Ecological determinants of mating system within and between three Fagus sylvatica populations along an elevational gradient

Studies addressing the variation of mating system between plant populations rarely account for the variability of these parameters between individuals within populations, although this variability is often non‐negligible. Here, we propose a new direct method based on paternity analyses (Mixed Effect Mating Model) to estimate individual migration (m_i) and selfing rates (s_i) together with the pollen dispersal kernel. Using this method and the KINDIST approach, we investigated the variation of mating system parameters within and between three populations of Fagus sylvatica along an elevational gradient. Among the mother trees, s_i varied from 0% to 48%, m_i varied from 12% to 86% and the effective number of pollen donors (Nep_i) varied from 2 to 364. The mating patterns differed along the gradient, the top population showing higher m and lower s, and a trend to higher Nep than the bottom populations. The phenological lag shaped long‐distance pollen flow both within population (by increasing m_i at mother‐tree level) and between populations (by increasing m at high elevation). Rather than the mate density, the canopy density was detected as a major mating system determinant within population; it acted as a barrier to pollen flow, decreasing the proportion of long‐distance pollen flow and increasing s_i. Overall, the effects of ecological factors on mating system were not the same within vs. between populations across the gradient, and these factors also differed from those traditionally found to shape variation at range‐wide scale, highlighting the interest of multiscale approaches.     

Forest aboveground biomass along an elevational transect in Sulawesi,Indonesia, and the role of Fagaceae in tropical montane rain forests

Aim This study investigates how estimated tree aboveground biomass (AGB) of tropical montane rain forests varies with elevation, and how this variation is related to elevational change in floristic composition, phylogenetic community structure and the biogeography of the dominant tree taxa. Location Lore Lindu National Park, Sulawesi, Indonesia. Methods Floristic inventories and stand structural analyses were conducted on 13 plots (each 0.24 ha) in four old‐growth forest stands at 1050, 1400, 1800 and 2400 m a.s.l. (submontane to upper montane elevations). Tree AGB estimates were based on d.b.h., height and wood specific gravity. Phylogenetic diversity and biogeographical patterns were analysed based on tree family composition weighted by AGB. Elevational trends in AGB were compared with other Southeast Asian and Neotropical transect studies (n = 7). Results AGB was invariant from sub‐ to mid‐montane elevation (309–301 Mg ha^?1) and increased slightly to 323 Mg ha^?1 at upper montane elevation. While tree and canopy height decreased, wood specific gravity increased. Magnoliids accounted for most of the AGB at submontane elevations, while eurosids I (including Fagaceae) contributed substantially to AGB at all elevations. Phylogenetic diversity was highest at upper montane elevations, with co‐dominance of tree ferns, Podocarpaceae, Trimeniaceae and asterids/euasterids II, and was lowest at lower/mid‐montane elevations, where Fagaceae contributed > 50% of AGB. Biogeographical patterns showed a progression from dominant tropical families at submontane to tropical Fagaceae (Castanopsis, Lithocarpus) at lower/mid‐montane, and to conifers and Australasian endemics at upper montane elevations. Cross‐continental comparisons revealed an elevational AGB decrease in transects with low/no presence of Fagaceae, but relatively high AGB in montane forests with moderate to high abundance of this family. Main conclusions AGB is determined by both changes in forest structure and shifts in species composition. In our study, these two factors traded off so that there was no net change in AGB, even though there were large changes in forest structure and composition along the elevational gradient. Southeast Asian montane rain forests dominated by Fagaceae constitute important carbon stocks. The importance of biogeography and species traits for biomass estimation should be considered by initiatives to reduce emissions from deforestation and forest degradation (REDD) and in taxon choice in reforestation for carbon offsetting.     

Variation in Drosophila melanogaster central metabolic genes appears driven by natural selection both within and between populations

In this report, we examine the hypothesis that the drivers of latitudinal selection observed in the eastern US Drosophila melanogaster populations are reiterated within seasons in a temperate orchard population in Pennsylvania, USA. Specifically, we ask whether alleles that are apparently favoured in northern populations are also favoured early in the spring, and decrease in frequency from the spring to autumn with the population expansion. We use SNP data collected for 46 metabolic genes and 128 SNPs representing the central metabolic pathway and examine for the aggregate SNP allele frequencies whether the association of allele change with latitude and that with increasing days of spring–autumn season are reversed. Testing by random permutation, we observe a highly significant negative correlation between these associations that is consistent with this expectation. This correlation is stronger when we confine our analysis to only those alleles that show significant latitudinal changes. This pattern is not caused by association with chromosomal inversions. When data are resampled using SNPs for amino acid change the relationship is not significant but is supported when SNPs associated with cis-expression are only considered. Our results suggest that climate factors driving latitudinal molecular variation in a metabolic pathway are related to those operating on a seasonal level within populations.     

Variation in floral scent composition within and between populations of Geonoma macrostachys (Arecaceae) in the western Amazon

In geonomoid palms floral scent is both an important pollinator attractant and an important factor in reproductive isolation. However, little is known about intraspecific variation in floral scent composition in these as well as in other plants. In this study the level of variation in floral scent composition found within and among five populations of Geonoma macrostachys var. macrostachys in the western Amazon is documented. Floral scent samples were collected using head-space adsorption and were analyzed by gas chromatography-mass spectrometry. Most of the 108 compounds recorded were of isoprenoid origin, but only 28 of the compounds were found in all 62 samples analyzed. No differentiation was found between the studied populations, confirming that G. macrostachys var. macrostachys is outbreeding and indicating that the individual populations are part of a metapopulation linked by sufficient gene flow to avoid local differentiation. However, a negative correlation between distance and similarity of floral scent chemistry indicates a case of clinal variation within the distribution area of G. macrostachys. Male euglossine bees are infrequent visitors to G. macrostachys, while other groups of insects are abundant. However, the level of variation and the chemical composition lend support to a suggested importance of male euglossine bees in long-distance pollen flow in G. macrostachys. Other insect groups are probably important in securing pollination of most flowers with pollen from nearby sources.     

Variation in scale numbers is consistent with ecologically based natural selection acting within and between lizard species

Recent studies have demonstrated that changes in scale number are correlated with ecological variables such as precipitation, and this suggests that scale number may be under selection to maintain water balance in reptiles. Here, we present new evidence that variation in scale numbers within and among species of Anolis lizards is under ecologically based natural selection. We measured scalation of the brown anole, Anolis sagrei, in two habitat types on each of five islands in the Bahamas. We also measured scalation for 12 species of anole representing six different ecomorphs from the Greater Antilles. Within populations of A. sagrei, scale numbers increased with increasing precipitation and with decreasing temperature in open arid habitats. Variation measured among species of Anolis from the Greater Antilles showed similar patterns with temperature, precipitation, and elevation. Independent contrasts using scale count data indicated that variation in scale number was congruent within and between species, even after accounting for the influence of phylogeny. We measured natural selection (survival to maturity) on scale number in A. sagrei over two different habitat types in the Bahamas. Patterns of natural selection were congruent with the correlational results described. Finally, results from a breeding experiment in the laboratory provide preliminary evidence that variation in scale number is heritable, and suggests a mechanism for generating these correlations. Our results provide new evidence that the diversification of anoles has been shaped by natural selection and that ecologically based selection pressures help explain diversification at both the population and species levels. Co-ordinating editor: M. Klaassen     

Unique elevational diversity patterns of geometrid moths in an Andean montane rainforest

Alpha‐diversity of geometrid moths was investigated along an elevational gradient in a tropical montane rainforest in southern Ecuador. Diversity was measured using 1) species number, 2) extrapolated species number (Chao 1 estimator), 3) rarefied species number, and 4) Fisher's alpha. When applied to the empirical data set, 1 and 2 strongly depended on the sample size, whereas 3 and 4 were suitable and reliable measures of local diversity. At single sites, up to 292 species were observed, and extrapolation estimates range from 244 to 445 species. Values for Fisher's alpha are among the highest ever measured for this moth family, and range from 69 to 131 per site. In contrast to theoretical assumptions and empirical studies in other regions of the world, the diversity of geometrid moths remained consistently high along the entire gradient studied. Diversity measures correlated with neither altitude nor ambient temperature. The large subfamily Ennominae has previously been assumed to be a group that occurs mainly at low and medium elevations. However, no decline in diversity was found in the study area. The diversity of the other large subfamily, Larentiinae, even increased from the lowest elevations and was highest at elevations above 1800 m. The roles of a decreasing diversity of potential host‐plants, decreasing structural complexity of the vegetation, increasingly unfavourable climatic conditions and possible physiological adaptations in determining herbivore species richness are discussed. A relatively low predation pressure might be an advantage of high‐altitude habitats. The physiognomy of the Andes (folded mountains, large areas at high altitudes) might also have allowed speciation events and the development of a species‐rich high‐altitude fauna. There is evidence that the species‐richness of other groups of herbivorous insects in the same area declines as altitude increases. This emphasises difficulties that are associated with biodiversity indicator groups, and calls for caution when making generalisations from case studies.     

Fern endemism and its correlates: contribution from an elevational transect in Costa Rica

We studied the distribution patterns of endemic ferns along an elevational gradient of 3400 m in Costa Rica, Central America. We related the endemism patterns of the whole species set and separated for life forms and microhabitats according to topography and environmental factors. Fern species were surveyed in 156 plots each with an area of 400 m², with up to five plots at every elevational step of 100 m. Global range size for every species was compiled from literature data, and species restricted to the mountain range from Costa Rica and adjacent western Panama were defined as endemic (24.5% of all species recorded). We found patterns of endemism rates mostly peaking at mid-elevation, but when separated for different life forms and microhabitats, some deviations from the overall pattern emerged. High constant humidity and reduced surface area were closely related to high levels of endemism. High humidity is discussed as a general predictor for high endemism rates in concert with highest overall richness. Restricted area of elevational belts, indicating a fragmented habitat, leads to a higher degree of population isolation and thus species differentiation. However, both interpretations were not fully supported by our data. Most importantly, endemism rates were fairly low on mountain tops that have the smallest available area in a topographically highly fragmented setting. In contrast, endemic species were more common than widespread species at the highest elevations. History and climatic shifts are assumed to play a role in this respect.     

Variation of body size within and between wild populations of Drosophila buzzatii

Four populations of the cactophilous species D. buzzatii have been compared with respect to the phenotypic variation of thorax and wing length of wild versus laboratory reared flies. Three of the strains were intercrossed to provide parent, F₁ and F₂ comparisons as a test of co-adaptation. The genetic contribution to phenotypic variation of laboratory reared flies was estimated from the correlation between sibs derived from random pair mating and reared individually in separate cultures. The average natural temperature during development was estimated from the relations between the wing/thorax ratio and temperature in laboratory tests.The variance of thorax and wing length of wild flies was several times greater than that of laboratory reared flies and the increase was attributed primarily to variation in larval food supply although temperature fluctuation is also important. There was no evidence of heterosis or F₂ break-down in the crosses. For two of the populations the heritability of thorax length was high, 60–70%, and substantially lower for the third. The average temperature estimated from the wing/thorax/temperature relationship differed between sites. The reduction of body size below the potential maximum averaged 30% for two and 20% for the other population, with a wide spread about these values. The evidence is discussed in relation to assessing the nature of ecological variation by comparing the variation of morphological traits in wild and laboratory reared flies.     

Onward but not always upward: individualistic elevational shifts of tree species in subtropical montane forests

Ongoing global climate change is driving widespread shifts in species distributions. Trends show frequent upwards shifts of treelines, but information on changes in montane forest below the treeline and in the tropics and subtropics is limited, despite the importance of these areas for biodiversity and ecosystem function. Patterns of species shifts in tropical and subtropical regions are likely to be more complex and individualistic than global averages suggest due to high species diversity and strong influence of competition, alongside direct climatic limitations on distributions. To address the question of how subtropical montane tree species are likely to move as climate changes, we used an extensive national forest inventory to estimate distribution shifts of 75 tree species in Taiwan by comparing the optimum elevation and range edges of adults and juveniles within species. Overall there was a significant difference in optimum elevation of adults and juveniles. Life stage mismatches suggested upward shifts in 35% of species but downward shifts of over half (56%), while 8% appeared stable. Upward elevation shifts were disproportionately common in high elevation species, whilst mid to low elevation species suggested greater variation in shift direction. Whilst previous research on mountain forest range shifts has been dominated by work addressing changes in treeline position, we show that although high elevation species shift up, below the treeline species may shift individualistically, heralding widespread changes in forest communities over coming decades. The wide variation of responses indicated is likely driven by individual species responses to interacting environmental factors such as competition, topography and anthropogenic influences across the broad range of forest types investigated. As global environmental changes continue, more detailed understanding of tree range shifts across a wide spectrum of forests will allow us to prepare for the implications of such changes for biodiversity, ecosystem function and dependent human populations.     

Variation in pika (Ochotona collaris,O. princeps) vocalizations within and between populations

Understanding geographic call variation can resolve evolutionary and behavioural questions, yet the factors influencing divergent acoustic signals remain poorly understood in mammals. We explored call variation between collared pikas in Yukon and Alaska and American pikas in Alberta, and between individuals within a population of collared pikas. Classification trees were used to determine the extent of call divergence between populations and the elements of calls driving these differences. Pika populations had significant differences in call structure, and individual pikas were classified to their correct populations with up to 94% accuracy. To investigate possible mechanisms responsible for interspecific variability, we tested the acoustic adaptation hypothesis by using a playback experiment to explore whether American and collared pika calls transmit with less degradation across their own species' habitat than the habitat of their congener. We found no support for the acoustic adaptation hypothesis. Geographic call variation in these two species of pikas likely reflects genetic divergence, and may be a result of separate evolutionary histories. We calculated the potential for individual coding for both time and frequency measurements of calls. High frequency harmonics showed greater between‐ than within‐individual variation, and may act as sources of information regarding individual identity.     

Genomic signatures reveal selection of characteristics within and between Meishan pig populations

The Chinese Meishan pig breed is well known for its high prolificacy. Moreover, this breed can be divided into three types based on their body size: big Meishan, middle Meishan (MMS) and small Meishan (SMS) pigs. Few studies have reported on the genetic signatures of Meishan pigs, particularly on a genome‐wide scale. Exploring for genetic signatures could be quite valuable for revealing the genetic architecture of phenotypic variation. Thus, we performed research in two parts based on the genome reducing and sequencing data of 143 Meishan pigs (74 MMS pigs, 69 SMS pigs). First, we detected the selection signatures among all Meishan pigs studied using the relative extended haplotype homozygosity test. Second, we detected the selection signatures between MMS and SMS pigs using the cross‐population extended haplotype homozygosity and F_ST methods. A total of 111 398 SNPs were identified from the sequenced genomes. In the population analysis, the most significant genes were associated with the mental development (RGMA), reproduction (HDAC4, FOXL2) and lipid metabolism (ACACB). From the cross‐population analysis, we detected genes related to body weight (SPDEF, PACSIN1) in both methods. We suggest that rs341373351, located within the PACSIN1 gene, might be the causal variant. This study may have achieved consistency between selection signatures and characteristics within and between Meishan pig populations. These findings can provide insight into investigating the molecular background of high prolificacy and body size in pig.     

Variations in the reproductive cycle of Bornean montane tree species along elevational gradients on ultrabasic and non-ultrabasic soils

Although lowland tree species in the ever-wet regions of Southeast Asia are characterized by the supra-annual cycle of reproduction, the reproductive phenology of montane tree species remains poorly understood. In this study, we investigated the reproductive phenology of montane tree species using litter samples that were collected every 2 weeks from six rainforest sites, consisting of three elevations (1700, 2700, and 3100 m), on Mount Kinabalu, Borneo. At each elevation, one site was on infertile ultrabasic soil and one was on relatively fertile non-ultrabasic soil. We used a composite sample from 10 or 20 litter traps per site and sorted it by species. Therefore, the obtained data captured reproductive phenology in the population of each species rather than in an individual tree. Ten-year time series of flower and fruit litterfall were obtained for 30 and 39 tree species, respectively. Fourier analysis was used to identify the dominant cycle of each time series. The most abundant cycle across species was supra-annual, followed by sub-annual, and annual cycles. Many species at higher elevations showed supra-annual cycles of flower litterfall, whereas species in the 1700 m sites often showed annual or sub-annual cycles regardless of soil types. No systematic differences were found among sites for fruit litterfall. Mechanisms underlying these elevational patterns in reproductive cycle remain unclear but may include more severe El Niño droughts, lower primary productivity, lower soil fertility, and the absence of some sub-annually or annually reproducing families at higher elevations.     

Diversity within and between populations of two sympatrically distributed Hordeum species in Jordan

Summary The diversity of two sympatrically distributed barley species (Hordeum vulgare L. and Hordeum spontaneum C. Koch.) has been assessed for 7 morphometric and 13 qualitative traits. Phenotypically, Hordeum vulgare was more stable than Hordeum spontaneum for all morphometric traits; this is a reflection of domestication and selection. The overall diversity indexes were 0.546±0.125 and 0.502±0.113 for Hordeum vulgare and Hordeum spontaneum, respectively (P=0.095). However, Hordeum spontaneum expressed a higher level of diversity for most qualitative traits. The observed similarity for a number of diversity indexes is probably due to gene flow between the two species.     

Genomic selection accuracies within and between environments and small breeding groups in white spruce

Background

Genomic selection (GS) may improve selection response over conventional pedigree-based selection if markers capture more detailed information than pedigrees in recently domesticated tree species and/or make it more cost effective. Genomic prediction accuracies using 1748 trees and 6932 SNPs representative of as many distinct gene loci were determined for growth and wood traits in white spruce, within and between environments and breeding groups (BG), each with an effective size of N_e ≈ 20. Marker subsets were also tested.

Results

Model fits and/or cross-validation (CV) prediction accuracies for ridge regression (RR) and the least absolute shrinkage and selection operator models approached those of pedigree-based models. With strong relatedness between CV sets, prediction accuracies for RR within environment and BG were high for wood (r = 0.71–0.79) and moderately high for growth (r = 0.52–0.69) traits, in line with trends in heritabilities. For both classes of traits, these accuracies achieved between 83% and 92% of those obtained with phenotypes and pedigree information. Prediction into untested environments remained moderately high for wood (r ≥ 0.61) but dropped significantly for growth (r ≥ 0.24) traits, emphasizing the need to phenotype in all test environments and model genotype-by-environment interactions for growth traits. Removing relatedness between CV sets sharply decreased prediction accuracies for all traits and subpopulations, falling near zero between BGs with no known shared ancestry. For marker subsets, similar patterns were observed but with lower prediction accuracies.

Conclusions

Given the need for high relatedness between CV sets to obtain good prediction accuracies, we recommend to build GS models for prediction within the same breeding population only. Breeding groups could be merged to build genomic prediction models as long as the total effective population size does not exceed 50 individuals in order to obtain high prediction accuracy such as that obtained in the present study. A number of markers limited to a few hundred would not negatively impact prediction accuracies, but these could decrease more rapidly over generations. The most promising short-term approach for genomic selection would likely be the selection of superior individuals within large full-sib families vegetatively propagated to implement multiclonal forestry.     

Variation in O-antigens, niche-specific selection and bacterial populations

Bacterial populations usually consist of distinct clones, often apparently adapted to specific niches. A formal model is developed whereby niche-specific selection maintains the polymorphisms involved in clonal adaptation. Infrequent transfer of non-adaptive alleles to a clone is balanced by the selection for the resident adaptive allele. The model can account for the extensive polymorphism in surface antigens observed in bacteria, and also for the existence of sympatric clones of pathogenic species which differ in host range and/or mode of pathogenesis. Niche-specific selection combined with low levels of genetic transfer can also account for the high level of neutral variation in bacteria, and indirectly for their ability to respond rapidly to environmental changes.     

Variation within and between white clover varieties in their preference for strains of Rhizobium trifolii

Variation within as well as between varieties of white clover (Trifolium repens L.) in their selection or preference for rhizobial strains in nodulation was studied using antibiotic-resistant mutant strains of Rhizobium trifolii. Significant differences between varieties were found. Cv. S100 was nodulated almost exclusively by 75 str but there was more variation within S184 and, in particular, Pajbjerg smalbladet. In this experiment 93% of the total variance was genotypic, of which 68% was due to the difference between varieties and 25% due to variance between genotypes within varieties. Significant correlations were found between the preference for rhizobial strains of plants grown from seeds and of stolon lines vegetatively propagated from the former plants, indicating that the preference for rhizobial strains is genetically controlled by the host. A considerable drift in preference towards selection of more compatible rhizobial strains by the clonally propagated stolons compared with the original white clover plants was observed. The results are discussed from the point of view of improving symbiotic nitrogen fixation by combining highly effective and competitive Rhizobium strains with a host variety with uniform preference for those strains.