Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences

Genetic variation and evolutionary demography of the shrimp Fenneropenaeus chinensis were investigated using sequence data of the complete mitochondrial control region (CR). Fragments of 993 bp of the CR were sequenced for 93 individuals from five localities over most of the species' range in the Yellow Sea and the Bohai Sea. There were 84 variable sites defining 68 haplotypes. Haplotype diversity levels were very high (0.95 ± 0.03-0.99 ± 0.02) in F. chinensis populations, whereas those of nucleotide diversity were moderate to low (0.66 ± 0.36%-0.84 ± 0.46%). Analysis of molecular variance and conventional population statistics (FST ) revealed no significant genetic structure throughout the range of F. chinensis. Mismatch distribution, estimates of population parameters and neutrality tests revealed that the significant fluctuations and shallow coalescence of mtDNA genealogies observed were coincident with estimated demographic parameters and neutrality tests, in implying important past-population size fluctuations or range expansion. Isolation with Migration (IM) coalescence results suggest that F. chinensis, distributed along the coasts of northern China and the Korean Peninsula (about 1000 km apart), diverged recently, the estimated time-split being 12,800 (7,400-18,600) years ago

Genetic population structure of penaeid prawns Penaeus monodon Fabricius 1798, Fenneropenaeus indicus H. Milne Edwards 1837 and Metapenaeus monoceros Fabricius 1798 in the Malindi–Ungwana Bay, Kenya

Thesis (MSc)--Stellenbosch University, 2013.ENGLISH ABSTRACT: Comparative analyses of genetic diversity, population structure and evolutionary relationships among co–distributed species can provide useful insights into fisheries management. In this study, mitochondrial DNA control region (mtCR) sequences were used to investigate genetic population structure and recruitment patterns of three co–occurring shallow water penaeid prawn species; Penaeus monodon, Fenneropenaeus indicus and Metapenaeus monoceros. These taxa dominate artisanal and commercial prawn catches in the Malindi–Ungwana Bay in Kenya, where juvenile prawns inhabit estuarine habitats, and adults occur further offshore, on mudbanks in the bay. A total of 296 [i.e. (P. monodon; n = 129), (F. indicus; n = 96), (M. monoceros; n = 71)] specimens were sampled from five sites; two estuarine nursery areas (juveniles), a nearshore mid–station (adults), and two offshore areas (adults). The sites were chosen to represent the bulk of the Kenyan fishery activities, and to include juvenile and adult cohorts that are presumably connected to each other through larval dispersal processes and migrations. Juveniles were obtained during 2010 from local fishermen, and adult prawns during 2011 using a commercial prawn trawler. Analysis of the mtCR sequences indicated high haplotype diversity (P. monodon; h = 0.9996 ± 0.0010; F. indicus; h = 0.9998 ± 0.0015; M. monoceros; h = 0.9815 ± 0.0110) for all three species. Genetic differentiation results for each species using AMOVA indicated no significant population differentiation (P. monodon; ΦST = 0.000, = p > 0.05; F. indicus; ΦST = 0.000, = p > 0.05; M. monoceros; ΦST = 0.0164, = p > 0.05) and pairwise ΦST statistics among sampling sites indicated the complete absence of spatial differentiation of female genes for all three species. In addition, the mtDNA data of P. monodon (i.e. n = 103) was augmented by using six polymorphic nuclear microsatellite loci. The pattern of panmixia was supported by the microsatellite analyses of P. monodon where AMOVA (i.e. RST = 0.00113, = p > 0.05), pairwise RST statistics (i.e. RST = 0.0000–0.0223, = p > 0.05) and STRUCTURE all confirmed the complete absence of genetic differentiation, among all sampled localities. Based on the absence of genetic population structure, each of the three species can be regarded as a single management unit throughout the Malindi–Ungwana Bay area. Spatial management strategies for prawn fisheries in the bay should therefore rely on factors other than genetic metapopulations, such as seasonal prawn recruitment and distribution patterns, ecosystem functioning and socio–economic implications to fishing communities and commercial trawl fishing companies.AFRIKAANSE OPSOMMING: Vergelykende analise van genetiese diversiteit, bevolkings stuktuur en evolutionêre verwantskappe tussen spesies wat 'n verspreidingsgebied deel kan nuttige insigte lewer oor vissery bestuur. In hierdie studie was die mitokondriale DNS kontrole area (mtCR) volgordebepalings gebruik om die bevolkings genetiese stuktuur en werwingspatrone van drie mede-verspreide vlak water penaeid garnaal spesies; Penaeus monodon, Fenneropenaeus indicus and Metapenaeus monoceros te ondersoek. Hierdie taksa domineer die ambagtelike en kommersiële vangste in die Malindi-Ungwanabaai in Kenya waar, onvolwasse garnale in riviermondings voorkom en volwassenes in dieper waters op modderbanke in die baai voorkom. 'n Totaal van 296 [(P. monodon; n = 129), (F. indicus; n = 96), (M. monoceros; n = 71)] monsters was geneem vanaf vyf lokaliteite; twee in riviermondings (onvolwassenes), 'n nabykus mid stasie (volwasse) en twee diep water (volwasse) areas. Hierdie lokaliteite was gekies om die oorgrote meerderheid van Kenya se vissery aktiwiteite, asook die onvolwasses en volwassene kohorte te verteenwoordig wat vermoedelik geneties verbind is aan mekaar deur larwale verspreidingsprosesse en migrasies. Onvolwasse diere was verkry in 2010 vanaf plaaslike vissermanne en volwasse diere was in 2011 gekollekteer deur gebruik te maak van 'n kommersiële garnaal vissersboot. Analise van die mtCR volgorde bepaling het gewys dat daar 'n hoë haplotipiese diversiteit (P. monodon; h = 0.9996 ± 0.0010; F. indicus; h = 0.9998 ± 0.0015; M. monoceros; h = 0.9815 ± 0.0110) vir al drie spesies bestaan. Genetiese differensiasie resultate vir elke spesie, bepaal deur 'n AMOVA toets, dui op geen beduidende bevolking differensiasie nie (P. monodon; ΦST = 0.000, = p > 0.05; F. indicus; ΦST = 0.000, = p > 0.05; M. monoceros; ΦST = 0.0164, = p > 0.05) en paarsgewyse ΦST statistiek tussen die lokaliteite waar monsters geneem was, dui op geen ruimtelike differensiasie van die vroulike gene in al drie spesies nie. Hierbenewens is die mtDNS datastel van P. monodon (i.e. n = 103) uitgebrei deur ses polimorfiese kern mikrosatelliete in te sluit. Die patroon van mtCR panmixia was ondersteun deur die mikro-satelliet analise van P. monodon waar die AMOVA (i.e. RST = 0.00113, = p > 0.05), paarsgewyse RST statistiek (i.e. RST = 0.0000-0.0223, = p > 0.05) en STRUCTURE bevestig het dat daar totale afwesigheid is van genetiese differensiasie tussen alle vergelyk-te lokaliteite. Gebaseer op die afwesigheid van genetiese bevolking-struktuur kan elk van die drie spesies beskou word as 'n enkele bestuurseenheid deur die Malindi-Ungwanabaai area. Die bestuurstrategieë vir garnaal vissery aktiwiteite in die baai moet dus steun op ander faktore as genetiese meta-bevolking. Belangrike faktore om in ag te neem is seisoenale garnaal werwing en verspreidings patrone, ekosisteem funksionering en sosio-ekonomiese implikasies van vissers gemeenskappe en kommersiële visserymaatskappye

Population genomics of the giant black tiger shrimp Penaeus monodon to understand wild fishery and aquaculture production

Nga Vu investigated the genetic structure of black tiger shrimp within the Indo-Pacific using genome-wide markers. She found evidence for the existence of genetic adaptation within and among populations as a consequence of geographic distance and/or environmental conditions. Her research will be used by the aquaculture industry to identify populations to use as foundation animals for genetic improvement programs

Genetic Management of the Atlantic halibut (Hippoglossus hippoglossus)

The Atlantic halibut (Hippoglossus hippoglossus) was selected as a new aquaculture candidate towards diversification from salmonid culture. The species was chosen because of its high market value and perceived good growth in the cold waters of the target farming regions. Extensive and collaborative research efforts formed the basis for the culture of this benthic marine species. Broodstock populations were established from a limited number of wild individuals due to the high costs involved in their capture. First generation hatchery reared offspring are now being selected as replacements but with no knowledge of a broodstock replacement strategy to manage this valuable genetic resource and to maximize the potential of this species the industry runs the risk of genetic degradation with the associated problems of inbreeding depression. This thesis investigates the processes involved with developing a genetic management strategy, using genetic profile technology, based on a population in Scotland at Otter Ferry Seafish Ltd. The level of genetic variability of 70 individuals in the parental population and 802 of their offspring (F1) in two year classes (1995 and 1998) was assessed at 7 microsatellite loci. The parental population which was comprised of three different stocks was genetically diverse, however, when compared with their offspring, substantial reductions in genetic variation, as judged by allelic diversity, were observed. The parentage of these F1 individuals was determined by exclusion principles and 91% of all the offspring genotyped were unambiguously assigned to a single parental pair. The assignment revealed that only half of the parents succeeded in contributing to the F1 generation. This problem was compounded by the fact that the family sizes were highly skewed such that the entire population consisted of a small number of large families resulting in an unacceptably low effective population size of 8.11. The inbreeding coefficient in the F1 generation was 6.16% however this differed markedly between the 1995 (7.74%) and 1998 (10.64%) year classes. The repeatability of reproductive performance defined by five performance traits reflecting quantity and quality of eggs, frequency of stripping events and viability was assessed by REML using data collected over three spawning seasons from 239 F1 females. The phenotypic correlations obtained between quality and quantity traits were low in magnitude and the study showed that with the exception of seasonal activity, all traits studied improved with age. There was also an effect of photoperiod in that fish kept under a 4 month-delayed regime did not perform as well as the fish under a one-month extended regime. Of all five traits, only volume of eggs collected was repeatable (r=0.37±0.07). This suggests that it is the only reproductive character influenced by the fish and all other traits, especially those pertaining to egg quality are determined by management practices. The heritability of body weight at four stages in the growout phase of production was estimated by REML using data from 486 F1 individuals. These animals were reared in two different sites, a land based tank and a sea cage. Significant effects of site, sex and grade were observed and by the end of the trial the average weight of fish in land based system was higher by 2 kg. Females were over 3 kg heavier than males and this difference was attributed to precocious maturation while fish in the smaller grade were consistently though decreasingly lighter than their larger counterparts. Heritabilities, derived from sire, dam and combined estimates ranged from 0.09 to 0.53 with wide confidence intervals. The poor precision of the estimates was due to the highly imbalanced family structure and the small number of offspring studied. Values varied depending on the age of fish and the source of variance used to estimate them. Heritabilities increased with age and although sire estimates were higher than dam estimates these differences were tested and the results obtained consistent with the conclusion that they represent nothing more than chance. The results suggested that selection for increased body weight in the halibut was likely to be successful. Based on the findings of the study a genetic management strategy for the Atlantic halibut was proposed structured on controlling the rate of inbreeding and a theory of domestication. The need to introduce additional individuals into the population was strongly recommended

Communal or Separate Rearing of Families in Selective Breeding of Common Carp (Cyprinus carpio L.)

This study reports on investigation of ways of improving the breeding programme for growth-related traits in common carp in Vietnam. The base population was synthesized following a single pair mating scheme from six carp stocks: (1) 2nd generation of family selection; (2) Hungarian 6th generation of mass selection; (3) Hungarian scaled carp; (4) Indonesian yellow 6th generation of mass selection; (5) Indonesian yellow carp; and (6) Vietnamese 6th generation of mass selection. The next two selected generations were produced using a partial factorial mating scheme, with each family being split and reared using communal early rearing (CER) or separate early rearing (SER) methods. The second generation (G2) was produced from selected fish from the CER G1 group. The total number of selection, control and reference families was 135 in the G1 and 101 in the G2 respectively. The control and reference (Hungarian P33 line) families were produced by single pair mating (reference families with the G2 only). Seven microsatellite loci were used for parentage assignment in the CER groups: 96.8% of the offspring (1284 individuals) and 96.2% offspring (1341 individuals) were unambiguously assigned to 113 families (selection, control) in the G1 and 99 families (selection, control and reference) in the G2 generations, respectively. Restricted maximum likelihood in the individual model was used to estimate phenotypic and genetic parameters. In CER, the estimated heritability values of common carp were from 0.20 ± 0.04 to 0.29 ± 0.05 for both weight and length at final harvest, indicating substantial additive genetic variation for selection on growth-related traits. The overall obtained maternal and common environmental effects were consistently close to zero. The average of direct response to selection for body weight was 15.0% per generation. In SER, the number of families in the G1 and G2 were 135 (selection and control) and 101 (selection, control and reference), respectively. The heritability estimates were from 0.20 ± 0.07 to 0.31 ± 0.08 at final measurement. Common environmental (full-sib family) effect were all lower at tagging and slightly higher at last measurement, ranging from 0.05 to 0.22. The response in each generation of selection as the difference between the selection and control lines was 8.1% on average for weight at final harvest, lower than under CER. The high genetic correlations of growth-related traits between the third (one year old, mature) and second (7 months old) measurements could allow selection to be based on the earlier assessment, reducing handling stress close to spawning. The benefits of using microsatellite markers to ascertain parentage, achieve greater growth rate (close to farming systems), shorten time to maturity and selection, and the overall relative merits of using CER v’s SER in this genetic improvement programme are discussed

Resource enhancement and sustainable aquaculture practices in Southeast Asia: challenges in responsible production of aquatic species : proceedings of the international workshop on resource enhancement and sustainable aquaculture practices in Southeast Asia 2014 (RESA)

The conference was held in order to promote and augment regional initiatives on resource enhancement and sustainable aquaculture practices, and to contribute to poverty alleviation, livelihood and food security in Southeast Asia. The contributions of the selected participants during the conference which are contained in this volume are cited individually.The Government of Japan through the Trust Fund Programs of the SEAFDEC Secretariat provided financial support for the conduct of the International Workshop on Resource Enhancement and Sustainable Aquaculture practices in Southeast Asia in March 2014 in Iloilo, Philippines, as well as, the publication of this proceedings. The editors also acknowledge the efforts of the Publication Review Committee of SEAFDEC/AQD especially Dr. Relicardo M. Coloso, Dr. Maria Lourdes Cuvin-Aralar, Dr. Evelyn Grace de Jesus Ayson, Dr. Rolando Pakingking and Dr. Myrna B. Teruel for reviewing the draft of the proceedings prior to its publication. Thanks are also due Ms. Imee S. Hacla for the copy-editing and layout.Collapse All Expand AllFOREWORDMESSAGESKEYNOTE ADDRESSPREFACEACKNOWLEDGEMENTSPLENARY PAPERSIs small-hold tropical aquaculture in a genetic plunge towards extinction?Roger W. DoyleRapid adaptation to a new environment: is it reversible?Hitoshi ArakiCOUNTRY PAPERSCambodiaCurrent status of sustainable aquaculture in CambodiaOuch LangJapanStatus of resource enhancement and sustainable aquaculture practices in JapanKoichi Okuzawa, Takayuki Takebe, Narisato Hirai and Kazumasa IkutaMalaysiaStatus of resource management and aquaculture in MalaysiaAishah YusoffMyanmarInland fisheries resource enhancement and conservation practices in MyanmarHtun TheinPhilippinesThe Philippine National Aquasilviculture ProgramRomeo E. Dieta and Florida C. DietaViet NamGood aquaculture practices (VietGAP) and sustainable aquaculture development in Viet NamNguyen Thi Bang TamLao PDRCountry status on sustainable aquaculture in Lao PDRThongkhoun KhonglalianeSingaporeCurrent status of aquaculture in SingaporeNeo Chin HengIndonesiaSustainable aquaculture and resources enhancement inIndonesiaSetiawan Soetardjo and Irham AdhityaThailandMilkish: new choice for aquaculture in ThailandPrapat KosawatpatCONTRIBUTED PAPERSAssessment of humphead wrasse (Cheilinus undulatus), spawningaggregations and declaration of marine protected area as strategy for enhancement of wildstocksFilemon G. Romero and Akkil S. InjaniStock assessment of christian crabs (Charybdis feriatus, Linnaeus,1758)in San Miguel bayPlutomeo M. Nieves, Nelson R. Olfindo and Aldrin Mel MacaleAbalone aquaculture for stock enhancement and community livelihoodproject in northern Palawan, PhilippinesBenjamin J. GonzalesSocial preparations towards community-based approach to stockenhancement in Sagay Marine Reserve, PhilippinesNerissa D. Salayo, Raisa Joy G. Castel, Dianne Hope M. Tormon, Rafael T. Barrido, MarieFrancesJ. Nievales and Teruo AzumaCommunity-based shrimp stock enhancement for coastal socio-ecological restoration in the PhilippinesJon Altamirano, Hisashi Kurokura, Nerissa Salayo, Didi Baticados, Jee Grace Suyo and Satoshi IshikawaBFAR-CHED Philippine National Aquasilviculture Program (PNAP) in BataanRudy C. Flores, Felicisima E. Tungol, Abraham S Antonio, Elizabeth D. Medairos and Jonathan M.SalasMarine fish hatchery: developments and future trendsClarissa L. Marte and Joebert D. ToledoHatchery management techniques for tiger-tail seahorse (Hippocampus comes)Shelah Mae B. Ursua and Teruo AzumaUpdates on the seed production of mud crabEmilia T. Quinitio, Fe D. Parado-Estepa, Joana Joy Huervana and Michael Ray BurlasMarker-aided genetic stock management: prospects in Philippine Aquatic Biodiversity conservation and aquacultureMaria Rowena R. Romana-Eguia, Minoru Ikeda and Akihiro KijimaFeed formulation for sustainable aquacultureRelicardo M. ColosoPotential of cowpea (Vigna unguiculata L.) meal as an alternativeprotein source in diets for giant freshwater prawn (Macrobrachium rosenbergii, de Man 1879)Frolan A. Aya, Maria Lourdes Cuvin-Aralar and Relicardo M. ColosoApplication of the United States Soybean Export Council program's soy-optimized floating feeds and low volume, high density cage aquaculture technologiesLevy Loreto L. Manalac, Michael Cremer, Hsiang Pin Lan and Lukas ManomaitisUtilization of sensors and SMS technology to remotely maintain thelevelof dissolved oxygen, salinity and temperature of fishpondsRodrigo C. Munoz, Reynan P. Calderon, Rudy C. Flores, Sisenando C. Masangcap, Jayson P.Angelesand Mark ColentavaReaching the poor through aquaculture: The case of technologyadoptionin rural communities at west central PhilippinesDidi B. BaticadosMarine biodiversity at the SEAFDEC/AQD research stations in IloiloandGuimaras, PhilippinesTeodora Uy BagarinaoTargeting essential gene utilizing RNA interference to protect theailing shrimp/prawn industry against WSSVJassy Mary S. Lazarte and Mary Beth B. ManingasABSTRACTS OF ORAL PRESENTATIONSSEAFDEC/AQD stock enhancement initiatives: releasestrategiesMa. Junemie Hazel Lebata-Ramos, Ellen Flor Doyola-Solis, Rema Sibonga, Joemel Sumbing, Jeff Bogart Abroguena, August Santillan and Mark DimzonResponsible shrimp culture through ecological approachEleonor A. TendenciaEstimation of energy budget of sea cucumber, Holothuria scabra, in integrated multi-trophic aquacultureSatoshi Watanabe, Masashi Kodama, Zenith Gaye A. Orozco, Joemel G. Sumbing, Schedar Rose M. Novilla and Ma. Junemie Hazel Lebata-RamosPost-larval rearing strategies in sandish (Holothuria scabra) cultureMarie Frances Nievales, Rema Sibonga and Harold FiguradoInduced breeding of giant trevally, maliputo (Caranx ignobilis)Ma. Theresa M. Mutia, Frederick B. Muyot and Myleen L. MagistradoSeed production of the blue swimming crab (Portunus pelagicus)Nonita S. Cabacaba and Jimmy E. SalamidaPotential genetic impacts of hatchery-based resource enhancementZubaida U. BasiaoGood aquaculture practices (GAqP): setting directions for harmonized regional standards - the Philippine experienceMark F. Matubang and Nelson A. LopezThe importance of mangroves to capture and culture fisheriesJurgenne H. PrimaveraStock enhancement? Why botherJose InglesABSTRACTS OF POSTER PRESENTATIONSResource assessment of sea cucumber in northern Iloilo, central PhilippinesPerry A. Alpasan and Romy A. BillonesOptimization of feeding and growth conditions for hatchery-bred larvae of indigenous Philippine silver perch, Leiopotherapon plumbeus (Perciformes: Terapontidae)Julie Andrea Añano, Frolan Aya, Mark Nell Corpuz and Maria Rowena R. Romana-EguiaDevelopment of a simple, rapid, cost-effective diagnostic kit for WSSVPocholo Mari T. Arabit, Amalea Dulcene D. Nicolasora, Patrick Ellis Z. Go, Christopher Marlowe A. Caipang and Mary Beth B. ManingasLarval rearing of silver therapon (Leiopotherapon plumbeus) in outdoor tanksFrolan A. Aya, Vicar Stella N. Nillasca, Mark Nell C. Corpuz and Luis Maria B. GarciaPreliminary trials on the effects of weaning and larval diets on survival and growth of silver therapon (Leiopotherapon plumbeus) larvaeFrolan A. Aya , Vicar Stella N. Nillasca and Luis Maria B. GarciaA preliminary study on the diagnosis of coral reef healthiness and establishment of coral replenishment technologyTeruo Azuma, Jemar Jed Roble Tan, Jacques Zarate, Jon Altamirano, Joey Gatus and Filipina SottoPreliminary assessment of the abundance and fishery of snapping shrimp (Alpheus sp.) in Calape, Bohol, PhilippinesJomel G. Baobao, Maria Danesa S. Rabia and Ernesto C. RulidaModelling the impact of different stress agents on Holothurian immunityLiudmila S. DolmatovaGrowth and survival of nile tilapia (Oreochromis niloticus) juveniles fed diets with varying levels of irradiated chitosanKristine Gonzales, Mark Nell Corpuz and Maria Rowena R. Romana-EguiaPerceptions on the effects of maritime activities on the Philippine aquatic ecosystemEnrique Java, Teresita Cruz and Isidro Yonggue HernandezPreliminary trials on the optimization of hormone dosages for induced breeding of Philippine silver perch, Leiopotherapon plumbeusMark Archei O. Javier, Frolan A. Aya and Maria Rowena R. Romana-EguiaDistribution and abundance of hard clam shells Meretrix meretrix along the coastal areas of Panguil bay, Lanao del Norte, PhilippinesCelestina Q. Jumawan , Rheino B. Palma and Renalyn O. SiaGrowth performance of brackishwater enhanced selected tilapia (BEST) reared in brackishwater pondsAnecito V. Labastida, Celestina Q. Jumawan, Antonio A. Abogado, Rheino B. Palma and Jerome J. SabilloFirst record of Laem-Singh virus in black tiger shrimp (Penaeus monodon) in the PhilippinesChristian Albert M. Cruz, Precious C. dela Cruz, Paul Christian D. Alcala, Florenz Giovanni M. Tagle, Erickson S. Santos, Mudjekeewis D. Santos and Mary Beth B. ManingasReproductive biology of christian crabs (Charybdis feriatus, Linnaeus, 1758) in San Miguel Bay, PhilippinesPlutomeo M. Nieves, Nelson R. Olfindo and Aldrin Mel MacaleShrimp metabolism: The roles of lactate dehydrogenase (c31), glycogen phosphorylase (c34) and protein kinase (PK) as revealed by RNA interferenceMaria Violeta R. Tare, Hidehiro Kondo, Ikuo Hirono and Mary Beth B. ManingasSUMMARY OF THE WORKSHOPANNEXESANNEX 1. Workshop CommitteesANNEX 2. Directory of Participants</div

Biodiversidade e evolução molecular da classe malacostraca

Doutoramento em BiologiaNo actual cenário de perda acelerada de biodiversidade, o nosso conhecimento dos ecossistemas marinhos, apesar da sua extensão e complexidade, continua muito inferior ao dos ecossistemas terrestres. A classe Malacostraca (Arthropoda, Crustacea), um grupo dos mais representativos nos ecossistemas marinhos, apresenta um elevado nível de diversidade morfológica e ecológica, mas difícil sua identificação ao nível de espécie requer frequentemente a ajuda de especialistas em taxonomia. A utilização recente do “barcoding” (código de barras do ADN), revelou ser um método rápido e eficaz para a identificação de espécies em diversos grupos de metazoários, incluindo os Malacostraca. No âmbito desta tese foi construída uma base de dados de código de barras de ADN envolvendo 132 espécies de Malacostraca vários locais de amostragem no Atlântico Nordeste e Mediterrâneo. As sequências de ADN mitocondrial provenientes de 601 espécimes formaram, em 95% dos casos, grupos congruentes com as identificações baseadas em características morfológicas. No entanto, foi detectado polimorfismo em seis casos e a divergência intra-específica foi elevada em exemplares pertencentes a duas espécies morfológicas, sugerindo, neste caso, a ocorrência de especiação críptica. Este estudo confirma a utilidade do código de barras de ADN para a identificação de Malacostraca marinhos. Apesar do sucesso obtido, este método apresenta alguns problemas, como por exemplo a possível amplificação de pseudogenes. A ocorrência de pseudogenes e as possíveisabordagens para a detecção e resolução deste tipo de problemas são discutidas com base em casos de estudo: análises dos códigos de barras ADN na espécie Goneplax rhomboides (Crustacea, Decapoda). A análise dos códigos de barras ADN revelou ainda grupos prioritários de decápodes para estudos taxonómicos e sistemáticos, nomeadamente os decápodes dos géneros Plesionika e Pagurus. Neste âmbito são discutidas as relações filogenéticas entre espécies seleccionadas dos géneros Plesionika e Pagurus. Este trabalho aponta para várias questões no âmbito da biodiversidade e evolução molecular da classe Malacostraca que carecem de um maior esclarecimento, podendo ser considerado como a base para estudo futuros. Análises filogenéticas adicionais integrando dados morfológicos e moleculares de um maior número de espécies e de famílias deverão certamente conduzir a uma melhor avaliação da biodiversidade e da evolução dentro da classe.The biodiversity of many habitats is under threat and although seas cover the majority of our planet’s surface, far less is known about the biodiversity of marine environments than that of terrestrial systems. The complexity of its species and ecosystems is immense. Marine malacostraca are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some malacostraca. Moreover, the generation of a larger comparative database allows additional insights into the tempo and mode of molecular evolution. Indeed, examination of diversity at the COI region yields an informative framework to identify and explore priority issues, demanding in turn a fully integrative approach utilising additional molecular, distributional and ecological information. Here we expand the DNA barcode database with a case study involving more than 132 malacostracan species from the Northeast Atlantic Ocean and Mediterranean Sea. DNA sequences from around 601 specimens grouped into clusters corresponding to known morphological species in 95% of cases. However shared polymorphism between sister-species was detected in six species. Intraspecific divergence was high in specimens belonging to two morphological species, suggesting the occurrence of cryptic speciation, allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.This study reconfirms the usefulness of DNA barcoding for the identification of marine malacostraca, despite complexities that sometimes arise due to pseudogenes (numts). Here, we study the effect of numts on DNA barcoding based on barcoding analyses in decapoda species: Goneplax rhomboides. DNA barcodes reveal priority groups for taxonomic and systematic focus of decapods. Here we discussed two cases of phylogenetic relationships among selected species of Plesionika and Pagurus, respectively. Issues relating to the molecular biodiversity and evolution of the Malacostraca arising from this study allow identification of future priorities. Further phylogenetic analyses including morphological and molecular data of selected families is required, especially encompassing broad geographic and ecological coverage, will lead to an improved evaluation of the biodiversity and evolution among selected Malacostraca specie

The future of cephalopod populations, fisheries, culture, and research in Europe

International audienc

Applications of microsatellite markers to genetic management of carps in aquaculture

Carp aquaculture in South Asia suffers severely from a lack of genetic management, which has eroded the genetic quality of both captive and wild populations. Use of molecular markers, especially microsatellites, has revolutionized genetic management of hatchery stocks through its ability to detect kinship between individuals and hence in controlling level of inbreeding and loss of genetic diversity. In the present PhD work, microsatellite markers were applied to breeding programmes for silver carp (Hypophthalmichthys molitrix) and common carp (Cyprinus carpio) to study different genetic management aspects and new markers were generated from rohu (Labeo rohita). A set of newly isolated microsatellite markers from silver carp were characterized and two pentaplex PCR reactions were optimized to enable rapid genotyping of large number of individuals at 10 microsatellite loci. The utility of these markers in parentage, sibship and relatedness analysis were assessed by applying them to groups of fish with known relationship. These markers were used for parentage analysis in a breeding programme designed to estimate heritability of harvest weight and length in silver carp. Full- and half-sib families were created in three sets of partly factorial mating and all the families from each set were reared in communal ponds from very early life stages. With ten microsatellites 96.3% of the offspring could be assigned to a single family. Heritability estimates were found to be 0.65 ± 0.13 for weight and 0.50 ± 0.13 for length. High estimates of h2 suggested that this population should respond rapidly to selection for increased harvest size. Microsatellite markers were also applied to monitor the early stages of a mass selection programme in common carp (Cyprinus carpio). The selection was initiated from a base population synthesized from six different stocks. The selected individuals were divided to create two separate lines. The aims of this study were to monitor whether the stocks were represented in the intended proportions in the F1 selected populations, to investigate the relative contribution of families and its impact on effective population size and to identify any loss of molecular genetic variation. Five highly polymorphic microsatellites were used for parentage analysis of the selected fish to track stock and family contribution. Overall, large perturbations were observed in the relative contributions of two major stocks. Family contribution was also highly variable, causing the Ne to drop to below half the census size. A loss of 6.9%-12.2% of microsatellite alleles was observed but loss of heterozygosity was not very prominent. The replicate lines showed significant differences in allelic distribution after the first generation of selection, but not in genotypic distribution. Finally, 52 microsatellite markers were isolated from a partial genomic library of rohu using a selective hybridization protocol. Characterization of these markers resulted in 36 polymorphic loci, which will be useful in future work on conservation and management of both wild and captive rohu populations