File Name: conservation and the genetics of populations .zip
Conservation genetics is an interdisciplinary subfield of population genetics that aims to understand the dynamics of genes in populations principally to avoid extinction. Therefore, it applies genetic methods to the conservation and restoration of biodiversity. Researchers involved in conservation genetics come from a variety of fields including population genetics, molecular ecology , biology , evolutionary biology , and systematics. Genetic diversity is one of the three fundamental levels of biodiversity, so it is directly important in conservation.
To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific microsatellite DNA loci.
All loci were variable, with the mean number of alleles per locus ranging from 5. Considerable genetic variability was detected for all populations at the seven loci ;. Moderate but statistically significant genetic differentiation was found among populations considering both 0. All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positive values due to inbreeding occurring in the species.
Altogether, these results indicate that genetic variation in Milicia excelsa is geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.
Tropical trees suffered from several threats which have considerable long-term effects on the demographic and genetic structure of populations worldwide [ 1 ]. Deforestation, habitat fragmentation, and selective logging result in the loss of genetic diversity, the extinction of local populations, the reduction of population size, and disruption of mutualisms within pollinators and seed-dispersal agents [ 1 — 4 ] Lemes et al.
To evaluate and reduce the genetic effect of deforestation and logging, it has become a priority to obtain information on the natural levels and distribution of genetic variation in population of tropical trees. Investigations on population genetic diversity and structure of populations within a species may not only illustrate evolutionary histories, processes, and mechanisms but also provide useful information for the biological conservation of endangered species [ 6 ].
Earliest studies of tropical trees have used isozymes as the primary genetic markers and have shown that most of the species investigated are outcrossed, exhibit high levels of genetic diversity and gene flow, and carry much of the variation within rather than among populations [ 2 , 7 ].
More accurately, recent studies using microsatellites with strong discriminatory power have reported high level of inbreeding, restricted gene flow and isolation by distance in some tropical trees due to fragmentation [ 1 , 8 , 9 ] Lemes et al. Indeed, many African countries were exporters of iroko timber, especially Ghana traded together with M. In Benin, as the species ranks the first among valuable timber species, superior individuals were almost all logged from forests.
Thus as a result of its overexploitation, the species was classified on the IUCN red list as close to vulnerable [ 11 ] and becomes the focus of conservation concern in many African countries. Therefore, there is an urgent need for effective conservation and management of the remnant populations.
For this purpose, estimates of population genetic parameters are essential. The variability observed at different loci with codominant markers provides estimates of inbreeding, heterozygosity, gene flow, and outcrossing rate, all of which are important measures for assessing the conservation and management status of tropical trees under intense human pressure Lemes et al.
In this work, we assessed the genetic diversity and population structure of the remnant natural populations of Milicia excelsa across its range in Benin using microsatellite markers recently developed for the species [ 12 ]. The specific questions addressed in this study were i what is the amount of genetic diversity and differentiation harboured within-and among populations?
Milicia excelsa is a dioecious species. Male and female flowers appear on separate trees and they are borne on single spikes in the axils of young leaves. Female flowers are greenish, in shorter and much fatter spikes, the styles of each flower project so that the inflorescence appears hairy.
Fruits, 5 to 7. Seeds are hard, small, and lie in the pulp. The fruit bat Eidolon helvum feeds on Milicia fruits and is considered as the principal agent of dispersal of this giant African tree both quantitatively and qualitatively. A part from bat, it was noticed that several other agents are involved in the Milicia seeds dispersion among which, the red-crowned parrot which defecate seeds primarily in the seed-hostile environment below parent tree crowns, elephants and monkeys or duikers which probably kill and defecate many seeds in large clumps which predisposes them to seed predation, seedling competition, or fungal attack.
It is noteworthy that these agents are poor dispersers compare to fruit bat. Milicia excelsa species is found in transitional vegetation between closed forest and savanna. It is often found in deciduous forests, semideciduous forests, and evergreen forest and sometimes in savannah woodlands. Young leaves samples from a total of Milicia excelsa mature trees 15 to 21 individuals per population were collected in twelve natural populations representing the geographical distribution of the species in Benin see Table 1 for more details.
Leaves were silicagel-dried and kept in freezer at C until DNA extraction. Total genomic DNA was extracted from about 0. DNA concentration was determined by electrophoresis on agarose-TAE gel stained with ethidium bromide [ 13 ]. Molecular variation at 7 microsatellite loci was investigated using the following primers designed for Milicia excelsa [ 12 ]: Mex, Mex63, Mex, Mex51, Mex, Mex81, Mex PCR products were analyzed on 6.
Allele sizes were determined using the v. Using the GDA program, genetic parameters for each population and overall loci were assessed by computing the average number of alleles per locus AR adjusted for the differences in sample size by resampling [ 17 ], observed heterozygosity , and heterozygosity expected under Hardy-Weinberg equilibrium.
For purpose of comparison, genetic differentiation was quantified using both statistics and differentiation based on allele size. Weir and Cockerham [ 19 ]; Excoffier et al. Jackknifing over samples and loci and bootstrapping over loci were automatically performed for the statistics , ,. Values of overall loci were estimated as weighted and unweighted [ 22 , 23 ].
Geographical trends in the distribution of genetic diversity were investigated by three different methods. This does not require conditioning on known population structure. The model-based clustering algorithm was applied to identify clusters of genetically similar individuals and to test the proportion of genetic admixture among the clusters using STRUCTURE version 2. This was to assign individual multilocus genotypes probabilistically to a user defined number K of cluster or gene pools [ 28 ], achieving linkage equilibrium within cluster.
We used an admixture model in which the fraction of ancestry from each cluster is estimated for each individual. Parameter of individual admixture alpha was chosen to be the same for all clusters and was given a uniform prior. The allele frequencies were kept independent among clusters to avoid overestimating the number of clusters [ 28 , 29 ]. Proportions of ancestry were averaged over individuals within each population sample and the corresponding pie charts were plotted onto the Benin map.
The clusters are referred to as gene pools [ 28 ]. Almost all loci met Hardy-Weinberg expectations except Mex81 in Bante population and Mex95 in Tamarou population which showed significant deviation from HWE equilibrium after Bonferroni corrections. Exact test for genotypic linkage disequilibrium showed significant deviations for 7 out of comparisons , which may be due to chance alone and these deviations are all associated with Mex81 and Mex95 suggesting that this disequilibrium could largely be due to the Hardy-Weinberg disequilibrium in these two loci since pairwise measures include both within- and among-loci disequilibrium.
A total number of alleles were recorded over the 7 loci in the individuals with a range from 13 alleles Mex to 32 alleles Mex63 and an overall average of 6.
Most of the loci were variables across populations with mean observed heterozygosity ranging from Mex95 to Mex Total gene diversity is high and similar for each locus with a range from Mex to Mex63 ; and gene diversity within populations ranging from Mex to Mex Allelic richness in populations varies from 3. The number of private alleles Pa across populations ranged from 1 to 5 with a total number of At the population level, the observed heterozygosity ranged from Niaouli and Aplahoue populations to Save population with an average value of 0.
The average gene diversity within population was a range from 0. Populations were on average inbred with a mean inbreeding coefficient of , indicating a significant excess of homozygotes relative to Hardy-Weinberg expectations Tables 1 and 2.
Bante and Tamarou Populations showed significant pairwise disequilibrium between Mex81 and Mex51, and Mex95 and Mex51 respectively. Genetic differentiation among populations estimated over loci by was moderate but within the range of the estimated values using 0. Mean values of and were 0. Differentiation among populations based on the allele sizes, was significantly larger than differentiation based on allele identities , indicating that stepwise-like mutations contributed to overall among population differentiation.
Based on the private allele method Gene flow estimated for the studied populations from the formula [ 14 ] equaled to migrant per generation suggesting a restricted extent of gene flow among populations. Correlation between geographical and genetic distances drawn from Mantel test was significantly positive ; as shown by Figure 1 , indicating an evidence for isolation by distance, that geographically close populations tended to be genetically more similar.
This result clearly showed the existence of heterogeneity in population genetic structure of Milicia excelsa. Southern east populations clustered to form group 1, southern west populations composed group 2, central and northern east populations grouped together except Biro which clustered with the first group.
Population of Djougou remained alone in the fourth group. The model-based clustering method with STRUCTURE confirmed the heterogeneity in patterns of population genetic structure in Milicia excelsa in Benin although the inference of the number of gene pool K was not straightforward. The proportion of an individual genome from each population that contributed to each of the four clusters under a model with the highest probability is given by Figure 3. Gene pool 3 makes the bulk part of northern west population but is also remarkably represented in some populations from the south.
Biro population which, clusters with southern east populations, is geographically located in the northern east and genetically shares some common features gene pool 1, gene pool 2, and gene pool 3 with central, southern east and north populations, respectively. The overall pattern of genetic variation at microsatellite loci in Milicia excelsa revealed considerable genetic diversity , , and. The very high level of polymorphism detected could be due to high number of repeats 14 to 29 repeats in the used loci [ 12 ] as SSRs with many repeats have been shown to be more polymorphic than ones with few repeats [ 4 , 31 , 32 ].
Genetic diversities observed in Milicia excelsa AR , H O , H E and H S are lower than the pattern found in other microsatellite studies of tropical tree species including Symphonia globulifera [ 1 ], Carapa guianensis [ 4 ], Swietenia humilis [ 8 ], Caryacar brasilense [ 9 ], and Swietenia macrophylla Lemes et al.
Estimates of genetic differentiation among populations from microsatellites ; indicated moderate but highly significant degree of differentiation among populations of Milicia excelsa in Benin. Since the species of concern is a tropical cross pollinated species with bat and bird dispersal-seeds [ 34 ] and some gravity-dispersed seed, this result may fit with the general observation that woody, perennial and outbreeding species maintain most of their variation within populations Hamrick et al.
Other studies that have assessed genetic variation in natural populations of tropical tree species using microsatellites exhibited much lower levels of genetic differentiation than found here 0. However, some authors have suggested that population differentiation is more accurately estimated by , because this measure better accounts for the high mutation rate of microsatellite markers while tends to underestimate population differentiation [ 9 , 14 , 36 ] Lemes et al.
On the other hand, different simulation studies [ 37 ] have shown that most of the microsatellite markers formed by short or imperfect repeat motifs tend to fit more closely the IAM than the SMM.
Inbreeding coefficient indicated that alleles within populations were not united at random and that mating between close relatives may play an important role in determining the genetic structure of these populations. The estimated gene flow was also low reflecting a reduced gene flow among populations.
The first possible explanation of such a situation is the occurrence of null alleles, which failed to amplify because of mutations in the flanking primer sequence Lemes et al. But this seems to be an unlikely explanation because amplification failures were rare in this study.
The second explanation which has been experienced in Swietenia macrophylla , a tropical outcrossing species is that, assortive mating caused by spatial clustering or coincidence in flowering time among related groups of trees, can lead to inbreeding and homozygote excess Lemes et al. Such explanation seems to be more favorable in the case of Milicia excelsa in Benin.
Indeed, Milicia excelsa is threatened throughout its range in Benin as a result of overexploitation and habitat destruction, which have clearly reduced local population size and led many populations to local extinction. The spatial clustering of M. Then the great majority of dispersal occurs between nearest-neighbour populations with only a few individuals moving longer distance.
Our data suggested that M. This hypothesis is supported by a significant Mantel test between a matrix of values and a matrix of geographical distances. Spatial analysis by the model-based clustering method also indicated a geographical structure and clustered populations into four groups which correspond to southern west, southern east including one population from the middle northern east , northern west, and central populations. Several studies dealing with spatial genetic structure reported either a lack or a weak geographical heterogeneity in various tropical or temperate tree species which, they argued by the limited seed dispersal but extensive gene flow by pollen [ 40 — 42 ] or by extensive gene flow by pollen, wide seed dispersal, self incompatibility and dispersal agent [ 43 , 44 ].
These authors made the general statement that for woody insect-pollinated species with seed widely and independently dispersed by birds, at most weak genetic structure will result. In the current study, the distribution of gene pool 2 and gene pool 4 in the south and the predominance of gene pool 1 in the center, suggested an impact of limited seed dispersal. Different factors could explain this genetic structure.
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This section incorporates all aspects of the genetics of animal populations including but not limited to: analysis of evolutionary, ecological and conservation genetics of animal populations. Long noncoding RNA lncRNA has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potenti Content type: Research article. Published on: 18 February In the past decade, the brown marmorated stink bug BMSB , Halyomorpha halys Hemiptera: Pentatomidae has caused extensive damage to global agriculture. As a high-risk pest for many countries, including New Zeal
Jetzt bewerten Jetzt bewerten. Loss of biodiversity is among the greatest problems facing theworld today. Conservation and the Genetics of Populationsgives a comprehensive overview of the essential background,concepts, and tools needed to understand how genetic informationcan be used to conserve species threatened with extinction, and tomanage species of ecological or commercial importance.
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To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific microsatellite DNA loci.Reply