Temperature‐dependent conformational change affecting Tyr11 and sweetness loops of brazzein

The sweet protein brazzein, a member of the Csβα fold family, contains four disulfide bonds that lend a high degree of thermal and pH stability to its structure. Nevertheless, a variable temperature study has revealed that the protein undergoes a local, reversible conformational change between 37 and 3°C with a midpoint about 27°C that changes the orientations and side‐chain hydrogen bond partners of Tyr8 and Tyr11. To test the functional significance of this effect, we used NMR saturation transfer to investigate the interaction between brazzein and the amino terminal domain of the sweet receptor subunit T1R2; the results showed a stronger interaction at 7°C than at 37°C. Thus the low temperature conformation, which alters the orientations of two loops known to be critical for the sweetness of brazzein, may represent the bound state of brazzein in the complex with the human sweet receptor. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Cytoplasmic diversity,phylogenetic relationships and molecular evolution of Tunisian Citrus species as inferred from mutational events and pseudogene of chloroplast trnL-trnF spacer

The genus Citrus L. is among the most important fruit trees in the world. In this report, cytoplasmic polymorphism of twenty seven Tunisian Citrus cultivars was explored using the chloroplast trnL-trnF intergenic spacer. Chloroplast sequences showed variation in length and nucleotide content. Haplotype and nucleotide diversity showed low variations. Molecular phylogenetic tree identifies Citrus maternal origins and demonstrates two major groups distinguishing between mandarin and pummelo groups. The trnL-trnF intergenic spacer showed one copy of pseudogene of the original trnF gene in 27 Citrus species at position 275 bp with a size varying from 49 to 63 bp. The anticodon domain was identified as the most conserved element, but one transversion (T−>C) was found in the D-domain. Meanwhile, one transversion (T−>A) and one transition (T−>G) were found in the T-domain. Neutrality tests (Tajima, Fu & Li and Fu) which revealed positive and non-significant values and Pi and θ_W assume a neutral model of evolution and advocated a constant population size. The study demonstrates the resolving power of trnL-trnF sequence data to prove both pummelo and mandarin gene pool’s contribution in the development of Tunisian secondary species and inferring their genetic and phylogenetic relationships.     

Temperature‐dependent oxygen limitation and the rise of Bergmann's rule in species with aquatic respiration

Bergmann's rule is the propensity for species‐mean body size to decrease with increasing temperature. Temperature‐dependent oxygen limitation has been hypothesized to help drive temperature–size relationships among ectotherms, including Bergmann's rule, where organisms reduce body size under warm oxygen‐limited conditions, thereby maintaining aerobic scope. Temperature‐dependent oxygen limitation should be most pronounced among aquatic ectotherms that cannot breathe aerially, as oxygen solubility in water decreases with increasing temperature. We use phylogenetically explicit analyses to show that species‐mean adult size of aquatic salamanders with branchial or cutaneous oxygen uptake becomes small in warm environments and large in cool environments, whereas body size of aquatic species with lungs (i.e., that respire aerially), as well as size of semiaquatic and terrestrial species do not decrease with temperature. We argue that oxygen limitation drives the evolution of small size in warm aquatic environments for species with aquatic respiration. More broadly, the stronger decline in size with temperature observed in aquatic versus terrestrial salamander species mirrors the relatively strong plastic declines in size observed previously among aquatic versus terrestrial invertebrates, suggesting that temperature‐dependent oxygen availability can help drive patterns of plasticity, micro‐ and macroevolution.     

Phylogeography and lineage‐specific patterns of genetic diversity and molecular evolution in a group of North American skinks

Geography influences the evolutionary trajectory of species by mediating opportunities for hybridization, gene flow, demographic shifts and adaptation. We sought to understand how geography and introgression can generate species‐specific patterns of genetic diversity by examining phylogeographical relationships in the North American skink species Plestiodon multivirgatus and P. tetragrammus (Squamata: Scincidae). Using a multilocus dataset (three mitochondrial genes, four nuclear genes; a total of 3455 bp) we discovered mito‐nuclear discordance, consistent with mtDNA introgression. We further tested for evidence of species‐wide mtDNA introgression by using comparisons of genetic diversity, selection tests and extended Bayesian skyline analyses. Our findings suggest that P. multivirgatus acquired its mitochondrial genome from P. tetragrammus after their initial divergence. This putative species‐wide mitochondrial capture was further evidenced by statistically indistinguishable substitution rates between mtDNA and nDNA in P. multivirgatus. This rate discrepancy was observed in P. multivirgatus but not P. tetragrammus, which has important implications for studies that combine mtDNA and nDNA sequences when inferring time since divergence between taxa. Our findings suggest that by facilitating opportunities for interspecific introgression, geography can alter the course of molecular evolution between recently diverged lineages.     

Temperature‐dependent development of Neoseiulus barkeri (Acari: Phytoseiidae) on Tetranychus urticae (Acari: Tetranychidae) at seven constant temperatures

Abstract The effect of seven constant temperatures of 15, 20, 25, 27, 30, 35 and 37°C on developmental time of Neoseiulus barkeri Hughes were determined in laboratory conditions under 65%± 5% RH and a photoperiod of 12 : 12 (L : D) h on nymphal stages of Tetranychus urticae Koch. Total developmental time of females (from egg to adult emergence) at the above‐mentioned temperatures was 26.59, 14.43, 6.32, 5.64, 4.59, 3.98 and 4.67 days, respectively. Developmental rate of the N. barkeri increased as temperature increased from 15 to 35°C, but declined at 37°C. A linear and two nonlinear models were fitted to developmental rate of immature stages of N. barkeri to predict the developmental rate as a function of temperature, as well as to estimate the thermal constant (K) and critical temperatures (i.e., T_min, T_opt and T_max). The estimated values of the T_min and K for total developmental time using the linear model were 12.07°C and 86.20 degree‐days (DD), respectively. The T_min and T_max estimated by the Sharpe‐Schoolfield‐Ikemoto (SSI) model were 11.90°C and 37.41°C, respectively. The estimated T_opt for overall immature stage development of N. barkeri by the Lactin and SSI models were 33.89°C and 24.51°C, respectively. Based on the biological criteria of model evaluation, the linear and SSI models were found to be the best models for describing the developmental rate of overall immature stages of N. barkeri and estimating the temperature thresholds.     

Environmental heterogeneity,species diversity and co‐existence at different spatial scales

The positive relationship between spatial environmental heterogeneity and species diversity is a widely accepted concept, generally associated with niche limitation. However, niche limitation cannot account for negative heterogeneity–diversity relationships (HDR) revealed in several case studies. Here we explore how HDR varies at different spatial scales and provide novel theories for small‐scale species co‐existence that explain both positive and negative HDR. At large spatial scales of heterogeneity (e.g. landscape level), different communities co‐exist, promoting large regional species pool size and resulting in positive HDR. At smaller scales within communities, species co‐existence can be enhanced by increasing the number of different patches, as predicted by the niche limitation theory, or alternatively, restrained by heterogeneity. We conducted meta‐regressions for experimental and observational HDR studies, and found that negative HDRs are significantly more common at smaller spatial scales. We propose three theories to account for niche limitation at small spatial scales. (1) Microfragmentation theory: with increasing spatial heterogeneity, large homogeneous patches lose area and become isolated, which in turn restrains the establishment of new plant individuals and populations, thus reducing species richness. (2) Heterogeneity confounded by mean: when heterogeneity occurs at spatial scales smaller than the size of individual plants, which forage through the patches, species diversity can be either positively or negatively affected by a change in the mean of an environmental factor. (3) Heterogeneity as a separate niche axis: the ability of species to tolerate heterogeneity at spatial scales smaller than plant size varies, affecting HDR. We conclude that processes other than niche limitation can affect the relationship between heterogeneity and diversity.     

Determining the relative roles of species replacement and species richness differences in generating beta‐diversity patterns

Aim To determine the relative contribution of species replacement and species richness differences to the emergence of beta‐diversity patterns. Innovation A novel method that disentangles all compositional differences (β_cc, overall beta diversity) in its two components, species replacement (β_‐3) and species richness differences (β_rich) is proposed. The performance of the method was studied with ternary plots, which allow visualization of the influence of the relative proportions of shared and unique species of two sites over each metric. The method was also tested in different hypothetical gradients and with real datasets. The novel method was compared with a previous proposal based on the partitioning of overall compositional differences (β_sor) in replacement (β_sim) and nestedness (β_nes). The linear response of β_cc contrasts with the curvilinear response of β_sor to linear gradients of dissimilarity. When two sites did not share any species, β_sim was always 1 and β_‐3 only reached 1 when the number of exclusive species of both sites was equal. β_‐3 remained constant along gradients of richness differences with constant replacement, while β_sim decreased. β_rich had a linear response to a linear gradient of richness differences with constant species replacement, whereas β_nes exhibited a hump‐shaped response. Moreover, β_sim > β_nes when clearly almost all species of one site were lost, whereas β_‐3 < β_rich in the same circumstances. Main conclusions The behaviour of the partition of β_cc into β_‐3 and β_rich is consistent with the variation of replacement and richness differences. The partitioning of β_sor into β_sim and β_nes overestimates the replacement component and underestimates richness differences. The novel methodology allows the discrimination of different causes of beta‐diversity patterns along latitudinal, biogeographic or ecological gradients, by estimating correctly the relative contributions of replacement and richness differences.     

Environmental factors affecting patterns of distribution and co‐occurrence of two competing raptor species

Habitat selection is a complex process, that is affected by several factors, including habitat characteristics, environmental conditions, and both intra‐ and interspecific interactions. We analysed habitat preferences of two top avian predators, Peregrine Falcon Falco peregrinus, a medium‐sized diurnal raptor, and Eagle Owl Bubo bubo, a large nocturnal raptor. These two species are known to compete for preferred nest‐sites, and proximity to cliffs with Eagle Owls may reduce Peregrine breeding output through predation of young Falcons. We investigated the environmental factors affecting occurrence and coexistence of the two species and the potential role of habitat suitability in favouring co‐occurrence in 3519 km² of the central pre‐Alps of Italy, where the two species breed on cliffs and sometimes co‐occur on the same cliff. Peregrines settled on long, steep and favourably orientated cliffs in woodland landscapes close to urban areas. Eagle Owls settled on topographically similar cliffs, but in lower rainfall areas compared with cliffs occupied by Peregrines and cliffs unoccupied by either species. Sites where the two species co‐occurred were characterized by more horizontally extended cliffs compared with sites of exclusive occurrence of each species. An analysis of relative habitat suitability revealed that sites where the two species co‐occurred had the highest predicted probability of occupancy for both species, suggesting that those sites should be regarded as high‐quality sites. Breeding productivity of Eagle Owls was negatively affected by the co‐occurrence of Peregrines, whereas the effect of Eagle Owl proximity on Peregrine productivity varied according to cliff suitability for the Peregrines. Habitat selection had fitness consequences for Eagle Owls because breeding productivity increased with cliff length. Environmental conditions, particularly climatic factors, could allow the widespread coexistence of these competing raptors at the landscape scale, whereas at the local scale co‐occurrence could take place only on larger cliffs. These were preferred sites for both species, presumably because breeding at such sites offsets the costs of settling close to the competitor species.     

Contrasting patterns of density‐dependent selection at different life stages can create more than one fast–slow axis of life‐history variation

There has been much recent research interest in the existence of a major axis of life‐history variation along a fast–slow continuum within almost all major taxonomic groups. Eco‐evolutionary models of density‐dependent selection provide a general explanation for such observations of interspecific variation in the "pace of life." One issue, however, is that some large‐bodied long‐lived “slow” species (e.g., trees and large fish) often show an explosive “fast” type of reproduction with many small offspring, and species with “fast” adult life stages can have comparatively “slow” offspring life stages (e.g., mayflies). We attempt to explain such life‐history evolution using the same eco‐evolutionary modeling approach but with two life stages, separating adult reproductive strategies from offspring survival strategies. When the population dynamics in the two life stages are closely linked and affect each other, density‐dependent selection occurs in parallel on both reproduction and survival, producing the usual one‐dimensional fast–slow continuum (e.g., houseflies to blue whales). However, strong density dependence at either the adult reproduction or offspring survival life stage creates quasi‐independent population dynamics, allowing fast‐type reproduction alongside slow‐type survival (e.g., trees and large fish), or the perhaps rarer slow‐type reproduction alongside fast‐type survival (e.g., mayflies—short‐lived adults producing few long‐lived offspring). Therefore, most types of species life histories in nature can potentially be explained via the eco‐evolutionary consequences of density‐dependent selection given the possible separation of demographic effects at different life stages.     

Gametophytic self-incompatibility in Lycium parishii (Solanaceae): allelic diversity, genealogical structure, and patterns of molecular evolution at the S-RNase locus

We characterized allelic diversity at the locus controlling self-incompatibility (SI) for a population of Lycium parishii (Solanaceae) from Organ Pipe National Monument, Arizona. Twenty-four partial sequences of S-RNase alleles were recovered from 25 individuals. Estimates of allelic diversity range from 23 to 27 alleles and, consistent with expectations for SI, individuals are heterozygous. We compare S-RNase diversity, patterns of molecular evolution, and the genealogical structure of alleles from L. parishii to a previously studied population of its congener L. andersonii. Gametophytic SI is well characterized for Solanaceae and although balancing selection is hypothesized to be responsible for high levels of allelic divergence, the pattern of selection varies depending on the portion of the gene considered. Site-specific models investigating patterns of selection for L. parishii and L. andersonii indicate that positive selection occurs in those regions of the S-RNase gene hypothesized as important to the recognition response, whereas positive selection was not detected for any position within regions previously characterized as conserved. A 10-species genealogy including S-RNases from a pair of congeners from each of five genera in Solanaceae reveals extensive transgeneric evolution of L. parishii S-RNases. Further, within Lycium, the Dn/Ds ratios for pairs of closely related alleles for intraspecific versus interspecific comparisons were not significantly different, suggesting that the S-RNase diversity recovered in these two species was present prior to the speciation event separating them. Despite this, two S-RNases from L. parishii are identical to two previously reported alleles for L. andersonii, suggesting gene flow between these species.     

Geography best explains global patterns of genetic diversity and postglacial co‐expansion in marine turtles

For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion, while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to postglacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial data set encompassing 23 previously identified lineages from all seven marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian model averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.     

Energy, range dynamics and global species richness patterns: reconciling mid-domain effects and environmental determinants of avian diversity

Spatial patterns of species richness follow climatic and environmental variation, but could reflect random dynamics of species ranges (the mid-domain effect, MDE). Using data on the global distribution of birds, we compared predictions based on energy availability (actual evapotranspiration, AET, the best single correlate of avian richness) with those of range dynamics models. MDE operating within the global terrestrial area provides a poor prediction of richness variation, but if it operates separately within traditional biogeographic realms, it explains more global variation in richness than AET. The best predictions, however, are given by a model of global range dynamics modulated by AET, such that the probability of a range spreading into an area is proportional to its AET. This model also accurately predicts the latitudinal variation in species richness and variation of species richness both within and between realms, thus representing a compelling mechanism for the major trends in global biodiversity.     

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation

? Premise of the study: Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. ? Methods: Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. ? Results: Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. ? Conclusions: Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.     

Why decadal to century timescale palaeoclimate data are needed to explain present‐day patterns of biological diversity and change

The current distribution of species, environmental conditions and their interactions represent only one snapshot of a planet that is continuously changing, in part due to human influences. To distinguish human impacts from natural factors, the magnitude and pace of climate shifts, since the Last Glacial Maximum, are often used to determine whether patterns of diversity today are artefacts of past climate change. In the absence of high‐temporal resolution palaeoclimate reconstructions, this is generally done by assuming that past climate change occurred at a linear pace between widely spaced (usually, ≥1,000 years) climate snapshots. We show here that this is a flawed assumption because regional climates have changed significantly across decades and centuries during glacial–interglacial cycles, likely causing rapid regional replacement of biota. We demonstrate how recent atmosphere‐ocean general circulation model (AOGCM) simulations of the climate of the past 21,000 years can provide credible estimates of the details of climate change on decadal to centennial timescales, showing that these details differ radically from what might be inferred from longer timescale information. High‐temporal resolution information can provide more meaningful estimates of the magnitude and pace of climate shifts, the location and timing of drivers of physiological stress, and the extent of novel climates. They also produce new opportunities to directly investigate whether short‐term climate variability is more important in shaping biodiversity patterns rather than gradual changes in long‐term climatic means. Together, these more accurate measures of past climate instability are likely to bring about a better understanding of the role of palaeoclimatic change and variability in shaping current macroecological patterns in many regions of the world.     

Individual species–area relationships and spatial patterns of species diversity in a Great Basin,semi‐arid shrubland

Traditional biodiversity metrics operate at the level of a plant community but do not capture spatial variation in diversity from a ‘plant's‐eye view’ of a community. Recently‐developed statistics consider the spatial patterns of plants as well as the number and distribution of species in local plant neighborhoods to quantitatively assess multispecies spatial patterns from a ‘plant's‐eye view’. We used one such statistic, the individual species area relationship (ISAR), to assess spatial patterns of species diversity in a Great Basin (USA) semi‐arid shrubland through an analysis of a spatial dataset on shrub species and locations. In conjunction with appropriate null models, the ISAR blends species area relationships with second‐order spatial statistics to measure the expected species richness in local neighborhoods of variable size around the individuals of a focal species within a community. We found that, contrary to a previous analysis using more traditional methods, the community was well‐mixed with a typical shrub surrounded on average by 4.9 shrub neighbors of 2.1 species at a neighborhood scale of 1.0 m. We also found statistically significant fine‐scale variation in diversity patterns, such that neighborhoods of two species were more diverse than expected by a heterogeneous Poisson null model that accounted for larger‐scale habitat heterogeneity. However, this effect was caused by intraspecific aggregation of these species and was not due to positive interspecific association. Contrary to previous findings in other semi‐arid shrublands, our analysis suggests that the spatial pattern of the shrub community was not significantly structured by interspecific facilitation. This result supports growing evidence for balanced species patterns of adult plants in multispecies communities. Our approach may be used in other communities to describe complex multispecies spatial patterns, quantify species‐specific associations with diversity patterns, and to generate hypotheses regarding relationships between patterns and community‐structuring processes.