Data for the sustainable management of an emerging fishery: Age, growth and stock structure of Atlantic saury Scomberesox saurus saurus (Walbaum), in the Northeastern Atlantic Ocean

Almost half of Ireland’s commercial stocks face overexploitation. As traditional species decrease in abundance and become less profitable, the industry is increasingly turning to alternate species. Atlantic saury (Scomberesox saurus saurus (Walbaum)) has been identified as a potential species for exploitation. Very little information is available on its biology or population dynamics, especially for Irish waters. This thesis aims to obtain sound scientific data, which will help to ensure that a future Atlantic saury fishery can be sustainably managed. The research has produced valuable data, some of which contradicts previous studies. Growth of Atlantic saury measured using otolith microstructure is found to be more than twice that previously calculated from annual structures on scales and otoliths. This results in a significant reduction of the expected life span from five to about two years. Investigation of maturity stage at age indicates that Atlantic saury will reproduce for the first time at age one and will survive for one or at most two reproduction seasons. It is concluded that a future Irish fishery will target mostly fish prior to their first reproduction. Finally the thesis gives some insights into the population structure of Atlantic saury, by analysis of otolith morphometric. Significant differences are detected between Northeastern Atlantic and western Mediterranean Sea specimens of the 0+ age class (less than one year old). The implications of these results for the management of an emerging fishery are discussed.

Comparative analysis of population structure of endemic Western Atlantic hermit crab Loxopagurus loxochelis (Decapoda, Anomura) in two regions of state of Sao Paulo, Brazil

This work characterized the population structure of the hermit crab Loxopagurus loxochelis (Moreira, 1901) in terms of size frequency distribution and sex ratio. Specimens were collected monthly, over a period of one year (from July 2002 to June 2003), in seven transects (from 5 to 35 m of depth) using fishing boat equipped with two double-rig trawl nets, in Caraguatatuba and Ubatuba regions (state of Sao Paulo, Brazil). A total of 366 hermit crabs were collected in Caraguatatuba [222 males (60.65%), 114 non-ovigerous females (31.15%) and 30 ovigerous females (8.20%)] and 126 hermit crabs in Ubatuba [81 males (64.28%), 38 non-ovigerous females (30.16%) and seven ovigerous females (5.56%)]. In Caraguatatuba the highest incidence of ovigerous females occurred during winter (July 2002), whereas in Ubatuba, the number was incipient. The cephalothoracic shield length ranged from 2.0 to 7.9mm (5.29 +/- 0.96mm) in Caraguatatuba, and from 2.7 to 7.5mm (5.32 +/- 0.95mm) in Ubatuba. The mean size of males was significantly larger than the mean size of females in both regions. Overall sex ratio was in favor of males (1.54:1 in Caraguatatuba and 1.9:1 in Ubatuba). Sexual dimorphism was recorded to L. loxochelis by the presence of males in the largest size classes, following the standard pattern observed in Decapoda. There was an unimodal size distribution for both sexes, with normal distributions in both regions. The higher number of males in relation to females may indicate the existence of different growth and mortality rates between the sexes. Despite of the different geomorphologic characteristics between Caraguatatuba and Ubatuba regions, the dynamics of development was similar for both populations.

Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales

In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we measured oxygen- isotope ratios (δ18O) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (δ15N: δ13C) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in δ15N and δ18O values in the layer deposited at age 3, considered to be the one best representing the baseline of the breeding ground, in δ15N, δ13C and δ18O values in the period up to age 20, and in the ontogenetic variation of δ15N and δ18O values. These differences evidence that diet composition, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted.

Population structure and breeding season of the South Atlantic hermit crab, Loxopagurus loxochelis (Anomura, Diogenidae) from the Ubatuba region, Brazil

A population of Loxopagurus loxochelis was studied in terms of seasonal abundance, size frequency distribution, sex ratio, and reproductive period (percentage of ovigerous females). Specimens were collected monthly over a period of two years (from September 1995 to August 1997) in the non-consolidated areas of the Ubatuba, Mar Virado, and Ubatumirim bays (northern coast of São Paulo State, Brazil) with a double-rig trawl net. A total of 1,084 individuals were analysed. Animal size (minimum, maximum, and mean +/- SD shield length) was 2.8, 9.1, and 6.88 +/- 1.13 mm for 625 males; 2.8, 8.2, and 5.78 +/- 0.98 mm for 236 non-ovigerous females; and 4.6, 8.0, and 6.24 +/- 0.68 mm for 223 ovigerous females, respectively. Sexual dimorphism was recorded by the presence of males in the largest size classes. The sex ratio was 1.4 : 1 in favour of males. The highest incidence of ovigerous females occurred during winter and spring (June to October), with a low percentage in summer and fall (November to May), indicating continuity in the reproductive cycle. This strategy of reproduction is related to temperature. The occurrence of L. loxochelis in the Ubatuba region represents the final point of northern distribution of this species as a function of water mass influence, and could be its real limit on the Atlantic coast of South America.

Population structure, distribution and abundance patterns of the patagonian smoothhound Musmlus schmitti springer, 1939 (Chondrichthyes,Elasmobranchii, Triakidae) in the rio de la plata and inner continental shelf, SW Atlantic ocean (34 degrees-30'-39 degrees-30's)

A total number of 4824 Mustelus schmitti was sampled. Females ranged from 25 to 93 em in spring and from 28 to 90 cm in summer. Males ranged from 34 to 82 and from 28 to 77 cm, respectively. Length composition of the population showed significant differences between spring and summer being females larger than males. Total length distribution did not show significant differences between cruises. Males density varied significantly between cruises while for the females no significant variation was observed. In the spring cruise, both sexes occurred at depths lower than 50 in. Females occurred in the whole area with adult occurrence only above 35 degrees 30'S. Mature males occurred throughout the area, immature males occurring in two trawls in Samborombon Bay. The summer cruise showed a discontinuous distribution of the species along the study area resulting in spatial segregation in two groups with immature females predominating in both of them.

Population structure, distribution and abundance patterns of the patagonian smoothhound Mustelus schmitti Springer, 1939 (Chondrichthyes, Elasmobranchii, Triakidae) in the rio de La Plata and inner continental shelf , sw Atlantic ocean (34º30'-39º30'S)

Um total de 4824 Mustelus schmitti foi amostrado. As fêmeas apresentaram comprimento total de 25-93 cm na primavera e 28-90 cm no verão enquanto os machos apresentaram 34-82 e de 28-77 cm, respectivamente. A composição de comprimentos da população mostrou diferenças significativas entre primavera e verão sendo as fêmeas maiores do que os machos. A distribuição de comprimento total não variou significativamente entre cruzeiros. A densidade variou significativamente entre cruzeiros nos machos sendo que a variação não foi expressiva nas fêmeas. No cruzeiro da primavera, ambos os sexos ocorreram em profundidades menores do que 50 m, as fêmeas ocorrendo em toda a área de estudo, as adultas somente acima da latitude 35°30'S. Os machos adultos foram observados em toda a área sendo que os imaturos somente em dois arrastos na Bahia de Samborombón. O cruzeiro de verão mostrou uma distribuição descontínua da espécie ao longo da área de estudo, resultando na segregação espacial em dois grupos, com predominância de fêmeas imaturas em ambos.

Length-weight relationships, condition and population structure of the genus Atlantoraja (Elasmobranchii, Rajidae, Arhynchobatinae) in Southeastern Brazilian waters, SW Atlantic Ocean

During the present study, 107 specimens of Atlantoraja castelnaui, 188 of A. platana, and 770 of A. cyclophora, were obtained by commercial vessels operating in Southeastern Brazil from March 2005 to April 2006. Males of A. castelnaui ranged from 17.9-111.0 cm and females from 17.4-116.0 cm total length. Males of A. platana ranged from 13.1-70.0 cm and females from 12.5-76.0 cm total length. Males of A. cyclophora ranged from 13.3-58.5 cm and females from 11.5-68.0 cm total length. Length-weight curves were sexually dimorphic in the three species. The analysis of the angular coefficient (b) demonstrated that growth (in weight) in relation to length was allometric (b>3) in males of A. castelnaui and A. platana, while isometric (b = 3) in females of these species. Conversely, growth of A. cyclphora was isometric in males, while in females it was allometric (b>3). The condition factor varied significantly throughout the year only in females of A. castelnaui.

Population structure and canopy use by Coussapoa microcarpa, a strangler hemiepiphyte from the Brazilian Atlantic Forest

We studied density, size structure, and establishment sites of Coussapoa microcarpa in the Brazilian Atlantic rain forest. This species is a hemiepiphyte that begins its life in the tops of trees and survives the death of its host to become a free-standing tree. All individuals of C. microcarpa already rooted in the ground were recorded in a 3.43 ha (1.75 ha in lowland and 1.68 ha in submontane) sample of forest plots. Data on total height, root diameter at breast height, host height and diameter at breast height, as well as height, type and diameter of the establishment site were collected. Coussapoa microcarpa present a high density (36.5 ind. ha-1) and the population studied was composed mainly of young individuals. Young and adults differed in establishment sites. The diameter of establishment sites of young was narrower than the diameter of establishment sites of adults, which points out to a limiting factor (diameter of establishment site) regulating the establishment of C. microcarpa. © 2013 Cambridge University Press.

Initial description of the phylogeography, population structure and genetic diversity of Atlantic spotted dolphins from Brazil and the Caribbean, inferred from analyses of mitochondrial and nuclear DNA

We provide initial information regarding the population structure and genetic diversity of Stenella frontalis from the Caribbean and southeastern Brazil from analyses of mitochondrial control region sequences and sequences from the first intron of the α-lactalbumin gene. Comparisons with previously described S. frontalis sequences showed a high number of haplotypes shared between populations throughout their distribution range. High diversity was found for southeastern Brazil and Caribbean samples, and population structure analyses indicate significant differentiation among population units at the FST level, but not at the ΦST level. Significant differentiation at the FST level was found between the Caribbean population unit and all other populations units. These results suggest historical or present connectivity between the Azores and Madeira and the southeastern Brazil groups and population differentiation between the Caribbean and southeastern Brazil, supporting the notion of two separate stocks in the waters around the Atlantic coast of South America. © 2013 Elsevier Ltd.

Population structure of Lutjanus purpureus (Lutjanidae - Perciformes) on the Brazilian coast: further existence evidence of a single species of red snapper in the western Atlantic

ABSTRACT: The present study focus on the mitochondrial control region to investigate phylogeographic patterns and population structure in Lutjanus purpureus, and to evaluate the genetic similarity between L. purpureus and L. campechanus. For the initial analysis, 810 base pairs sequence from control region were obtained from 239 specimens of L. purpureus collected from four localities off the Brazilian coast. The results revealed the presence of a single panmictic population characterized by high values of genetic diversity. The 299 base pairs hypervariable portion were used for the combined analysis of L. purpureus and L. campechanus, being 275 haplotypes identified in the 414 specimens. Phylogenetic tree and haplotype network did not indicate phylogeographic substructuring between the two species, but rather an intense intermingling of individuals. Considering their marked morphological similarity, the molecular data presented here indicatethat only one species of red snapper exists in the western Atlantic.

Distribution and population structure of the flecked box crab Hepatus pudibundus (Decapoda, Brachyura) in the western South Atlantic

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Population structure of a native and an alien species of snail in an urban area of the Atlantic Rainforest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Assessment of the population structure and temporal changes in spatial dynamics and genetic characteristics of the Atlantic bluefin tuna under a fishery independent framework.

As a large and long-lived species with high economic value, restricted spawning areas and short spawning periods, the Atlantic bluefin tuna (BFT; Thunnus thynnus) is particularly susceptible to over-exploitation. Although BFT have been targeted by fisheries in the Mediterranean Sea for thousands of years, it has only been in these last decades that the exploitation rate has reached far beyond sustainable levels. An understanding of the population structure, spatial dynamics, exploitation rates and the environmental variables that affect BFT is crucial for the conservation of the species. The aims of this PhD project were 1) to assess the accuracy of larval identification methods, 2) determine the genetic structure of modern BFT populations, 3) assess the self-recruitment rate in the Gulf of Mexico and Mediterranean spawning areas, 4) estimate the immigration rate of BFT to feeding aggregations from the various spawning areas, and 5) develop tools capable of investigating the temporal stability of population structuring in the Mediterranean Sea. Several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials are reviewed. Barcoding of scombrid larvae revealed important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. Using a Genotyping-by-Sequencing a panel of 95 SNPs was developed and used to characterize the population structuring of BFT and composition of adult feeding aggregations. Using novel molecular techniques, DNA was extracted from bluefin tuna vertebrae excavated from late iron age, ancient roman settlements Byzantine-era Constantinople and a 20th century collection. A second panel of 96 SNPs was developed to genotype historical and modern samples in order to elucidate changes in population structuring and allele frequencies of loci associated with selective traits.