Genetic diversity among geographically separated populations of Nepenthes mirabilis

The distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H _T) and inter-population genetic diversity (H _S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G _ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.     

Analysis of the Phylogenetic Relationships Among Several Species of Gramineae Using ACGM Markers

To study the transferability of rice (Oryza sativa L.) genome data, we used amplified consensus genetic markers to analyze the phylogenetic relationships among several species and genera in Gramineae. Ten accessions representing five grass genera (Oryza, Zea, Setaria, Triticum, and Phyllostachys) were used. According to the genetic distances, a cluster tree was constructed. The relationships among the five genera could be simply described as ((Oryza + (Zea + Setaria)) + Triticum) + Phyllostachys. The results suggest that the genetic distance between rice and maize (Z. mays L.) or rice and millet (Setaria italica L.) is closer than that between rice and wheat (Triticum aestivum L) or rice and bamboo.     

Molecular Approaches Revealing Prehistoric, Historic, or Recent Translocations and Introductions of Hares (Genus Lepus) by Humans

Although only of medium size, and thus of little nutritional value compared to big game such as mammoths and ungulates, hares (Lepus spp.) probably have always been a food source for humans, as documented in archaeological finds. Nowadays, hares, particularly such species as the brown hare (L. europaeus), are among the most important game species in many European countries. For hunting, perhaps religious reasons, and in connection with certain myths, hares have been and are still being intentionally translocated. Ancient translocations by humans can be inferred from the presence of hares on islands that had no mainland connections, at least during the Pleistocene, the major evolutionary period of the genus Lepus. We review some of the literature on anthropogenic translocations of hares. We focus on three examples [the brown hare (L. europaeus), the Corsican hare (L. corsicanus), and the Sardinian hare (L. capensis)], where some molecular data could be used to trace the translocation routes and possible origins of introduced hare populations. Certain molecular marker systems, such as sequences of the hypervariable part I (HV-1) of the mitochondrial control region, show high variability in hare species and are thus promising for tracing both recent and ancient origins of translocated hares. Some other molecular marker systems as well as caveats connected with the use of such marker systems in the genus Lepus are also discussed.     

Clonality in South African isolates and evidence for a European origin of the root pathogen Thielaviopsis basicola

Thielaviopsis basicola is a soil-borne fungal pathogen with a wide host range and a cosmopolitan distribution. It causes disease on many agricultural crops, and in South Africa is the causal agent of black pod rot of groundnuts and black root rot on chicory. Knowledge of the population diversity of T. basicola could provide valuable information regarding management strategies, the possible movement, origin, and reproductive strategies of the fungus. The objective of this study was to determine the population diversity of T. basicola isolates from groundnuts and chicory in South Africa using co-dominant polymorphic markers. These markers were also used to compare isolates from South Africa with those from other hosts and geographic regions. Seven loci revealed nine alleles and two genotypes, one on groundnut and one on chicory, differing at only two loci. T. basicola isolates from eight different countries and ten different hosts revealed 17 genotypes across the seven loci with 39 different alleles. The lack of diversity for the two South African host-related populations of isolates suggests that T. basicola was introduced into South Africa. Some evidence is provided for a European origin of the pathogen, possibly linked to trade in root crops.     

Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B

Bread wheat (Triticum aestivum) is one of the most important crops worldwide. However, because of its large, hexaploid, highly repetitive genome it is a challenge to develop efficient means for molecular analysis and genetic improvement in wheat. To better understand the composition and molecular evolution of the hexaploid wheat homoeologous genomes and to evaluate the potential of BAC-end sequences (BES) for marker development, we have followed a chromosome-specific strategy and generated 11 Mb of random BES from chromosome 3B, the largest chromosome of bread wheat. The sequence consisted of about 86% of repetitive elements, 1.2% of coding regions, and 13% remained unknown. With 1.2% of the sequence length corresponding to coding sequences, 6000 genes were estimated for chromosome 3B. New repetitive sequences were identified, including a Triticineae-specific tandem repeat (Fat) that represents 0.6% of the B-genome and has been differentially amplified in the homoeologous genomes before polyploidization. About 10% of the BES contained junctions between nested transposable elements that were used to develop chromosome-specific markers for physical and genetic mapping. Finally, sequence comparison with 2.9 Mb of random sequences from the D-genome of Aegilops tauschii suggested that the larger size of the B-genome is due to a higher content in repetitive elements. It also indicated which families of transposable elements are mostly responsible for differential expansion of the homoeologous wheat genomes during evolution. Our data demonstrate that BAC-end sequencing from flow-sorted chromosomes is a powerful tool for analysing the structure and evolution of polyploid and highly repetitive genomes.     

Hybrid origin and differentiation of two tetraploid Achillea species in East Asia: molecular, morphological and ecogeographical evidence

Achillea (Asteraceae-Anthemideae) offers classical models for speciation by hybridization and polyploidy. Here, we test the suspected allotetraploid origin of two species, Achillea alpina and Achillea wilsoniana between phylogenetically distinct lineages in East Asia. A total of 421 AFLP bands from 169 individuals and 19 populations of five 2x- and two 4x-species were obtained. The data set was analysed with a newly developed model that accounts for polyploidy and assumes lack of recombination between the parental chromosome sets (i.e. disomic inheritance). A. alpina and A. wilsoniana then appear to be allotetraploids between Achillea acuminata-2x (sect. Ptarmica) and Achillea asiatica-2x (sect. Achillea). The two 4x-species share 44% and 48% of their AFLP bands with A. acuminata-2x, and 39% and 38% with A. asiatica-2x, respectively. Eight plastid haplotypes (A-H) were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses. A. alpina-4x and A. wilsoniana-4x share haplotype F only with A. asiatica-2x. This is consistent with the hybrid origin(s) involving the latter as the maternal ancestor. This result corroborates our previous DNA sequence data, where A. alpina-4x and A. wilsoniana-4x are also placed close to A. asiatica-2x. Morphology, ecology, and amplified fragment length polymorphism (AFLP) profiles of the two 2x-species are distinct, whereas the two 4x-species, grouped as A. alpina aggregate, form a nearly continuous link between them. Considering all evidence, this 4x-aggregate is regarded as the product of a hybridization between genetically distant 2x-ancestors limited to China and adjacent areas: one A. acuminata-like, and the other A. asiatica-like. The allopolyploid A. alpina agg. exhibits considerable morphological variation and ecological flexibility, and has expanded throughout eastern Asia and to northern North America, far beyond the ranges of their presumed 2x-ancestors.     

Conservation genetics and the resilience of reef-building corals

Coral reefs have suffered long-term decline due to a range of anthropogenic disturbances and are now also under threat from climate change. For appropriate management of these vulnerable and valuable ecosystems it is important to understand the factors and processes that determine their resilience and that of the organisms inhabiting them, as well as those that have led to existing patterns of coral reef biodiversity. The scleractinian (stony) corals deposit the structural framework that supports and promotes the maintenance of biological diversity and complexity of coral reefs, and as such, are major components of these ecosystems. The success of reef-building corals is related to their obligate symbiotic association with dinoflagellates of the genus Symbiodinium. These one-celled algal symbionts (zooxanthellae) live in the endodermal tissues of their coral host, provide most of the host's energy budget and promote rapid calcification. Furthermore, zooxanthellae are the main primary producers on coral reefs due to the oligotrophic nature of the surrounding waters. In this review paper, we summarize and critically evaluate studies that have employed genetics and/or molecular biology in examining questions relating to the evolution and ecology of reef-building corals and their algal endosymbionts, and that bear relevance to coral reef conservation. We discuss how these studies can focus future efforts, and examine how these approaches enhance our understanding of the resilience of reef-building corals.     

What should we weigh to estimate heterozygosity,alleles or loci?

The interest to study the effects of inbreeding in natural populations has increased in the last years. Several microsatellite-derived metrics have recently been developed to infer inbreeding from multilocus heterozygosity data without requiring detailed pedigrees that are difficult to obtain in open populations. Internal relatedness (IR) is currently the most widespread used index and its main attribute is that allele frequency is incorporated into the measure. However, IR underestimates heterozygosity of individuals carrying rare alleles. For example, descendants of immigrants paired with natives (normally more outbred) bearing novel or rare alleles would be considered more homozygous than descendants of native parents. Thus, the analogy between homozygosity and inbreeding that generally is carried out would have no logic in those cases. We propose an alternative index, homozygosity by loci (HL) that avoids such problems by weighing the contribution of each locus to the homozygosity index depending on their allelic variability. Under a wide range of simulated scenarios, we found that our index (HL) correlated better than both IR and uncorrected homozygosity (H(O)), measured as proportion of homozygous loci) with genome-wide homozygosity and inbreeding coefficients in open populations. In these populations, which are likely to prevail in nature, the use of HL instead of IR reduced considerably the sample sizes required to achieve a given statistical power. This is likely to have important consequences on the ability to detect heterozygosity fitness correlations assuming the relationship between genome-wide heterozygosity and fitness traits.     

Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

Background and Aims

The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest.

Methods

Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers.

Key Results

For nuclear microsatellites, allelic richness (R) and heterozygosity (H_e,nuc) differed between types of forest: R = 7·36 and R = 9·55, H_e,nuc = 0·64 and H_e,nuc = 0·80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (N_a,nuc) and the fixation index F_IS differed significantly: N_a,nuc = 9·41 and N_a,nuc = 13·18, F_IS = 0·06 and F_IS = 0·15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (F_ST,nuc = 0·08) and moderate for chloroplast microsatellites (F_ST,cp = 0·49). A clear relationship was observed between genetic and geographic distance (r = 0·42 P < 0·01 and r = 0·42 P = 0·03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations.

Conclusions

Residual diversity and genetic structure of populations of D. monticola in Madagascar suggest a limited impact of fragmentation on molecular genetic parameters.