Yield potential of Miscanthus energy crops in the Loess Plateau of China

Growing second‐generation energy crops on marginal land is conceptualized as one of the primary means of future bioenergy development. However, the extent to which marginal land can support energy crop production remains unclear. The Loess Plateau of China, one of the most seriously eroded regions of the world, is particularly rich in marginal land. On the basis of the previous field experiment of planting Miscanthus species in Qingyang of the Gansu Province, herein, we estimated the yield potential of Miscanthus lutarioriparius, the species with the highest biomass, across the Loess Plateau. On the basis of the radiation model previously developed from Miscanthus field trials, annual precipitation was introduced as an additional variable for yield estimate in the semiarid and semihumid regions of the Loess Plateau. Of 62 million hectares (Mha) of the Loess Plateau, our model estimated that 48.7 Mha can potentially support Miscanthus growth, with the average yield of 17.8 t ha^?1 yr^?1. After excluding high‐quality cropland and pasture and land suitable for afforestation, a total of 33.3 Mha of presumably marginal land were left available for producing the energy crop at the average yield of 16.8 t ha^?1 yr^?1 and the total annual yield of 0.56 billion tons. The analysis of environmental factors indicated that erosion, aridity, and field steepness were the primary contributors to the poor quality of the marginal land. The change of land uses from traditional agriculture to energy crop production may prevent further erosion and land degradation and consequently establish a sustainable economy for the region.     

Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones

Miscanthus × giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type‐specimen. A subset of accessions was also evaluated by restriction‐site associated DNA sequencing (RAD‐seq). In addition, we assessed the potential of new crosses to increase Mxg genetic diversity by comparing eight new triploid Mxg progeny grown from seed, along with samples of the parental species M. sacchariflorus and M. sinensis. Estimates of genotyping error rates were essential for distinguishing between experimental error and true genotypic differences among accessions. Given differences in estimated error rates and costs per marker for SSRs and RAD‐seq, the former is currently more cost‐effective for determining if two accessions are genetically identical. We concluded that all of the Mxg legacy cultivars were derived via vegetative propagation from a single genet. In contrast with the Mxg legacy cultivars, genetic similarity to the type‐specimen of eight new triploid Mxg progeny ranged from 0.46 to 0.56. Though genetic diversity among the Mxg legacy cultivars is critically low, new crosses can provide much‐needed variation to growers.     

Population structure and gene flow in the Sheepnose mussel (Plethobasus cyphyus) and their implications for conservation

North American freshwater mussel species have experienced substantial range fragmentation and population reductions. These impacts have the potential to reduce genetic connectivity among populations and increase the risk of losing genetic diversity. Thirteen microsatellite loci and an 883 bp fragment of the mitochondrial ND1 gene were used to assess genetic diversity, population structure, contemporary migration rates, and population size changes across the range of the Sheepnose mussel (Plethobasus cyphyus). Population structure analyses reveal five populations, three in the Upper Mississippi River Basin and two in the Ohio River Basin. Sampling locations exhibit a high degree of genetic diversity and contemporary migration estimates indicate that migration within river basins is occurring, although at low rates, but there is no migration is occurring between the Ohio and Mississippi river basins. No evidence of bottlenecks was detected, and almost all locations exhibited the signature of population expansion. Our results indicate that although anthropogenic activity has altered the landscape across the range of the Sheepnose, these activities have yet to be reflected in losses of genetic diversity. Efforts to conserve Sheepnose populations should focus on maintaining existing habitats and fostering genetic connectivity between extant demes to conserve remaining genetic diversity for future viable populations.     

Genotypic variation of cell wall composition and its conversion efficiency in Miscanthus sinensis,a potential biomass feedstock crop in China

Plant cell walls are composed of cellulose microfibrils embedded in a cross‐linked‐net of matrix polysaccharides and co‐polymerized with lignin. The study presented the genotypic variations of cell wall composition, biohydrogen production, and lignocellulose degradation ratio in a collection of 102 Miscanthus sinensis (M. Sinensis, hereafter) accessions collected from a wide geographical range in China. Significant variations were observed for the determined traits, cellulose content, hemicellulose content, cellulose and hemicellulose degradation efficiency, and biohydrogen yield. The cellulose, hemicellulose, and lignin contents ranged from 30.20–44.25, 28.97–42.65, and 6.96–20.75%, respectively. The degradation ratio of cellulose and hemicellulose varied from 2.08% to 37.87% and from 14.71% to 52.50%, respectively. The feedstock was fermented to produce biohydrogen, and the production varied from 14.59 to 40.66 ml per gram of Miscanthus biomass. The expression profile of three cellulose synthase (MsCesA) genes was initially established to indicate the genotypic difference among the M. sinensis accessions. Pearson's correlations were conducted to reveal the perplexing relationship between the tested traits, biohydrogen yield, cell wall composition and their degradation efficiency. In addition, the relationship pattern, between the test traits and the geographic factors corresponding with the original place, was investigated. The result showed that the significant variation among the M. sinensis genotypes is the result of natural selection in different environments of their original habitats. Improvement in cell wall composition and structure and enhancement of lignocellulose degradation ratio could significantly increase sustainable bioenergy production.     

Genetic diversity and differentiation of Daphnia galeata in the middle and lower reaches of the Yangtze River,China

Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F‐statistics (F_ST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.     

Genetic diversity and phylogeography of Daphnia similoides sinensis located in the middle and lower reaches of the Yangtze River

Geographical patterns, climate, and environmental change have important influences on the distribution and spread of aquatic organisms. However, the relationships between the geographical pattern and phylogenetics of Daphnia as well as environmental change are not well known. The genetic diversity and phylogeography of seven D. similoides sinensis populations located in the middle and lower reaches of the Yangtze River were investigated based on the combination of mitochondrial (COI gene) and nuclear (14 microsatellite primers) markers. Based on the mitochondrial gene markers, D. similoides sinensis from the middle and lower reaches of the Yangtze River had one ancestral haplotype and two evolutionary clades. In addition, D. similoides sinensis population deviated from neutral evolution, showing signs of a bottleneck effect followed by population expansion. Based on the microsatellite markers, the seven D. similoides sinensis populations formed three main groups. The dendrogram (NJ/ME) showed that D. similoides sinensis based on the mitochondrial genes marker were obviously clustered two main clades, whereas there were three clades based on the microsatellite markers. Our results suggested that the habitat fragmentation due to the barrier of the dams and sluices promoted the genetic differentiation and phylogeography of D. similoides sinensis populations in the middle and lower reaches of the Yangtze River.     

Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis

Species and hybrids of Miscanthus are a promising energy crop, but their outcrossing mating systems and perennial life cycles are serious challenges for breeding programs. One approach to accelerating the domestication of Miscanthus is to harness the tremendous genetic variation that is present within this genus using phenotypic data from extensive field trials, high‐density genotyping and sequencing technologies, and rapidly developing statistical methods of relating phenotype to genotype. The success of this approach, however, hinges on detailed knowledge about the population genetic structure of the germplasm used in the breeding program. We therefore used data for 120 single‐nucleotide polymorphism and 52 simple sequence repeat markers to depict patterns of putatively neutral population structure among 244 Miscanthus genotypes grown in a field trial near Aberystwyth (UK) and delineate a population of 145 M . sinensis genotypes that will be used for association mapping and genomic selection. Comparative multivariate analyses of molecular marker and phenotypic data for 17 traits related to phenology, morphology/biomass, and cell wall composition revealed significant geographic patterns in this population. A longitudinal cline accounted for a substantial proportion of molecular marker variation (R² = 0.60, P = 3.4 × 10^?15). In contrast, genetic variation for phenotypic traits tended to follow latitudinal and altitudinal gradients, with several traits appearing to have been affected by divergent selection (i.e., Q_ST >> F_ST). These contrasting geographic trends are unusual relative to other plants and provide opportunities for powerful studies of phenotype–genotype associations and the evolutionary history of M. sinensis.     

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. F_ST outlier analysis revealed that promoter, 5′‐UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within‐population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.     

The effects of time,temperature and plant variety on pollen viability and its implications for gene flow risk

• Pollen viability affects the probability that a pollen grain deposited on a plant's stigma will produce a viable seed. Because a mature seed is needed before a gene flow event can occur, pollen viability will influence the risk of escape for genetically engineered (GE) crops.
• Pollen viability was measured at intervals for up to 2 h following removal of the pollen from the anthers. It was quantified at three temperatures and for different alfalfa varieties, including both conventional and Roundup Ready (RR) varieties. Pollen viability was assessed using in vitro germination.
• Time since removal from the anthers was the most prevalent factor affecting pollen viability in alfalfa. Pollen viability declined with increasing time at all three temperatures and for all varieties tested. Pollen viability was not affected by temperatures ranging between 25 and 37 °C and did not vary among plant varieties, including conventional and RR varieties.
• Bee foraging behaviour suggested pollen viability within the first 10 min following pollen removal from a flower to most affect seed production. Pollen longevity was predicted to have little impact on seed set and gene flow. Linking pollinator behaviour to pollen viability improved our understanding of its impact on gene flow risk.

     

Short‐term variations in gene flow related to cyclic density fluctuations in the common vole

In highly fluctuating populations with complex social systems, genetic patterns are likely to vary in space and time due to demographic and behavioural processes. Cyclic rodents are extreme examples of demographically instable populations that often exhibit strong social organization. In such populations, kin structure and spacing behaviour may vary with density fluctuations and impact both the composition and spatial structure of genetic diversity. In this study, we analysed the multiannual genetic structure of a cyclic rodent, Microtus arvalis, using a sample of 875 individuals trapped over three complete cycles (from 1999 to 2007) and genotyped at 10 microsatellite loci. We tested the predictions that genetic diversity and gene flow intensity vary with density fluctuations. We found evidences for both spatial scale‐dependant variations in genetic diversity and higher gene flow during high density. Moreover, investigation of sex‐specific relatedness patterns revealed that, although dispersal is biased toward males in this species, distances moved by both sexes were lengthened during high density. Altogether, these results suggest that an increase in migration with density allows to restore the local loss of genetic diversity occurring during low density. We then postulate that this change in migration results from local competition, which enhances female colonization of empty spaces and male dispersal among colonies.     

A new approach to quantify the adaptive potential of gene expression variation in gymnosperms

Variation in patterns of gene expression contributes to phenotypic diversity and can ultimately predict adaptive responses. However, in many cases, the consequences of regulatory mutations on patterns of gene expression and ultimately phenotypic differences remain elusive. A standard way to study the genetic architecture of expression variation in model systems has been to map gene expression variation to genetic loci (Fig. 1a). At the same time, in many nonmodel species, especially for long‐lived organisms, controlled crosses are not feasible. If we are to expand our understanding of the role of regulatory mutations on phenotypes, we need to develop new methodologies to study species under ecologically relevant conditions. In this issue of Molecular Ecology, Verta et al. ( 2013 ) present a new approach to analyse gene expression variation and regulatory networks in gymnosperms (Fig. 1b). They capitalized on the fact that gymnosperm seeds contain an energy storage tissue (the megagametophyte) that is directly derived from a single haploid cell (the megaspore). The authors identified over 800 genes for which expression segregated in this maternally inherited haploid tissue. Based on the observed segregation patterns, these genes (Mendelian Expression Traits) are most probably controlled by biallelic variants at a single locus. Most of these genes also belonged to different regulatory networks, except for one large group of 180 genes under the control of a putative trans‐acting factor. In addition, the approach developed here may also help to uncover the effect of rare recessive mutations, which usually remain hidden in a heterozygous state in diploid individuals. The appeal of the work by Verta et al. ( 2013 ) to study gene expression variation is in its simplicity, which circumvents several of the hurdles behind traditional expression quantitative trait locus (eQTL) studies, and could potentially be applied to a large number of species.     

Comparative phylogeography of five bumblebees: impact of range fragmentation,range size and diet specialization

We characterised the phylogeographic patterns displayed by five species of bumblebees with largely overlapping ranges in Eurasia, but different levels of range fragmentation, range size and food specialization. Genetic variation across the range of each species was explored by using sequence variation of a total of 368 specimens at one mitochondrial and two nuclear DNA fragments (total of ~2380 bp). Comparing patterns of genetic variation across species allowed us to investigate whether diet specialization, relative range size and/or fragmentation, impact phylogeographic patterns in bumblebees. As expected, stronger fragmentations of the species range are associated with a stronger overall geographic differentiation. Furthermore, diet specialization appears to increase population structure at the landscape level, presumably due to the less widespread and more heterogeneously distributed food resources. Conversely, no clear association was highlighted between diet specialization or overall range size and genetic diversity. Surprisingly, the two generalist and co‐distributed species investigated, B. pratorum and B. hortorum, displayed widely divergent patterns in terms of genetic diversity and population structure. We suggest these differences are best explained by contrasting responses to past climate changes, possibly involving different glacial refuges. Overall, our results are compatible with a combined impact of two interacting parameters on intraspecific genetic variation: environment disturbances (presumably related to past climate changes) and features specific to the organism, such as diet specialization. They thus further highlight the challenge of dissociating both parameters in phylogeographic studies.     

Genetic variation in Plethodon cinereus and Plethodon hubrichti from in and around a contact zone

Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk—particularly in range‐restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red‐backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1,008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.     

Human‐aided and natural dispersal drive gene flow across the range of an invasive mosquito

Human‐aided transport is responsible for many contemporary species introductions, yet the contribution of human‐aided transport to dispersal within non‐native regions is less clear. Understanding dispersal dynamics for invasive species can streamline mitigation efforts by targeting routes that contribute disproportionally to spread. Because of its limited natural dispersal ability, rapid spread of the Asian tiger mosquito (Aedes albopictus) has been attributed to human‐aided transport, but until now, the relative roles of human‐aided and natural movement have not been rigorously evaluated. Here, we use landscape genetics and information‐theoretic model selection to evaluate 52 models representing 9240 pairwise dispersal paths among sites across the US range for Ae. albopictus and show that recent gene flow reflects a combination of natural and human‐aided dispersal. Highways and water availability facilitate dispersal at a broad spatial scale, but gene flow is hindered by forests at the current distributional limit (range edge) and by agriculture among sites within the mosquito's native climatic niche (range core). Our results show that highways are important to genetic structure between range‐edge and range‐core pairs, suggesting a role for human‐aided mosquito transport to the range edge. In contrast, natural dispersal is dominant at smaller spatial scales, reflecting a shifting dominance to natural movement two decades after introduction. These conclusions highlight the importance of (i) early intervention for species introductions, particularly those with readily dispersed dormant stages and short generation times, and (ii) strict monitoring of commercial shipments for transported immature stages of Ae. albopictus, particularly towards the northern edge of the US range.     

Connectivity in the cold: the comparative population genetics of vent‐endemic fauna in the Scotia Sea,Southern Ocean

We report the first comparative population genetics study for vent fauna in the Southern Ocean using cytochrome C oxidase I and microsatellite markers. Three species are examined: the kiwaid squat lobster, Kiwa tyleri, the peltospirid gastropod, Gigantopelta chessoia, and a lepetodrilid limpet, Lepetodrilus sp., collected from vent fields 440 km apart on the East Scotia Ridge (ESR) and from the Kemp Caldera on the South Sandwich Island Arc, ~95 km eastwards. We report no differentiation for all species across the ESR, consistent with panmixia or recent range expansions. A lack of differentiation is notable for Kiwa tyleri, which exhibits extremely abbreviated lecithotrophic larval development, suggestive of a very limited dispersal range. Larval lifespans may, however, be extended by low temperature‐induced metabolic rate reduction in the Southern Ocean, muting the impact of dispersal strategy on patterns of population structure. COI diversity patterns suggest all species experienced demographic bottlenecks or selective sweeps in the past million years and possibly at different times. ESR and Kemp limpets are divergent, although with evidence of very recent ESR‐Kemp immigration. Their divergence, possibility indicative of incipient speciation, along with the absence of the other two species at Kemp, may be the consequence of differing dispersal capabilities across a ~1000 m depth range and/or different selective regimes between the two areas. Estimates of historic and recent limpet gene flow between the ESR and Kemp are consistent with predominantly easterly currents and potentially therefore, cross‐axis currents on the ESR, with biogeographic implications for the region.     

Parabolic variation in sexual selection intensity across the range of a cold‐water pipefish: implications for susceptibility to climate change

While an understanding of evolutionary processes in shifting environments is vital in the context of rapid ecological change, one of the most potent selective forces, sexual selection, remains curiously unexplored. Variation in sexual selection across a species range, especially across a gradient of temperature regimes, has the potential to provide a window into the possible impacts of climate change on the evolution of mating patterns. Here, we investigated some of the links between temperature and indicators of sexual selection, using a cold‐water pipefish as model. We found that populations differed with respect to body size, length of the breeding season, fecundity, and sexual dimorphism across a wide latitudinal gradient. We encountered two types of latitudinal patterns, either linear, when related to body size, or parabolic in shape when considering variables related to sexual selection intensity, such as sexual dimorphism and reproductive investment. Our results suggest that sexual selection intensity increases toward both edges of the distribution and that the large differences in temperature likely play a significant role. Shorter breeding seasons in the north and reduced periods for gamete production in the south certainly have the potential to alter mating systems, breeding synchrony, and mate monopolization rates. As latitude and water temperature are tightly coupled across the European coasts, the observed patterns in traits related to sexual selection can lead to predictions regarding how sexual selection should change in response to climate change. Based on data from extant populations, we can predict that as the worm pipefish moves northward, a wave of decreasing selection intensity will likely replace the strong sexual selection at the northern range margin. In contrast, the southern populations will be followed by heightened sexual selection, which may exacerbate the problem of local extinction at this retreating boundary.     

Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient

In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common‐garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common‐garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net‐house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations.