Correlation between Climatic Factors and Genetic Diversity of Phrynocephalus forsythii

Global climate change is a threat to animals in nearly all biomes and ecosystems, especially for ectotherm whose life activities highly depend on environmental thermal regime. Population genetic diversity which is essential for adaptation to environmental change is a useful index for long-term species survival. In this paper, genetic diversity of eight Phrynocephalus forsythii population which distributed in Tarim Basin, China, were evaluated based on three mtDNA gene and its correlation with environment factors were investigated using RDA. Our result revealed that, the level of genetic diversity of P. forsythii populations was related to its location but there was no significant correlation between genetic distances and geographic distances in P. forsythii. However, we find that mtDNA of P. forsythii was subjected to selection pressure during evolution and population genetic diversity was significantly positively related to variation coefficient of rainfall(VCR) and altitude(AL), while significantly negatively related to longitude(N) and annual average temperature(AAT). Our result supported the previous prediction that excessive ambient heat is a threat to P. forsythii.     

Environmental adaptations as windows on molecular evolution

Changes in gene regulation may play an important role in adaptive evolution, particularly during adaptation to a changing environment. However, little is known about the molecular mechanisms underlying adaptively significant variation in gene regulation. To address this question, we are using environmental adaptations in populations of a fish, Fundulus heteroclitus as a window into the molecular evolution of gene regulation. F. heteroclitus are found along the East Coast of North America, with populations distributed along a steep thermal gradient. At the extremes of the species range, populations have undergone local adaptation to their habitat temperatures. A variety of genes differ in their regulation between these populations. We have determined the mechanism responsible for changes in lactate dehydrogenase-B (Ldh-B) gene regulation. A limited number of mutations in the regulatory sequence of this gene result in changes in its expression. Both the phenotypic (increased LDH activity) and genotypic (changes in Ldh-B regulatory sequences) differences between populations have been shown to be affected by natural selection, rather than genetic drift. Therefore, even a small number of mutations within important regulatory sequences can provide evolutionarily significant variation and have an impact on environmental adaptation.     

A genome‐wide search for local adaptation in a terrestrial‐breeding frog reveals vulnerability to climate change

Terrestrial‐breeding amphibians are likely to be vulnerable to warming and drying climates, as their embryos require consistent moisture for successful development. Adaptation to environmental change will depend on sufficient genetic variation existing within or between connected populations. Here, we use Single Nucleotide Polymorphism (SNP) data to investigate genome‐wide patterns in genetic diversity, gene flow and local adaptation in a terrestrial‐breeding frog (Pseudophryne guentheri) subject to a rapidly drying climate and recent habitat fragmentation. The species was sampled across 12 central and range‐edge populations (192 samples), and strong genetic structure was apparent, as were high inbreeding coefficients. Populations showed differences in genetic diversity, and one population lost significant genetic diversity in a decade. More than 500 SNP loci were putatively under directional selection, and 413 of these loci were correlated with environmental variables such as temperature, rainfall, evaporation and soil moisture. One locus showed homology to a gene involved in the activation of maturation in Xenopus oocytes, which may facilitate rapid development of embryos in drier climates. The low genetic diversity, strong population structuring and presence of local adaptation revealed in this study shows why management strategies such as targeted gene flow may be necessary to assist isolated populations to adapt to future climates.     

Genetic diversity in butterflies: Interactive effects of habitat fragmentation and climate-driven range expansion

Some species are expanding their ranges polewards during current climate warming. However, anthropogenic fragmentation of suitable habitat is affecting expansion rates and here we investigate interactions between range expansion, habitat fragmentation and genetic diversity. We examined three closely related Satyrinae butterflies, which differ in their habitat associations, from six sites along a transect in England from distribution core to expanding range margin. There was a significant decline in allozyme variation towards an expanding range margin in Pararge aegeria, which has the most restricted habitat availability, but not in Pyronia tithonus whose habitat is more widely available, or in a non-expanding 'control species' (Maniola jurtina). Moreover, data from another transect in Scotland indicated that declines in genetic diversity in P. aegeria were evident only on the transect in England, which had greater habitat fragmentation. Our results indicate that fragmentation of breeding habitats leads to more severe founder events during colonization, resulting in reduced diversity in marginal populations in more specialist species. The continued widespread loss of suitable habitats in the future may increase the likelihood of loss of genetic diversity in expanding species, which may affect whether or not species can adapt to future environmental change.     

Specialization and habitat: spatial and environmental effects on abundance and genetic diversity of forest generalist and specialist Carabus species

Habitat specialist species are supposed to be more susceptible to variations in local environmental characteristics than generalists. To test this hypothesis, we conducted a comparative analysis on abundance and genetic diversity of forest carabids differing in their habitat requirements. Four species were sampled in forests characterized by abiotic, landscape and biotic environmental variables. A statistical framework based on canonical correspondence analysis was used for one habitat generalist and one habitat specialist species to determine the relative contribution of environmental variables in structuring inter- and intrapopulational genetic diversity depicted by microsatellites. Our results showed that sympatric species differed in their sensitivity to environmental variables. The same variables were found to be important in analyses of abundance and genetic data. However, specialization was not related to a greater sensitivity to local environmental characteristics. The strong impact of spatial variables on genetic data suggested that genetic variation among populations would largely reflect the response of individual species to dispersal opportunities more than the effect of habitat quality.     

Biotechnological approaches for conservation and improvement of rare and endangered plants of Saudi Arabia

Genetic variation is believed to be a prerequisite for the short-and long-term survival of the plant species in their natural habitat. It depends on many environmental factors which determine the number of alleles on various loci in the genome. Therefore, it is important to understand the genetic composition and structure of the rare and endangered plant species from their natural habitat to develop successful management strategies for their conservation. However, rare and endangered plant species have low genetic diversity due to which their survival rate is decreasing in the wilds. The evaluation of genetic diversity of such species is very important for their conservation and gene manipulation. However, plant species can be conserved by in situ and in vitro methods and each has advantages and disadvantages. DNA banking can be considered as a means of complimentary method for the conservation of plant species by preserving their genomic DNA at low temperatures. Such approach of preservation of biological information provides opportunity for researchers to search novel genes and its products. Therefore, in this review we are describing some potential biotechnological approaches for the conservation and further manipulation of these rare and endangered plant species to enhance their yield and quality traits.     

杨属遗传多样性研究进展

 生物多样性的研究和保护是目前全世界普遍关注的问题,其中研究较多的是遗传多样性、物种多样性及生态系统多样性,遗传多样性作为生物多样性的重要组成部分,是生态系统多样性和物种多样性的基础方面。杨树是世界各国普遍种植的木本植物,研究其遗传多样性具有重要的理论和实践意义,国内外都开展了广泛研究。本文综述了杨属(Populus)植物的派、种及无性系等在表型、染色体、蛋白质及DNA水平的遗传多样性的研究进展。其表型多样性主要体现在不同水平上的种群大小、形态特征、物候期、材性以及对生物或非生物逆境的抗性等方面;在杨属植物中已发现有天然的三倍体及三倍体/非整倍体的杂交种存在;蛋白质的多态性主要集中于同工酶的研究,用于不同杨属植物的遗传差异,无性系或品种的特征、分化和遗传研究;DNA多态性是研究最多的,RFLP、RAPD、AFLP和SSR等分子标记已广泛用于杨属的遗传多样性研究中,根据不同的研究目的所选择的DNA（nDNA, cpDNA或mtDNA）也不同。并根据国内的研究现状,提出了几点建议。     

Genetically depauperate but widespread: the case of an emblematic Mediterranean pine

Genetic variation is generally considered a prerequisite for adaptation to new environmental conditions. Thus the discovery of genetically depauperate but geographically widespread species is unexpected. We used 12 paternally inherited chloroplast microsatellites to estimate population genetic variation across the full range of an emblematic circum-Mediterranean conifer, stone pine (Pinus pinea L.). The same chloroplast DNA haplotype is fixed in nearly all of the 34 investigated populations. Such a low level of variation is consistent with a previous report of very low levels of diversity at nuclear loci in this species. Stone pine appears to have passed through a severe and prolonged demographic bottleneck, followed by subsequent natural- and human-mediated dispersal across the Mediterranean Basin. No other abundant and widespread plant species has as little genetic diversity as P. pinea at both chloroplast and nuclear markers. However, the species harbors a nonnegligible amount of variation at adaptive traits. Thus a causal relationship between genetic diversity, as measured by marker loci, and the evolutionary precariousness of a species, cannot be taken for granted.     

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation‐sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat‐related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.     

Canalization breakdown and evolution in a source-sink system

Understanding the process of adaptation to novel environments may help to elucidate several ecological phenomena, from the stability of species range margins to host-pathogen specificity and persistence in degraded habitats. We study evolution in one type of novel environment: a sink habitat where populations cannot persist without recurrent immigration from a source population. Previous studies on source-sink evolution have focused on how extrinsic environmental factors influence adaptation to a sink, but few studies have examined how intrinsic genetic factors influence adaptation. We use an individual-based model to explore how genetic canalization that evolves in gene regulation networks influences the adaptation of a population to a sink. We find that as canalization in the regulation network increases, the probability of adaptation to the novel habitat decreases. When adaptation to the habitat does occur, it is usually preceded by a breakdown of canalization. As evolution continues in the novel habitat, canalization reemerges, but a legacy of the breakdown may remain, even after several generations. We also find that environmental noise tends to increase the probability of adaptation to the novel habitat. Our results suggest that the details of genetic architecture can significantly influence the likelihood of niche evolution in novel environments.     

Epigenetic variation associated with responses to different habitats in the context of genetic divergence in Phragmites australis

The mechanisms underlying heritable phenotypic divergence associated with adaptation in response to environmental stresses may involve both genetic and epigenetic variations. Several prior studies have revealed even higher levels of epigenetic variation than genetic variation. However, few population‐level studies have explored the effects of epigenetic variation on species with high levels of genetic diversity distributed across different habitats. Using AFLP and methylation‐sensitive AFLP markers, we tested the hypothesis that epigenetic variation may contribute to differences in plants occupying different habitats when genetic variation alone cannot fully explain adaptation. As a cosmopolitan invasive species, Phragmites australis (common reed) together with high genetic diversity and remarkable adaptability has been suggested as a model for responses to global change and indicators of environmental fluctuations. We found high levels of genetic and epigenetic diversity and significant genetic/epigenetic structure within each of 12 studied populations sampled from four natural habitats of P. australis. Possible adaptive epigenetic variation was suggested by significant correlations between DNA methylation‐based epigenetic differentiation and adaptive genetic divergence in populations across the habitats. Meanwhile, various AMOVAs indicated that some epigenetic differences may respond to various local habitats. A partial Mantel test was used to tease out the correlations between genetic/epigenetic variation and habitat after controlling for the correlation between genetic and epigenetic variations. We found that epigenetic diversity was affected mostly by soil nutrient availability, suggesting that at least some epigenetic differentiation occurred independently of genetic variation. We also found stronger correlations between epigenetic variation and phenotypic traits than between genetic variation and such traits. Overall, our findings indicate that genetically based differentiation correlates with heterogeneous habitats, while epigenetic variation plays an important role in ecological differentiation in natural populations of P. australis. In addition, our results suggest that when assessing global change responses of plant species, intraspecific variation needs to be considered.     

Less can be more: loss of MHC functional diversity can reflect adaptation to novel conditions during fish invasions

The ability of invasive species to adapt to novel conditions depends on population size and environmental mismatch, but also on genetic variation. Away from their native range, invasive species confronted with novel selective pressures may display different levels of neutral versus functional genetic variation. However, the majority of invasion studies have only examined genetic variation at neutral markers, which may reveal little about how invaders adapt to novel environments. Salmonids are good model systems to examine adaptation to novel pressures because they have been translocated all over the world and represent major threats to freshwater biodiversity in the Southern Hemisphere, where they have become invasive. We examined patterns of genetic differentiation at seven putatively neutral (microsatellites) loci and one immune‐related major histocompatibility complex (MHC class II‐β) locus among introduced rainbow trout living in captivity (farmed) or under natural conditions (naturalized) in Chilean Patagonia. A significant positive association was found between differentiation at neutral and functional markers, highlighting the role of neutral evolutionary forces in shaping genetic variation at immune‐related genes in salmonids. However, functional (MHC) genetic diversity (but not microsatellite diversity) decreased with time spent in the wild since introduction, suggesting that there was selection against alleles associated with captive rearing of donor populations that do not provide an advantage in the wild. Thus, although high genetic diversity may initially enhance fitness in translocated populations, it does not necessarily reflect invasion success, as adaptation to novel conditions may result in rapid loss of functional MHC diversity.     

Evidence for Frozen-Niche Variation in a Cosmopolitan Parthenogenetic Soil Mite Species (Acari,Oribatida)

Parthenogenetic lineages may colonize marginal areas of the range of related sexual species or coexist with sexual species in the same habitat. Frozen-Niche-Variation and General-Purpose-Genotype are two hypotheses suggesting that competition and interclonal selection result in parthenogenetic populations being either genetically diverse or rather homogeneous. The cosmopolitan parthenogenetic oribatid mite Oppiella nova has a broad ecological phenotype and is omnipresent in a variety of habitats. Morphological variation in body size is prominent in this species and suggests adaptation to distinct environmental conditions. We investigated genetic variance and body size of five independent forest - grassland ecotones. Forests and grasslands were inhabited by distinct genetic lineages with transitional habitats being colonized by both genetic lineages from forest and grassland. Notably, individuals of grasslands were significantly larger than individuals in forests. These differences indicate the presence of specialized genetic lineages specifically adapted to either forests or grasslands which coexist in transitional habitats. Molecular clock estimates suggest that forest and grassland lineages separated 16-6 million years ago, indicating long-term persistence of these lineages in their respective habitat. Long-term persistence, and morphological and genetic divergence imply that drift and environmental factors result in the evolution of distinct parthenogenetic lineages resembling evolution in sexual species. This suggests that parthenogenetic reproduction is not an evolutionary dead end.