Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation

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.     

Contrasting patterns of genetic structure in Caryocar (Caryocaraceae) congeners from flooded and upland Amazonian forests

In the present study, we compare the genetic structure of a flooded forest tree Caryocar microcarpum and a terra firme forest tree Caryocar villosum in the lower Rio Negro region and test the hypothesis that the Rio Negro, the largest tributary on the left bank of the Amazon River, has been acting as a geographical barrier to gene flow between populations from the left and right banks. Seventeen adult individuals on the left bank and 27 on the right bank of Rio Negro were sampled for C. microcarpum, whereas 27 on the left and 20 on the right bank were sampled for C. villosum. Two chloroplast DNA regions were sequenced: the intron of trnL gene and the intergenic region between psbA and trnH genes; and all individuals were genotyped using ten microsatellite loci. The trnL intron and psbA‐trnH intergenic spacer generated fragments of 459 bp and 424 bp, respectively. For C. microcarpum, six haplotypes were identified for trnL and seven for psbA‐trnH. By contrast, only one haplotype was found for C. villosum for both sequences. The results obtained showed that the Rio Negro has not been a barrier to gene flow by pollen and seeds for either species. No genetic differentiation and a high migration rate between populations from the left and right banks of the Rio Negro were detected for the chloroplast sequences and nuclear microsatellites, for both C. villosum and C. microcarpum. Although the two analysed sequences showed a sharp topology difference, both indicated that multiple lineages may have contributed to the origin of C. microcarpum populations in the Rio Negro basin. Nevertheless, for C. villosum, from terra firme, the results obtained may provide evidence of a recent expansion of one maternal lineage from an ancient relic population surviving in one of the few moist forest refuges of the Guiana Shield during extended droughts of the glacial periods. We hypothesize that the contrasting environments colonized by this congener pair may have played an important role in shaping the genetic structure of both species. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 278–290.     

Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754-0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, theta = 0.097 and rho = 0.147, respectively. Estimates of theta and rho were significantly greater than zero for all pairwise population comparisons. Pairwise rho-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil.     

Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera

We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited less stability in allelic composition across sites and stages. The number of alleles per hectare (ha) of forest was similar when continuous forest plots were compared to plots from fragmented forest for all three stages. This pattern also held for the number of unique multilocus adult and sapling genotypes, but the number of unique seedling genotypes per ha of fragmented forest greatly exceeded expectations based on continuous forest data, probably due to the concentration of seeds into remnant forest patches by foraging bats. Significant inbreeding and genetic differentiation were most often associated with the fragmented forest and the seedlings. Finally, principal component analysis reaffirmed that a bottleneck, acting in concert with pre-existing genetic structure in the adults, had led to enhanced and rapid divergence in the seedlings following deforestation, a result that is of central interest for landscape management.     

Population structure and genetic diversity in four tropical tree species in Costa Rica

Despite intensified interest in conservation of tropical forests, knowledge of the population genetics of tropical forest trees remains limited. We used random amplified polymorphic DNA (RAPD) data to evaluate trends in genetic diversity and differentiation for four tropical tree species, Alchornea latifolia, Dendropanax arboreus, Inga thibaudiana and Protium glabrum . These species occur at contrasting population densities along an elevational gradient and we use RAPD and ecological data to examine natural levels of genetic diversity of each species, trends in genetic variability with population density and structure, genetic differentiation along the elevation gradient, and the relationship between genetic diversity and such factors as seed dispersal and pollination syndrome. At the distances we examined (plot distances ranging from 0.8 to 8.6 km) there was very little genetic structuring at any distance along the gradient. All four species exhibited levels of variation expected for spatial distribution, mating system and pollinator syndrome; greater than 96% of the genetic variation occurred within plots for Inga thibaudiana, Protium glabrum and Dendropanax arboreus. Alchornea latifolia only occurred in a single plot. The results of this study contribute to a growing database of genetic diversity data that can be utilized to make predictions about the effect of disturbance and subsequent reductions in population size on genetic variation and structure in tropical tree species.     

Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.     

Population genetic structure of the lemon shark (Negaprion brevirostris) in the western Atlantic: DNA microsatellite variation

DNA microsatellite markers were used to characterize the population genetic structure of the lemon shark, Negaprion brevirostris, in the western Atlantic. This study demonstrates for the first time the usefulness of microsatellites to study population genetic structure and mating systems in the Chondricthyes. Lemon sharks (mostly juveniles) were sampled non-destructively from four locations, Gullivan Bay and Marquesas Key in Florida, Bimini, Bahamas, and Atol das Rocas, Brazil. At least 545 individuals were genotyped at each of four dinucleotide loci. The number of alleles per locus ranged from 19 to 43, and expected heterozygosities ranged from 0.69 to 0.90. Relatively little genetic structure was found in the western Atlantic, with small but significant values for estimators of F(ST) and R(ST) among populations, theta (0.016) and rho (0.026), respectively. No sharp discontinuities were found between the Caribbean sites and Brazil, and most alleles were found at all four sites, indicating that gene flow occurs throughout the western Atlantic with no evidence for distinct stocks.     

Isolation and characterization of nuclear microsatellite loci in the tropical tree Corythophora alta (Lecythidaceae)

Studies of tropical plant population structure and gene flow are needed to estimate genetic repercussions of tropical deforestation. Twelve microsatellite loci were isolated for Corythophora alta (Lecythidaceae), a canopy tree at the Biological Dynamics of Forest Fragments Project, near Manaus, Brazil. These microsatellites will be used to estimate population structure and infer seed paternity. Loci were isolated with a subtractive hybridization method. Loci averaged 10.7 alleles per locus with high levels of heterozygosity. Four loci had significant deficits and one locus had a significant excess of heterozygotes compared to Hardy–Weinberg expectations. Many loci had high average probabilities of paternity exclusion.     

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.     

Characterization of 15 polymorphic microsatellite loci in an endangered tropical tree Hopea bilitonensis (Dipterocarpaceae) in Peninsular Malaysia

This study reports the isolation and characterization of 15 polymorphic microsatellite loci in an endangered tropical tree Hopea bilitonensis (Dipterocarpaceae). The primers were designed from a genomic library enriched for dinucleotide (CT) repeats and screened on 24 adult trees from a natural population. The number of alleles ranged from two to eight, and the observed heterozygosity ranged from 0.042 to 1.000. These loci will allow mating system and population analyses to be carried out in this species.     

Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagle

The fragmentation of a population may have important consequences for population genetic diversity and structure due to the effects of genetic drift and reduced gene flow. We studied the genetic consequences of the fragmentation of the Spanish imperial eagle (Aquila adalberti) population into small patches through a temporal analysis. Thirty‐four museum individuals representing the population predating the fragmentation were analysed for a 345‐bp segment of the mitochondrial control region and a set of 10 nuclear microsatellite loci. Data from a previous study on the current population (N = 79) were re‐analysed for this subset of 10 microsatellite markers and results compared to those obtained from the historical sample. Three shared mitochondrial haplotypes were found in both populations, although fluctuations in haplotype frequencies and the occurrence of a fourth haplotype in the historical population resulted in lower current levels of haplotype and nucleotide diversity. However, microsatellite markers revealed undiminished levels of nuclear diversity. No evidence for genetic structure was observed for the historical Spanish imperial eagle population, suggesting that the current pattern of structure is the direct consequence of population fragmentation. Temporal fluctuations in mitochondrial and microsatellite allelic frequencies were found between the historical and the current population as well as for each pairwise comparison between historical and current Centro and historical and current Parque Nacional de Doñana nuclei. Our results indicate an ancestral panmictic situation for the species that management policies should aim to restore. A historical analysis like the one taken here provides the baseline upon which the relative role of recent drift in shaping current genetic patterns in endangered species can be evaluated and this knowledge is used to guide conservation actions.     

Isolation and characterization of microsatellite loci in the Guanacaste tree, Enterolobium cyclocarpum

We isolated nine microsatellite loci from the Guanacaste tree (Enterolobium cyclocarpum) and optimized them for future research on breeding populations of this species. Loci were screened across 53 individuals from one population and were shown to be variable with the number of alleles per locus ranging from five to 15. Polymorphic information content ranged from 0.420 to 0.900 and observed heterozygosity ranged from 0.547 to 0.906.     

Characterization and isolation of DNA microsatellite primers for the tropical tree,Symphonia globulifera Linn. f.

Five highly polimorphic microsatellite markers for Symphonia globulifera were developed from enriched repeat libraries screened for microsatellite repeats. An average of 5.8 alleles per locus and expected heterozygosity ranging from 0.649 to 0.806 were found in a sample of 12 S. globulifera individuals from the Tapajos National Forest, in the state of Pará in the Brazilian Amazon. These loci are being used for analysis of precise paternity testing, estimation of gene flow and parentage coefficients in a managed forest in Pará, Brazil, as part of the Dendrogene Project.     

Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.     

基于微卫星的中国红火蚁种群遗传结构的研究

[背景]自入侵中国之后,红火蚁已给农林业、健康卫生、生态环境等造成了危害。红火蚁在中国的入侵、扩散路径及方式等仍然是待解决的问题。[方法]利用微卫星分子标记,对来自国内14个地区和国外1个地区共15个红火蚁地理种群的遗传多样性水平及种群遗传结构进行了研究。[结果]应用7对微卫星引物共检测到28个等位基因,15个红火蚁种群在各微卫星位点的基因型频率均符合Hardy-Weinberg平衡。各种群的平均表观杂合度HO、预期杂合度HE、Shannon信息指数Ⅰ、基因多样性指数Nei＇s和多态位点百分率P分别为0.2848、0.2708、0.3174、0.2629和43.63%,研究结果表明这15个红火蚁种群具有比较丰富的遗传多样性。种群间平均分化系数FST为0.4258,说明有42.58%的变异来源于种群间,表明红火蚁各种群之间有较高程度的分化,且遗传分化可能是由地理隔离和基因流障碍（Nem=0.7442）共同引起。遗传距离D显示,河源种群与其他种群间的遗传距离均相对高于其他各种群间的遗传距离,表明河源种群与其他地理种群之间存在较大的遗传差异,可能是较为原始的类型。[结论与意义]短距离的种群主要通过自然扩散方式传播,地理距离与亲缘关系有一定的相关性;长距离的种群主要依靠人为传播,因此地理距离与遗传距离不成正比。对于长距离的入侵事件,监控与检疫是关键的预防措施。     

Population genetic structure and diversity of the endangered Cantabrian capercaillie

The Cantabrian capercaillie (Tetrao urogallus cantabricus) occupies the southwestern edge of the grouse family distribution range in Eurasia. It is endemic to the Cantabrian Mountains in northwestern Spain and is geographically isolated and separated from the neighboring population in the Pyrenees by a distance of 300 km. Over the last decades, the population has undergone a dramatic decline and is now threatened with extinction. This study presents the genetic analysis of the Cantabrian capercaillie population using non-invasive samples. We performed genotyping of 45 individuals using 20 microsatellites and a sex marker. The data highlight the need for using a large number of markers when considering fragmented small populations. Genetic diversity (H_E = 0.50) and average number of alleles (3.40) in the population were low. The population is fragmented into 2 clusters (F_ST = 0.113) that fit with areas on both sides of the transportation ways that divide its range. Both clusters exhibited additional heterozygote deficits. Geographical distance was negatively correlated with genetic relatedness (r = −0.44, P ≤ 0.001). The data show a recent decline in effective population size that can be related to an ongoing process of population reduction and fragmentation. Conservation actions should focus on the protection of local demes by maintaining a dense network of suitable patches to maximize reproductive output and the number of potential dispersers to reconnect the 2 subpopulations. © 2012 The Wildlife Society.     

Microsatellite variation and assessment of genetic structure in tea tree (Melaleuca alternifolia– Myrtaceae)

Analysis of five microsatellite loci in 500 Melaleuca alternifolia individuals produced 98 alleles that were useful for population genetic studies. Considerable levels of observed heterozygosity were recorded (HO = 0.724), with approximately 90% of the variability being detected within populations. A low level of selfing (14%) was suggested to be the principal cause of excess homozygosity in a number of populations (overall FIS = 0.073). This study showed low levels of inbreeding in certain populations as well as a significant isolation-by-distance model. Only two groups of populations (Queensland and New South Wales) constituted different genetic provenances as a result of geographical isolation. The M. alternifolia data suggest that microsatellite loci did not always arise by a stepwise mutation process but that larger jumps in allele size may be involved in their evolution.     

Isolation and characterization of eight polymorphic microsatellite loci in the endangered Hawaiian tree snail, Achatinella sowerbyana

Achatinella is a genus of highly endangered native Hawaiian tree snails. Eight polymorphic microsatellite markers were isolated for one species, Achatinella sowerbyana, to be used in assessing remaining genetic diversity and gene flow in the often small and isolated populations. All loci amplified consistently in every individual tested. The number of alleles per locus in a sample of 40 individuals varied from three to 13, and the observed heterozygosity ranged from 0.308 to 0.846. These markers will be used to assist in the development of conservation and management plans.