strongly reject the monophyletic origin of the melanic forms and suggest that the two populations of the nominal subspecies A. p. nigra may have arisen independently from different ancestral populations in a parallel evolutionary response to selection in cool, coastal habitats.