MADS-box out of the black box

The compelling elegance of using genome‐wide scans to detect the signature of selection is difficult to resist, but is countered by the low demonstrated efficacy of pinpointing the actual genes and traits that are the targets of selection in nonmodel species. While the difficulty of going from a suggestive signature to a functional nucleotide polymorphism should not prevent researchers from using genome scans, it does lessen their long‐term utility within and across study systems. In a new study published in this issue of Molecular Ecology ( Mariac et al. 2011 ), researchers have gone a long way towards increasing the relevance of genome‐wide scans for selection via two approaches: (i) they tailored the markers used in the scan to target a family of developmental genes that were good candidates for controlling a trait of interest and (ii) they used an independent mapping population to confirm the association of the gene with polymorphism in the trait of interest. All of this was completed in the nonmodel system of pearl millet (Pennisetum glaucum) and may provide a road map for other researchers hoping to pin down solid candidate genes for selected traits in natural or cultivated systems. Outside of these broad methodological innovations, the paper specifically focuses on a trait (flowering time) that varies across an environmental gradient (rainfall). This environmental gradient potentially serves as a model for environmental change over time, and allele frequencies at the gene can therefore be used to track how populations of pearl millet will adapt to future climate shifts at the genetic level.     

The Role of Pseudo-Endoglucanases in the Evolution of Nematode Cell Wall-Modifying Proteins

In this article, the characterization and evolution of pseudo-endoglucanases and a putative expansin-like gene in the migratory nematode Ditylenchus africanus are described. Four genes were cloned with a very high similarity to the endoglucanase Da-eng1, which, however, lack a part of the catalytic domain most probably due to homologous recombination. Owing to this deletion, at least one of the catalytic residues of the corresponding protein is missing, and hence these genes are possibly pseudogenes. In two of the pseudo-endoglucanase genes, the deletions cause a frameshift (Da-engdel2, Da-engdel4), while two others (Da-engdel1, Da-engdel3) code for protein sequences with an intact carbohydrate-binding module (CBM). Recombinant proteins for Da-ENG1, Da-ENGDEL1, and Da-ENGDEL3 were demonstrated to bind to cellulose, while only Da-ENG1 showed cellulose-degrading activity. This indicates that Da-ENGDEL1 and Da-ENGDEL3 which lack cellulase activity, could still exert a function similar to cellulose-binding proteins (CBPs). Next to the pseudo-endoglucanases, a putative expansin-like gene (Da-exp1) was identified, consisting of a signal peptide, an expansin-like domain, and a CBM. This domain structure was never found before in nematode expansin-like proteins. Interestingly, the CBM of the expansin-like gene is very similar to the endoglucanase CBMs, and a conserved intron position in the CBM of nematode endoglucanases, expansin-like genes, and CBPs indicates a common origin for these domains. This suggests that domain shuffling is an important mechanism in the evolution of cell wall-modifying enzymes in nematodes.     

Variable evolutionary response to regional climate change in a polymorphic species

The evolutionary response to regional and global climate change may vary in widespread polymorphic species, so predicting future genetic responses will require careful tracking of genetic variability in local populations. We surveyed chromosomal inversion polymorphisms in 25 populations of Drosophila robusta, many of which have been sampled repeatedly starting in the 1940s, 50s, and 60s up until 2007, across its range in the USA. Frequencies of some northerly, or cold‐adapted, gene arrangements have declined in the face of increasing temperatures, whereas frequencies of several southern, or warm‐adapted, gene arrangements were positively correlated with increasing temperature changes. Over a finer geographic scale, populations from the west‐central part of the species range from the Ozark Plateau, Ouachita mountains, and eastern Oklahoma showed genetic differentiation between south‐central Ozark and western Ozark/Ouachita regions that has persisted in the face of recent shifts in gene arrangement frequencies. Overall, populations of D. robusta exhibited dynamic genetic changes over time, with some populations shifting chromosome frequencies in just 10–15 years. Some temporal genetic shifts were widespread and significantly correlated with temperature increases, but regions of the genome marked by different gene arrangements have responded in different sections of the species range. In some parts of the species range, chromosome frequencies shifted but were not associated with changing temperatures, showed little or no temporal change, or temporal shifts stopped for temperature sensitive gene arrangements near fixation. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 702–718.     

Experimental evidence of genome‐wide impact of ecological selection during early stages of speciation‐with‐gene‐flow

Theory predicts that speciation‐with‐gene‐flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome‐wide impacts of host‐associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation‐with‐gene‐flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co‐occurring apple and hawthorn flies in nature. This striking genome‐wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco‐evolutionary dynamics and genome divergence.     

Effects of External Mass Transfer and Product Inhibition on a Simulated Immobilized Enzyme‐Catalyzed Reactor for Lactose Hydrolysis

A mathematical model has been developed for predicting the performance and simulation of a packed bed immobilized enzyme reactor performing lactose hydrolysis, which follows Michaelis‐Menten kinetics with competitive product (galactose) inhibition. The performance characteristics of a packed bed immobilized enzyme reactor have been analyzed taking into account the effects of various diffusional phenomena like axial dispersion and external mass transfer limitations. The model design equations are then solved by Galerkin's method and orthogonal collocation on finite elements. The effects of external mass transfer and axial dispersion have been studied and their effects were shown to reduce the external effectiveness factor. The effects of product inhibition have been investigated at different operating conditions correlated at different regimes using dimensionless moduli (St, γ, θ, Da)¹⁾. The product inhibition was shown to reduce the substrate conversion, and, additionally, to decrease the effectiveness factor when Da > Da_xo, however, it increases the effectiveness factor when Da < Da_xo. The effectiveness factor is found to be independent of the product inhibition at a crossover point at which Da_xo is defined. Effects of St and Pe have been investigated at different kinetic regimes and the results show that their effects have a strong dependency on the kinetic parameters θ, γ (i.e., K_m/K_p), and Da_xo.     

Population demography influences climatic niche evolution: evidence from diploid American Hordeum species (Poaceae)

In this study, we explore the interplay of population demography with the evolution of ecological niches during or after speciation in Hordeum. While large populations maintain a high level of standing genetic diversity, gene flow and recombination buffers against fast alterations in ecological adaptation. Small populations harbour lower allele diversity but can more easily shift to new niches if they initially survive under changed conditions. Thus, large populations should be more conservative regarding niche changes in comparison to small populations. We used environmental niche modelling together with phylogenetic, phylogeographic and population genetic analyses to infer the correlation of population demography with changes in ecological niche dimensions in 12 diploid Hordeum species from the New World, forming four monophyletic groups. Our analyses found both shifts and conservatism in distinct niche dimensions within and among clades. Speciation due to vicariance resulted in three species with no pronounced climate niche differences, while species originating due to long‐distance dispersals or otherwise encountering genetic bottlenecks mostly revealed climate niche shifts. Niche convergence among clades indicates a niche‐filling pattern during the last 2 million years in South American Hordeum. We provide evidence that species, which did not encounter population reductions mainly showed ecoclimatic niche conservatism, while major niche shifts occurred in species which have undergone population bottlenecks. Our data allow the conclusion that population demography influences adaptation and niche shifts or conservatism in South American Hordeum species.     

Genetic divergence in nuclear genomes between populations of <Emphasis Type="Italic">Fagus crenata</Emphasis> along the Japan Sea and Pacific sides of Japan

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species’ range. Although population differentiation was very low (F _ST = 0.027; R _ST = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H _E = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.     

Phenotypic differentiation of the Solidago virgaurea complex along an elevational gradient: Insights from a common garden experiment and population genetics

Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations. Leaf mass per area was lower, while leaf nitrogen and chlorophyll concentrations were greater for higher elevations at which seeds were originally collected. For reproductive traits, plants derived from higher elevations had larger flower heads on shorter stems and flowering started earlier. These elevational changes in morphology were consistent with the clines in the field, indicating that phenotypic variation along the elevational gradient would have been caused by genetic differentiation. However, population genetic analysis using 16 microsatellite loci suggested an extremely low level of genetic differentiation of neutral genes among the nine populations. Analysis of molecular variance also indicated that most genetic variation was partitioned into individuals within a population, and the genetic differentiation among the populations was not significant. This study suggests that genome regions responsible for adaptive traits may differ among the populations despite the existence of gene flow and that phenotypic variation of the S. virgaurea complex along the elevational gradient is maintained by strong selection pressure.     

Differential Influence of Life Cycle on Growth and Toxin Production of three Pseudo‐nitzschia Species (Bacillariophyceae)

We used a multistrain approach to study the intra‐ and interspecific variability of the growth rates of three Pseudo‐nitzschia species – P. australis, P. fraudulenta, and P. pungens – and of their domoic acid (DA) production. We carried out mating and batch experiments to investigate the respective effects of strain age and cell size, and thus the influence of their life cycle on the physiology of these species. The cell size – life cycle relationship was characteristic of each species. The influence of age and cell size on the intraspecific variability of growth rates suggests that these characteristics should be considered cautiously for the strains used in physiological studies on Pseudo‐nitzschia species. The results from all three species do not support the hypothesis of a decrease in DA production with time since isolation from natural populations. In P. australis, the cellular DA content was rather a function of cell size. More particularly, cells at the gametangia stage of their life cycle contained up to six times more DA than smaller or larger cells incapable of sexual reproduction. These findings reveal a link between P. australis life cycle and cell toxicity. This suggest that life cycle dynamics in Pseudo‐nitzschia natural populations may influence bloom toxicity.     

Postglacial ecotype formation under outcrossing and self‐fertilization in Arabidopsis lyrata

The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here, we addressed whether substrate‐related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems. The North American subspecies colonized both rocky and sandy habitats during postglacial range expansion and shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole‐genome sequence data of 20 selfing or outcrossing populations, which suggested genes involved in adaptation to substrate. Motivated by enriched gene ontology terms, we compared root growth between plants from the two substrates in a common environment and found that plants originating from sand grew roots faster and produced more side roots, independent of mating system. Furthermore, single nucleotide polymorphisms associated with substrate‐related ecotypes were more clustered among selfing populations. Our study provides evidence for substrate‐related ecotypes in A. lyrata and divergence in the genomic footprint between mating systems. The latter is the likely result of selfing populations having experienced divergent selection on larger genomic regions due to higher genome‐wide linkage disequilibrium.     

Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the Himalaya-Hengduan Mountains across elevational gradients

Aim

How species respond to ongoing climate change has been a hot research topic, especially with the controversy in shifting range (movement) or persisting in local habitat (in situ) as the primary response. Assessing the relative roles of range shifts, phenotypic plasticity and genetic adaptation helps us predict the evolutionary fate of species. We aim to explore the evolutionary strategies of plants under climate change from a keystone herb in alpine ecosystems, Mirabilis himalaica, along its elevational gradient.

Location

Himalaya-Hengduan Mountains, China.

Methods

We combined evidence from population genomics and ecological data in both space and time to investigate the state of “staying” or “moving”. We identified migration events by assessing historical and contemporary gene flow and changes in species distribution. Morphological variation was compared by measuring five traits using specimen data. Moreover, we explored climate-driven genetic variation and local selection regimes acting on populations in the alpine landscape along an elevational gradient.

Results

Our results argue that staying in situ by morphological variation and local genetic evolution rather than range shifting plays an important role in M. himalaica response to climate change. We first found trace evidence of upward or climatic-driven shifting along an elevational gradient, although asymmetric gene flow was restricted within microenvironments of mid-elevational populations. Furthermore, morphological variation comparisons revealed clinal variation, as resource allocation showed a declining pattern in vegetative growth but increased reproductive growth with increasing elevation. Outlier tests and environment association analyses indicated adaptative loci primarily related to thermal-driven selection and continuous adaptations to high elevation in the Himalaya-Hengduan Mountains.

Main Conclusions

Our findings show M. himalaica may persist in local habitats rather than shifting range under climate change, exhibiting a low risk of genomic vulnerability in current habitats. This study has important implications in improving our understanding of the evolutionary response in alpine plants to climate change.     

<Emphasis Type="Italic">Drosophila</Emphasis> gustatory preference behaviors require the atypical soluble guanylyl cyclases

The intracellular messenger cGMP has been suggested to play a role in taste signal transduction in both vertebrates and invertebrates. In the present study, we have examined the role of the Drosophila atypical soluble guanylyl cyclases (sGCs), Gyc-89Da and Gyc-89Db, in larval and adult gustatory preference behaviors. We showed that in larvae, sucrose attraction requires Gyc-89Db and caffeine avoidance requires Gyc-89Da. In adult flies, sucrose attraction is unaffected by mutations in either gene whereas avoidance of low concentrations of caffeine is eliminated by loss of either gene. Similar defective behaviors were observed when cGMP increases were prevented by the expression of a cGMP-specific phosphodiesterase. We also showed that both genes were expressed in gustatory receptor neurons (GRNs) in larval and adult gustatory organs, primarily in a non-overlapping pattern, with the exception of a small group of cells in the adult labellum. In addition, in adults, several cells co-expressed the bitter taste receptor, Gr66a, with either Gyc-89Da or Gyc-89Db. We also showed that the electrophysiological responses of a GRN to caffeine were significantly reduced in flies mutant for the atypical sGCs, suggesting that at least part of the adult behavioral defects were due to a reduced ability to detect caffeine.     

Ploidy level and genome size of locally adapted populations of <Emphasis Type="Italic">Silene ciliata</Emphasis> across an altitudinal gradient

Silene ciliata Poiret is a small perennial that presents several ploidy levels and inhabits the mountain ranges of the European Mediterranean basin. Recent studies have shown evidence of local adaptation in populations located across an altitudinal gradient in Sierra de Guadarrama (Central Spain) at the species’ southernmost distribution limit. In this study, we assessed whether the existence of local adaptation in these populations was related to differences in karyological features (ploidy level or chromosome number modification) or in nuclear DNA amount. Optical microscope (phase contrast and epifluorescence after DAPI staining) and flow cytometry were used to estimate the ploidy level and genome size of several family lines in three populations across the altitude gradient. With a sampling three times higher than usual in genome size assessments, all individuals showed a constant diploid set (2n = 24), so that polyploidy or other chromosome number modifications were discarded. The small genome size found (mean ± SD; 2C = 1.76 ± 0.06 pg) was within the range of those found in other Silene species. Significant differences in genome size were found when the three populations of S. ciliata were compared. The largest genome size found at the intermediate population may be associated to lower environmental stress at the mid elevation, in line with the recent studies in this area.     

Variation in plant functional traits across and within four species of Western Australian Banksia (Proteaceae) along a natural climate gradient

Plant traits are fundamental components of the ecological strategies of plants, relating to how plants acquire and use resources. Their study provides insight into the dynamics of species geographical ranges in changing environments. Here, we assessed the variation in trait values at contrasting points along an environmental gradient to provide insight into the flexibility of species response to environmental heterogeneity. Firstly, we identified how commonly measured functional traits of four congeneric species (Banksia baxteri, B. coccinea, B. media and B. quercifolia) varied along a longitudinal gradient in the South Western Australian Floristic Region. This regional gradient provides significant variation in moisture, temperature and soil nutrients: soil nitrogen content decreases with declining rainfall and increasing temperature. We hypothesized that (i) the regional pattern in trait–environment associations across the species would match those observed on a global scale and (ii) that the direction and slopes of the within‐species relationships would be similar to those across species for each of the measured traits. Along the regional gradient we observed strong shifts in trait values, and cross‐species relationships followed the expected trend: specific leaf area was significantly lower, and leaf N_area and seed dry mass significantly higher, at the drier end of the rainfall gradient. However, traits within species were generally not well correlated with habitat factors: we found weak patterns among populations, either due to the small ecological gradient or perhaps because fine‐scale structuring among populations (at a micro‐evolutionary scale) was low due to high gene flow within species. Understanding how species traits shift as a result of climatic influences, both at the regional (across species) and local (within species) scale, provides insight into plant adaptation to the environment. Such studies have important applications for conservation biology and population management in the face of global change.     

Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community?

Species responses to environmental change are likely to depend on existing genetic and phenotypic variation, as well as evolutionary potential. A key challenge is to determine whether gene flow might facilitate or impede genomic divergence among populations responding to environmental change, and if emergent phenotypic variation is dependent on gene flow rates. A general expectation is that patterns of genetic differentiation in a set of codistributed species reflect differences in dispersal ability. In less dispersive species, we predict greater genetic divergence and reduced gene flow. This could lead to covariation in life‐history traits due to local adaptation, although plasticity or drift could mirror these patterns. We compare genome‐wide patterns of genetic structure in four phenotypically variable grasshopper species along a steep elevation gradient near Boulder, Colorado, and test the hypothesis that genomic differentiation is greater in short‐winged grasshopper species, and statistically associated with variation in growth, reproductive, and physiological traits along this gradient. In addition, we estimate rates of gene flow under competing demographic models, as well as potential gene flow through surveys of phenological overlap among populations within a species. All species exhibit genetic structure along the elevation gradient and limited gene flow. The most pronounced genetic divergence appears in short‐winged (less dispersive) species, which also exhibit less phenological overlap among populations. A high‐elevation population of the most widespread species, Melanoplus sanguinipes, appears to be a sink population derived from low elevation populations. While dispersal ability has a clear connection to the genetic structure in different species, genetic distance does not predict growth, reproductive, or physiological trait variation in any species, requiring further investigation to clearly link phenotypic divergence to local adaptation.     

Genetic structure of a reef-building coral from thermally distinct environments on the Great Barrier Reef

Adaptation to localised thermal regimes is facilitated by restricted gene flow, ultimately leading to genetic divergence among populations and differences in their physiological tolerances. Allozyme analysis of six polymorphic loci was used to assess genetic differentiation between nine populations of the reef-building coral Acropora millepora over a latitudinal temperature gradient on the inshore regions of the Great Barrier Reef (GBR). Small but significant genetic differentiation indicative of moderate levels of gene flow (pairwise F _ST 0.023 to 0.077) was found between southern populations of A. millepora in cooler regions of the GBR and the warmer, central or northern GBR populations. Patterns of genetic differentiation at these putatively neutral allozyme loci broadly matched experimental variation in thermal tolerance and were consistent with local thermal regimes (warmest monthly-averages) for the A. millepora populations examined. It is therefore hypothesized that natural selection has influenced the thermal tolerance of the A. millepora populations examined and greater genetic divergence is likely to be revealed by examination of genetic markers under the direct effects of natural selection.     

DNA metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient

Resource variation along abiotic gradients influences subsequent trophic interactions and these effects can be transmitted through entire food webs. Interactions along abiotic gradients can provide clues as to how organisms will face changing environmental conditions, such as future range shifts. However, it is challenging to find replicated systems to study these effects. Phytotelmata, such as those found in carnivorous plants, are isolated aquatic communities and thus form a good model for the study of replicated food webs. Due to the degraded nature of the prey, molecular techniques provide a useful tool to study these communities. We studied the pitcher plant Sarracenia purpurea L. in allochthonous populations along an elevational gradient in the Alps and Jura. We predicted that invertebrate richness in the contents of the pitcher plants would decrease with increasing elevation, reflecting harsher environmental conditions. Using metabarcoding of the COI gene, we sequenced the invertebrate contents of these pitcher plants. We assigned Molecular Operational Taxonomic Units at ordinal level as well as recovering species‐level data. We found small but significant changes in community composition with elevation. These recovered sequences could belong to invertebrate prey, rotifer inquilines, pollinators and other animals possibly living inside the pitchers. However, we found no directional trend or site‐based differences in MOTU richness with elevational gradient. Use of molecular techniques for dietary or contents analysis is a powerful way to examine numerous degraded samples, although factors such as DNA persistence and the relationship with species presence still have to be completely determined.     

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present‐day tropical biota. Using genome‐wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post‐Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as “isolation by instability,” highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.     

Insertional mutagenesis in <Emphasis Type="Italic">Populus</Emphasis>: relevance and feasibility

The recent sequencing of the first tree genome, that of the black cottonwood (Populus trichocarpa), opens a new chapter in tree functional genomics. While the completion of the genome is a milestone, mobilizing this significant resource for better understanding the growth and development of woody perennials will be an even greater undertaking in the years to come. In other model organisms, a critical tool for high-throughput analysis of gene function has been the generation of large mutagenized populations. Some mutagenesis technologies and approaches cannot be applied to trees because of their typically outcrossing breeding systems, high heterozygosity, large body size, and delayed flowering. In contrast, gene-tagging approaches that use insertional mutagenesis to create dominant phenotypes are ideally suited for trees and, especially, Populus. Both activation tagging and enhancer trap programs have been successful in identifying new genes important to tree development. The generation of genome-wide insertional mutant populations, which provide direct functional links between genes and phenotypes, should help to integrate in silico analyses of gene and protein expression, association studies of natural genetic polymorphism, and phenotypic analyses of adaptation and development.