Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Survival in the Rainforest : Change and Resilience among the Punan Vuhang of Eastern Sarawak, Malaysia

This dissertation concerns the Punan Vuhang, former hunter-gatherers who are now part-time farmers living in an area of remote rainforest in the Malaysian state of Sarawak. It covers two themes: first, examining their methods of securing a livelihood in the rainforest, and second looking at their adaptation to a settled life and agriculture, and their response to rapid and large-scale commercial logging. This study engages the long-running debates among anthropologists and ecologists on whether recent hunting-gathering societies were able to survive in the tropical rainforest without dependence on farming societies for food resources. In the search for evidence, the study poses three questions: What food resources were available to rainforest hunter-gatherers? How did they hunt and gather these foods? How did they cope with periodic food shortages? In fashioning a life in the rainforest, the Punan Vuhang survived resource scarcity by developing adaptive strategies through intensive use of their knowledge of the forest and its resources. They also adopted social practices such as sharing and reciprocity, and resource tenure to sustain themselves without recourse to external sources of food. In the 1960s, the Punan Vuhang settled down in response to external influences arising in part from the Indonesian-Malaysian Confrontation. This, in turn, initiated a series of processes with political, economic and religious implications. However, elements of the traditional economy have remained resilient as the people continue to hunt, fish and gather, and are able to farm on an individual basis, unlike neighboring shifting cultivators who need to cooperate with each other. At the beginning of the 21st century, the Punan Vuhang face a new challenge arising from the issue of rights in the context of the state and national law and large-scale commercial logging in their forest habitat. The future seems bleak as they face the social problems of alcoholism, declining leadership, and dependence on cash income and commodities from the market.

A physical mechanism for North Atlantic SST influence on the Indian summer monsoon

A link between the Atlantic Multidecadal Oscillation (AMO) and multidecadal variability of the Indian summer monsoon rainfall is unraveled and a long sought physical mechanism linking Atlantic climate and monsoon has been identified. The AMO produces persistent weakening (strengthening) of the meridional gradient of tropospheric temperature (TT) by setting up negative (positive) TT anomaly over Eurasia during northern late summer/autumn resulting in early (late) withdrawal of the south west monsoon and persistent decrease (increase) of seasonal monsoon rainfall. On inter-annual time scales, strong North Atlantic Oscillation (NAO) or North Annular mode (NAM) influences the monsoon by producing similar TT anomaly over Eurasia. The AMO achieves the interdecadal modulation of the monsoon by modulating the frequency of occurrence of strong NAO/NAM events. This mechanism also provides a basis for explaining the observed teleconnection between North Atlantic temperature and the Asian monsoon in paleoclimatic proxies. Citation: Goswami, B. N., M. S. Madhusoodanan, C. P. Neema, and D. Sengupta (2006), A physical mechanism for North Atlantic SST influence on the Indian summer monsoon

Optimal management of conflicting species: Grey seal (Halichoerus grypus) and Atlantic salmon (Salmo salar) in the Baltic Sea

The objective of this thesis is to examine the economic effects in the conflict between grey seal population and the salmon fishery in the Baltic Sea. We will formulate a bioeconomic model which provides new insights on the optimal management of Atlantic salmon with respect to the effects brought about by the grey seal population. As the catch losses caused by seals have an effect on salmon fishery in Baltic, we will study how seal population affects the present value of the salmon fishery. The study considers the Finnish coastal trap net fishery. The bioeconomic model considers a scenario of sole salmon fishery and a scenario of salmon fishery affected by the grey seal population. On the basis of these scenarios, a seal compensation scheme is introduced. We can observe a significant economic seal-induced effect on the salmon fishery. The results suggest that the present seal compensation scheme emploid by the Finnish government is suboptimal. This thesis is part of the TARMO –project, in which the conflict between grey seal population and salmon fishery is studied using the methods of environmental economics.

Recovery of tropical rainforest avifauna in relation to vegetation succession following shifting cultivation in Mizoram, north-east India

1. Recovery of rainforest bird community structure and composition, in relation to forest succession after slash-and-burn shifting cultivation or jhum was studied in Mizoram, north-east India. Replicate fallow sites abandoned after shifting cultivation 1, 5, 10, 25 and approximate to 100 years ago, were compared with primary evergreen and semi-evergreen forest using transect and quadrat sampling. 2. Vegetation variables such as woody plant species richness, tree density and vertical stratification increased with fallow age in a rapid. nun-linear, asymptotic manner. Principal components analysis of vegetation variables summarized 92.8% of the variation into two axes: PC1 reflecting forest development and woody plant succession (variables such as tree density, woody plant species richness), and PC2 depicting bamboo density, which increased from 1 to 25 years and declined thereafter. 3. Bird species richness, abundance and diversity, increased rapidly and asymptotically during succession paralleling vegetation recovery as shown by positive correlations with fallow age and PC1 scores of sites. Bamboo density reflected by PC2 had a negative effect on bird species richness and abundance. 4. The bird community similarity (Morisita index) of sites with primary forest also increased asymptotically with fallow age indicating sequential species turnover during succession. Bird community similarity of sites with primary forest (or between sites) was positively correlated with both physiognomic and floristic similarities with primary forest (or between sites). 5. The number of bird species in guilds associated with forest development and woody plants (canopy insectivores, frugivores: bark feeders) was correlated with PCI scores of the sites. Species in other guilds (e. g. granivores, understorey insectivores) appeared to dominate during early and mid-succession. 6. The non-linear relationships imply that fallow periods less than a threshold of 25 years for birds, and about 50-75 years for woody plants, are likely to cause substantial community alteration. 7. As 5-10-year rotation periods or jhum cycles prevail in many parts of north-east India. there is a need to protect and conserve tracts of late-successional and primary forest.

Whales, dolphins, and porpoises of the western North Atlantic: a guide to their identification

This is an identification guide for cetaceans (whales, dolphins, and porpoises). It was designed to assist laypersons in identifying cetaceans encountered in the western North Atlantic Ocean and was intended for use by ongoing cetacean observer programs. This publication includes sections on identifying cetaceans at sea as well as stranded animals on shore. Species accounts are divided by body size and presence or lack of a dorsal fin. Appendices cover tags used on cetacean species; how to record and report cetacean observations at see and for stranded cetaceans; and a list of contacts for reporting cetacean strandings. (Document pdf contains 183 pages - file takes considerable time to open)

Influence of the northeastern Atlantic oceano-meteorological variability on the northern hake ("merluccius merluccius"). Analysis of the 1978-2006 period

316 p. : il., graf., map.

The frequency of muscle protein polymorphism in Menidia menidia (Atherinidae) along the Atlantic coast

(PDF has 6 pages.)

Interactions between adult migratory striped bass (Morone saxatilis) and their prey during winter off the Virginia and North Carolina Atlantic coast from 1994 through 2007

The migratory population of striped bass (Morone saxatilis) (>400 mm total length[TL]) spends winter in the Atlantic Ocean off the Virginia and North Carolina coasts of the United States. Information on trophic dynamics for these large adults during winter is limited. Feeding habits and prey were described from stomach contents of 1154 striped bass ranging from 373 to 1250 mm TL, collected from trawls during winters of 1994-96, 2000, and 2002-03, and from the recreational fishery during 2005-07. Nineteen prey species were present in the diet. Overall, Atlantic menhaden (Brevoortia tyrannus) and bay anchovy (Anchoa mitchilli) dominated the diet by boimass (67.9%) and numerically (68.6%). The percent biomass of Atlantic menhaden during 1994-2003 to 87.0% during 2005-07. Demersal fish species such as Atlantic croaker (Micropogonias undulatus) and spot (Leiostomus xanthurus) represented <15% of the diet biomass, whereas alosines (Alosa spp.) were rarely observed. Invertebrates were least important, contributing <1.0% by biomass and numerically. Striped bass are capable of feeding on a wide range of prey sizes (2% to 43% of their total length). This study outlines the importance of clupeoid fishes to striped bass winter production and also shows that predation may be exerting pressure on one of their dominant prey, the Atlantic menhaden.

An Integrated Assessment of the Introduction of Lionfish (Pterois volitans/miles complex) to the Western Atlantic Ocean.

Lionfish (Pterois volitans/miles complex) are venomous coral reef fishes from the Indian and western Pacific oceans that are now found in the western Atlantic Ocean. Adult lionfish have been observed from Miami, Florida to Cape Hatteras, North Carolina, and juvenile lionfish have been observed off North Carolina, New York, and Bermuda. The large number of adults observed and the occurrence of juveniles indicate that lionfish are established and reproducing along the southeast United States coast. Introductions of marine species occur in many ways. Ballast water discharge, a very common method of introduction for marine invertebrates, is responsible for many freshwater fish introductions. In contrast, most marine fish introductions result from intentional stocking for fishery purposes. Lionfish, however, likely were introduced via unintentional or intentional aquarium releases, and the introduction of lionfish into United States waters should lead to an assessment of the threat posed by the aquarium trade as a vector for fish introductions. Currently, no management actions are being taken to limit the effect of lionfish on the southeast United States continental shelf ecosystem. Further, only limited funds have been made available for research. Nevertheless, the extent of the introduction has been documented and a forecast of the maximum potential spread of lionfish is being developed. Under a scenario of no management actions and limited research, three predictions are made: ● With no action, the lionfish population will continue to grow along the southeast United States shelf. ● Effects on the marine ecosystem of the southeast United States will become more noticeable as the lionfish population grows. ● There will be incidents of lionfish envenomations of divers and/or fishers along the east coast of the United States. Removing lionfish from the southeast United States continental shelf ecosystem would be expensive and likely impossible. A bounty could be established that would encourage the removal of fish and provide specimens for research. However, the bounty would need to be lower than the price of fish in the aquarium trade (~$25-$50 each) to ensure that captured specimens were from the wild. Such a low bounty may not provide enough incentive for capturing lionfish in the wild. Further, such action would only increase the interaction between the public and lionfish, increasing the risk of lionfish envenomations. As the introduction of lionfish is very likely irreversible, future actions should focus on five areas. 1) The population of lionfish should be tracked. 2) Research should be conducted so that scientists can make better predictions regarding the status of the invasion and the effects on native species, ecosystem function, and ecosystem services. 3) Outreach and education efforts must be increased, both specifically toward lionfish and more generally toward the aquarium trade as a method of fish introductions. 4) Additional regulation should be considered to reduce the frequency of marine fish introduction into U.S. waters. However, the issue is more complicated than simply limiting the import of non-native species, and these complexities need to be considered simultaneously. 5) Health care providers along the east coast of the United States need to be notified that a venomous fish is now resident along the southeast United States. The introduction and spread of lionfish illustrates the difficulty inherent in managing introduced species in marine systems. Introduced species often spread via natural mechanisms after the initial introduction. Efforts to control the introduction of marine fish will fail if managers do not consider the natural dispersal of a species following an introduction. Thus, management strategies limiting marine fish introductions need to be applied over the scale of natural ecological dispersal to be effective, pointing to the need for a regional management approach defined by natural processes not by political boundaries. The introduction and success of lionfish along the east coast should change the long-held perception that marine fish invasions are a minimal threat to marine ecosystems. Research is needed to determine the effects of specific invasive fish species in specific ecosystems. More broadly, a cohesive plan is needed to manage, mitigate and minimize the effects of marine invasive fish species on ecosystems that are already compromised by other human activities. Presently, the magnitude of marine fish introductions as a stressor on marine ecosystems cannot be quantified, but can no longer be dismissed as negligible. (PDF contains 31 pages)

Preliminary guide to the identification of the early life history stages of Priacanthid fishes of the Western Central Atlantic

The family Priacanthidae contains four genera and four species that occur in the western central North Atlantic (Starnes, 1988). Pristigenys alta is distributed in the Caribbean, Gulf of Mexico and along the east coast of North America. Although juveniles have been reported from as far north as southern New England waters, adults are not reported north of Cape Hatteras, NC. Priacanthus arenatus is distributed in tropical and tropically influenced areas of the western central North Atlantic in insular and continental shelf waters. Adult P. arenatus are distributed north to North Carolina and Bermuda, juveniles have been collected as far north as Nova Scotia. Cookeolus japonicus and Heteropriacanthus cruentatus are circumglobally distributed species and are both common in insular habitats. In the western central North Atlantic, C. japonicus ranges from New Jersey to Argentina; H. cruentatus from New Jersey and northern Gulf of Mexico to southern Brazil (Starnes, 1988). (PDF contains 6 pages)

Preliminary guide to the identification of the early life history stages of Gerreid fishes of the Western Central Atlantic

The family Gerreidae contains four genera and 13 species that occur in the western central North Atlantic. Adult gerreids are small to medium size fishes that are abundant in coastal waters, bays, and estuaries in tropical and warm temperate regions and sometimes occur in freshwaters. They are generally associate~ with grassy or open bottoms, but not with reefs. Gerreids are silvery fishes, with deeply forked tails, and extremely protrusible mouth that points downward when protracted. They apparently feed on bottom-dwelling organisms and at least one species (Eucinostomus gula) shows a distinct transition, during the juvenile period, from a planktivore (exclusively copepods) to a carnivore that includes a diet of almost solely polychaetes (Carr & Adams, 1973; Robins and Ray, 1987; Murdy et al., 1997). (PDF contains 10 pages)