Incomplete congruence between morphobiological characters and sex-specific molecular markers in pacific salmons: 2. Population and temporal variability of the phenomenon

The congruence between secondary sexual characters and molecular markers, linked to the Ychromosome was examined in Asian populations of five Pacific salmon species of the genus Oncorhynchus. Our results support the existence of discrepancy between secondary sexual characters and sex-linked molecular markers in all species examined, which suggests the existence of similar or identical mechanism responsible for this phenomenon in Pacific salmons. Clinal latitudinal directional variation of the character confirmed the possibility that this phenomenon could be adaptively important, including its importance for regulation of the population number. In addition to natural factors affecting the degree of discrepancy between morphobiological characters and molecular markers in the Pacific salmon populations, anthropogenic factors, in particular intense fishery of certain population or population group, is also important.     

Incomplete congruence between morphobiological characters and sex-specific molecular markers in Pacific salmons: 1. Analysis of discrepancy in five species of the genus <Emphasis Type="Italic">Oncorhynchus</Emphasis>

The congruence between molecular markers, identifying the presence of the Y chromosome, and secondary sexual characters was examined in Asian populations of five Pacific salmon species: pink salmon (Oncorhynchus gorbuscha), chum salmon (O. keta), sockeye salmon (O. nerka), chinook salmon (O. tschawytscha), and sima (O. masou). It was demonstrated that in all species examined, the presence or absence of sex-specific molecular markers was to a considerable degree congruent with secondary sexual characters, but in some cases, an incongruence was found. These findings suggested that the mechanism underlying this phenomenon was similar or identical in all species examined. Possible genetic and physiological explanations of this phenomenon are discussed.     

Sex ratio control in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations: the possible causes and mechanisms of changes in the sex ratio

Long-term changes in the sex ratio have been studied in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations of Kamchatka and Sakhalin. It has been demonstrated that these changes are an adaptation to population dynamics: an increase in the population size is accompanied by a shift towards a higher proportion of males; a decrease in population size, by a shift towards a higher proportion of females. The correspondence between morphological and molecular characters in populations of the two species has been analyzed in order to determine the mechanism of sex ratio control. In some pink salmon and chum salmon populations, there is a discrepancy between sex identifications based on morphological characters and molecular markers. This discrepancy is assumed to be accounted for by sex inversion mechanisms, which may be population- or region-specific. In two cases, it has been found that the sex ratio discrepancy in populations is related to the numbers of fish in subsequent generations. These findings suggest that sex inversion may be related to population size control.     

Sex ratio control in pink salmon (<Emphasis Type="Italic">Oncorhynchus gorbuscha</Emphasis> and chum salmon (<Emphasis Type="Italic">O. keta</Emphasis>) populations: The possible causes and mechanisms of changes in the sex ratio

Long-term changes in the sex ratio have been studied in pink salmon (Oncorhynchus gorbuscha and chum salmon (O. keta) populations of Kamchatka and Sakhalin. It has been demonstrated that these changes are an adaptation to population dynamics: an increase in the population size is accompanied by a shift towards a higher proportion of males; a decrease in population size, by a shift towards a higher proportion of females. The correspondence between morphological and molecular characters in populations of the two species has been analyzed in order to determine the mechanism of sex ratio control. In some pink salmon and chum salmon populations, there is a discrepancy between sex identifications based on morphological characters and molecular markers. This discrepancy is assumed to be accounted for by sex inversion mechanisms, which may be population-or region-specific. In two cases, it has been found that the sex ratio discrepancy in populations is related to the numbers of fish in subsequent generations. These findings suggest that sex inversion may be related to population size control.     

Molecular population divergence and sexual selection on morphology in the banded demoiselle (Calopteryx splendens)

The importance of sexual selection in population divergence is of much interest, mainly because it is thought to cause reproductive isolation and hence could lead to speciation. Sexually selected traits have been hypothesized to diverge faster between populations than other traits, presumably because of differences in the strength, mechanism or dynamics of selection. We investigated this by quantifying population divergence in eight morphological characters in 12 south Swedish populations of a sexually dimorphic damselfly, the banded demoiselle (Calopteryx splendens). The morphological characters included a secondary sexual character, the male melanized wing spot, which has an important function in both inter- and intrasexual selection. In addition, we investigated molecular population divergence, revealed by amplified fragment length polymorphism (AFLP) analysis. Molecular population divergence was highly significant among these Northern European populations (overall F(st)=0.054; pairwise population F(st)'s ranged from approximately 0 to 0.13). We found evidence for isolation-by-distance (r=0.70) for the molecular markers and a significant correlation between molecular and phenotypic population divergence (r=0.39). One interpretation is that population divergence for the AFLP loci are affected by genetic drift, but is also indirectly influenced by selection, due to linkage with loci for the phenotypic traits. Field estimates of sexual and natural selection from two of the populations revealed fairly strong sexual selection on wing spot length, indicating that this trait has the potential to rapidly diverge, provided that variation is heritable and the observed selection is chronic.     

Use of population viability analysis models for Atlantic and Pacific salmon recovery planning

Uncertainty and risk abound in making natural resource management decisions. Population viability analysis (PVA) includes a variety of qualitative or quantitative analyses to predict the future status of a population or collection of populations and to predict the risk of extinction (or quasi-extinction) over time given some assumptions of the factors driving population dynamics. In this paper, we review the various PVA models applied to Atlantic and Pacific salmon for determination of listing under the Endangered Species Act and in planning recovery actions. We also review the numerous cautions involved in developing PVA models and in interpreting their results. There have been a larger number of PVA models applied to Pacific salmon compared to Atlantic salmon due to the greater geographic range and number of species of Pacific salmon. Models for both Atlantic and Pacific salmon have ranged from simple models that view populations as simply a number of organisms to complex age- or stage-structured models depending on the purpose of the model and available data for model parameterization. The real value of PVA models to salmon conservation is not in making absolute predictions of the risk of extinction, but rather in evaluating relative effects of management alternatives on extinction risk and informing decision making within an adaptive management framework. As computing power, quantitative techniques, and knowledge of mechanistic linkages between terrestrial, freshwater, and marine environments advance, PVA models will become an even more powerful tool in conservation planning for salmon species.     

The extent of variation in male song, wing and genital characters among allopatric Drosophila montana populations

Drosophila montana, a species of the Drosophila virilis group, has distributed around the northern hemisphere. Phylogeographic analyses of two North American and one Eurasian population of this species offer a good background for the studies on the extent of variation in phenotypic traits between populations as well as for tracing the selection pressures likely to play a role in character divergence. In the present paper, we studied variation in the male courtship song, wing and genital characters among flies from Colorado (USA), Vancouver (Canada) and Oulanka (Finland) populations. The phenotypic divergence among populations did not coincide with the extent of their genetic divergence, suggesting that the characters are not evolving neutrally. Divergence in phenotypic traits was especially high between the Colorado and Vancouver populations, which are closer to each other in terms of their mtDNA genotypes than they are to the Oulanka population. The males of the Colorado population showed high divergence especially in song traits and the males of the Vancouver population in wing characters. Among the male song traits, two characters known to be under sexual selection and a trait important in species recognition differed clearly between populations, implying a history of directional and/or diversifying rather than balancing selection. The population divergence in wing characters is likely to have been enhanced by natural selection associated with environmental factors, whereas the male genitalia traits may have been influenced by sexual selection and/or sexual conflict.     

Population genetic structure of the lettuce root aphid,Pemphigus bursarius (L.), in relation to geographic distance,gene flow and host plant usage

Microsatellite markers were used to examine the population structure of Pemphigus bursarius, a cyclically parthenogenetic aphid. Substantial allele frequency differences were observed between populations on the primary host plant (collected shortly after sexual reproduction) separated by distances as low as 14 km. This suggested that migratory movements occur over relatively short distances in this species. However, the degree of allele frequency divergence between populations was not correlated with their geographical separation, indicating that isolation by distance was not the sole cause of spatial genetic structuring. Significant excesses of homozygotes were observed in several populations. Substantial allele frequency differences were also found between aphids on the primary host and those sampled from a secondary host plant after several parthenogenetic generations at the same location in two successive years. This could have been due to the existence of obligately parthenogenetic lineages living on the secondary host or genetically divergent populations confined to different secondary host plant species but sharing a common primary host.     

THE QUANTITATIVE AND MOLECULAR GENETIC ARCHITECTURE OF A SUBDIVIDED SPECIES

In an effort to elucidate the evolutionary mechanisms that determine the genetic architecture of a species, we have analyzed 17 populations of the microcrustacean Daphnia pulex for levels of genetic variation at the level of life-history characters and molecular markers in the nuclear and mitochondrial genomes. This species is highly subdivided, with approximately 30% of the variation for nuclear molecular markers and 50% of the variation for mitochondrial markers being distributed among populations. The average level of genetic subdivision for quantitative traits is essentially the same as that for nuclear markers, which superficially suggests that the life-history characters are diverging at the neutral rate. However, the existence of a strong correlation between the levels of population subdivision and broadsense heritabilities of individual traits argues against this interpretation, suggesting instead that the among-population divergence of some quantitative traits (most notably body size) is being driven by local adaptation to different environments. The fact that the mean phenotypes of the individual populations are also strongly correlated with local levels of homozygosity indicates that variation in local inbreeding plays a role in population differentiation. Rather than being a passive consequence of local founder effects, levels of homozygosity may be selected for directly for their effects on the phenotype (adaptive inbreeding depression). There is no relationship between the levels of variation within populations for molecular markers and quantitative characters, and this is explained by the fact that the average standing genetic variation for life-history characters in this species is equivalent to only 33 generations of variation generated by mutation.     

Temporal patterns in adult salmon migration timing across southeast Alaska

Pacific salmon migration timing can drive population productivity, ecosystem dynamics, and human harvest. Nevertheless, little is known about long‐term variation in salmon migration timing for multiple species across broad regions. We used long‐term data for five Pacific salmon species throughout rapidly warming southeast Alaska to describe long‐term changes in salmon migration timing, interannual phenological synchrony, relationships between climatic variation and migratory timing, and to test whether long‐term changes in migration timing are related to glaciation in headwater streams. Temporal changes in the median date of salmon migration timing varied widely across species. Most sockeye populations are migrating later over time (11 of 14), but pink, chum, and especially coho populations are migrating earlier than they did historically (16 of 19 combined). Temporal trends in duration and interannual variation in migration timing were highly variable across species and populations. The greatest temporal shifts in the median date of migration timing were correlated with decreases in the duration of migration timing, suggestive of a loss of phenotypic variation due to natural selection. Pairwise interannual correlations in migration timing varied widely but were generally positive, providing evidence for weak region‐wide phenological synchrony. This synchrony is likely a function of climatic variation, as interannual variation in migration timing was related to climatic phenomenon operating at large‐ (Pacific decadal oscillation), moderate‐ (sea surface temperature), and local‐scales (precipitation). Surprisingly, the presence or the absence of glaciers within a watershed was unrelated to long‐term shifts in phenology. Overall, there was extensive heterogeneity in long‐term patterns of migration timing throughout this climatically and geographically complex region, highlighting that future climatic change will likely have widely divergent impacts on salmon migration timing. Although salmon phenological diversity will complicate future predictions of migration timing, this variation likely acts as a major contributor to population and ecosystem resiliency in southeast Alaska.     

Identification of multiple genetically distinct populations of Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in a small coastal watershed

Management and restoration planning for Pacific salmon is often characterized by efforts at broad multi-basin scales. However, finer-scale genetic and phenotypic variability may be present within individual basins and can be overlooked in such efforts, even though it may be a critical component for long-term viability. Here, we investigate Chinook salmon (Oncorhynchus tshawytscha) within the Siletz River, a small coastal watershed in Oregon, USA. Adult Chinook salmon were genotyped using neutral microsatellite markers, single nucleotide polymorphisms and “adaptive” loci, associated with temporal variation in migratory behavior in many salmon populations, to investigate genetic diversity based upon both spatial and temporal variation in migratory and reproductive behavior. Results from all three marker types identified two genetically distinct populations in the basin, corresponding to early returning fish that spawn above a waterfall, a spring-run population, and later returning fish spawning below the waterfall, a fall-run population. This finding is an important consideration for management of the species, as spring-run populations generally only have been recognized in large watersheds, and highlights the need to evaluate population structure of salmon within smaller watersheds, and thereby increase the probability of successful conservation of salmon species.     

Discovery and characterization of single nucleotide polymorphisms in coho salmon,Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population‐ and pedigree‐based analyses across the southern part of the species native range.     

Host-associated populations in the lettuce root aphid, Pemphigus bursarius (L.)

Pemphigus bursarius is a host-alternating aphid in which annual rounds of sexual reproduction on its primary host, Populus nigra, are interspersed with parthenogenesis on a range of secondary hosts. Evidence was sought for the existence of genetically distinct populations, associated with different secondary hosts, in P. bursarius. Microsatellite markers revealed that genetically distinct populations were present on three different secondary host species. Microsatellites were also used, in conjunction with mitochondrial DNA sequence variation, to investigate the relationships between aphids on Populus, following sexual reproduction, and those on the secondary hosts. Evidence was found for a distinct, cyclically parthenogenetic population that exploited Lactuca sativa as its secondary host. In contrast, populations associated with Matricaria inodora appeared to be largely composed of obligate parthenogens or may even have been another species of Pemphigus. Populations on Lapsana communis appeared to be a mixture of cyclical and obligate parthenogens and were more genetically heterogeneous than those on other secondary hosts, possibly due to founder effects. Experiments to measure the performance of P. bursarius clones on different secondary hosts were inconclusive, failing to demonstrate either the presence or absence of adaptations to secondary hosts.     

Geographical and host distribution patterns of Parvicapsula minibicornis (Myxozoa) small subunit ribosomal RNA genetic types

Parvicapsula minibicornis is a myxozoan parasite implicated in mortalities of both juvenile and pre-spawning adult salmon in the Pacific Northwest of North America. Disease severity and presentation varies between salmon species and geographical localities. To better characterize population structure of the parasite, we sought genetic markers in the P. minibicornis ribosomal RNA gene. We compared samples from California with the type specimen from British Columbia, identified sequence variations, and then sequenced 197 samples from fish, river water and the parasite's polychaete worm host. Although DNA sequences of the parasite were >98·9% similar, there was enough variation to define 15 genotypes. All genotypes were detected in fish samples, although not in all species. A single genotype only was found in sockeye and pink salmon in the Fraser River Basin, but was not detected in sockeye from the adjacent Columbia River Basin. All coho salmon, irrespective of river basin, were infected with a unique mix of 2 genotypes. These data indicated that the P. minibicornis population exhibited strong signals of structuring by both geography and salmonid host species. Particular genotypes may correlate with disease differences seen in salmon populations in the Pacific Northwest.     

Juvenile salmon in estuaries: comparisons between North American Atlantic and Pacific salmon populations

All anadromous fishes, including juvenile salmon, encounter estuarine habitats as they transition from riverine to marine environments. We compare the estuarine use between juvenile Atlantic salmon (Salmo salar) in the Penobscot River estuary and Pacific salmon (Oncorhynchus spp.) in the Columbia River estuary. Both estuaries have been degraded by anthropogenic activities. Atlantic and Pacific salmon populations in both basins rely heavily on hatchery inputs for persistence. Pacific salmon, as a group, represent a continuum of estuarine use, from species that move through rapidly to those that make extensive use of estuarine habitats. While Atlantic salmon estuarine use is predominantly similar to rapidly moving Pacific salmon, they can exhibit nearly the entire range of Pacific salmon estuarine use. Both slow and rapidly migrating Atlantic and Pacific salmon actively feed in estuarine environments, consuming insect and invertebrate prey. Interactions between juvenile salmon and estuarine fish communities are poorly understood in both estuaries, although they experience similar avian and marine mammal predators. Estuaries are clearly important for Atlantic and Pacific salmon, yet our understanding of this use is currently insufficient to make informed judgments about habitat quality or overall estuary health. This review of salmonid migration through and residency within estuaries identifies actions that could hasten restoration of both Atlantic and Pacific salmon populations.     

Species distinction in Irish populations of Quercus petraea and Q. robur: morphological versus molecular analyses

BACKGROUND AND AIMS: Populations of oak (Quercus petraea and Q. robur) were investigated using morphological and molecular (AFLP) analyses to assess species distinction. The study aimed to describe species distinction in Irish oak populations and to situate this in a European context. METHODS: Populations were sampled from across the range of the island of Ireland. Leaf morphological characters were analysed through clustering and ordination methods. Putative neutral molecular markers (AFLPs) were used to analyse the molecular variation. Cluster and ordination analyses were also performed on the AFLP markers in addition to calculations of genetic diversity and F-statisitcs. KEY RESULTS: A notable divergence was uncovered between the morphological and molecular analyses. The morphological analysis clearly differentiated individuals into their respective species, whereas the molecular analysis did not. Twenty species-specific AFLP markers were observed from 123 plants in 24 populations but none of these was species-diagnostic. Principal Coordinate Analysis of the AFLP data revealed a clustering, across the first two axes, of individuals according to population rather than according to species. High F(ST) values calculated from AFLP markers also indicated population differentiation (F(ST) = 0.271). Species differentiation accounted for only 13 % of the variation in diversity compared with population differentiation, which accounted for 27 %. CONCLUSIONS: The results show that neutral molecular variation is partitioned more strongly between populations than between species. Although this could indicate that the populations of Q. petraea and Q. robur studied may not be distinct species at a molecular level, it is proposed that the difficulty in distinguishing the species in Irish oak populations using AFLP markers is due to population differentiation masking species differences. This could result from non-random mating in small, fragmented woodland populations. Hybridization and introgression between the species could also have a significant role.     

New polymorphic microsatellite markers for the masu salmon (Oncorhynchus masou masou) from Korea and their application to wild and hatchery populations

Masu salmon, Oncorhynchus masou masou, is an economically important fish species in the Far East and occurs in two life history forms: sea-run migratory (anadromous) and freshwater resident (non-anadromous). The non-anadromous form has recently become a popular freshwater food and game fish during a well-known Korean winter festival. However, the genetic background of this species remains largely unknown, partly due to a lack of molecular genetic markers. In this study, we developed new polymorphic microsatellite markers for masu salmon using next-generation sequencing technology. From 40 primer sets, 11 primer sets (27.5% of the primer sets selected) were successfully amplified with 106 alleles (range 2–9) in 64 individuals from different populations: two wild and one hatchery. Observed and expected heterozygosities ranged from 0.304 to 0.947 and 0.278 to 0.865, respectively. Significant departures from the Hardy–Weinberg equilibrium were detected for four markers (OMM11, OMM17, OMM28, and OMM33) in a single population. All pair-wise F_ST values were highly significant between the wild and hatchery populations (range 0.084–0.183, P < 0.0001). We identified a set of robust microsatellite markers that worked well even in formalin-fixed samples, which will be suitable for biogeographical and population structure analyses of the masu salmon.     

Asynchrony in population dynamics of sockeye salmon in southwest Alaska

Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population‐specific responses to regional environmental change. We used long‐term data on sockeye salmon Oncorhynchus nerka from pristine watersheds of southwestern Alaska to show that populations spawning in close proximity (<40 km) to one another have a limited degree of synchrony in their dynamics, even after accounting for density‐dependent processes. In fact, the dynamics of local populations of stream‐spawning sockeye salmon were no more coherent than those of stocks at a much coarser resolution across this region of Alaska. We examined four hypotheses to explain the observed patterns of asynchrony among stream‐spawning populations, and found that populations spawning in dissimilar habitats, and using different nursery lakes were less synchronized in their productivity. Similarity in the age structure of spawning adults was less correlated with synchrony in productivity. These results emphasize the importance of maintaining diverse spawning and rearing habitat for the conservation of Pacific salmon, and should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over‐fishing.     

Signals of large scale climate drivers,hatchery enhancement,and marine factors in Yukon River Chinook salmon survival revealed with a Bayesian life history model

Understanding how species might respond to climate change involves disentangling the influence of co‐occurring environmental factors on population dynamics, and is especially problematic for migratory species like Pacific salmon that move between ecosystems. To date, debate surrounding the causes of recent declines in Yukon River Chinook salmon (Oncorhynchus tshawytscha) abundance has centered on whether factors in freshwater or marine environments control variation in survival, and how these populations at the northern extremity of the species range will respond to climate change. To estimate the effect of factors in marine and freshwater environments on Chinook salmon survival, we constructed a stage‐structured assessment model that incorporates the best available data, estimates incidental marine bycatch mortality in trawl fisheries, and uses Bayesian model selection methods to quantify support for alternative hypotheses. Models fitted to two index populations of Yukon River Chinook salmon indicate that processes in the nearshore and marine environments are the most important determinants of survival. Specifically, survival declines when ice leaves the Yukon River later in the spring, increases with wintertime temperature in the Bering Sea, and declines with the abundance of globally enhanced salmon species consistent with competition at sea. In addition, we found support for density‐dependent survival limitations in freshwater but not marine portions of the life cycle, increasing average survival with ocean age, and age‐specific selectivity of bycatch mortality in the Bering Sea. This study underscores the utility of flexible estimation models capable of fitting multiple data types and evaluating mortality from both natural and anthropogenic sources in multiple habitats. Overall, these analyses suggest that mortality at sea is the primary driver of population dynamics, yet under warming climate Chinook salmon populations at the northern extent of the species’ range may be expected to fare better than southern populations, but are influenced by foreign salmon production.     

Environmental and evolutionary effects on horn growth of male bighorn sheep

The development of male secondary sexual characters such as antlers or horns has substantial biological and socio‐economic importance because in many species these traits affect male fitness positively through sexual selection and negatively through trophy hunting. Both environmental conditions and selective hunting can affect horn growth but their relative importance remains unexplored. We first examined how a large‐scale climate index, the Pacific Decadal Oscillation (PDO), local weather and population density influenced both absolute and relative annual horn growth from birth to three years of male bighorn sheep Ovis canadensis over 42 years. We then examined the relative influence of environmental conditions and evolution mainly driven by trophy hunting on male horn length at three years of age. Horn growth was positively influenced by low population density and warm spring temperature, suggesting that ongoing climate change should lead to larger horns. Seasonal values of PDO were highly correlated. Horn growth increased with PDO in spring or summer at low density, but was weak at high density regardless of PDO. The interaction between population density and PDO in spring or summer accounted for a similar proportion of the observed annual variation in horn growth (32% or 37%) as did the additive effects of spring temperature and density (34%). When environmental conditions deteriorated, males allocated relatively more resources to summer mass gain than to horn growth, suggesting a conservative strategy favoring maintenance of condition over allocation to secondary sexual characters. Population density explained 27% of the variation in horn length, while evolutionary effects explained 9% of the variance. Thus, our study underlines the importance of both evolution and phenotypic plasticity on the development of a secondary sexual trait.