Genetic diversity and population structure of Brazilian native bovine breeds

Conservation and improvement strategies should be based on the association between genetic and phenotypic characteristics. The objective of this work was to characterize five native Brazilian cattle breeds (Caracu, Crioulo Lageano, Curraleiro, National Polled and Pantaneiro) and two commercial breeds (Holstein and Nellore) using RAPD technique to estimate genetic distances and variability between and within breeds. Genetic relationships were investigated using 22 primers which generated 122 polymorphic bands. Analysis of molecular variance indicated that most of the genetic variation lay among individuals within populations. The genetic variabilities between pairs of breeds were statistically significant. The smallest genetic divergence was between Crioulo Lageano and Curraleiro.The National Polled, although historically considered to be of Bos taurus aquitanicus origin,similar to theCaracu, was grouped together with the other breeds of Bos taurus ibericus origin. Generally, the individual breeds formed distinct clusters except the National Polled. The RAPD technique was capable to distinguish genetically between the breeds studied; the Caracu, Crioulo Lageano, Curraleiro and Pantaneiro may be considered distinct genetic entities thereby proving the uniqueness of the populations; the National Polled has not been able to re-establish itself after its decline in the 1950s, thereby losing its genetic identity.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants.

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.

Genetic improvement and population structure of the Nelore breed in Northern Brazil

The objective of this work was to evaluate the population structure and the genetic and phenotypic progress of Nelore cattle in Northern Brazil. Pedigree information concerning animals born between 1942 and 2006 were analyzed. Population structure was performed using the Endog program. Out of the 140,628 animals studied, 67.7, 14.52 and 3.18% had complete pedigree record of the first, second and third parental generation, respectively. Inbreeding and average relatedness coefficients were low: 0.2 and 0.13%, respectively. However, these parameters may have been underestimated, since information on pedigree was incomplete. The effective number of founders was 370 and the genetic contribution of 10, 50 and 448 most influent ancestors explained 13.2, 28 and 50% of the genetic variability in the population, respectively. The genetic variability for growth traits and population structure demonstrates high probability of increasing productivity through selective breeding. Moreover, management strategies to reduce the currently observed age at first calving and generation intervals are important for Nelore cattle genetic improvement.

Species-specific population structure in rock-specialized sympatric cichlid species in Lake Tanganyika, East Africa.

Species richness and geographical phenotypic variation in East African lacustrine cichlids are often correlated with ecological specializations and limited dispersal. This study compares mitochondrial and microsatellite genetic diversity and structure among three sympatric rock-dwelling cichlids of Lake Tanganyika, Eretmodus cyanostictus, Tropheus moorii, and Ophthalmotilapia ventralis. The species represent three endemic, phylogenetically distinct tribes (Eretmodini, Tropheini, and Ectodini), and display divergent ecomorphological and behavioral specialization. Sample locations span both continuous, rocky shoreline and a potential dispersal barrier in the form of a muddy bay. High genetic diversity and population differentiation were detected in T. moorii and E. cyanostictus, whereas much lower variation and structure were found in O. ventralis. In particular, while a 7-km-wide muddy bay curtails dispersal in all three species to a similar extent, gene flow along mostly continuous habitat appeared to be controlled by distance in E. cyanostictus, further restricted by site philopatry and/or minor habitat discontinuities in T. moorii, and unrestrained in O. ventralis. In contrast to the general pattern of high gene flow along continuous shorelines in rock-dwelling cichlids of Lake Malawi, our study identifies differences in population structure among stenotopic Lake Tanganyika species. The amount of genetic differentiation among populations was not related to the degree of geographical variation of body color, especially since more phenotypic variation is observed in O. ventralis than in the genetically highly structured E. cyanostictus.

Evolutionary aspects of population structure for molecular and quantitative traits in the freshwater snail Radix balthica.

Detecting the action of selection in natural populations can be achieved using the QST-FST comparison that relies on the estimation of FST with neutral markers, and QST using quantitative traits potentially under selection. QST higher than FST suggests the action of directional selection and thus potential local adaptation. In this article, we apply the QST-FST comparison to four populations of the hermaphroditic freshwater snail Radix balthica located in a floodplain habitat. In contrast to most studies published so far, we did not detect evidence of directional selection for local optima for any of the traits we measured: QST calculated using three different methods was never higher than FST. A strong inbreeding depression was also detected, indicating that outcrossing is probably predominant over selfing in the studied populations. Our results suggest that in this floodplain habitat, local adaptation of R. balthica populations may be hindered by genetic drift, and possibly altered by uneven gene flow linked to flood frequency.

Population structure of three Psammodromus species in the Iberian Peninsula.

The knowledge of a species' population structure is essential for the development of adequate conservation actions as well as for the understanding of its evolution. The population structure is unknown in all species of the Genus Psammodromus, including the Western Sand Racer (Psammodromus occidentalis; a recently described species), the Edward's Sand Racer (P. edwardsianus) and the Spanish Sand Racer (P. hispanicus). In this article, the genetic variability and population structure of Psammodromus edwardsianus, P. hispanicus, and P. occidentalis were studied in the Iberian Peninsula covering their natural geographic distribution. Mitochondrial DNA showed genetically different units in all species with higher genetic variability in their southern populations (latitudinal variation). Genetic differentiation was different among species and contrasted to those of species with similar characteristics. Our results therefore highlight the importance of species-specific studies analysing population structure.

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori.

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

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 in a highly pelagic seabird, the Cory's shearwater (Calonectris diomedea): an examination of genetics, morphology and ecology

Increasing evidence suggests oceanic traits may play a key role in the genetic structuring of marine organisms. Whereas genetic breaks in the open ocean are well known in fishes and marine invertebrates, the importance of marine habitat characteristics in seabirds remains less certain. We investigated the role of oceanic transitions versus population genetic processes in driving population differentiation in a highly vagile seabird, the Cory"s shearwater, combining molecular, morphological and ecological data from 27 breeding colonies distributed across the Mediterranean (Calonectris diomedea diomedea) and the Atlantic (C. d. borealis). Genetic and biometric analyses showed a clear differentiation between Atlantic and Mediterranean Cory"s shearwaters. Ringing-recovery data indicated high site fidelity of the species, but we found some cases of dispersal among neighbouring breeding sites (<300 km) and a few long distance movements (>1000 km) within and between each basin. In agreement with this, comparison of phenotypic and genetic data revealed both current and historical dispersal events. Within each region, we did not detect any genetic substructure among archipelagos in the Atlantic, but we found a slight genetic differentiation between western and eastern breeding colonies in the Mediterranean. Accordingly, gene flow estimates suggested substantial dispersal among colonies within basins. Overall, genetic structure of the Cory"s shearwater matches main oceanographic breaks (Almería-Oran Oceanic Front and Siculo-Tunisian Strait), but spatial analyses suggest that patterns of genetic differentiation are better explained by geographic rather than oceanographic distances. In line with previous studies, genetic, phenotypic and ecological evidence supported the separation of Atlantic and Mediterranean forms, suggesting the 2 taxa should be regarded as different species.

Population structure and density of Attalea phalerata Mart. ex Spreng. (Arecaceae) in a semideciduous forest

The structure of a population can be seen as the result of biotic and abiotic interacting forces. The studies of population characteristics are vital to improve the understanding of ecosystem functioning. In this study, we attempted to answer the two following questions: What are the population structure of Attalea phalerata? and Are there any influence of reproducers presence, canopy openness, declivity, basal area and soil coverage on recruitment of individuals in this population? We distinguished four ontogenetic stages in A. phalerata. Reproducers and virgins were sampled by using 25 plots (400 m²), juveniles and seedlings were sampled in sub-plots (100 m²). We found 2,328 Attalea phalerata individuals per hectare, first two ontogenetic stages accounted for 89.8% of the total, describing a relatively stable population. None of the analyzed factors were affecting the natural regeneration of Attalea phalerata in the fragment. The density and distribution pattern found for the population are probably signs of formation of oligarchic forests, moreover, the species seems to be able to colonize clearings and open areas.

POPULATION STRUCTURE AND SPATIAL DISTRIBUTION OF Bauhinia cheilantha (Bong.) Steud. IN TWO FRAGMENTS AT DIFFERENT REGENERATION STAGES IN THE CAATINGA, IN SERGIPE, BRAZIL

ABSTRACTThis study aimed to analyze the vertical and diameter structure and the spatial distribution pattern of Bauhinia cheilantha in two Caatinga fragments in Sergipe, Brazil, at different regeneration stages. Thirty plots were demarcated in area I (Canindé de São Francisco and Poço Redondo), which has vegetation regeneration, and 25 plots in area II (Porto da Folha) with preserved vegetation, both having 400 m2. All B. cheilanthaindividuals had their height and circumference (circumference at breast height > 6 cm) measured. Possible differences in height and diameter at breast height were tested in the two populations by using Student’s T-test. The distribution pattern of species was calculated through Payandeh’s index. We sampled 154 B. cheilantha individuals, equivalent to 33.3% of the plots in area I and in 1,027 individuals in area II, totaling 100% frequency. Height and the diameter of the two populations were statistically different, where AI achieved all values lower than AII. The spatial distribution pattern of B. cheilantha found in both areas was aggregate, with values of 11.85 and 9.00, respectively. Thus, it became clear that the population in AII is at a more advanced successional status than AI, due to its longer conservation time.

POPULATION STRUCTURE AND PRODUCTION OF COPAIBA OLEORESIN BETWEEN VALLEYS AND HILLSIDES OF THE MINING AREA OFTROMBETAS RIVER - PARÁ1

ABSTRACT We aimed in this work to study natural populations of copaiba (Copaifera multijuga Hayne) on the Monte Branco mountain at Porto Trombetas-PA, in order to support sustainable management and the exploitation of oleoresin from copaiba. We studied the population structure of copaiba on hillsides and valleys of the south face of Monte Branco, within Saracá Taquera National Forest, where bauxite ore was extracted in the biennium 2013-2014 by Mineração Rio do Norte (MRN). We produced a 100% forest inventory of the specie and of oleoresin extraction in order to quantify the potential production of the remaining area. The density of copaiba individuals with DBH > 30 cm was 0.33 individuals per hectare in the hillside and 0.25 individuals per hectare in the valley. Both environments presented a density of 0.28 individuals per hectare. The average copaiba oleoresin yield was 0.661±0.334 liters in the hillside and 0.765±0.280 liters in the valley. The average value of both environments together (hillside and valley) was 0.714±0.218 liters. From all individuals with DBH over 30 cm, 38 (58%) produced some amount of oleoresin, averaging 1.113±0.562 liters in the hillside, 1.329±0.448 liters in the valley and 1.190±0.355 liters in both environments together. The results show the need for planning the use of the surroundings of the study area in order to reach the required volume of copaiba to make feasible the sustainable management of oleoresin extraction in the region.

Inter-annual variations in the floristic and population structure of an herbaceous community of "caatinga" vegetation in Pernambuco, Brazil

The influence of climatic variations on the herbaceous component of the "caatinga" vegetation was examined in the state of Pernambuco, Brazil. A total of 105 1 × 1 m-plots were established, of which 35 were in a level micro-habitat, 35 in a riparian micro-habitat, and 35 in a stony microhabitat. During two consecutive years all herbaceous plants in these plots were counted, measured (height and diameter), and collected for identification. The Shannon-Wiener diversity index and the equitability were calculated for each year, as well as the density, frequency, dominance, total basal area and importance index for each species. The total annual pluviometric was 819.5 and 448.8 mm in 2002 and 2003, respectively. The herbaceous flora in the study area was composed of 71 species, of which 58 were sampled in the plots. The families with the greatest species richness were Malvaceae (8 species), Euphorbiaceae (7), Poaceae (6), Convolvulaceae (4), Fabaceae (4), and Portulacaceae (4). The diversity indices were 2.66 and 3.01 nats ind-1 in 2002 and 2003, respectively. The density, frequency, dominance and importance value of herbaceous populations, as well as, the height and diameter of plants were low in the dryer year. The riparian group was the most isolated of the microhabitats examined, both in terms of its floristic and its population structure. Annual seasonal climatic variations greatly modified these populations structure during the course of this study, emphasizing the fact that long-term studies are needed in order to better understand the dynamics of the herbaceous component of the "caatinga" vegetation.

Population structure of Eschweilera coriacea (DC.) S. A. Mori in forest fragments in eastern Brazilian Amazonia

The population structure of a common canopy tree was examined in three sites to investigate the possible effects of forest fragmentation in eastern Amazonia. Evidence for the escape hypothesis of differential seed/seedling survival was evaluated. Two 1 ha plots were established at each site and all individuals of Eschweilera coriacea (DC.) S. A. Mori over 1 m tall were tagged, measured and mapped. Smaller individuals were recorded in the same way within subplots. Mature individuals were abundant at all sites with densities of 32-52 ha-1. The species exhibited substantial regeneration, although total population density varied fourfold among sites (1,256-4,805 individuals ha-1). Overall, juveniles were clumped while adults were randomly distributed. The difference between the dispersion pattern of adults and juveniles supported the escape hypothesis. However, no difference in population structure among sites could be related to the forest fragmentation.