Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

Brown trout Salmo trutta is endemic to Europe, western Asia, north‐western Africa and is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river‐resident, lake‐resident) and three main facultative migratory life histories (downstream–upstream within a river system, fluvial–adfluvial potamodromous; to and from a lake, lacustrine–adfluvial (inlet)–allucustrine (outlet) potamodromous; to and from the sea, anadromous). River‐residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial–adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine–adfluvial–allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold‐trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non‐genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river‐resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr–smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonids. Identification of genetic markers linked to migration components and especially to the migration–residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes

Seasonal changes in broodstock spawning performance and egg quality in ballan wrasse (Labrus bergylta)

Sea lice continue to be one of the largest issues for the salmon farming industry and the use of ballan wrasse (Labrus bergylta) as a biological control is considered to be one of the most sustainable solutions in development. Broodstock management has proved challenging in the initial phases due to the significant lack of understanding of basic reproductive physiology and behaviour in the species. The aim of the study was to monitor captive breeding populations throughout a spawning season to examine timing and duration of spawning, quantify egg production, and look at seasonal changes in egg quality parameters as well as investigate the parental contribution to spawning events. A clear spawning rhythm was shown with 3–5 spawning periods inclusive of spawning windows lasting 1–9days followed by interspawning intervals of 8–12days. Fertilization rate remained consistently high (>87.5%) over the spawning season and did not differ significantly between spawning populations. Hatch rate was variable (0–97.5%), but peaked in the middle of the spawning season. Mean oocyte diameter and gum layer thickness decreased slightly over the spawning season with no significant differences between spawning populations. Fatty acid (FA) profile of eggs remained consistent throughout the season and with the exception of high levels of ARA (3.8±0.5% of total FA) the FA profile was similar to that observed in other marine fish species. Parental contribution analysis showed 3 out of 6 spawning events to be single paired mating while the remaining 3 had contributions from multiple parents. Furthermore, the proposed multiple batch spawning nature of this species was confirmed with proof of a single female contributing to two separate spawning events. Overall this work represents the first comprehensive dataset of spawning activity of captive ballan wrasse, and as such and will be helpful in formulating sustainable broodstock management plans for the species

Microsatellite DNA Profiling in the Blue Shark Prionace glauca : Development and Potential Application for Population Studies.

he world-wide increase in shark fisheries is thought to be resulting in declining population numbers of many species. The blue shark ( Prionace glauca ), possibly the most abundant of the larger pelagic sharks, is no exception. In addition to a directed fishery, large numbers of blue sharks make up the bycatch in the tuna and swordfish fishery. Increased fishing pressure and inadequate management strategies have prompted concerns about the sustainable health of blue shark populations. The main reason for inadequate management measures is the paucity of information on population genetic structure and life history strategy for this species. Traditional methods used to gather this type of information such as allozyme electrophoresis and RFLP analysis of mitochondrial DNA have proved to be only of limited use due to the apparent low rate of molecular evolution in this and other shark species. Recently, microsatellite DNA profiling techniques have been proposed as an alternative source of highly informative molecular makers. This new class of markers has not yet been fully exploited for shark population studies. Here we report on the development of blue shark microsatellite markers from an enriched library. Their potential for blue shark population genetic studies with examples is also discussed

Global Phylogeography of the Great (Sphyrna mokarran) and Smooth (Sphyrna zygaena) Hammerhead Sharks

The great (Sphyrna mokarran) and smooth hammerhead (S. zygaena) sharks are globally distributed species of significant conservation concern because they have high bycatch rates and high value fins. The great hammerhead has been assessed as endangered and the smooth hammerhead as Lower Risk / Near Threatened by the IUCN Redlist. There is no information on the population structure of either species to inform management and conservation efforts. We report on an ongoing assessment of the global population structure of both species using nuclear microsatellite markers and complete mitochondrial control region (mtCR) sequences (approximately 1098 nucleotides) from 78 great and 85 smooth hammerheads. Great hammerhead samples analyzed thus far included 59 North Atlantic and 6 Indo-Pacific individuals. Smooth hammerhead samples analyzed included 14 Atlantic, 23 North Pacific, 28 Southeast Pacific and 19 Indo-Pacific individuals. Analyses of the great hammerhead mtCR revealed strong geographical subdivision into two distinct evolutionary lineages with little exchange of haplotypes between the lineages (FST 0.704, P\u3c 0.005) and little to no detectable genetic structure within either lineage. Smooth hammerhead mtCR revealed strong geographical subdivision into four separate populations with no evidence of gene flow between the populations (FST= 0.802, P\u3c 0.00000) and little to no detectable genetic structure within the populations. Analyses of microsatellite loci from both species are currently underway. Despite the modest regional distribution of samples analyzed thus far, the data suggest that genetic population subdivision in these species may be extensive, making it likely that proper management will require a multi-regional approach

Taxonomy and phylogeography of the Irish Arctic char (<i>Salvelinus alpinus</i>). Report No. 444

A comprehensive genetic analysis of Arctic char (Salvelinus alpinus) populations in Irish loughs was undertaken to address several aspects relevant to conservation and management. First, the study aimed to clarify the taxonomic status of this species, investigating whether there is scientific evidence supporting the existence of multiple char species in Ireland. Second, it sought to uncover the phylogeographical history and population structure of contemporary Arctic char populations in Ireland. Third, it assessed the impact of scientific communication on conservation decisions made by policymakers, using an environmental economics analytical framework. Finally, the study aimed to provide insights into the development of effective conservation measures for Arctic char in Ireland, using the genetic data generated in conjunction with other available information.The study involved sampling Arctic char from 37 loughs in Ireland, representing 82% of the loughs where the species has been recorded as naturally present. Archived samples were also available from 18 additional loughs where Arctic char is now thought to be extinct. Limited samples from Scotland (UK), England (UK) and Sweden were included in the dataset for comparison. Historical specimens, collected during the late 1800s and early 1900s, were sourced from the Natural History Museum in London and the National Museum of Ireland. These included holotypes and syntypes associated with species previously described in Ireland by Günther (1862, 1863) and Regan (1908, 1911). In total, over 3200 Arctic char specimens were analysed during the study.The analysis involved the examination of genetic data from both nuclear and mitochondrial DNA (mtDNA), in addition to morphometric data. Single nucleotide polymorphism (SNP) markers were developed for both nuclear DNA and mtDNA, based on a sample set of 288 individuals representing 29 Irish Arctic char loughs, along with specimens from England and Scotland for reference. Nuclear SNP markers were employed to screen the 3072 samples collected for the project. The results revealed that all Arctic char loughs hosted genetically distinct populations, with varying degrees of divergence. There was no major correlation between geographical location and genetic similarity, indicating that geographical proximity is not an indicator of genetic similarity. Several loughs were found to host multiple genetically distinct populations, a phenomenon known as sympatric populations.Comparative analysis of 342 Arctic char mitochondrial genomes unveiled 173 distinct mtDNA haplotypes. Results indicate that Arctic char populations in Ireland’s loughs are represented by four genetically distinct, rich (i.e. represented by several genetic variants) evolutionary lineages. Genetic divergence among these lineages suggests separate evolution in distinct refugia prior to the Last Glacial Maximum. As the ice retreated between 20,000 and 13,000 years ago, these lineages independently colonised Irish freshwater habitats. Two of these lineages appeared to be unique to Ireland, possibly representing the first colonisers following the ice retreat. The remaining lineages were also found in other North Atlantic countries. Within-lough diversity explained most of the mitochondrial genetic diversity, further emphasising the lack of a geographical pattern. The disjunct contemporary geographical distribution of lineages indicates that the recolonisation of Ireland was complex, involving colonisation, extinction, recolonisation, and/or secondary contact and admixture among Arctic char populations representing different lineages.The results of the study challenge the species status of Arctic char populations based on Victorian-era taxonomy. Neither genetic nor morphometric data support the existence of multiple char species in Ireland. While scientific evidence does not substantiate the presence of distinct species, the study highlights the uniqueness, richness and potentially endemic nature of mtDNA diversity among Irish Arctic char. Much of this diversity has evolved in isolation since the Last Glacial Maximum. This unique biodiversity warrants conservation attention and protection. The results of the environmental economics analysis reveal that policymakers’ conservation decisions are influenced by the inclusion or exclusion of uncertainties in the conservation context. Building on these findings, to assist with the development of effective conservation measures, a prioritisation list ranking Arctic char conservation needs in Ireland was devised. This ranking system, based on a straightforward points-based approach, uses the novel genetic and morphometric data generated by the study, combined with other available information on the loughs under investigation. This prioritisation list could be a valuable tool for relevant stakeholders, to assist with the development and implementation of sound conservation measures for Arctic char in Ireland

A Genetic Investigation Into a Shark \u27Virgin-Birth\u27: Asexual Reproduction, Inter-Specific Hybridization or Long-Term Sperm Retention?

Asexual reproduction via parthenogenesis is relatively rare among chordates and has never been recorded in the class Chondrichthyes. In December 2001, a female Bonnethead Shark, Sphyrna tiburo, gave birth in captivity to a single female pup, despite having been separated from any male S. tiburo for a period of at least three years. Widespread media attention quickly led to this case being billed as the shark-virgin birth (i.e., asexual reproduction), however other explanations (sexual reproduction coupled with long-term sperm storage, inter-specific hybridization with a male leopard shark, Triakis semifasciata, tank-mate) could not be ruled out. We present the results of a genetic investigation aimed at ruling out these alternatives and determining whether this birth is the first known case of asexual reproduction in this ancient lineage

Microsatellite DNA Profiling in the Bonnethead Shark, Sphyrna tiburo: Application to Mating System and Population Structure Studies.

Although application of microsatellite markers to shark biology is in its infancy, these markers are already proving useful for elucidating relationships at population and individual levels. Herein, we provide a preliminary evaluation of microsatellite loci to investigate life history traits and population structure of the bonnethead shark, Sphyrna tiburo. Mature female bonnetheads are known to store sperm in their oviducal gland for a period of about five months after insemination. Although there are no published observations of bonnethead sharks mating, recent studies on other sharks suggest that multiple males often participate in mating events involving a single female. If the bonnethead shark has evolved this type of multiple-male (polyandrous) mating system coupled with protracted sperm storage, it is possible that females are fertilized by multiple males in a single reproductive cycle. Using 8 microsatellite markers, we have assayed several litters of this species for multiple paternity. Three of the 8 microsatellite loci were isolated from the genome of S. tiburo. The remaining five were previously isolated from the blue shark, Prionace glauca, and were also found to be informative for S. tiburo. We also report on a preliminary assessment of micro-geographic population structure in this species from the SE United States

Mating Systems of the Bonnethead and Scalloped Hammerhead Sharks in the Southeast United States, as Revealed by Microsatellite DNA Profiling

Just as DNA-profiling has revolutionized our understanding of the reproductive biology of many animal groups, this technology has begun to provide significant new insights into the mating practices and parentage of free-living sharks. Genetic profiling of two shark species (nurse [Ginglymostoma cirratum] and lemon [Negaprion brevirostris]) have revealed almost ubiquitous multiple paternity of litters within the sampled study populations. In contrast, our recent studies have revealed that female bonnethead sharks (Sphyrna tiburo; Family Sphyrnidae [hammerhead sharks]) demonstrate a relatively low frequency of multiple paternity within a given reproductive cycle (p\u3c20% of 22 litters directly tested by microsatellite genotyping). Collectively, these studies indicate diversity in the mating systems of sharks, raising interesting questions as to what factors drive the evolution of female promiscuity and multiple paternity in these ancient fishes. To further explore this issue, we have expanded our analysis of parentage in S. tiburo to include a total of 70 litters (\u3e650 embryos), originating from breeding grounds along the Gulf coast of Florida and South Carolina. Despite an increase in sample size, multiple paternity remained low overall and we tested the hypothesis that it is more common in larger females. We also genotyped 20 litters (\u3e400 embryos) of scalloped hammerheads (S. lewini), a larger, ecologically dissimilar congener of S. tiburo. Although we document the first records of multiple paternity in S. lewini, the mating system of this species appears to be more akin to that of S. tiburo than it is to that of N. brevirostris and G. cirratum

Data from: New insights on postglacial colonisation in Western Europe: the phylogeography of the Leisler's bat (Nyctalus leisleri)

Despite recent advances in the understanding of the interplay between a dynamic physical environment and phylogeography in Europe, the origins of contemporary Irish biota remain uncertain. Current thinking is that Ireland was colonized post-glacially from southern European refugia, following the end of the last glacial maximum (LGM), some 20 000 years BP. The Leisler's bat (Nyctalus leisleri), one of the few native Irish mammal species, is widely distributed throughout Europe but, with the exception of Ireland, is generally rare and considered vulnerable. We investigate the origins and phylogeographic relationships of Irish populations in relation to those across Europe, including the closely related species N. azoreum. We use a combination of approaches, including mitochondrial and nuclear DNA markers, in addition to approximate Bayesian computation and palaeo-climatic species distribution modelling. Molecular analyses revealed two distinct and diverse European mitochondrial DNA lineages, which probably diverged in separate glacial refugia. A western lineage, restricted to Ireland, Britain and the Azores, comprises Irish and British N. leisleri and N. azoreum specimens; an eastern lineage is distributed throughout mainland Europe. Palaeo-climatic projections indicate suitable habitats during the LGM, including known glacial refugia, in addition to potential novel cryptic refugia along the western fringe of Europe. These results may be applicable to populations of many species

Shark Virgin Birth Produces Multiple, Viable Offspring

Facultative automictic parthenogenesis has only recently been confirmed in the most ancient jawed vertebrates, the chondrichthyan fishes (sharks, batoids, and chimeras). To date, however, in both documented cases, the females have only produced a single parthenogen offspring, and none of these have lived for more than 3 days. We present a genetically verified case of automictic parthenogenesis by a white-spotted bamboo shark (Chiloscyllium plagiosum), in which at least 2 parthenogens were produced and survived for 5 years or more. These findings demonstrate that some female sharks are capable of producing, multiple, viable offspring through parthenogenesis