Demographic and Genetic Patterns of Variation among Populations of Arabidopsis thaliana from Contrasting Native Environments

Background

Understanding the relationship between environment and genetics requires the integration of knowledge on the demographic behavior of natural populations. However, the demographic performance and genetic composition of Arabidopsis thaliana populations in the species'' native environments remain largely uncharacterized. This information, in combination with the advances on the study of gene function, will improve our understanding on the genetic mechanisms underlying adaptive evolution in A. thaliana.

Methodology/Principal Findings

We report the extent of environmental, demographic, and genetic variation among 10 A. thaliana populations from Mediterranean (coastal) and Pyrenean (montane) native environments in northeast Spain. Geographic, climatic, landscape, and soil data were compared. Demographic traits, including the dynamics of the soil seed bank and the attributes of aboveground individuals followed over a complete season, were also analyzed. Genetic data based on genome-wide SNP markers were used to describe genetic diversity, differentiation, and structure. Coastal and montane populations significantly differed in terms of environmental, demographic, and genetic characteristics. Montane populations, at higher altitude and farther from the sea, are exposed to colder winters and prolonged spring moisture compared to coastal populations. Montane populations showed stronger secondary seed dormancy, higher seedling/juvenile mortality in winter, and initiated flowering later than coastal populations. Montane and coastal regions were genetically differentiated, montane populations bearing lower genetic diversity than coastal ones. No significant isolation-by-distance pattern and no shared multilocus genotypes among populations were detected.

Conclusions/Significance

Between-region variation in climatic patterns can account for differences in demographic traits, such as secondary seed dormancy, plant mortality, and recruitment, between coastal and montane A. thaliana populations. In addition, differences in plant mortality can partly account for differences in the genetic composition of coastal and montane populations. This study shows how the interplay between variation in environmental, demographic, and genetic parameters may operate in natural A. thaliana populations.     

Contrasting Patterns of Genetic Structuring in Natural Populations of Arabidopsis lyrata Subsp. petraea across Different Regions in Northern Europe

Level and partitioning of genetic diversity is expected to vary between contrasting habitats, reflecting differences in strength of ecological and evolutionary processes. Therefore, it is necessary to consider processes acting on different time scales when trying to explain diversity patterns in different parts of species'' distributions. To explore how historical and contemporary factors jointly may influence patterns of genetic diversity and population differentiation, we compared genetic composition in the perennial herb Arabidopsis lyrata ssp. petraea from the northernmost parts of its distribution range on Iceland to that previously documented in Scandinavia. Leaf tissue and soil were sampled from ten Icelandic populations of A. lyrata. Seedlings were grown from soil samples, and tissue from above-ground and seed bank individuals were genotyped with 21 microsatellite markers. Seed bank density in Icelandic populations was low but not significantly different from that observed in Norwegian populations. While within-population genetic diversity was relatively high on Iceland (H _E = 0.35), among-population differentiation was low (F _ST = 0.10) compared to Norwegian and Swedish populations. Population differentiation was positively associated with geographical distance in both Iceland and Scandinavia, but the strength of this relationship varied between regions. Although topography and a larger distribution range may explain the higher differentiation between mountainous Norwegian relative to lowland populations in Sweden, these factors cannot explain the lower differentiation in Icelandic compared to Swedish populations. We propose that low genetic differentiation among Icelandic populations is not caused by differences in connectivity, but is rather due to large historical effective population sizes. Thus, rather than contemporary processes, historical factors such as survival of Icelandic lineages in northern refugia during the last glacial period may have contributed to the observed pattern.     

Environmental Tolerances of Miscanthus sinensis in Invasive and Native Populations

Miscanthus sinensis is a moderately invasive ornamental grass species being considered as a bioenergy species in the USA and elsewhere. In this study, we show the range of environmental conditions tolerated by this species in wild populations in the USA and in Japan. Six naturalized populations in the USA and five native populations in Japan were sampled in summer 2009. In each population, environmental factors (canopy cover and soil fertility) were measured, along with measurements of size and morphology for 30 plants. Relationships between M. sinensis size and environmental variables in the two countries were determined using linear mixed effects models. Results indicated that M. sinensis can tolerate extremely wide variation in soil and climate conditions in the populations we sampled across both ranges, suggesting that it could be successfully grown across a wide distribution in the USA, both intentionally as a bioenergy crop and unintentionally as an escaped invader. Plant size generally responded to different environmental conditions in both ranges, with USA plants being negatively influenced by canopy cover and Japanese plants being positively influenced by soil fertility measures. We recommend caution in growing M. sinensis for bioenergy or ornamental purposes to minimize escape outside of its native range.     

Patterns of Privet: Urbanizing Watersheds,Invasive Ligustrum sinense,and Performance of Native Plant Species in Piedmont Floodplain Forests

Floodplain forests in rapidly changing landscapes with increased urbanization may reshape habitat conditions to the detriment of native biota and favor invasive species. We assessed whether introduced Ligustrum sinense distribution and abundance are causally linked to urbanization and whether mechanisms that promote L. sinense cause the demise of native plant species. We surveyed vegetation in 12 independent floodplain forests along an urban to rural gradient in South Carolina, USA. We then used a seedling transplant experiment in nine watersheds to assess how increased urban development affects survival and growth of L. sinense and three native species over two growing seasons. Urban development ranged from 1 to 45% and L. sinense cover was positively associated with development. However, in our transplant experiment, growth and survival of L. sinense did not differ significantly among watersheds. Native species were able to survive at all sites, but performance varied greatly among sites and species but not as a function of urban development. Our results suggest that although L. sinense invasion and urbanization are related (likely due to proximity of propagules from urban sources), the demise of native species cannot be explained by increased urbanization or changes in edaphic conditions and points to L. sinense as an agent of change in our floodplain forests. These results indicate that all floodplain forests are at risk of invasion if propagules arrive and that land managers need to be vigilant against new species introductions regardless of the proximity to urban areas.     

Seasonal and Regional Dynamics of M. ulcerans Transmission in Environmental Context: Deciphering the Role of Water Bugs as Hosts and Vectors

Background

Buruli ulcer, the third mycobacterial disease after tuberculosis and leprosy, is caused by the environmental mycobacterium M. ulcerans. Various modes of transmission have been suspected for this disease, with no general consensus acceptance for any of them up to now. Since laboratory models demonstrated the ability of water bugs to transmit M. ulcerans, a particular attention is focused on the transmission of the bacilli by water bugs as hosts and vectors. However, it is only through detailed knowledge of the biodiversity and ecology of water bugs that the importance of this mode of transmission can be fully assessed. It is the objective of the work here to decipher the role of water bugs in M. ulcerans ecology and transmission, based on large-scale field studies.

Methodology/Principal Findings

The distribution of M. ulcerans-hosting water bugs was monitored on previously unprecedented time and space scales: a total of 7,407 water bugs, belonging to large number of different families, were collected over one year, in Buruli ulcer endemic and non endemic areas in central Cameroon. This study demonstrated the presence of M. ulcerans in insect saliva. In addition, the field results provided a full picture of the ecology of transmission in terms of biodiversity and detailed specification of seasonal and regional dynamics, with large temporal heterogeneity in the insect tissue colonization rate and detection of M. ulcerans only in water bug tissues collected in Buruli ulcer endemic areas.

Conclusion/Significance

The large-scale detection of bacilli in saliva of biting water bugs gives enhanced weight to their role in M. ulcerans transmission. On practical grounds, beyond the ecological interest, the results concerning seasonal and regional dynamics can provide an efficient tool in the hands of sanitary authorities to monitor environmental risks associated with Buruli ulcer.     

Patterns of genetic variation in Native America.

Allele frequencies from seven polymorphic red cell antigen loci (ABO, Rh, MN, S, P, Duffy, and Diego) were examined in 144 Native American populations. Mean genetic distances (Nei's D) and the fixation index FST are approximately equal for the North and South American samples but are reduced in the Central American geographic area. The relationship between genetic distance and geographic distance differs markedly across geographic areas. The correlation between geographic distance and genetic distance for the North and Central American data is twice as large as that observed for the South American samples. This geographic difference is confirmed in spatial autocorrelation analyses; no geographic structure is apparent in the South American data but geographic structure is prominent in North and Central American samples. These results confirm earlier observations regarding differences between North and South American gene frequency patterns.     

Native Prey and Invasive Predator Patterns of Foraging Activity: The Case of the Yellow-Legged Hornet Predation at European Honeybee Hives

Contrary to native predators, which have co-evolved with their prey, alien predators often benefit from native prey naïveté. Vespa velutina, a honeybee predator originating from Eastern China, was introduced into France just before 2004. The present study, based on video recordings of two beehives at an early stage of the invasion process, intends to analyse the alien hornet hunting behaviour on the native prey, Apis mellifera, and to understand the interaction between the activity of the predator and the prey during the day and the season. Chasing hornets spent most of their time hovering facing the hive, to catch flying honeybees returning to the hive. The predation pressure increased during the season confirming previous study based on predator trapping. The number of honeybee captures showed a maximum peak for an intermediate number of V. velutina, unrelated to honeybee activity, suggesting the occurrence of competition between hornets. The number of honeybees caught increased during midday hours while the number of hornets did not vary, suggesting an increase in their efficacy. These results suggest that the impact of V. velutina on honeybees is limited by its own biology and behaviour and did not match the pattern of activity of its prey. Also, it could have been advantageous during the invasion, limiting resource depletion and thus favouring colonisation. This lack of synchronization may also be beneficial for honeybee colonies by giving them an opportunity to increase their activity when the hornets are less effective.     

Distribution Patterns in the Native Vascular Flora of Iceland

The aim of our study was to reveal biogeographical patterns in the native vascular flora of Iceland and to define ecological factors responsible for these patterns. We analysed dataset of more than 500,000 records containing information on the occurrence of vascular plants. Analysis of ecological factors included climatic (derived from WORLDCLIM data), topographic (calculated from digital elevation model) and geological (bedrock characteristics) variables. Spherical k-means clustering and principal component analysis were used to detect biogeographical patterns and to study the factors responsible for them. We defined 10 biotic elements exhibiting different biogeographical patterns. We showed that climatic (temperature-related) and topographic variables were the most important factors contributing to the spatial patterns within the Icelandic vascular flora and that these patterns are almost completely independent of edaphic factors (bedrock type). Our study is the first one to analyse the biogeographical differentiation of the native vascular flora of Iceland.     

Patterns of Testa-imposed Seed Dormancy in Native Australian Legumes

The testa-imposed seed dormancy of 34 native Australian speciesof Faboideae and Mimosoideae was examined immediately afterthe seeds matured and again after 3.5 years of dry storage inthe laboratory. Three groups of dormancy patterns are recognized:17 species (of the Mirbelieae and Acacieae) that have a relativelysmall nondormant fraction (0–10%) of their ripe seedsand that maintain this fraction through time; ten species (ofthe Mirbelieae) that have a relatively large non-dormant fraction(10–40%) of their ripe seeds and that maintain this fractionthrough time; and seven species (of the Bossiaeeae and Phaseoleae)that have a relatively small non-dormant fraction when the seedsripen, and have this fraction increase significantly throughtime. The species in the second group have smaller seeds thando those of the first and third groups, while the species inthe third group have a different testa construction from thosein the first and second groups. For all of the non-dormant seedstested, the water permeability is not localized only at thelens. Leguminosae, Fabaceae, Mimosoideae, Papilionoideae, Faboideae, legume seeds, seed dormancy, hard-seededness, dormancy loss, germination     

Establishment and Control of Hay-scented Fern: A Native Invasive Species

Hay-scented fern (Dennstaedtia punctilobula (Michx.) Moore) is a native forest understory species that behaves as an invasive plant under certain conditions. Previous work has shown that both increased understory light intensity following overstory thinning and removal of competing plants by herbivores can lead to accelerated growth of hay-scented fern, allowing it to develop dense, nearly monospecific understories that inhibit tree seedling regeneration. To study the relationship between these two factors, we sampled 28 forest stands thinned at different times and subjected to different levels of browsing by white-tailed deer (Odocoileus virginianus), and concluded that more than 15 years of intensive browsing following thinning was necessary for ferns to form closed understory canopies with densities of >90 fronds/m² and canopy heights of 60–80 cm; thinning alone or intensive browsing alone was not sufficient to cause this level of fern invasion. We applied three treatments to dense fern understories to determine the relative importance of the fern canopy and the dense mat of roots, rhizomes, and dead fronds in the inhibition of tree seedling establishment. Results after two years were: (1) complete removal of the organic mat produced a large germination response of woody and herbaceous species; (2) mixing the organic mat into the mineral soil produced an initial germination response but poor seedling survivorship, as the fern canopy regrew to near pretreatment density; (3) repeatedly clipping the ferns for two years without disturbing the organic mat resulted in a lower germination response than the removal treatment, but rapid growth of seedlings.     

Nutrient Limitation of Native and Invasive N2-Fixing Plants in Northwest Prairies

Nutrient rich conditions often promote plant invasions, yet additions of non-nitrogen (N) nutrients may provide a novel approach for conserving native symbiotic N-fixing plants in otherwise N-limited ecosystems. Lupinus oreganus is a threatened N-fixing plant endemic to prairies in western Oregon and southwest Washington (USA). We tested the effect of non-N fertilizers on the growth, reproduction, tissue N content, and stable isotope δ¹⁵N composition of Lupinus at three sites that differed in soil phosphorus (P) and N availability. We also examined changes in other Fabaceae (primarily Vicia sativa and V. hirsuta) and cover of all plant species. Variation in background soil P and N availability shaped patterns of nutrient limitation across sites. Where soil P and N were low, P additions increased Lupinus tissue N and altered foliar δ¹⁵N, suggesting P limitation of N fixation. Where soil P was low but N was high, P addition stimulated growth and reproduction in Lupinus. At a third site, with higher soil P, only micro- and macronutrient fertilization without N and P increased Lupinus growth and tissue N. Lupinus foliar δ¹⁵N averaged −0.010‰ across all treatments and varied little with tissue N, suggesting consistent use of fixed N. In contrast, foliar δ¹⁵N of Vicia spp. shifted towards 0‰ as tissue N increased, suggesting that conditions fostering N fixation may benefit these exotic species. Fertilization increased cover, N fixation, and tissue N of non-target, exotic Fabaceae, but overall plant community structure shifted at only one site, and only after the dominant Lupinus was excluded from analyses. Our finding that non-N fertilization increased the performance of Lupinus with few community effects suggests a potential strategy to aid populations of threatened legume species. The increase in exotic Fabaceae species that occurred with fertilization further suggests that monitoring and adaptive management should accompany any large scale applications.     

Temperature,Herbivory and Epibiont Acquisition as Factors Controlling the Distribution and Ecological Role of an Invasive Seaweed

The invasive canopy alga, Codium fragile ssp. tomentosoides, first observed at the Isles of Shoals in 1983, has become the dominant canopy species to 8 m throughout the islands. Codium populations are replacing themselves at most sites in what appears to be a new, climax, canopy species. However, Codium densities have declined in protected Gosport Harbor areas where it first became established. Codium has only slowly expanded its presence in adjacent nearshore subtidal habitats. Recent studies suggest a combination of factors that may be influencing the relative success of populations between habitats. The herbivorous sea slug, Placida dendritica, may be reducing populations in protected areas in spite of predators such as the green crab, Carcinus maenas, while surge may inhibit herbivore buildup in exposed habitats. Temperature instability due to localized, wind-driven upwelling may be slowing the buildup of subtidal Codium populations in nearshore sites. The combination of Codium dominance and the acquisition of increasing epibiont diversity are producing a new, potentially more complex community state than the previous kelp-dominated climax typical of the Gulf of Maine.     

Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies

The top-view, two-dimensional spatial patterning of non-uniform growth in a Saccharomyces cerevisiae yeast colony is considered. Experimental images are processed to obtain data sets that provide spatial information on the cell-area that is occupied by the colony. A method is developed that allows for the analysis of the spatial distribution with three metrics. The growth of the colony is quantified in both the radial direction from the centre of the colony and in the angular direction in a prescribed outer region of the colony. It is shown that during the period of 100–200 hours from the start of the growth of the colony there is an increasing amount of non-uniform growth. The statistical framework outlined in this work provides a platform for comparative quantitative assays of strain-specific mechanisms, with potential implementation in inferencing algorithms used for parameter-rate estimation.     

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.     

Native Useful Plants of Chile: A Review and Use Patterns

Economic Botany - Native Useful Plants of Chile: A Review and Use Patterns. We compiled an inventory of the uses of the native flora of Chile by extracting uses cited in the literature until 2015....     

Spatial Patterns and Natural Recruitment of Native Shrubs in a Semi-arid Sandy Land

Passive restoration depending on native shrubs is an attractive approach for restoring desertified landscapes in semi-arid sandy regions. We sought to understand the relationships between spatial patterns of native shrubs and their survival ability in sandy environments. Furthermore, we applied our results to better understand whether passive restoration is feasible for desertified landscapes in semi-arid sandy regions. The study was conducted in the semi-arid Mu Us sandy land of northern China with the native shrub Artemisia ordosica. We analyzed population structures and patterns of A. ordosica at the edges and centers of land patches where sand was stabilized by A. ordosica-dominated vegetation. Saplings were more aggregated than adults, and both were more aggregated at the patch edges than at the patch centers. At the patch edges, spatial association of the saplings with the adults was mostly positive at distances 0.3–6.6 m, and turned from positive to neutral, and even negative, at other distances. At the patch centers, the saplings were spaced almost randomly around the adults, and their distances from the adults did not seem to affect their locations. A greater number of A. ordosica individuals emerged at the patch edges than at the patch centers. Such patterns may have resulted from their integrative adjustment to specific conditions of soil water supply and sand drift intensity. These findings suggest that in semi-arid sandy regions, native shrubs that are well-adapted to local environments may serve as low-cost and competent ecological engineers that can promote the passive restoration of surrounding patches of mobile sandy land.     

Morphological and Functional Divergence of the Lower Jaw Between Native and Invasive Red Foxes

Journal of Mammalian Evolution - The introduction of European red foxes in Australia in the late mid-nineteenth century has resulted in the spread of this invasive species across the continent. The...