Adaptation to environmental stress: a rare or frequent driver of speciation?

The Impact of Urbanization on Taxonomic Diversity and Functional Similarity among Butterfly Communities in Waterfront Green Spaces

Urbanization has been shown to cause biodiversity loss. However, its effects on butterfly taxonomic and functional diversity still need to be studied, especially in urban waterfront green spaces where mechanisms of impact still need to be explored. We used butterflies as indicators to study how urbanization affects their taxonomic and functional diversity and identify indicator species in different urban ecological gradient areas. From July to September 2022, we surveyed 10 urban waterfront green spaces in Fuzhou City, China. We recorded 1163 butterflies of 28 species from 6 families. First, we explored the effects of urbanization on butterfly communities and made pairwise comparisons of different urban ecological gradients (α-diversity); secondly, we looked for differences between butterfly communities across urban ecological gradients (β-diversity); finally, we investigated differences in the response of butterfly functional groups to different urban ecological gradient areas and identified ecological indicative species. This study found the following: (1) Urbanization has led to the simplification of butterfly community structure, but there are also favorable factors that support the survival of individual butterflies; (2) Urbanization has led to significant differences in butterfly communities and plant-feeding polyphagous butterfly groups; (3) Urbanization has led to differences in the functional diversity of butterfly diet and activity space groups; (4) We identified five eco-indicator species in different urban ecological gradients.

Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex

Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importance on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scale. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.

Varieties of the highly dispersible and hypervariable tree, Metrosideros polymorpha, differ in response to mechanical stress and light across a sharp ecotone

PREMISE

The drivers of isolation between sympatric populations of long-lived and highly dispersible conspecific plants are not well understood. In the Hawaiian Islands, the landscape-dominant tree, Metrosideros polymorpha, displays extraordinary phenotypic differences among sympatric varieties despite high dispersibility of its pollen and seeds, thereby presenting a unique opportunity to investigate how disruptive selection alone can maintain incipient forms. Stenophyllous M. polymorpha var. newellii is a recently evolved tree endemic to the waterways of eastern Hawai'i Island that shows striking neutral genetic differentiation from its ancestor, wet-forest M. polymorpha var. glaberrima, despite sympatry of these forms. We looked for evidence for, and drivers of, differential local adaptation of these varieties across the range of M. polymorpha var. newellii.

METHODS

For paired populations of these varieties, we compared seedling performance under contrasting light conditions and a strong water current characteristic of the riparian zone. We also conducted a reciprocal transplant experiment and contrasted adult leaf anatomy.

RESULTS

Results suggest that the riparian zone is harsh and that selection involving the mechanical stress of rushing water, and secondarily, light, led to significant reciprocal immigrant inviability in adjacent forest and riparian environments. The strongest adaptive divergence between varieties was seen in leaves and seedlings from the site with the sharpest ecotone, coincident with the strongest genetic isolation of M. polymorpha var. newellii observed previously.

CONCLUSIONS

These findings suggest that disruptive selection across a sharp ecotone contributes to the maintenance of an incipient riparian ecotype from within a continuous population of a long-lived and highly dispersible tree species.

Asymmetrical selection maintains heritable phenotypic variation between two subspecies of Monardella villosa

PREMISE

Monardella villosa is an evolutionarily young species complex distributed across a large geographic range. Our goal was to determine whether the phenotypic difference between two subspecies of M. villosa was heritable and whether the alternative phenotypes were adaptive to their respective local habitats.

METHODS

We collected seeds from 25 populations of M. villosa, 14 from subspecies franciscana, which grows closer to the coast, and 11 from subspecies villosa, which has a larger and more inland geographic distribution. We reciprocally transplanted the two subspecies into their respective habitats and compared plant germination, post-emergence survival, and growth. We used linear mixed models to quantify the effects of genotype and environment to determine whether subspecies were locally adapted and whether leaf traits that distinguish these subspecies were genetically based.

RESULTS

Plants of both subspecies grown at the coastal site had significantly lower survival and biomass than the inland site. The subspecies were not locally adapted; however, the coastal subspecies franciscana did have a home site advantage. We also found that distinctive leaf morphological traits were genetically based, with high broad-sense heritability of traits.

CONCLUSIONS

The two subspecies of Monardella villosa were not locally adapted to their respective habitat, but rather we found that selection for local genotypes may be stronger at the coastal site. Despite the lack of evidence for local adaptation in the strict sense, the subspecies had heritable variation in several leaf phenotypes, indicating that heterogeneous selection imposes an adaptive trade-off for leaf trichome production within this species.

The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass

Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.

Species-Specific Means and Within-Species Variance in Glucocorticoid Hormones and Speciation Rates in Birds

At macroevolutionary scales, stress physiology may have consequences for species diversification and subspecies richness. Populations that exploit new resources or undergo range expansion should cope with new environmental challenges, which could favor higher mean stress responses. Within-species variation in the stress response may also play a role in mediating the speciation process: in species with broad variation, there will always be some individuals that can tolerate an unpredictable environment, whereas in species with narrow variation there will be fewer individuals that are able to thrive in a new ecological niche. We tested for the evolutionary relationship between stress response, speciation rate, and subspecies richness in birds by relying on the HormoneBase repository, from which we calculated within- and among-species variation in baseline (BL) and stress-induced (SI) corticosterone levels. To estimate speciation rates, we applied Bayesian analysis of macroevolutionary mixtures that can account for variation in diversification rate among clades and through time. Contrary to our predictions, lineages with higher diversification rates were not characterized by higher BL or SI levels of corticosterone either at the tips or at the deeper nodes of the phylogeny. We also found no association between mean hormone levels and subspecies richness. Within-species variance in corticosterone levels showed close to zero repeatability, thus it is highly unlikely that this is a species-specific trait that influences diversification rates. These results imply that stress physiology may play a minor, if any, role in determining speciation rates in birds.

Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species

BACKGROUND

Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses.

RESULTS

Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in Z. kawagoii than in Z. shuanglongensis explains the more widespread distribution of Z. kawagoii in Taiwan.

CONCLUSIONS

Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.

Conceptualizing plant systems evolution

Organisms inhabiting extreme environments are emerging models in systems evolution, enabling us to identify the molecular alterations effecting major phenotypic divergence through comparative approaches. Here I discuss possible physiological mechanisms underlying evolutionary adaptations to extreme environments both theoretically and in relation to experimental observations. Reasoning leads me to the 'conserved steady-state' hypothesis of evolutionary adaptation: Between closely related plants adapted to differently composed soils, the homeostatically controlled steady-state set point cytosolic (buffered) concentrations of mineral ions are conserved. Subsequently, I compare molecular alterations expected to contribute to physiological adaptations with our present knowledge. Key roles of enhanced gene product dosage in plant evolutionary adaptations question the widespread stimulus response-centric paradigm. As a broader implication, co-regulation networks can lack decisive functional network elements. With this article, I hope to stimulate a discussion across research fields and provide an initial conceptual framework for future experimental testing and for quantitative modelling.

Tight species cohesion among sympatric insular wild gingers (Asarum spp. Aristolochiaceae) on continental islands: Highly differentiated floral characteristics versus undifferentiated genotypes

The Amami Island group of the Ryukyu Archipelago, Japan, harbors extensive species diversity of Asarum in a small landmass. The fine-scale population genetic structure and diversity of nine insular endemic Asarum species were examined using nuclear DNA microsatellite loci and ITS sequences. High population genetic diversity (HS = 0.45-0.79) was estimated based on the microsatellites, implying outcrossing of Asarum species within populations accompanied by inbreeding. Bayesian clustering analyses revealed that species were divided into three robust genetic clusters and that the species within each cluster had a homogeneous genetic structure, indicating incomplete lineage sorting. This conclusion was supported by an ITS phylogeny. The degree of genetic differentiation among species was very low both within and between clusters (FST = 0.096-0.193, and 0.096-0.266, respectively). Although species can be crossed artificially to produce fertile hybrids, our results indicate that there is very little evidence of hybridization or introgression occurring among species in the wild, even within stands composed of multiple sympatric species. The highly differentiated floral morphology of the studied species is likely to impose reproductive isolation between them and maintain their integrity in the wild. A lack of genetic differentiation between sympatric species suggests that speciation within this group occurred rapidly and recently.

Photosynthetic plasticity in the green algal species Klebsormidium flaccidum (Streptophyta) from a terrestrial and a freshwater habitat

The genus Klebsormidium (Klebsormidiales, Streptophyta) has a worldwide distribution in terrestrial habitats. In the present study, we focused on two strains of Klebsormidium flaccidum, the type species of the genus. The isolates used in this study were isolated from a soil and freshwater habitat. Photosynthetic activity was evaluated under different controlled gradients of light, temperature and desiccation. The data clearly indicate that both isolates of K. flaccidum exhibit conspicuously different photosynthetic response patterns to photon fluence rate, temperature and desiccation, and thus can be related to their different habitats. Although both strains represent the same species, their physiological response patterns to abiotic gradients, as well as their morphology differed to some extent, indicating high phenotypic plasticity of K. flaccidum, which was maintained even after long-term culture and thus can be explained by the formation of physiologically distinct ecotypes.

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks

Background

Reference transcriptomes provide valuable resources for understanding evolution within and among species. We de novo assembled and annotated a reference transcriptome for Quercus lobata and Q. garryana and identified single-nucleotide polymorphisms (SNPs) to provide resources for forest genomicists studying this ecologically and economically important genus. We further performed preliminary analyses of genes important in interspecific divergent (positive) selection that might explain ecological differences among species, estimating rates of nonsynonymous to synonymous substitutions (d_N/d_S) and Fay and Wu’s H. Functional classes of genes were tested for unusually high d_N/d_S or low H consistent with divergent positive selection.

Results

Our draft transcriptome is among the most complete for oaks, including 83,644 contigs (23,329 ≥ 1 kbp), 14,898 complete and 13,778 partial gene models, and functional annotations for 9,431 Arabidopsis orthologs and 19,365 contigs with Pfam hits. We identified 1.7 million possible sequence variants including 1.1 million high-quality diallelic SNPs — among the largest sets identified in any tree. 11 of 18 functional categories with significantly elevated d_N/d_S are involved in disease response, including 50+ genes with d_N/d_S > 1. Other high-d_N/d_S genes are involved in biotic response, flowering and growth, or regulatory processes. In contrast, median d_N/d_S was low (0.22), suggesting that purifying selection influences most genes. No functional categories have unusually low H.

Conclusions

These results offer preliminary support for the hypothesis that divergent selection at pathogen resistance are important factors in species divergence in these hybridizing California oaks. Our transcriptome provides a solid foundation for future studies of gene expression, natural selection, and speciation in Quercus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1761-4) contains supplementary material, which is available to authorized users.

Direct and indirect selection on flowering time, water-use efficiency (WUE, δ (13)C), and WUE plasticity to drought in Arabidopsis thaliana

Flowering time and water-use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time, WUE, and WUE plasticity to drought in Arabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genetically correlated within and between different soil moisture environments? (2) Does terminal drought select for early flowering and drought escape? (3) Is WUE plasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions of A. thaliana grown in well-watered and season-ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment. WUE and flowering time were consistently positively genetically correlated. WUE was correlated with WUE plasticity, but the direction changed between treatments. Selection generally favored early flowering and low WUE, with drought favoring earlier flowering significantly more than well-watered conditions. Selection for lower WUE was marginally stronger under drought. There were no net fitness costs of WUE plasticity. WUE plasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation between WUE and flowering time may facilitate the evolution of drought escape, or constrain independent evolution of these traits. Terminal drought favored drought escape in these spring flowering accessions of A. thaliana. WUE plasticity may be favored over completely fixed development in environments with periodic drought.

What is environmental stress? Insights from fish living in a variable environment

Although the term environmental stress is used across multiple fields in biology, the inherent ambiguity associated with its definition has caused confusion when attempting to understand organismal responses to environmental change. Here I provide a brief summary of existing definitions of the term stress, and the related concepts of homeostasis and allostasis, and attempt to unify them to develop a general framework for understanding how organisms respond to environmental stressors. I suggest that viewing stressors as environmental changes that cause reductions in performance or fitness provides the broadest and most useful conception of the phenomenon of stress. I examine this framework in the context of animals that have evolved in highly variable environments, using the Atlantic killifish, Fundulus heteroclitus, as a case study. Consistent with the extreme environmental variation that they experience in their salt marsh habitats, killifish have substantial capacity for both short-term resistance and long-term plasticity in the face of changing temperature, salinity and oxygenation. There is inter-population variation in the sensitivity of killifish to environmental stressors, and in their ability to acclimate, suggesting that local adaptation can shape the stress response even in organisms that are broadly tolerant and highly plastic. Whole-organism differences between populations in stressor sensitivity and phenotypic plasticity are reflected at the biochemical and molecular levels in killifish, emphasizing the integrative nature of the response to environmental stressors. Examination of this empirical example highlights the utility of using an evolutionary perspective on stressors, stress and stress responses.

Incipient radiation within the dominant Hawaiian tree Metrosideros polymorpha

Although trees comprise a primary component of terrestrial species richness, the drivers and temporal scale of divergence in trees remain poorly understood. We examined the landscape-dominant tree, Metrosideros polymorpha, for variation at nine microsatellite loci across 23 populations on young Hawai'i Island, sampling each of the island's five varieties throughout its full geographic range. For four varieties, principal coordinate analysis revealed strong clustering of populations by variety across the 10 430 km(2) island, indicating partitioning of the species into multiple evolutionarily significant units. The single island-endemic form, riparian var. newellii, showed especially strong differentiation from other varieties despite occurring in sympatry with other varieties and likely evolved from a bog form on the oldest volcano, Kohala, within the past 500 000 years. Along with comparable riparian forms on other Pacific Islands, var. newellii appears to represent parallel incipient ecological speciation within Metrosideros. Greater genetic distance among the more common varieties on the oldest volcano and an inverse relationship between allelic diversity and substrate age appear consistent with colonization of Hawai'i Island by older, partially diverged varieties followed by increased hybridization among varieties on younger volcanoes. This study demonstrates that broad population-level sampling is required to uncover patterns of diversification within a ubiquitous and long-lived tree species. Hawaiian Metrosideros appears to be a case of incipient radiation in trees and thus should be useful for studies of divergence and the evolution of reproductive isolating barriers at the early stages of speciation.

Hormetic concentrations of hydrogen peroxide but not ethanol induce cross-adaptation to different stresses in budding yeast

The biphasic-dose response of microorganisms to hydrogen peroxide is a phenomenon of particular interest in hormesis research. In different animal models, the dose-response curve for ethanol is also nonlinear showing an inhibitory effect at high doses but a stimulatory effect at low doses. In this study, we observed the hormetic-dose response to ethanol in budding yeast S. cerevisiae. Cross-protection is a phenomenon in which exposure to mild stress results in the acquisition of cellular resistance to lethal stress induced by different factors. Since both hydrogen peroxide and ethanol at low concentrations were found to stimulate yeast colony growth, we evaluated the role of one substance in cell cross-adaptation to the other substance as well as some weak organic acid preservatives. This study demonstrates that, unlike ethanol, hydrogen peroxide at hormetic concentrations causes cross-resistance of S. cerevisiae to different stresses. The regulatory protein Yap1 plays an important role in the hormetic effects by low concentrations of either hydrogen peroxide or ethanol, and it is involved in the yeast cross-adaptation by low sublethal doses of hydrogen peroxide.

Transcriptional homeostasis of a mangrove species, Ceriops tagal, in saline environments, as revealed by microarray analysis

BACKGROUND

Differential responses to the environmental stresses at the level of transcription play a critical role in adaptation. Mangrove species compose a dominant community in intertidal zones and form dense forests at the sea-land interface, and although the anatomical and physiological features associated with their salt-tolerant lifestyles have been well characterized, little is known about the impact of transcriptional phenotypes on their adaptation to these saline environments.

METHODOLOGY AND PRINCIPAL FINDINGS

We report the time-course transcript profiles in the roots of a true mangrove species, Ceriops tagal, as revealed by a series of microarray experiments. The expression of a total of 432 transcripts changed significantly in the roots of C. tagal under salt shock, of which 83 had a more than 2-fold change and were further assembled into 59 unigenes. Global transcription was stable at the early stage of salt stress and then was gradually dysregulated with the increased duration of the stress. Importantly, a pair-wise comparison of predicted homologous gene pairs revealed that the transcriptional regulations of most of the differentially expressed genes were highly divergent in C. tagal from that in salt-sensitive species, Arabidopsis thaliana.

CONCLUSIONS/SIGNIFICANCE

This work suggests that transcriptional homeostasis and specific transcriptional regulation are major events in the roots of C. tagal when subjected to salt shock, which could contribute to the establishment of adaptation to saline environments and, thus, facilitate the salt-tolerant lifestyle of this mangrove species. Furthermore, the candidate genes underlying the adaptation were identified through comparative analyses. This study provides a foundation for dissecting the genetic basis of the adaptation of mangroves to intertidal environments.

Shared and unique patterns of embryo development in extremophile poeciliids

BACKGROUND

Closely related lineages of livebearing fishes have independently adapted to two extreme environmental factors: toxic hydrogen sulphide (H(2)S) and perpetual darkness. Previous work has demonstrated in adult specimens that fish from these extreme habitats convergently evolved drastically increased head and offspring size, while cave fish are further characterized by reduced pigmentation and eye size. Here, we traced the development of these (and other) divergent traits in embryos of Poecilia mexicana from benign surface habitats ("surface mollies") and a sulphidic cave ("cave mollies"), as well as in embryos of the sister taxon, Poecilia sulphuraria from a sulphidic surface spring ("sulphur mollies"). We asked at which points during development changes in the timing of the involved processes (i.e., heterochrony) would be detectible.

METHODS AND RESULTS

Data were extracted from digital photographs taken of representative embryos for each stage of development and each type of molly. Embryo mass decreased in convergent fashion, but we found patterns of embryonic fat content and ovum/embryo diameter to be divergent among all three types of mollies. The intensity of yellow colouration of the yolk (a proxy for carotenoid content) was significantly lower in cave mollies throughout development. Moreover, while relative head size decreased through development in surface mollies, it increased in both types of extremophile mollies, and eye growth was arrested in mid-stage embryos of cave mollies but not in surface or sulphur mollies.

CONCLUSION

Our results clearly demonstrate that even among sister taxa convergence in phenotypic traits is not always achieved by the same processes during embryo development. Furthermore, teleost development is crucially dependent on sufficient carotenoid stores in the yolk, and so we discuss how the apparent ability of cave mollies to overcome this carotenoid-dependency may represent another potential mechanism explaining the lack of gene flow between surface and cave mollies.

Local infection with oilseed rape mosaic virus promotes genetic rearrangements in systemic Arabidopsis tissue

We have previously shown that local infection of tobacco plants with tobacco mosaic virus (TMV) or oilseed rape mosaic virus (ORMV) results in a systemic increase in the homologous recombination frequency (HRF). Here, we analyzed what other changes in the genome are triggered by pathogen infection. For the analysis of HRF, mutation frequency (MF) and microsatellite instability (MI), we used three different transgenic Arabidopsis lines carrying β-glucuronidase (GUS)-based substrates in their genome. We found that local infection of Arabidopsis with ORMV resulted in an increase of all three frequencies, albeit to differing degrees. The most prominent increase was observed in microsatellite instability. The increase in HRF was the lowest, although still statistically significant. The analysis of methylation of the 35S promoter and transgene expression showed that the greater instability of the transgene was not attributed to these changes. Strand breaks brought about a significant increase in non-treated tissues of infected plants. The expression of genes associated with various repair processes, such as KU70, RAD51, MSH2, DNA POL α and DNA POL δ, was also increased. To summarize, our data demonstrate that local ORMV infection destabilizes the genome in systemic tissues of Arabidopsis plants in various ways resulting in large rearrangements, point mutations and microsatellite instability.

Nitrogen stress response of a hybrid species: a gene expression study

BACKGROUND AND AIMS

Low soil fertility limits growth and productivity in many natural and agricultural systems, where the ability to sense and respond to nutrient limitation is important for success. Helianthus anomalus is an annual sunflower of hybrid origin that is adapted to desert sand-dune substrates with lower fertility than its parental species, H. annuus and H. petiolaris. Previous studies have shown that H. anomalus has traits generally associated with adaptation to low-fertility habitats, including a lower inherent relative growth rate and longer leaf lifetime.

METHODS

Here, a cDNA microarray is used to identify gene expression differences that potentially contribute to increased tolerance of low fertility of the hybrid species by comparing the nitrogen stress response of all three species with high- and low-nutrient treatments.

KEY RESULTS

Relative to the set of genes on the microarray, the genes showing differential expression in the hybrid species compared with its parents are enriched in stress-response genes, developmental genes, and genes involved in responses to biotic or abiotic stimuli. After a correction for multiple comparisons, five unique genes show a significantly different response to nitrogen limitation in H. anomalus compared with H. petiolaris and H. annuus. The Arabidopsis thaliana homologue of one of the five genes, catalase 1, has been shown to affect the timing of leaf senescence, and thus leaf lifespan.

CONCLUSIONS

The five genes identified in this analysis will be examined further as candidate genes for the adaptive stress response in H. anomalus. Genes that improve growth and productivity under nutrient stress could be used to improve crops for lower soil fertility which is common in marginal agricultural settings.

Life history traits of the pseudometallophyte Thlaspi caerulescens in natural populations from Northern Europe

We examined recruitment, survival, life cycle and fecundity of two metallicolous (M, on metalliferous calamine soils) and two non-metallicolous (NM, on normal soils) populations of Thlaspi caerulescens in Belgium and Luxemburg. In each population, permanent plots were monitored over two reproductive seasons. In M populations, plots were located in two contrasting environments (grass versus grove) in order to test the influence of vegetation cover on life strategy. Our results show that the monocarpic life cycle is dominant in all populations of T. caerulescens. However the length of the pre-reproductive period varies from several months (winter annuals) to 1 year or more (perennials), and is partly related to plant origin (M versus NM). Most plants growing in metalliferous environments were annuals, whereas NM plants were mostly perennials. These differences in life cycle were related to differences in survival during summer, which was better in NM than in M populations. Within each M population, different survival conditions and life cycles were observed according to vegetation cover. Plants growing in grass areas were mostly annuals and had a low survival rate in summer whereas grove plants were mostly perennials and survived better in summer. Our results suggest the selection of stress avoiders (shortening of life cycle) in M populations of T. caerulescens but only for individuals growing in grass areas. Summer survival seems to play a key role in selection of life strategy in T. caerulescens.

Ecological barriers to gene flow between riparian and forest species of Ainsliaea (Asteraceae)

Understanding the role of habitat-associated adaptation in reducing gene flow resulting in population differentiation and speciation is a major issue in evolutionary biology. We demonstrate a significant role for habitat divergence in species isolation between two naturally hybridizing riparian and nonriparian plants, Ainsliaea faurieana and A. apiculata (Asteraceae), on Yakushima Island, Japan. By analyzing the fine-scale population structure at six sympatric sites, we found that variations in leaf shape, geography, light conditions, and genotype were strongly correlated across riverbank-forest transitions. No evidence of effective gene flow was found between the two species across the majority of the transition zones, although the NewHybrid clustering analysis confirmed interspecific hybridization. However, a relatively high level of gene flow was observed across one zone with a more diffuse ecotone and intermediate flooding and light conditions, possibly generated by human disturbances. These results suggest that the barriers to gene flow between the riparian and forest species are primarily ecological. Additional common garden experiments indicated that the two species are adaptively differentiated to contrasting flooding and light environments. Overall, our study suggests that adaptations to different habitats can lead to the formation of reproductive isolating barriers and the maintenance of distinct species boundaries.

Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event

Background

Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H₂S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood.

Results

Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre.

Conclusions

The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations to physico-chemical stressors may directly affect the survival probability in divergent habitat types.

Genetic and physiological basis of adaptive salt tolerance divergence between coastal and inland Mimulus guttatus

Local adaptation is a well-established phenomenon whereby habitat-mediated natural selection drives the differentiation of populations. However, little is known about how specific traits and loci combine to cause local adaptation. Here, we conducted a set of experiments to determine which physiological mechanisms contribute to locally adaptive divergence in salt tolerance between coastal perennial and inland annual ecotypes of Mimulus guttatus. Quantitative trait locus (QTL) mapping was used to discover loci involved in salt spray tolerance and leaf sodium (Na(+)) concentration. To determine whether these QTLs confer fitness in the field, we examined their effects in reciprocal transplant experiments using recombinant inbred lines (RILs). Coastal plants had constitutively higher leaf Na(+) concentrations and greater levels of tissue tolerance, but no difference in osmotic stress tolerance. Three QTLs contributed to salt spray tolerance and two QTLs to leaf Na(+) concentration. All three salt-spray tolerance QTLs had a significant fitness effects at the coastal field site but no effects inland. Leaf Na(+) QTLs had no detectable fitness effects in the field. * Physiological results are consistent with adaptation of coastal populations to salt spray and soil salinity. Field results suggest that there may not be trade-offs across habitats for alleles involved in local salt spray adaptations.

Divergence in an obligate mutualism is not explained by divergent climatic factors

Adaptation to divergent environments creates and maintains biological diversity, but we know little about the importance of different agents of ecological divergence. Coevolution in obligate mutualisms has been hypothesized to drive divergence, but this contention has rarely been tested against alternative ecological explanations. Here, we use a well-established example of coevolution in an obligate pollination mutualism, Yucca brevifolia and its two pollinating yucca moths, to test the hypothesis that divergence in this system is the result of mutualists adapting to different abiotic environments as opposed to coevolution between mutualists. We used a combination of principal component analyses and ecological niche modeling to determine whether varieties of Y. brevifolia associated with different pollinators specialize on different environments. Yucca brevifolia occupies a diverse range of climates. When the two varieties can disperse to similar environments, they occupy similar habitats. This suggests that the two varieties have not specialized on distinct habitats. In turn, this suggests that nonclimatic factors, such as the biotic interaction between Y. brevifolia and its pollinators, are responsible for evolutionary divergence in this system.

Rapid speciation in a newly opened postglacial marine environment, the Baltic Sea

BACKGROUND

Theory predicts that speciation can be quite rapid. Previous examples comprise a wide range of organisms such as sockeye salmon, polyploid hybrid plants, fruit flies and cichlid fishes. However, few studies have shown natural examples of rapid evolution giving rise to new species in marine environments.

RESULTS

Using microsatellite markers, we show the evolution of a new species of brown macroalga (Fucus radicans) in the Baltic Sea in the last 400 years, well after the formation of this brackish water body ~8-10 thousand years ago. Sympatric individuals of F. radicans and F. vesiculosus (bladder wrack) show significant reproductive isolation. Fucus radicans, which is endemic to the Baltic, is most closely related to Baltic Sea F. vesiculosus among north Atlantic populations, supporting the hypothesis of a recent divergence. Fucus radicans exhibits considerable clonal reproduction, probably induced by the extreme conditions of the Baltic. This reproductive mode is likely to have facilitated the rapid foundation of the new taxon.

CONCLUSION

This study represents an unparalleled example of rapid speciation in a species-poor open marine ecosystem and highlights the importance of increasing our understanding on the role of these habitats in species formation. This observation also challenges presumptions that rapid speciation takes place only in hybrid plants or in relatively confined geographical places such as postglacial or crater lakes, oceanic islands or rivers.

Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants?

BACKGROUND

The presence of chloroplast-related DNA sequences in the nuclear genome is generally regarded as a relic of the process by which genes have been transferred from the chloroplast to the nucleus. The remaining chloroplast encoded genes are not identical across the plant kingdom indicating an ongoing transfer of genes from the organelle to the nucleus.

SCOPE

This review focuses on the active processes by which the nuclear genome might be acquiring or removing DNA sequences from the chloroplast genome. Present knowledge of the contribution to the nuclear genome of DNA originating from the chloroplast will be reviewed. In particular, the possible effects of stressful environments on the transfer of genetic material between the chloroplast and nucleus will be considered. The significance of this research and suggestions for the future research directions to identify drivers, such as stress, of the nuclear incorporation of plastid sequences are discussed.

CONCLUSIONS

The transfer to the nuclear genome of most of the protein-encoding functions for chloroplast-located proteins facilitates the control of gene expression. The continual transfer of fragments, including complete functional genes, from the chloroplast to the nucleus has been observed. However, the mechanisms by which the loss of functions and physical DNA elimination from the chloroplast genome following the transfer of those functions to the nucleus remains obscure. The frequency of polymorphism across chloroplast-related DNA fragments within a species will indicate the rate at which these DNA fragments are incorporated and removed from the chromosomes.

Ecological reproductive isolation of coast and inland races of Mimulus guttatus

Adaptive divergence due to habitat differences is thought to play a major role in formation of new species. However it is rarely clear the extent to which individual reproductive isolating barriers related to habitat differentiation contribute to total isolation. Furthermore, it is often difficult to determine the specific environmental variables that drive the evolution of those ecological barriers, and the geographic scale at which habitat-mediated speciation occurs. Here, we address these questions through an analysis of the population structure and reproductive isolation between coastal perennial and inland annual forms of the yellow monkeyflower, Mimulus guttatus. We found substantial morphological and molecular genetic divergence among populations derived from coast and inland habitats. Reciprocal transplant experiments revealed nearly complete reproductive isolation between coast and inland populations mediated by selection against immigrants and flowering time differences, but not postzygotic isolation. Our results suggest that selection against immigrants is a function of adaptations to seasonal drought in inland habitat and to year round soil moisture and salt spray in coastal habitat. We conclude that the coast and inland populations collectively comprise distinct ecological races. Overall, this study suggests that adaptations to widespread habitats can lead to the formation of reproductively isolated species.

Phenotypic plasticity, costs of phenotypes, and costs of plasticity: toward an integrative view

Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic basis of plasticity. In this vein, microbial work is especially illuminating and has three additional strengths. First, information about the machinery underlying plasticity--such as structural and regulatory genes, sensory proteins, and biochemical pathways--helps link population-level studies with underlying physiological and genetic mechanisms. Second, microbial studies involve many generations, large populations, and replication. Finally, empirical estimation of key parameters (e.g., mutation rates) is tractable. Together, these allow for rigorous investigation of gene interactions, drift, mutation, and selection--all potential factors influencing the maintenance or loss of inducible traits along with phenotypic and plasticity costs. Messages emerging from microbial work can guide future efforts to understand the evolution of plastic traits in diverse organisms.

Cool temperatures interfere with D1 synthesis in tomato by causing ribosomal pausing

Photodamage occurs when leaves are exposed to light in excess of what can be used for photosynthesis and in excess of the capacity of ancillary photoprotective as well as repair mechanisms. An important site of photodamage is the chloroplast encoded D1 protein, a component of the photosystem II (PSII) reaction center. Even under optimal growth irradiance, D1 is photodamaged necessitating rapid turnover to prevent the accumulation of photodamaged PSII reaction centers and consequent inhibition of photosynthesis. However, this on-going process of D1 turnover and replacement was impeded in the chilling-sensitive tomato (Solanum lycopersicum) plants when exposed to high-growth light at cool temperature. The decrease in D1 turnover and replacement was found not to be due to changes in the steady-state level of the psbA message. While the recruitment of ribosomes to psbA transcript, initiation of D1 translation, and the association of polysomes with the thylakoid membrane occurred normally, chilling temperatures caused ribosomal pausing during D1 peptide elongation in tomato. The pause locations were non-randomly located on the D1 transcript. The interference with translation caused by ribosomal pausing allowed photodamaged PSII centers to accumulate leading to the consequent inhibition of photosynthesis.

A broad-scale analysis of population differentiation for Zn tolerance in an emerging model species for tolerance study: Arabidopsis halleri (Brassicaceae)

Although current knowledge about the overall distribution of zinc (Zn) tolerance in Arabidopsis halleri populations is scarce, the species is an emerging model for the study of heavy metal tolerance in plants. We attempted to improve this knowledge by testing the Zn tolerance of scattered European metallicolous (M) and nonmetallicolous (NM) populations of A. h. subsp. halleri and A. h. subsp. ovirensis in hydroponic culture. The occurrence of constitutive tolerance was unconditionally established in A. h. halleri and tolerance was extended to the subspecies ovirensis. M populations were the most tolerant but there was a continuous range of variation in tolerance from NM to M populations. Finally, relatively high levels of tolerance were detected in some NM populations, suggesting that enhanced tolerance could be present at high frequency in populations that have not experienced metal exposure. We used our results to argue the evolutionary dynamics and origin of Zn tolerance in A. halleri.