Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

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Genetic diversity and population structure of burbot Lota lota in Germany: Implications for conservation and management

The genetic structure of the gadiform fish species, burbot Lota lota L., was investigated across Germany to derive management options for facilitating the preservation of genetic diversity. Sequence analysis of the mitochondrial control region (n = 244) and microsatellite analysis (n = 861) of specimens from 20 sites revealed genetic structuring between major river basins, and particularly between lake and river habitats. The admixture zone between the Eurasian and West European phylogenetic clades in Lake Constance was confirmed and expanded to include the drainage basins of the rivers Rhine and Schlei/Trave. Haplotype distribution and private haplotypes in single river basins indicated population differentiation and imply that German burbot constituted an important part of the entire species' diversity. The derived genetic structuring has implications for future stocking programmes and the preservation of the adaptive potential of burbot, a guiding species for oligotrophic lakes in Europe.     

Managing global shark fisheries: suggestions for prioritizing management strategies

• 1. Over the past two decades the number of fisheries targeting shark resources has increased dramatically. A combination of factors, including relatively slow growth rate, low fecundity and late age of maturity, result in low recovery rates from exploitation for most shark species. This, in turn, is reflected in the poor record of sustainability of shark fisheries.
• 2. One of the greatest challenges is to find a way to deal with the substantial levels of shark bycatch taken in many non‐target fisheries. Poor general recording of shark landings and paucity of shark landing data at the species level also undermine the development of effective shark management strategies. 3. This paper reviews the problems that must be faced worldwide if shark resources are to be managed sustainably and lays out a comprehensive set of prioritized management strategies to facilitate the sustainable management of global shark fisheries. It is acknowledged that the majority of sharks are harvested in developing countries and that the management of shark resources in developing and developed countries will need to incorporate different management strategies relevant to local socio‐economic agendas. The management recommendations deal with methods to improve the global regulation of fisheries, ways to improve global conservation ethics and encourage active participation in management, as well as means by which specific management strategies may be implemented.

Copyright © 2004 John Wiley & Sons, Ltd.     

An unfished area enhances a spiny lobster,Panulirus argus,fishery: implications for management and conservation within a Biosphere Reserve in the Mexican Caribbean

The Caribbean spiny lobster, Panulirus argus, Latreille, is the main source of income for the communities in the Sian Ka'an Biosphere Reserve Mexico. The fishery has recently been certified as sustainable by the Marine Stewardship Council provided that further stock assessment is carried out. A total of 379 lobsters were tagged in an unfished area offshore from the Bahía del Espíritu Santo fishing grounds to assess whether lobsters remained within these areas and were thus fully protected. The lobsters recaptured in the shallow area (5.3%) were sufficient to develop a multistate mark recapture model, which takes into account fishing and natural mortality, tag reporting rate and tag loss. This estimated that between 15 and 20% of all adult lobsters dwelling in the unfished area moved into the fishery and were subjected to exploitation. This study suggests that the offshore unfished area provides protection to the majority of the stock in this area while adding to and maintaining fishing yields within the inshore commercial fishery.     

Gear restrictions create conservation and fisheries trade-offs for management

Gear-based management for coral reef fisheries is often overlooked in the scientific literature. Empirical studies have demonstrated the conservation benefits of gear-restricted areas (i.e. prohibiting fishing gears), which can support greater biomass than unrestricted areas and protect species that play key functional roles. However, population dynamics of functional feeding groups of reef fishes under specific gear-restriction regimes remains uncertain. Here, we constructed a multi-species, length-based fisheries model to observe relative biomass and catch of reef fishes under various gear-restriction management scenarios. We used fishery-dependent and fishery-independent data to determine the catchability of functional groups and selectivity of size classes for hook-and-line, net and spear fishing, which are widely used gear types on coral reefs globally. Our model revealed trade-offs involved with gear-restriction management such that no single management strategy was able to maximize biomass or catch of all functional groups simultaneously. Also, we found that spear fishing (i.e. prohibiting hook-and-line and net fishing) maintained the highest total biomass summed across functional groups, whilst hook-and-line fishing (i.e. prohibiting net and spear fishing) and a ban on spears maintained the lowest biomass. However, hook-and-line fishing generated the highest catch-per-unit-effort. Our model results were primarily driven by differential growth rates, maximum per capita production of recruits, and catchability of functional groups targeted by each fishing gear. We demonstrate that gear restrictions can be a critical management tool for maintaining biomass and catch of certain functional groups but will likely require additional management to protect all key functional feeding groups of coral reef fishes.     

Global phylogeography of the smooth hammerhead shark: Glacial refugia and historical migration patterns

1. Extreme climate changes during the Cenozoic Era strengthened different biogeographical barriers that decreased the connectivity among populations, triggering lineage diversification of different species worldwide.
2. The mitochondrial DNA control region was employed to explore the phylogeography of Sphyrna zygaena, a globally distributed species threatened by unsustainable, illegal, unreported and unregulated fisheries triggered by the international shark fin trade. It is listed as ‘Vulnerable’ by the IUCN Red List and its trade is regulated by CITES Appendix II.
3. Only 13 haplotypes were found with low genetic diversity levels (hd = 0.686 ± 0.014; π = 0.00206 ± 0.00004) compared with other species of the Sphyrnidae family. The species has a very strong phylogeographic population structure among the Atlantic, Indian and Pacific Oceans (Φ_ST = 0.79132). Worldwide, there are six distinct populations with some haplotype sharing.
4. These populations are probably connected by a stepping-stone dispersal of a small number of migrants per generation from the Indo-Pacific towards the Atlantic. Modelling suggests that S. zygaena diverged into two lineages around 6.96 million years ago which have been isolated in glacial refuges in the Atlantic and Indo-Pacific oceans; and after deglaciation, a population expansion probably permitted secondary contact.
5. Conservation plans to establish differentiated management units should be adopted in each of the identified populations. Among these, the Eastern Central Atlantic and West Indo-Pacific are the most important areas for the species considering the historical migration routes that act as a bridge connecting the Atlantic and Indo-Pacific Oceans while the Gulf of Guinea connects the Atlantic populations. Still, further studies are required to know if these populations are also linked with nursery areas for the species.
6. The results herein can help to delimit the main evolutionarily significant units to implement effective policies to establish differentiated management units as starting points to genetic monitoring programmes for Sphyrna zygaena.

     

Diversity and genetic population structure of the Brazilian sharpnose shark Rhizoprionodon lalandii

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The future of stock enhancements: lessons for hatchery practice from conservation biology

The world's fish species are under threat from habitat degradation and over‐exploitation. In many instances, attempts to bolster stocks have been made by rearing fish in hatcheries and releasing them into the wild. Fisheries restocking programmes have primarily headed these attempts. However, a substantial number of endangered species recovery programmes also rely on the release of hatchery‐reared individuals to ensure long‐term population viability. Fisheries scientists have known about the behavioural deficits displayed by hatchery‐reared fish and the resultant poor survival rates in the wild for over a century. Whilst there remain considerable gaps in our knowledge about the exact causes of post‐release mortality, or their relative contributions, it is clear that significant improvements could be made by rethinking the ways in which hatchery fish are reared, prepared for release and eventually liberated. We emphasize that the focus of fisheries research must now shift from husbandry to improving post‐release behavioural performance. In this paper we take a leaf out of the conservation biology literature, paying particular attention to the recent developments in reintroduction biology. Conservation reintroduction techniques including environmental enrichment, life‐skills training, and soft release protocols are reviewed and we reflect on their application to fisheries restocking programmes. It emerges that many of the methods examined could be implemented by hatcheries with relative ease and could potentially provide large increases in the probability of survival of hatchery‐reared fish. Several of the necessary measures need not be time‐consuming or expensive and many could be applied at the hatchery level without any further experimentation.     

Current conservation genetics: building an ecological approach to the synthesis of molecular and quantitative genetic methods

Abstract Although neutral molecular markers have long been important tools for describing genetic variation in threatened fish species, many of the most critical questions in conservation relate more to quantitative genetic variation than to neutral markers. Quantitative genetic studies are typically expensive and time-consuming to conduct, especially in some of the long-lived vertebrates of conservation concern. The present review of recent literature in fish conservation genetics examines the traditional role of molecular studies in describing conservation units and providing indirect inference about local adaptation and adaptive potential. Of special interest are approaches that use a combination of molecular and quantitative genetic methods. Such studies are likely to provide important new insights into many conservation-related problems. The review also explores how increasing interest in non-neutral molecular markers is contributing to our understanding of the geographic scale and evolutionary importance of local adaptation in threatened populations. It is increasingly clear that advanced genetic technologies for the exploration of neutral and non-neutral molecular variation are leading to a fundamental shift in the way complex phenotypic traits are studied. This new synthesis of methods will have dramatic implications for fish conservation genetics and biology in general.     

The mitigation hierarchy for sharks: A risk‐based framework for reconciling trade‐offs between shark conservation and fisheries objectives

Sharks and their cartilaginous relatives are one of the world's most threatened species groups. The primary cause is overfishing in targeted and bycatch fisheries. Reductions in fishing mortality are needed to halt shark population declines. However, this requires complex fisheries management decisions, which often entail trade‐offs between conservation objectives and fisheries objectives. We propose the mitigation hierarchy (MH)—a step‐wise precautionary approach for minimizing the impacts of human activity on biodiversity—as a novel framework for supporting these management decisions. We outline a holistic conceptual model for risks to sharks in fisheries, which includes biophysical, operational and socioeconomic considerations. We then demonstrate how this model, in conjunction with the MH, can support risk‐based least cost shark conservation. Through providing examples from real‐world fishery management problems, we illustrate how the MH can be applied to a range of species, fisheries and contexts, and explore some of the opportunities and challenges hereto. Finally, we outline next steps for research and implementation. This is important in the context of increasing international regulation of shark fishing and trade, which must lead to reductions in shark mortality, while managing trade‐offs between conservation objectives and the socioeconomic value of fisheries.     

Colonization history and human translocations explain the population genetic structure of the noble crayfish (Astacus astacus) in Fennoscandia: Implications for the management of a critically endangered species

1. The noble crayfish (Astacus astacus) is an endangered freshwater species in Europe. The main threat is from lethal crayfish plague, caused by the oomycete Aphanomyces astaci that has been spread over Europe by introduced North American crayfish species, acting as chronic carriers of the disease.
2. Most of the remaining noble crayfish populations are found in the Baltic Sea area, and there is an urgent need to implement conservation actions to slow down or halt the extinction rate in this region. However, limited knowledge about the genetic structure of populations in this area has so far precluded the development of conservation strategies that take genetic aspects into consideration.
3. Key objectives of this large-scale genetic study, covering 77 locations mainly from northern Europe, were to describe the contemporary population genetic structure of the noble crayfish in the Fennoscandian peninsula (Sweden, Norway, and Finland), taking postglacial colonization history into account, and to evaluate how human activities such as stocking have affected the genetic structure of the populations.
4. Analyses of 15 microsatellite markers revealed three main genetic clusters corresponding to populations in northern, middle, and southern Fennoscandia, with measures of genetic diversity being markedly higher within populations in the southern cluster. The observed genetic structure probably mirrors two main colonizations of the Baltic Sea basin after the last glaciation period. At the same time, several deviations from this pattern were observed, reflecting past human translocations of noble crayfish.
5. The results are discussed in relation to the conservation and management of this critically endangered species. In particular, we recommend increased efforts to protect the few remaining noble crayfish populations in southern Fennoscandia and the use of genetic information when planning stocking activities, such as reintroductions following local extinctions.

     

Genetic diversity and population history of the migratory catfishes Pangasianodon hypophthalmus and Pangasius bocourti in the Cambodian Mekong River

ABSTRACT:   Polymerase chain reaction (PCR) restriction fragment length polymorphism analysis of mitochondrial DNA was applied to the genetic structure and evolutionary history of the more ancestral Pangasianodon hypophthalmus ( n  = 82), and the recently speciated catfish Pangasius bocourti ( n  = 90) from the Cambodian Mekong River. Both pangasiids were characterized by a lack of genetic population structure that may result from high levels of contemporary gene flow. Genetic diversity was lower in P. hypophthalmus than in P. bocourti . However, a different evolutionary history was inferred for both species based on genealogical and demographic analyses (mismatch analysis, Tajima's D- and Fu's F _S-tests). The genetic profile of the more ancestral P. hypophthalmus shows indications of a recent population bottleneck, whereas the recently speciated P. bocourti shows signatures of historical population expansion. This study stresses the importance of preserving the migration routes in the Cambodian Mekong basin in order to maintain the genetic diversity and long-term integrity of both species.     

Analysis of the population genetics of the Yangtze finless porpoise population in the Poyang Lake Basin: Insight of conservation recommendations

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Population genetic structure of Atlantic salmon,Salmo salar L., in the River Tamar,southwest England

Abstract Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L., population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment‐specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment‐specific studies of stock abundance. Implications for implementing management actions are considered.     

A simple approach for assigning the conservation status of freshwater fish based on their natural variability – a case study from the Iberian Ecoregion

A simple, non‐lethal method for assigning conservation status is proposed based on three conservation classes (favourable, unfavourable/inadequate and unfavourable/bad) to fish species based on their natural population variability. To demonstrate this approach, conservation classes were allocated to three native fish species (brown trout Salmo trutta L., northern Iberian chub Squalius carolitertii (Doadrio), and northern straight‐mouth nase, Pseudochondrostoma duriense (Coelho) based on basic population variables (density and biomass) using a 9‐year dataset (2004–2012) from 15 different sampling sites in Spain. The classification of the population variables into conservation classes was made using previously described nonparametric methods and percentiles categorisation, and the current conservation status of the studied species was established. Temporal trend analyses showed that S. carolitertii experienced a progressive significant decrease during the study period, whereas both S. trutta and P. duriense exhibited weak increases in density. The study exemplifies the need to quantify the natural variability of fish resources to reveal their current conservation status and to determine whether short‐term and long‐term management actions are needed to rehabilitate native fish assemblages. The proposed approach could easily be employed by fisheries managers to monitor the conservational status of other native species.     

Historical and contemporary habitat use of sperm whales around the Galápagos Archipelago: Implications for conservation

1. Sperm whales have occupied the waters off the Galápagos Islands, Ecuador, for at least the past 200 years. During the 19^th century, they were the target of intensive whaling that severely depleted the population. In recent times, after commercial whaling ended, sperm whales in the region remain vulnerable to multiple threats, especially potential entanglement in fishing gear, which may hinder their ability to recover from the whaling era.
2. As a highly mobile, long-lived species, long-term analysis of the habitat use of sperm whales is necessary to establish effective conservation and management strategies. Here, contemporary (1985–2014) and historical (1830–1850) sperm whale habitat use off the Galápagos Islands was analysed and contrasted to the extent of the Galápagos Marine Reserve (GMR). Contemporary habitat use and its variability over time were modelled as a function of geographic, oceanographic, and topographic variables using generalized additive models.
3. The fine-scale habitat (<50 km) used by sperm whales was associated with topographic (i.e. depth and slope) and oceanographic characteristics (i.e. relative sea surface temperature and standard deviation of sea surface temperature), but these preferences varied over time.
4. While historical and contemporary data indicate that sperm whale habitat primarily occurred within the boundaries of the GMR, in recent years, whales were found up to 30.1% of the time outside the GMR, potentially overlapping with commercial fisheries operating in the area.
5. The dynamic nature of the relationship of this nomadic species with its habitat highlights the need of large-scale conservation efforts across the Eastern Tropical Pacific region, including the wide-scale enforcement of regulations requiring the use of Automatic Identification System in fishing vessels, the promotion of on-board fisheries observer programmes, the development of adaptive management strategies, and international collaboration to identify and mitigate threats.

     

From endangered to sustainable: Multi‐faceted management in rivers and coasts improves Atlantic salmon (Salmo salar) populations in Denmark

The status of Atlantic salmon, Salmo salar L., over the last decades has been of concern across its entire distribution area. Its anadromous nature exposes the species to human pressures in both freshwater and marine environments, and over long periods, thus exacerbating its decline. Given its value within the food industry, the recreational angling community as well as culturally, the status of Atlantic salmon is regarded as a matter of national and international conservation interest, providing great incentive for its management. The literature currently lacks specific examples of successful and unsuccessful management strategies and practices for Atlantic salmon populations at a broader scale. To address this, the present article describes how the multi‐faceted management approach taken for Danish Atlantic salmon, which included changes in legislation, stocking practices, habitat restoration, population genetics and barrier removals, successfully rehabilitated salmon populations in four major Danish rivers. Specific recommendations are provided for the successful management of Atlantic salmon elsewhere.     

Conservation genetics and management implications for European grayling, Thymallus thymallus: synthesis of phylogeography and population genetics

Abstract  European grayling, Thymallus thymallus (L.), populations have steadily declined since the mid-1980s, mostly because of habitat degradation and increased predation pressure. To provide guidelines for conservation strategies and future management programmes, delineation of conservation and management units is warranted. Over the last decade, several studies have investigated the phylogeography and population genetic structure of T. thymallus using mitochondrial and nuclear microsatellite DNA markers. However, no study has covered the distribution range of T. thymallus across Europe; thus, a comprehensive survey of the evolutionary history of the species is lacking. This paper synthesises the major findings of the molecular studies and provides guidelines for the conservation and management of genetic resources of T. thymallus . At least five major mtDNA lineages have evolved in geographical isolation during the Pleistocene and these lineages should be recognised as the basic evolutionary significant units for T. thymallus in northern, central and southern Europe. There is also evidence for a high level of admixture among major lineages and sublineages, especially in the contact zones of drainages (e.g. in mainland Sweden and Norway and in central Germany), most probably resulting from a complex process of post-glacial and inter-glacial colonisation and re-colonisation events from different refugia during the Pleistocene ice ages. Based on the microsatellite data, T. thymallus shows a substantial level of inter-population genetic differentiation and, compared with other freshwater fish species, a relatively low level of within-population genetic diversity. The species develops discrete population structure, both within hydrologically connected rivers or lakes on comparatively small scales as well as in large river systems.     

Fish spawning aggregations: where well‐placed management actions can yield big benefits for fisheries and conservation

Marine ecosystem management has traditionally been divided between fisheries management and biodiversity conservation approaches, and the merging of these disparate agendas has proven difficult. Here, we offer a pathway that can unite fishers, scientists, resource managers and conservationists towards a single vision for some areas of the ocean where small investments in management can offer disproportionately large benefits to fisheries and biodiversity conservation. Specifically, we provide a series of evidenced‐based arguments that support an urgent need to recognize fish spawning aggregations (FSAs) as a focal point for fisheries management and conservation on a global scale, with a particular emphasis placed on the protection of multispecies FSA sites. We illustrate that these sites serve as productivity hotspots – small areas of the ocean that are dictated by the interactions between physical forces and geomorphology, attract multiple species to reproduce in large numbers and support food web dynamics, ecosystem health and robust fisheries. FSAs are comparable in vulnerability, importance and magnificence to breeding aggregations of seabirds, sea turtles and whales yet they receive insufficient attention and are declining worldwide. Numerous case‐studies confirm that protected aggregations do recover to benefit fisheries through increases in fish biomass, catch rates and larval recruitment at fished sites. The small size and spatio‐temporal predictability of FSAs allow monitoring, assessment and enforcement to be scaled down while benefits of protection scale up to entire populations. Fishers intuitively understand the linkages between protecting FSAs and healthy fisheries and thus tend to support their protection.