Building genetic networks using relatedness information : a novel approach for the estimation of dispersal and characterization of group structure in social animals

Natal dispersal is an important life history trait driving variation in individual fitness, and therefore, a proper understanding of the factors underlying dispersal behaviour is critical to many fields including population dynamics, behavioural ecology and conservation biology. However, individual dispersal patterns remain difficult to quantify despite many years of research using direct and indirect methods. Here, we quantify dispersal in a single intensively studied population of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps) using genetic networks created from the combination of pairwise relatedness data and social networking methods and compare this to dispersal estimates from re-sighting data. This novel approach not only identifies movements between social groups within our study sites but also provides an estimation of immigration rates of individuals originating outside the study site. Both genetic and re-sighting data indicated that dispersal was strongly female biased, but the magnitude of dispersal estimates was much greater using genetic data. This suggests that many previous studies relying on mark–recapture data may have significantly underestimated dispersal. An analysis of spatial genetic structure within the sampled population also supports the idea that females are more dispersive, with females having no structure beyond the bounds of their own social group, while male genetic structure expands for 750 m from their social group. Although the genetic network approach we have used is an excellent tool for visualizing the social and genetic microstructure of social animals and identifying dispersers, our results also indicate the importance of applying them in parallel with behavioural and life history data.

Quantifying the positive effects of sponsor level, length, prominence and relatedness on recall and residual recall rates over time

This study is the first multi-year examination of the relative influence of the four main variables said to influence sponsorship recall. Sponsor recall data were collected from season ticket holders (STHs) of 10 professional sports teams, over periods ranging from 3 to 5 years per team. Across those teams and over that time, 309 sponsor–team relationships were examined, and sponsor recall data from over 117,000 individual STHs were collected. Sponsorship length and level were shown to have the strongest impact on recall, followed by relatedness and prominence. These variables affected both the recall of current sponsors and the decay rates of residual recall following the end of a sponsorship. The average rates of sponsor recall growth and decline have been derived from these data, giving managers a tool by which to benchmark sport sponsorship recall performance.

The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness

Co-flowering plant species commonly share flower visitors, and thus have the potential to influence each other's pollination. In this study we analysed 750 quantitative plant-pollinator networks from 28 studies representing diverse biomes worldwide. We show that the potential for one plant species to influence another indirectly via shared pollinators was greater for plants whose resources were more abundant (higher floral unit number and nectar sugar content) and more accessible. The potential indirect influence was also stronger between phylogenetically closer plant species and was independent of plant geographic origin (native vs. non-native). The positive effect of nectar sugar content and phylogenetic proximity was much more accentuated for bees than for other groups. Consequently, the impact of these factors depends on the pollination mode of plants, e.g. bee or fly pollinated. Our findings may help predict which plant species have the greatest importance in the functioning of plant-pollination networks.

Sequential polyandry through divorce and re-pairing in a cooperatively breeding bird reduces helper-offspring relatedness

Polyandry is an important component of both sexual selection and kin structuring within cooperatively breeding species. A female may have multiple partners within a single reproductive attempt (simultaneous polyandry) or across multiple broods within and/or across years (sequential polyandry). Both types of polyandry confer a range of costs and benefits to individuals and alter the genetic structure of social groups over time. To date, many molecular studies of cooperative breeders have examined the evolution of cooperative breeding in relation to simultaneous polyandry. However, cooperatively breeding vertebrates are iteroparous, and thus sequential polyandry is also likely, but more rarely considered in this context. We examined sequential polyandry in a cooperatively breeding bird that has a low level of within-brood polyandry. Over a 5-year period (2006–2010), we monitored individual mating relationships using molecular markers in a population of individually marked apostlebirds (Struthidea cinerea). Divorce occurred between reproductive seasons in 17 % (8/48) of pairs and appeared to be female-driven. The level of sequential polyandry was also driven by the disappearance of males after breeding, and over 90 % of females, for whom we had suitable data, bred with multiple males over the period of study. This sequential polyandry significantly altered the relatedness of group members to the offspring in the nest. However, in about half of the cases, the second male was related (first- or second-order relative) to the first male of a sequentially polyandrous female and this alleviated the reduction in relatedness caused by polyandry. Our findings suggest that even in species with high within-brood parentage certainty, helper-offspring relatedness values can quickly erode through sequential polyandry.

Genetic relatedness among wild, domestic and Brazilian fighting roosters

Except for the meat- and egg-type strains used in commercial poultry farms in Brazil, there are no scientific reports about the origin of birds from the genus Gallus that have been introduced in this country with domestication or fighting purposes. Therefore, the aim of this study was to identify the position of the Brazilian Game Bird in the phylogenetic tree of the genus Gallus by nucleotide sequence analysis of the mitochondrial DNA D-loop region. The results indicate that fighting roosters comprise two different clusters within the species Gallus gallus domesticus. One of the clusters is related to the wild ancestors, while the other one is more related to the birds raised by the poultry industry. In conclusion, Brazilian fighting roosters have originated from the red jungle fowl (Gallus gallus) and belong to the subspecies Gallus gallus domesticus.

Genetic relatedness of commensal strains of Candida albicans carried in the oral cavity of patients' dental prosthesis users in Brazil

The aim of this study is to describe the degree of yeast-colonization in diabetic and hemodialysed-users of dental prostheses. Individuals (306) were examined using an oral rinse technique in order to evaluate the incidence of yeast-carriage, and genotype of C. albicans. Yeasts were isolated from 68.4% (91/133) individual's dental prostheses users. Dental prostheses were found to be a significant factor for the yeast colonization (P < 0.05). Overall, the intensity of carriage was higher in diabetic patients as compared with health and hemodialysed individuals (P < 0.05). The isolation rates were: C. albicans (51.7%), C. parapsilosis (20.9%), C. tropicalis (14.3%), C. glabrata (6.6%), C. krusei (3.3%), C. rugosa (1.1%), and Pichia (Pichia ohmeri, 2.2%). Ready-To-Go RAPD Analysis Beads were used and primer OPJ 6 distinguished the C. albicans isolates found in prostheses users. All the isolates were grouped into 11 RAPD profiles in four main clusters and, the average S (AB) for the entire collection of 47 C. albicans isolates were 0.779 +/- 0.178. Over 85% of isolates had a similarity level higher than or equal to 0.8 reinforcing the idea that the use of dental prostheses, independently of the host's clinical condition, probably provides the necessary conditions for these strains to gain a growth-specific advantage over others.

Molecular characterization and relatedness of Haematobia irritans (horn fly) populations, by RAPD-PCR

Haematobia irritans is a hematophagous parasite of cattle that causes significant economic losses in many parts of the world, including Brazil. In the present work, one American and four Brazilian populations of this species were studied by Random Amplified Polymorpht DNA (RAPD) to assess basically genetic variability within and between populations. Ten different decamer random primers were employed in the genomic DNA amplification, yielding 117 fragments in the five H.. irritans populations. In Drosophila prosaltans, used as an outgroup, 81 fragments were produced. Forty-three of these fragments were shared by both species. Among the H. irritans samples, that from Rio Branco (Acre State, Brazil) produced the smallest numbers of fragments and polymorphic bands. This high genetic homogenity may be ascribed to its geographic origin (in the Northwest of Brazil), which causes high isolation and low gene flow, unlike the other Brazilian populations, from the South Central region, in which cattle trade is very intensive. Marker fragments (exclusive bands) detected in every sample enabled the population origin to be characterized, but they are also potentially useful for further approaches such as the putative origin of Brazilian populations from North America. Similarity indices [Nei & Li, 1979, Proc. Natl. Acad. Sci. USA 76: 5269-5273] and phylogenetic trees, rooted by using the outgroup and produced by the Phylogenetic Analysis using Parsimony (PAUP 4.0-Swofford, 2001) program showed the closest relationships between flies from Sao Jose do Rio Preto and Turiuba (both from São Paulo State, Brazil) while flies from the geographically distant Rio Branco showed the greatest differentiation relative to the others.

Intrageneric Karyotypic Variation in Pseudopaludicola (Anura: Leiuperidae) and Its Taxonomic Relatedness

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

Genetic relatedness of Plasmodium falciparum isolates and the origin of allelic diversity at the merozoite surface protein-1 (MSP-1) locus in Brazil and Vietnam

Background: Despite the extensive polymorphism at the merozoite surface protein-1 (MSP-1) locus of Plasmodium falciparum, that encodes a major repetitive malaria vaccine candidate antigen, identical and nearly identical alleles frequently occur in sympatric parasites. Here we used microsatellite haplotyping to estimate the genetic distance between isolates carrying identical and nearly identical MSP-1 alleles. Methods: We analyzed 28 isolates from hypoendemic areas in north-western Brazil, collected between 1985 and 1998, and 23 isolates obtained in mesoendemic southern Vietnam in 1996. MSP-1 alleles were characterized by combining PCR typing with allele-specific primers and partial DNA sequencing. The following single-copy microsatellite markers were typed: Polyα, TA42 (only for Brazilian samples), TA81, TA1, TA87, TA109 (only for Brazilian samples), 2490, ARAII, PfG377, PfPK2, and TA60. Results: The low pair-wise average genetic distance between microsatellite haplotypes of isolates sharing identical MSP-1 alleles indicates that epidemic propagation of discrete parasite clones originated most identical MSP-1 alleles in parasite populations from Brazil and Vietnam. At least one epidemic clone propagating in Brazil remained relatively unchanged over more than one decade. Moreover, we found no evidence that rearrangements of MSP-1 repeats, putatively created by mitotic recombination events, generated new alleles within clonal lineages of parasites in either country. Conclusion: Identical MSP-1 alleles originated from co-ancestry in both populations, whereas nearly identical MSP-1 alleles have probably appeared independently in unrelated parasite lineages.

Genetic polymorphism, molecular characterization and relatedness of Macrobrachium species (Palaemonidae) based on RAPD-PCR.

The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species.

Inbreeding, Average Relatedness Coefficient and Effective Population Size In Jaffarabadi Buffaloes Raised In Brazil

The major aim of this study was to evaluate the inbreeding (F), average relatedness coefficient (AR) and effective population size (Ne) in the Jaffarabadi buffalo breed from Brazil. Pedigree information of 1,272 animals born from 1966 was used. The effective population size was calculated in two ways: first, computed via individual increase in inbreeding and second estimated by individual increase in coancestry. The known generation numbers were 1.24, 1.76 and 2.64 for complete, equivalent and maximum generation, respectively. The effective size computed via individual increase in coancestry was small with a value of 10.82 +/- 1.29. The effective size computed by individual increase in inbreeding (10.40 +/- 3.69) was very similar but a little smaller than the previous reported value. The average values of F and AR for the population reference (1,059) were 4.22 and 12.5 percent. The mean of F for inbred animals (319) was 14.0%. The F and AR means were 5.7 and 13.3% for animals with at least 1.5 known equivalent generation and 9.3 and 15.97% for individuals having at least 2.5 equivalent generations known. It was found 78 matings between half sibs (6.14%) and 67 matings (5.27%) between parent-offspring. The estimated inbreeding increase per generation by considering maximum generation, complete generation and equivalent generation were 1.21%, 5.18% and 3.57%, respectively. Considering the uncompleted pedigree, the estimated inbreeding for the reference population could be underestimated.

Coeffcients of herdability and relatedness in a forest fragment of Araucaria angustifolia (Bertol.) Kuntze using genetic markers

Methods based on genetic markers to estimate the coefficient of heritability in natural populations are important to understand the effects of natural selection on inheritance of quantitative traits. The objective of this study was to investigate the genetic control of the trait plant height in a fragmented population of Araucaria angustifolia. This study was conducted in a forest fragment of 5.4 ha of area, located in the State of Parana, Brazil. Estimates of heritability were performed using data from genotypes and height of regenerating individuals of the population. Four methods to estimate the relatedness between pairs of individuals (RITLAND, 1996; LYNCH; RITLAND, 1999; QUELLER; GOODNIGHT, 1989; WANG, 2002) for three distances (without criteria, 25 and 50 m) were used. The coefficient of heritability estimated using the estimator of relatedness of Ritland (1996), suggest that the genetic control of the trait height is low in the regeneration, thus the natural selection as well as the artificial selection have a low potential to change the mean of the population. The estimates based on the other methods to calculate the relatedness presented low precision, indication that these methods are not adequate for the data used.

Clonal relatedness and resistance patterns of Salmonella Corvallis from poultry carcasses in a Brazilian slaughterhouse

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic relatedness of Plasmodium falciparum isolates and the origin of allelic diversity at the merozoite surface protein-1 (MSP-1) locus in Brazil and Vietnam

Abstract Background Despite the extensive polymorphism at the merozoite surface protein-1 (MSP-1) locus of Plasmodium falciparum, that encodes a major repetitive malaria vaccine candidate antigen, identical and nearly identical alleles frequently occur in sympatric parasites. Here we used microsatellite haplotyping to estimate the genetic distance between isolates carrying identical and nearly identical MSP-1 alleles. Methods We analyzed 28 isolates from hypoendemic areas in north-western Brazil, collected between 1985 and 1998, and 23 isolates obtained in mesoendemic southern Vietnam in 1996. MSP-1 alleles were characterized by combining PCR typing with allele-specific primers and partial DNA sequencing. The following single-copy microsatellite markers were typed : Polyα, TA42 (only for Brazilian samples), TA81, TA1, TA87, TA109 (only for Brazilian samples), 2490, ARAII, PfG377, PfPK2, and TA60. Results The low pair-wise average genetic distance between microsatellite haplotypes of isolates sharing identical MSP-1 alleles indicates that epidemic propagation of discrete parasite clones originated most identical MSP-1 alleles in parasite populations from Brazil and Vietnam. At least one epidemic clone propagating in Brazil remained relatively unchanged over more than one decade. Moreover, we found no evidence that rearrangements of MSP-1 repeats, putatively created by mitotic recombination events, generated new alleles within clonal lineages of parasites in either country. Conclusion Identical MSP-1 alleles originated from co-ancestry in both populations, whereas nearly identical MSP-1 alleles have probably appeared independently in unrelated parasite lineages.