Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer,Cryptomeria japonica

Local adaptation is important in evolutionary processes and speciation. We used multiple tests to identify several candidate genes that may be involved in local adaptation from 1026 loci in 14 natural populations of Cryptomeria japonica, the most economically important forestry tree in Japan. We also studied the relationships between genotypes and environmental variables to obtain information on the selective pressures acting on individual populations. Outlier loci were mapped onto a linkage map, and the positions of loci associated with specific environmental variables are considered. The outlier loci were not randomly distributed on the linkage map; linkage group 11 was identified as a genomic island of divergence. Three loci in this region were also associated with environmental variables such as mean annual temperature, daily maximum temperature, maximum snow depth, and so on. Outlier loci identified with high significance levels will be essential for conservation purposes and for future work on molecular breeding.     

Clonal structure of natural populations of Cryptomeria japonica growing at different positions on slopes,detected using RAPD markers

Cryptomeria japonica D. Don (Japanese cedar), an economically important timber species endemic to Japan, is dominant on ridges and upper slopes in cool-temperate natural forests of Kyoto Prefecture. Recruitment of sexual progeny in the area near the Japan Sea is extremely rare, and propagation occurs predominantly through clonal growth by layering. The development pattern that occurs with layering and the resulting complexity of the population structure make it difficult to identify distinct clones, even by excavation. Therefore, we used the randomly amplified polymorphic DNA (RAPD) technique to examine the clonal structure of upper- and lower-slope plots established in two C. japonica populations in Kyoto Prefecture. A total of 263 plants sampled from four plots were analyzed using 10 arbitrarily chosen decamer primers, which produced 50 highly reproducible RAPD bands. There was a different clonal structure in upper- and lower-slope plots. Lower-slope plots were made up of a small number of genets with many ramets, while upper-slope plots were made up of a large number of genets with a few ramets. Clonal diversity measured using PD, Simpson’s D, and Fager’s E was higher in the upper-slope plots. These results show that natural C. japonica populations maintain relatively high clonal variation, compared with other clonal plant species, and that repeated seedling recruitment occurred more frequently in upper-slope plots than in lower-slope plots.     

A genome scan to detect candidate regions influenced by local natural selection in human populations

As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic variation. A potential approach for detecting local selection is to screen random loci across the genome; those loci that exhibit unusually large genetic distances between human populations are then potential markers of genomic regions under local selection. We investigated this approach by genotyping 332 short tandem repeat (STR) loci in Africans and Europeans and calculating the genetic differentiation for each locus. Patterns of genetic diversity at these loci were consistent with greater variation in Africa and with local selection operating on populations as they moved out of Africa. For 11 loci exhibiting the largest genetic differences, we genotyped an additional STR locus located nearby; the genetic distances for these nearby loci were significantly larger than average. These genomic regions therefore reproducibly exhibit larger genetic distances between populations than the "average" genomic region, consistent with local selection. Our results demonstrate that genome scans are a promising means of identifying candidate regions that have been subjected to local selection.     

Demographic genetic structure of Cryptomeria japonica var. sinensis in Tianmushan Nature Reserve, China

Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations.However,compared with spatial genetic structure,few studies have been conducted on genetic changes over time.In this study,we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan,Cryptomeria japonica var.sinensis,in the Tianmushan National Nature Reserve,whose origin was debatable.The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively,lower than other conifers with the same life history characteristics.FST was 0.002 4- 0.003,and the pairwise test revealed no significant differentiation in any pair of size classes.Significant heterozygosity excesses were detected in five size classes except the oldest one,indicating bottleneck event(s).The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.     

Population genetic structure and the effect of historical human activity on the genetic variability of Cryptomeria japonica core collection,in Japan

Population structure and genome-wide linkage disequilibrium (LD) were investigated in a Cryptomeria japonica core collection consisting of 510 individuals and providing comprehensive coverage of the natural distribution range of the species, using 4,896 SNP markers. Both Bayesian clustering and principal coordinate analyses clearly subdivided the sample into two distinct groups corresponding to the Japan Sea side and the Pacific Ocean side of Japan. The clustering analysis also detected two subgroups located in Northern Tohoku and Yakushima Island, as was also the case in the natural population. This finding is in accord with the ecogeographical origin of the cultivars; however, the spatial distribution of these clusters was slightly different between the natural population and the core collection, especially in the Chugoku district, an effect which might have resulted from historical human activity. The genetic diversity of the core collection is comparable to, or a little higher than, that of natural populations, indicating that the individuals in the core collection have not suffered from diversity losses caused by a domestication bottleneck. LD analysis with mapped markers indicated that the LD decays rapidly, within approximately 5 cM, in both the core collection and natural populations. The results show that the population described here is a valuable resource for both basic and applied research on C. japonica.     

Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period

Using 11 microsatellite markers, we investigated the allelic variation and genetic structure of Cryptomeria japonica, across most of its natural distribution. The markers displayed high levels of polymorphism (average gene diversity=0.77, average number of alleles=24.0), in sharp contrast to the lower levels of polymorphism found in allozyme and cleaved amplified polymorphic sequence markers in previous studies. Little genetic differentiation was found among populations (F_ST=0.028, P<0.001), probably because the species is wind-pollinated and long-lived. No clear relationship between Neis genetic distances and geographical locations of the populations were found using the principal coordinate and unweighted pair-group method with arithmetic averaging analyses. The lack of such trends might be due partly to microsatellite homoplasy arising from mutation blurring the genealogical record. However, there was a trend towards high allelic diversity in five populations (Ashitaka, Ashiu, Oki-Island, Yakushima-Island-1 and -2), which are very close to, or in, refugial areas of the last glacial period as defined by Tsukada based on pollen analysis data and current climatic divisions. We postulate that these refugial populations might have been less affected by genetic drift than the other populations due to their relatively large size.     

Landscape genetic structure of natural populations of Acacia caven in Argentina

Acacia caven is a South American species which shows remarkable climate tolerance and ecological adaptability; as such, this species is suitable for colonizing anthropogenically degraded sites. This species is widely distributed, and six varieties have been described based on both morphological traits and molecular markers. Moreover, Aronson (1992) suggests that, for this species, geographical separation could be associated with ecological differentiation. In this study, amplified fragment length polymorphisms were used to study genetic variation within and among 15 populations of A. caven from five eco-regions of Argentina and to investigate (1) whether the varieties are genetically coherent, (2) whether the varieties correspond consistently to a single eco-region, (3) the proportion of the species diversity explained within and among varieties and eco-regions. Eight of the 225 bands appear to be under positive selection. The remaining 217 neutral loci showed a high percentage of polymorphism (99.1%). The estimates of genetic diversity H _j were generally high. The F _ST (0.315) was highly significant, providing evidence for genetic structure among populations. Hierarchical analysis of molecular variance indicated that variation among eco-regions was 8.2% and highly significant. The higher component of variance was found within populations (67.5%). STRUCTURE analysis suggested that the optimal number of K?=?11. The results showed that, in most cases, geographic separation is associated with ecological differentiation. Since differentiation of A. caven populations studied here in eco-regions was highly significant, sampling should include a large number of trees within populations as well as covering the wide ecological diversity of the species.     

Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis

Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

     

Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato)

We investigated DNA variation within and between two closely related conifers, Cryptomeria japonica and Taxodium distichum, at nuclear loci encoding ferredoxin, glutamyl-tRNA reductase, lycopene beta cyclase, and phosphoribosylanthranilate transferase. Average nucleotide diversity at silent sites was estimated to be 0.0035 (SE 0.0012) in C. japonica and 0.0058 (SE 0.0006) in T. distichum. One population in C. japonica was differentiated from the others but generally there was not much differentiation among populations or varieties within the two species. However, the two species seemed to differ in frequency spectra of DNA polymorphisms. Excesses of intermediate-frequency variants were found in C. japonica, whereas excesses of both rare and high-frequency variants were found in T. distichum, which suggested different histories of population structures in the two species. Deviations from the standard neutral expectations in DNA polymorphisms were found by applications of neutrality tests. The results show that actions of selection to respective loci seem to differ between the two species, indicating differences of interaction among evolutionary factors.     

Site-specific selfish genes as tools for the control and genetic engineering of natural populations

Site-specific selfish genes exploit host functions to copy themselves into a defined target DNA sequence, and include homing endonuclease genes, group II introns and some LINE-like transposable elements. If such genes can be engineered to target new host sequences, then they can be used to manipulate natural populations, even if the number of individuals released is a small fraction of the entire population. For example, a genetic load sufficient to eradicate a population can be imposed in fewer than 20 generations, if the target is an essential host gene, the knockout is recessive and the selfish gene has an appropriate promoter. There will be selection for resistance, but several strategies are available for reducing the likelihood of it evolving. These genes may also be used to genetically engineer natural populations, by means of population-wide gene knockouts, gene replacements and genetic transformations. By targeting sex-linked loci just prior to meiosis one may skew the population sex ratio, and by changing the promoter one may limit the spread of the gene to neighbouring populations. The proposed constructs are evolutionarily stable in the face of the mutations most likely to arise during their spread, and strategies are also available for reversing the manipulations.     

Spatial genetic structure within two populations of a self-incompatible perennial,Chionographis japonica var.japonica (Liliaceae)

Intrapopulational spatial genetic structure was examined in two populations ofChionographis japonica var.japonica, a self-incompatible perennial, by spatial autocorrelation analysis of enzyme polymorphism. Although most spatial autocorrelation indices (Moran'sI) in the shortes distance class were significantly positive, most in the other distance classes did not significantly deviate from the values expected from random distributions of genotypes in both populations. This contrasts with a spatial genetic pattern previously reported for a population of the predominantly selfing congener,C. japonica var.kurohimensis, indicating that pollen-mediated gene flow highly impedes genetic substructuring within populations of outcrossingC. japonica var.japonica. Genetic similarity in very proximate distance found in outcrossingC. japonica var.japonica is probably due to restricted dispersal of seeds.     

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.     

Quantitative genetic analysis of natural populations

Quantitative genetic studies in natural populations have been rare because they require large breeding programmes or known pedigrees. The relatedness that has been estimated from molecular markers can now be used to substitute for breeding, allowing studies of previously inaccessible species. Many behavioural ecologists have a sufficient number of markers and study species with characteristics that are amenable to this approach. It is now time to combine studies of selection with studies of genetic variation for a more complete understanding of behavioural evolution.     

On adaptive accuracy and precision in natural populations

Adaptation is usually conceived as the fit of a population mean to a fitness optimum. Natural selection, however, does not act only to optimize the population mean. Rather, selection normally acts on the fitness of individual organisms in the population. Furthermore, individual genotypes do not produce invariant phenotypes, and their fitness depends on how precisely they are able to realize their target phenotypes. For these reasons we suggest that it is better to conceptualize adaptation as accuracy rather than as optimality. The adaptive inaccuracy of a genotype can be measured as a function of the expected distance of its associated phenotype from a fitness optimum. The less the distance, the more accurate is the adaptation. Adaptive accuracy has two components: the deviance of the genotypically set target phenotype from the optimum and the precision with which this target phenotype can be realized. The second component, the adaptive precision, has rarely been quantified as such. We survey the literature to quantify how much of the phenotypic variation in wild populations is due to imprecise development. We find that this component is often substantial and highly variable across traits. We suggest that selection for improved precision may be important for many traits.     

AFLP and CAPS linkage maps of Cryptomeria japonica

We have used two DNA marker systems, AFLP and CAPS, in a two-way pseudo-testcross strategy applied to an F₁ population to construct genetic linkage maps of two local sugi cultivars. The AFLP markers detected about eight polymorphisms per parent per primer combination. Using 38 primer combinations, 612 AFLPs were detected in ’Haara 4’ and ’Kumotooshi’, of which 305 segregated in a 1:1 ratio (P>0.05). A total of 91 markers (83 AFLP and 8 CAPS) in ’Haara 4’ and 132 (123 AFLP and 9 CAPS) in ’Kumotooshi’ were distributed among 19 and 23 linkage groups, respectively, each of which included 2–17 markers. Maps of ’Haara 4’ and ’Kumotooshi’ spanned 1266.1 cM and 1992.3 cM, and covered approximately 50% and 80% of the sugi genome, respectively. Sequences derived from cDNA, which were previously used to construct a sugi linkage map, were also placed on our linkage maps as CAPS markers. Where a ’two-way pseudo-testcross’ is used, more than half of the sugi CAPS developed can be used to construct linkage maps for each parental family. The saturation of mapped markers, and the integration of several linkage maps derived from different mapping populations, is anticipated in the near future. Received: 15 August 1999 / Accepted: 27 August 1999     

The influence of natural barriers in shaping the genetic structure of Maharashtra populations

Background

The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level.

Methodology/Principal Findings

To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a.

Conclusions/Significance

Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (∼10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations.