This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons

We report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of theta and R(ST) showed important genetic differentiation among populations. theta was much lower than R(ST), suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (R(IS) = 0.04). Differentiation (pairwise F(ST)) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (approximately 60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.

In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10-locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median-joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.

The results strongly support that the disjunct distribution of L. ericoides may represent a climatic relict and that long-distance gene flow is unlikely. With an estimated time to most recent common ancestor (T(MRCA)) dated from approx. 790,655 +/- 36,551 years bp (chloroplast) and approx. 623,555 +/- 55,769 years bp (ITS), it was hypothesized that the disjunct distribution may be a consequence of an expansion of the geographical distribution favoured by the drier and colder conditions that prevailed in much of Brazil during the Kansan glaciation, followed by the retraction of the distribution due to the extinction of populations in some areas as climate became warmer and moister.

No abstract

Complex and integrative approaches may be necessary to understand the abundant-centre model and the patterns in genetic diversity that may be explained by this model. Here we developed an integrated framework to study spatial patterns in genetic diversity within local populations, coupling genetic data, niche modelling and landscape genetics, and applied this framework to evaluate population structure of Caryocar brasiliense, an endemic tree from the Brazilian Cerrado. We showed different geographical patterns for genetic diversity, allelic richness and inbreeding levels, estimated using microsatellite data for ten local populations. Ecological suitability was estimating by combining five niche modelling techniques. Genetic diversity tend to follow a central-periphery model and is associated with ecological variables. On the other hand, inbreeding levels may be alternatively explained by isolation processes and habitat fragmentation more related to intense recent human occupation in the southern border of the biome, or by deeper historical patterns in the origin of the populations. Although still suffering from some of the problems of central-periphery analysis (small number of local populations), our analyses show how these patterns can be better investigated and offering a better understanding of the processes structuring genetic diversity within species' geographic ranges.

Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species' distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21 000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species' paleodistribution 21 kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence.

In this work we investigate the mating system of four populations of the endangered tropical tree species Caryocar brasiliense, using genetic data from 10 microsatellite loci. Eight to 10 openpollinated progeny arrays of 16 individuals, together with their mother tree, were sampled per population. Mating system parameters were estimated under the mixed mating model, implemented by the software MLTR MLTR. The single-locus outcrossing rate (t s ) varied among loci and populations, but multilocus outcrossing rates (t m ) were equal to one for all four populations. Nevertheless, biparental inbreeding (t m ) t s ) was dierent from zero for all populations, indicating that outcrossing events may occur between relatives. Our results also indicate that the high polymorphism of microsatellite markers provide an extraordinary resolution to discriminate precisely sel®ng events from outcrossing events between close relatives. Our results indicate that, although highly outcrossed, C. brasiliense shows high levels of biparental inbreeding, most likely due to the limited¯ight range of pollinators and restriction in seed dispersal. Furthermore, these results suggest that Cerrado fragmentation could limit gene¯ow by isolating seed dispersers and territorial small sized bat pollinators inside fragments, increasing the rate of mating between close relatives. The conservation of nonisolated populations in large preserved areas may be necessary to foster outcrossing events between unrelated individuals and thus maintain species viability.Keywords: Caryocar brasiliense, Caryocaraceae, fragmentation, mating system, microsatellites, tropical tree. IntroductionThe Brazilian Cerrado biome covers nearly 22% of the Brazilian territory (2 million km 2 ) consisting of a very heterogeneous vegetation. This biome displays high biodiversity, with nearly 160 000 described species, including plants, animals and fungi. The number of trees and shrubs in savannah-like vegetation (cerrado sensu stricto) exceeds 800 species, nearly 40% of which are endemic (Ratter et al., 1997). Cerrado has been intensively fragmented in the last 60 years because of agricultural expansion resulting in continental islands of wild habitat surrounded by an`ocean' of crops, jeopardising species viability.Despite the high biodiversity and endemism and the high rate of deforestation and fragmentation, studies of the reproductive biology of cerrado species are scarce (but see Gribel & Hay, 1993; Oliveira & Silva, 1993 60and Anoura georoyi) (Gribel & Hay, 1993). The seeds are surrounded by a woody endocarp coated with a yellow¯eshy mesocarp rich in oil and vitamin A, and are eaten by several wild animals, such as birds, including greater rhea (Rhea americana), macaws (Ara spp.) and parrots (Amazona spp.), pampas deer (Ozotocerus berzoarticus) and paca (Agouti paca) (Gribel & Hay, 1993). Furthermore, C. brasiliense is a source of raw material for small and middle-sized industries, playing an important role in the economy of the inhabitants of central Brazil (Arau jo, 1994)....