Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives

Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.     

Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota

Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.     

Reciprocal chromosome painting shows that genomic rearrangement between rat and mouse proceeds ten times faster than between humans and cats.

Reciprocal chromosome painting between mouse and rat using complete chromosome probe sets of both species permitted us to assign the chromosomal homology between these rodents. The comparative gene mapping data and chromosome painting have a better than 90% correspondence. The reciprocal painting results graphically show that mouse and rat have strikingly different karyotypes. At least 14 translocations have occurred in the 10-20 million years of evolution that separates these two species. The evolutionary rate of chromosome translocations between these two rodents appears to be up to 10 times greater than that found between humans and cats, or between humans and chimpanzees, where over the last 5-6 million years just one translocation has occurred. Outgroup comparison shows that the mouse genome has incorporated at least three times the amount of interchromosomal rearrangements compared to the rat genome. The utility of chromosome painting was also illustrated by the assignment of two new chromosome homologies between rat and mouse unsuspected by gene mapping: between mouse 11 and rat 20 and between mouse 17 and rat 6. We conclude that reciprocal chromosome painting is a powerful method, which can be used with confidence to chart the genome and predict the chromosome location of genes. Reciprocal painting combined with gene mapping data will allow the construction of large-scale comparative chromosome maps between placental mammals and perhaps other animals.     

Sex-linked mammalian sperm proteins evolve faster than autosomal ones

X-linked genes can evolve slower or faster depending on whether most recessive, or at least partially recessive alleles are deleterious or beneficial due to their hemizygous expression in males. Molecular studies of X chromosome divergence have provided conflicting evidence for both a higher and lower rate of nucleotide substitution at both synonymous and nonsynonymous sites, depending on the nucleotide sites sampled. Using human and mouse orthologous genes, we tested the hypothesis that genes encoding male-specific sperm proteins are evolving faster on the X chromosome compared with autosomes. X-linked sperm proteins have an average nonsynonymous mutation rate almost twice as high as sperm genes found on autosomes, unlike other tissue-specific genes, where no significant difference in the nonsynonymous mutation rate between the X chromosome and autosomes was found. However, no difference was found in the average synonymous mutation rate of X-linked versus autosomal sperm proteins, which along with corresponding higher values of Ka/Ks in X-linked sperm proteins suggest that differences in selective forces and not mutation rates are the underlying cause of higher X-linked mammalian sperm protein divergence.     

莱州湾鱼类群落优势种生态位

根据2011年5月、8月、10月和12月莱州湾底拖网调查资料,对该海域鱼类群落优势种的生态位进行了研究。结果表明,全年调查共捕获鱼类49种,各季节优势种种类数分别为春季3种,夏季5种,秋季3种,冬季4种。夏、冬季优势种的丛生指数较低,春、秋季较高;冬、春季优势种的平均拥挤度较低,夏、秋季较高。基于欧氏距离的优势种丰度聚类结果同优势度排序结果吻合。主成分分析(PCA)表明,青鳞小沙丁鱼(Sardinella zunasi)和赤鼻棱鳀(Thryssa kammalensis)分别是影响第一轴和第二轴的主要种类。绯鱼衔(Callionymus beniteguri)、鲬(Platycephalus indicus)、髭缟虾虎鱼(Tridentiger barbatus)和短吻红舌鳎(Cynoglossus joyneri)是时空二维生态位宽度最高的种类(2)。时空生态位显著重叠(0.6)的种类有7组,其中银姑鱼(Pennahia argentata)和皮氏叫姑鱼(Johnius belengerii)重叠值最高(0.798)。δ~(13)C值变幅(CR)最大的种类为斑鱼祭(Konosirus punctatus),δ~(15)N值变幅(NR)最大的种类为青鳞小沙丁鱼;青鳞小沙丁鱼和鱼祭生态位总面积超过20,皮氏叫姑鱼生态位总面积最小(1.38)且与其他优势种营养生态位重叠较高。等级聚类、排序、PCA和优势种排序结果较一致,而与时空生态位宽度分析结果差异较大,表明莱州湾鱼类群落结构受洄游鱼类的影响较大。时空生态位宽度较高的种类主要为集群特征不明显的周年定居种(绯鱼衔、鲬、短吻红舌鳎等底层鱼类),而季节洄游种(青鳞小沙丁鱼、鱼祭、赤鼻棱鳀等中上层鱼类)因时间生态位宽度较低导致时空生态位宽度较低。时空生态位和营养生态位分析表明,生态位重叠导致的资源利用性竞争并不是导致莱州湾鱼类群落结构现状的决定性因素,而更多可能是人为干扰形成的。     

Predicting species distribution: offering more than simple habitat models

In the last two decades, interest in species distribution models (SDMs) of plants and animals has grown dramatically. Recent advances in SDMs allow us to potentially forecast anthropogenic effects on patterns of biodiversity at different spatial scales. However, some limitations still preclude the use of SDMs in many theoretical and practical applications. Here, we provide an overview of recent advances in this field, discuss the ecological principles and assumptions underpinning SDMs, and highlight critical limitations and decisions inherent in the construction and evaluation of SDMs. Particular emphasis is given to the use of SDMs for the assessment of climate change impacts and conservation management issues. We suggest new avenues for incorporating species migration, population dynamics, biotic interactions and community ecology into SDMs at multiple spatial scales. Addressing all these issues requires a better integration of SDMs with ecological theory.     

The species chromatogram,a new graphical method to represent,characterize, and compare the ecological niches of different species

The ecological niche sensu Hutchinson is defined as the set of environmental conditions allowing a species to grow, maintain, and reproduce. This conception of the niche, which is assimilated to a p‐dimensional hypervolume, with p representing all environmental variables, has been widely applied in ecology. However, displaying the niche hypervolume has proved challenging when more than three environmental dimensions are considered simultaneously. We propose a simple method (implemented in the specieschrom R package) that displays the full multidimensionality of the ecological niche of a species into a two‐dimensional space by means of a graphic we call species chromatogram. This method gives a graphical summary of the niche by representing together abundance gradients with respect to all environmental variables. A chromatogram enables niche optimums and breaths to be rapidly quantified, and when several chromatograms are examined (one per species), rapid comparisons can be made. From our chromatograms, we proposed a procedure that quantifies niche optimum and breadth as well as niche overlapping (index D) and the identification of the most discriminant combination of environmental variables. We apply these analyses on eight planktonic species collected by the Continuous Plankton Recorder (CPR) survey in the North Atlantic Ocean using 10 environmental variables. We display their full multidimensional niches and quantify their niche optimums and breadths along each dimension. We also compare our index D with other indices by means of hypervolume and dynRB R packages. By catching the full complexity of the niche, species chromatograms allow many different niche properties to be rapidly assessed and compared among species from niche optimums and breadths to the identification of the most relevant environmental parameters and the degree of niche overlapping among species. Species chromatograms may be seen as species’ fingerprint and may also allow a better identification of the mechanisms involved in species assembly.     

Towards a trait-based quantification of species niche

Aims Although the niche concept is of prime importance in ecology, the quantification of plant species' niches remains difficult. Here we propose that plant functional traits, as determinants of species performance, may be useful tools for quantifying species niche parameters over environmental gradients.Important findings Under this framework, the mean trait values of a species determine its niche position along gradients, and intraspecific trait variability determines its niche breadth. This trait-based approach can provide an operational assessment of niche for a potentially large number of species, making it possible to understand and predict species niche shifts under environmental changes. We further advocate a promising method that recently appeared in the literature, which partitions trait diversity into among- and within-community components as a way to quantify the species niche in units of traits instead of environmental parameters. This approach allows the switch of the focus from ecological niches to trait niches, facilitating the examination of species coexistence along undefined environmental gradients. Altogether, the trait-based approach provides a promising toolkit for quantifying the species ecological niche and for understanding the evolution of species niche and traits.     

Haploids adapt faster than diploids across a range of environments

Despite a great deal of theoretical attention, we have limited empirical data about how ploidy influences the rate of adaptation. We evolved isogenic haploid and diploid populations of Saccharomyces cerevisiae for 200 generations in seven different environments. We measured the competitive fitness of all ancestral and evolved lines against a common competitor and find that in all seven environments, haploid lines adapted faster than diploids, significantly so in three environments. We apply theory that relates the rates of adaptation and measured effective population sizes to the properties of beneficial mutations. We obtained rough estimates of the average selection coefficients in haploids between 2% and 10% for these first selected mutations. Results were consistent with semi-dominant to dominant mutations in four environments and recessive to additive mutations in two other environments. These results are consistent with theory that predicts haploids should evolve faster than diploids at large population sizes.     

Specialists make faster decisions than generalists: experiments with aphids

Theoretical studies and a few recent experimental reports suggest that the evolution of diet breadth in herbivorous insects is constrained by a limited neural ability to efficiently process large amounts of information in short periods of time. This neural-constraints hypothesis predicts that generalist herbivores should make slower or poorer decisions than specialists when selecting plants, because generalists must discriminate and decide among stimuli from a wider variety of potential hosts. The present study compares the speed with which host-associated decisions are made in specialist versus generalist populations of the aphid Uroleucon ambrosiae. Populations of U. ambrosiae from eastern North America are highly specific to the host plant Ambrosia trifida (Asteraceae), whereas those from the American southwest also feed on a variety of other taxa from the Asteraceae. Experiments with winged (alate) and wingless (apterous) individuals showed that host-finding, host-selection, host-acceptance, host-sampling and host-settling were more efficiently performed by the eastern specialists. These very consistent results provide evidence that strongly supports the neural-constraints hypothesis.     

Tree species distribution in temperate forests is more influenced by soil than by climate

Knowledge of the ecological requirements determining tree species distributions is a precondition for sustainable forest management. At present, the abiotic requirements and the relative importance of the different abiotic factors are still unclear for many temperate tree species. We therefore investigated the relative importance of climatic and edaphic factors for the abundance of 12 temperate tree species along environmental gradients. Our investigations are based on data from 1,075 forest stands across Switzerland including the cold‐induced tree line of all studied species and the drought‐induced range boundaries of several species. Four climatic and four edaphic predictors represented the important growth factors temperature, water supply, nutrient availability, and soil aeration. The climatic predictors were derived from the meteorological network of MeteoSwiss, and the edaphic predictors were available from soil profiles. Species cover abundances were recorded in field surveys. The explanatory power of the predictors was assessed by variation partitioning analyses with generalized linear models. For six of the 12 species, edaphic predictors were more important than climatic predictors in shaping species distribution. Over all species, abundances depended mainly on nutrient availability, followed by temperature, water supply, and soil aeration. The often co‐occurring species responded similar to these growth factors. Drought turned out to be a determinant of the lower range boundary for some species. We conclude that over all 12 studied tree species, soil properties were more important than climate variables in shaping tree species distribution. The inclusion of appropriate soil variables in species distribution models allowed to better explain species' ecological niches. Moreover, our study revealed that the ecological requirements of tree species assessed in local field studies and in experiments are valid at larger scales across Switzerland.     

Complex relationships between species niches and environmental heterogeneity affect species co-occurrence patterns in modelled and real communities

Species co-occurrence analysis is commonly used to assess how interspecific interactions dictate community assembly. Non-random co-occurrences, however, may also emerge from niche differences as well as environmental heterogeneity. The relationships between species co-occurrence patterns, environmental heterogeneity and species niches are not fully understood, due to complex interactions among them. To analyse the relationships among these patterns and processes, I developed synthetic community models and analysed a large dataset of tree species across the conterminous United States. Niche overlap and environmental heterogeneity had significant and contrasting effects on species co-occurrence patterns, in both modelled and real communities. Niche breadth, in turn, affected the effect sizes of both variables on species co-occurrence patterns. The effect of niche breadth on the relationship between co-occurrence and niche overlap was markedly consistent between modelled and real communities, while its effect on the relationship between co-occurrence and environmental heterogeneity was mostly consistent between real and modelled data. The results of this analysis highlight the complex and interactive effects of species niche overlap, niche breadth and environmental heterogeneity on species co-occurrence patterns. Therefore, inferring ecological processes from co-occurrence patterns without accounting for these fundamental characteristics of species and environments may lead to biased conclusions.     

Litter dynamics recover faster than arthropod biodiversity during tropical forest succession

Litterfall and litter decomposition are key elements of nutrient cycling in tropical forests, a process in which decomposer communities such as macro-arthropods play a critical role. Understanding the rate and extent to which ecosystem function and biodiversity recover during succession is useful to managing the growing area of tropical successional forest globally. Using a replicated chronosequence of forest succession (5–15, 15–30, 30–45 years, and primary forest) on abandoned pastures in lowland tropical wet forest, we examined litterfall, litter chemistry, and effects of macro-arthropod exclusion on decomposition of two litter types (primary and 5- to 15-years-old secondary forest). Further, we assessed macro-arthropod diversity and community composition across the chronosequence. Overstory cover, litterfall, and litter nutrients reached levels similar to primary forest within 15–30 years. Young secondary forest litter (5–15 years) had lower initial N and P content, higher C:N, and decayed 60 percent faster than primary forest litter. The presence of macro-arthropods strongly mediated decomposition and nutrient release rates, increasing litter mass loss by 35–44 percent, N released by 53 percent, and P release by 84 percent. Forest age had no effect on soil nutrients, rates of litter decomposition, nutrient release, or macro-arthropod influence. In contrast, abundance and community composition of macro-arthropods remained significantly lower and distinct in all ages of secondary compared with primary forest. Order richness was lower in 5–15 years of secondary compared with primary forest. Our results suggest that in highly productive tropical wet forest, functional recovery of litter dynamics precedes recovery of decomposer community structure and biodiversity.     

Deletions in processed pseudogenes accumulate faster in rodents than in humans

Summary The relative rates of point nucleotide substitution and accumulation of gap events (deletions and insertions) were calculated for 22 human and 30 rodent processed pseudogenes. Deletion events not only outnumbered insertions (the ratio being 71 and 31 for human and rodent pseudogenes, respectively), but also the total length of deletions was greater than that of insertions. Compared with their functional homologs, human processed pseudogenes were found to be shorter by about 1.2%, and rodent pseudogenes by about 2.3%. DNA loss from processed pseudogenes through deletion is estimated to be at least seven times faster in rodents than in humans. In comparison with the rate of point substitutions, the abridgment of pseudogenes during evolutionary times is a slow process that probably does not retard the rate of growth of the genome due to the proliferation of processed pseudogenes.