Mendelian inheritance, linkage and genotypic disequilibrium in microsatellite loci isolated from Hymenaea courbaril (Leguminosae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Fluxo de pólen e sementes em população isolada de Copaifera langsdorfii Desf. (LEGUMINOSAE - CAESALPINIOIDEAE) em um fragmento florestal localizado em área urbana

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Uso de marcadores microssatélites para estimar parentescos dentro de progênies de polinização aberta de espécies arbóreas dióicas: um estudo de caso de Myracrodruon urundeuva (F.F. & M.F. Allemão)

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

Variabilidade genética de população selecionada e teste de paternidade de uma progênie de polinização aberta de Eucalyptus Grandis Hill ex Maiden

Pós-graduação em Ciência Florestal - FCA

Avaliação da variabilidade genética em uma população base de Eucalyptus camaldulensis Dehnh para fins de conservação e melhoramento genético

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

Development and characterization of 32 microsatellite loci in Genipa americana (Rubiaceae)

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

Development and characterization of microsatellite markers for Vriesea simplex (Bromeliaceae) and cross-amplification in other species of Bromeliaceae

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo hierárquico do sistema de reprodução entre e dentro de frutos, fluxo de pólen e estrutura genética espacial em um fragmento e em árvores isoladas na pastagem de hymenaea stigonocarpa mart. ex hayne na região de cerrado

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

DEVELOPMENT OF MICROSATELLITE PRIMERS FOR JATROPHA CURCAS (EUPHORBIACEAE) AND TRANSFERABILITY TO CONGENERS

Premise of the study: Microsatellite primers were developed for Jatropha curcas (Euphorbiaceae), a tree species with large potential for biofuel production, to investigate its natural genetic diversity and mating system to facilitate the establishment of tree improvement and conservation programs. Methods and Results: Using a protocol for genomic library enrichment, 104 clones containing 195 repeat motifs were identified. Primer pairs were developed for 40 microsatellite loci and validated in 41 accessions of J. curcas from six provenances. Nine loci were polymorphic revealing from two to eight alleles per locus, and six primers were able to amplify alleles in the congeners J. podagrica, J. pohliana, and J. gossypifolia, but not in other Euphorbiaceae species, such as Hevea brasiliensis, Manihot esculenta, or Ricinus communis. Conclusions: The primers developed here revealed polymorphic loci that are suitable for genetic diversity and structure, mating system, and gene flow studies in J. curcas, and some congeners.

DEVELOPMENT OF MICROSATELLITE MARKERS FOR ANADENANTHERA COLUBRINA (LEGUMINOSAE), A NEOTROPICAL TREE SPECIES

Premise of the study: We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. Methods and Results: Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirao Preto in Sao Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. Conclusions: A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.

Isolation and characterization of microsatellite loci from mother-of-millions, Bryophyllum delagoense (Crassulaceae), and its hybrid with Bryophyllum daigremontianum, 'Houghton's hybrid'

Nine microsatellite loci were developed, and are transferable, across the Madagascan succulents Bryophyllum daigremontianum, Bryophyllum delagoense (mother-of-millions) and their horticultural hybrid (Houghton's), from enriched libraries of the later two species. For B. delagoense, a tetraploid, three to 13 alleles per locus were found for native Madagascan (H-O = 0.4-1.0), and one to nine in invasive Australian (H-O = 0.0-1.0) samples. In addition for 91 Australian samples, only five multilocus genotypes were found (95% of individuals were of two genotypes), suggesting extensive clonality in its introduced range. These loci will be used to examine genetic diversity, hybrid origin and mating system in natural and introduced populations.

Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees

The theoretical impacts of anthropogenic habitat degradation on genetic resources have been well articulated. Here we use a simulation approach to assess the magnitude of expected genetic change, and review 31 studies of 23 neotropical tree species to assess whether empirical case studies conform to theory. Major differences in the sensitivity of measures to detect the genetic health of degraded populations were obvious. Most studies employing genetic diversity (nine out of 13) found no significant consequences, yet most that assessed progeny inbreeding (six out of eight), reproductive output (seven out of 10) and fitness (all six) highlighted significant impacts. These observations are in line with theory, where inbreeding is observed immediately following impact, but genetic diversity is lost slowly over subsequent generations, which for trees may take decades. Studies also highlight the ecological, not just genetic, consequences of habitat degradation that can cause reduced seed set and progeny fitness. Unexpectedly, two studies examining pollen flow using paternity analysis highlight an extensive network of gene flow at smaller spatial scales (less than 10 km). Gene flow can thus mitigate against loss of genetic diversity and assist in long-term population viability, even in degraded landscapes. Unfortunately, the surveyed studies were too few and heterogeneous to examine concepts of population size thresholds and genetic resilience in relation to life history. Future suggested research priorities include undertaking integrated studies on a range of species in the same landscapes; better documentation of the extent and duration of impact; and most importantly, combining neutral marker, pollination dynamics, ecological consequences, and progeny fitness assessment within single studies.

Genetic evidence for polygynandry in the black-striped pipefish syngnathus abaster: a microsatellite-based parentage analysis

Sexual selection theory predicts that, in organisms with reversed sex roles, more polyandrous species exhibit higher levels of sexual dimorphism. In the family Syngnathidae (pipefish, seahorses, and seadragons), males provide all parental care by carrying developing embryos on their ventral surfaces, and females develop secondary sex characters. Syngnathids exhibit a variety of genetic mating patterns, making them an ideal group to test predictions of sexual selection theory. Here, we describe the mating system of the black-striped pipefish Syngnathus abaster, using 4 highly variable microsatellites to analyze parentage of 102 embryos. Results revealed that 1) both sexes mate multiple times over the course of a pregnancy (polygynandrous mating system), 2) eggs are spatially segregated by maternity within each brood pouch, and 3) larger females have higher mating success (Kolmogorov–Smirnov test; P < 0.05). Together with similar studies of other syngnathid species, our results support the hypothesis that the mating system is related to the intensity of sexual dimorphism.

Genetic resources in wild and cultured stocks of the Asian mud crab, Scylla paramamosain

The mud crab (Scylla spp.) aquaculture industry has expanded rapidly in recent years in many countries in the Indo - West Pacific (IWP) region as an alternative to marine shrimp culture because of significant disease outbreaks and associated failures of many shrimp culture industries in the region. Currently, practices used to produce and manage breeding crabs in hatcheries may compromise levels of genetic diversity, ultimately compromising growth rates, disease resistance and stock productivity. Therefore, to avoid “genetic pollution” and its harmful effects and to promote further development of mud crab aquaculture and fisheries in a sustainable way, a greater understanding of the genetic attributes of wild and cultured mud crab stocks is required. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations for multiple purposes including for commercial production, recreation and conservation and to increase profitability and sustainability of newly emerging crab culture industries. Phylogeographic patterns and the genetic structure of Asian mud crab populations across the IWP were assessed to determine if they were concordant with those of other widespread taxa possessing pelagic larvae of relatively long duration. A 597 bp fragment of the mitochondrial DNA COI gene was amplified and screened for variation in a total of 297 individuals of S. paramamosain from six sampling sites across the species’ natural geographical distribution in the IWP and 36 unique haplotypes were identified. Haplotype diversities per site ranged from 0.516 to 0.879. Nucleotide diversity estimates among haplotypes were 0.11% – 0.48%. Maximum divergence observed among S. paramamosain samples was 1.533% and samples formed essentially a single monophyletic group as no obvious clades were related to geographical location of sites. A weak positive relationship was observed however, between genetic distance and geographical distance among sites. Microsatellite markers were then used to assess contemporary gene flow and population structure in Asian mud crab populations sampled across their natural distribution in the IWP. Eight microsatellite loci were screened in sampled S. paramamosain populations and all showed high allelic diversity at all loci in sampled populations. In total, 344 individuals were analysed, and 304 microsatellite alleles were found across the 8 loci. The mean number of alleles per locus at each site ranged from 20.75 to 28.25. Mean allelic richness per site varied from 17.2 to 18.9. All sites showed high levels of heterozygosity as average expected heterozygosities for all loci ranged from 0.917 – 0.953 while mean observed heterozygosity ranged from 0.916 – 0.959. Allele diversities were similar at all sites and across all loci. The results did not show any evidence for major differences in allele frequencies among sites and patterns of allele frequencies were very similar in all populations across all loci. Estimates of population differentiation (FST) were relatively low and most probably largely reflect intra – individual variation for very highly variable loci. Results from nDNA analysis showed evidence for only very limited population genetic structure among sampled S. paramamosain, and a positive and significant association for genetic and geographical distance among sample sites. Microsatellite markers were then employed to determine if adequate levels of genetic diversity has been captured in crab hatcheries for the breeding cycle. The results showed that all microsatellite loci were polymorphic in hatchery samples. Culture populations were in general, highly genetically depauperate, compared with comparable wild populations, with only 3 to 8 alleles recorded for the same loci set per population. In contrast, very high numbers of alleles per locus were found in reference wild S. paramamosain populations, which ranged from 18 to 46 alleles per locus per population. In general, this translates into a 3 to 10 fold decline in mean allelic richness per locus in all culture stocks compared with wild reference counterparts. Furthermore, most loci in all cultured S. paramamosain samples showed departures from HWE equilibrium. Allele frequencies were very different in culture samples from that present in comparable wild reference samples and this in particular, was reflected in a large decline in allele diversity per locus. The pattern observed was best explained by significant impacts of breeding practices employed in hatcheries rather than natural differentiation among wild populations used as the source of brood stock. Recognition of current problems and management strategies for the species both for the medium and long-term development of the new culture industry are discussed. The priority research to be undertaken over the medium term for S. paramamosain should be to close the life cycle fully to allow individuals to be bred on demand and their offspring equalised to control broodstock reproductive contributions. Establishing a broodstock register and pedigree mating system will be required before any selection program is implemented. This will ensure that sufficient genetic variation will be available to allow genetic gains to be sustainably achieved in a future stock improvement program. A fundamental starting point to improve hatchery practices will be to encourage farmers and hatchery managers to spawn more females in their hatcheries as it will increase background genetic diversity in culture stocks. Combining crablet cohorts from multiple hatcheries into a single cohort for supply to farmers or rotation of breeding females regularly in hatcheries will help to address immediate genetic diversity problems in culture stocks. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations more efficiently. Over the long-term, application of data on genetic diversity in wild and cultured stocks of Asian mud crab will contribute to development of sustainable and productive culture industries in Vietnam and other countries in the IWP and can contribute towards conservation of wild genetic resources.

Social Organisation of the Short-finned Pilot Whale, Globicephala macrorhynchus, with Special Reference to the Comparative Social Ecology of Delphinids

As a contribution to the understanding of comparative social trends within the cetacean family Delphinidae, a 22-month study was conducted on the shortfinned pilot whale, Globicephala macrorhynchus, which has been suggested to have a unique social system in which males and females in the same group are related and mating occurs outside of the group. The individual identification of 495 pilot whales, analysed in daily group association patterns, allowed identification of 46 pods. They were classified as productive or non-productive based on the presence or absence of immature animals. Productive pods were a significantly larger, although 12% of them lacked adult males. Two classes of whales (residents and visitors) were defined by patterns of occurrence,suggesting differential patterns of habitat use. Resident pods occasionally travelled together (41% of all groups) and associations between age and sex classes showed that in mixed-pod groups, the highest ranked associations of the reproductive females were with males from other pods, while within pods, adult males and females associated less. During summer, the proposed peak conception period, pilot whale groups were significantly larger and contained individuals from a significantly greater number of pods. These findings support the hypothesis that males and females mate when associating with individuals from other pods. A comparative analysis of sexual dimorphism, brain size, and testes size, habitat, prey and group size within the 17 delphinid genera identified a correlation between sexual dimorphism and body size, but relative measures of brain size and testes size did not correlate with broad ecological or social classifications. However, a comparison of three delphinid societies identified two distinct male mating systems: males of the small, mono-morphic Tursiops truncatus live in age/sex segregated groups and mate with a number of discrete female communities. Males in the large sexually dimorphic Glob icephala spp. and Orcinus orca mate with associated female pods and yet remain with their female kin. This corresponds to the avunculate social system described in some human societies. It could evolve from a promiscuous mating system where there is little guarantee of paternity and where males that live with their kin increase their inclusive fitness.