Habitat primary production and the evolution of body size within the hartebeest clade

Local adaptation is a key process in the evolution of biological diversity but relatively few studies have identified the selective forces that drive trait divergence at low taxonomic levels, particularly amongst mammals. Variation in body size across taxa is fundamental as shown by allometric relationships with numerous physiological, morphological and life-history traits. Differences in adult size across cohorts within populations of temperate ungulates are determined by variation in trophic resource availability during growth, suggesting that natural selection might promote the evolution of size divergence across sister taxa through local adaptation to variation in habitat productivity. We tested this hypothesis in the hartebeest ( Alcelaphu s sp.), an antelope lineage including eight extant (or recently extinct) allopatric subspecies that evolved within the last million years and colonized all the African savannahs. We predicted that body size across the subspecies should correlate positively with habitat productivity across taxon ranges. Mean body size of all the hartebeest taxa was quantified using skull length from museum specimens, and climatic variables were used as surrogates of habitat productivity. Body size across subspecies was positively correlated with rainfall, suggesting that variation in habitat primary production may drive morphological evolution between taxa. Focusing at a low taxonomic level has allowed us to identify a critical selective force that may shape divergence in body size, without the confounding effect of variation in trophic niche. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 431–440.     

Extreme variation in rates of evolution in the plastid Clp protease complex

Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi‐subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid‐encoded gene ( clpP1 ) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid‐encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns and RNA ‐editing sites) within seed plants. Although clpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus Silene , which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear‐encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino acid substitution rates in clpP1 and the nuclear‐encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.     

Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa

The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon‐primed intron‐crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate‐driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.     

Grasshopper community response to climatic change: variation along an elevational gradient

Background

The impacts of climate change on phenological responses of species and communities are well-documented; however, many such studies are correlational and so less effective at assessing the causal links between changes in climate and changes in phenology. Using grasshopper communities found along an elevational gradient, we present an ideal system along the Front Range of Colorado USA that provides a mechanistic link between climate and phenology.

Methodology/Principal Findings

This study utilizes past (1959–1960) and present (2006–2008) surveys of grasshopper communities and daily temperature records to quantify the relationship between amount and timing of warming across years and elevations, and grasshopper timing to adulthood. Grasshopper communities were surveyed at four sites, Chautauqua Mesa (1752 m), A1 (2195 m), B1 (2591 m), and C1 (3048 m), located in prairie, lower montane, upper montane, and subalpine life zones, respectively. Changes to earlier first appearance of adults depended on the degree to which a site warmed. The lowest site showed little warming and little phenological advancement. The next highest site (A1) warmed a small, but significant, amount and grasshopper species there showed inconsistent phenological advancements. The two highest sites warmed the most, and at these sites grasshoppers showed significant phenological advancements. At these sites, late-developing species showed the greatest advancements, a pattern that correlated with an increase in rate of late-season warming. The number of growing degree days (GDDs) associated with the time to adulthood for a species was unchanged across the past and present surveys, suggesting that phenological advancement depended on when a set number of GDDs is reached during a season.

Conclusions

Our analyses provide clear evidence that variation in amount and timing of warming over the growing season explains the vast majority of phenological variation in this system. Our results move past simple correlation and provide a stronger process-oriented and predictive framework for understanding community level phenological responses to climate change.     

Environmental variation and population responses to global change

Species' responses to environmental changes such as global warming are affected not only by trends in mean conditions, but also by natural and human‐induced environmental fluctuations. Methods are needed to predict how such environmental variation affects ecological and evolutionary processes, in order to design effective strategies to conserve biodiversity under global change. Here, we review recent theoretical and empirical studies to assess: (1) how populations respond to changes in environmental variance, and (2) how environmental variance affects population responses to changes in mean conditions. Contrary to frequent claims, empirical studies show that increases in environmental variance can increase as well as decrease long‐term population growth rates. Moreover, environmental variance can alter and even reverse the effects of changes in the mean environment, such that even if environmental variance remains constant, omitting it from population models compromises their ability to predict species' responses to changes in mean conditions. Drawing on theory relating these effects of environmental variance to the curvatures of population growth responses to the environment, we outline how species' traits such as phylogenetic history and body mass could be used to predict their responses to global change under future environmental variability.     

TPR重复和ELTR排型:重复的长度变化是一种功能进化的机制

TPR重复最初定义为一个34个氨基酸的蛋白结构重复。本文用PATTINPROT软件对基因库中TPR重复长度多样性进行了分析,发现40和42个氨基酸TPR重复大量存在。含40和42个氨基酸TPR重复序列蛋白的功能分析说明,这些长的TPR重复可以赋予蛋白新的功能。根据以上分析,提出重复序列的长度变化可能是功能进化的一种发生机制。     

The phylogeographic pattern of mitochondrial DNA variation in the Dall's porpoise Phocoenoides dalli

We used 11 restriction endonucleases to study mtDNA variation in 101 Dall's porpoises Phocoenoides dalli from the Bering Sea and western North Pacific. There was little phylogeographic patterning among the 34 mtDNA haplotypes identified in this analysis, suggesting a strong historical connection among populations across this region. Nonetheless, mtDNA variation does not appear to be randomly distributed in this species. Both G_ST and AMOVA uncovered significant differences in the distribution of mtDNA variation between the Bering Sea and western North Pacific populations. These mtDNA results, coupled with differences in allozyme variation and parasite infestation, support the demographic distinctiveness of Bering Sea and western North Pacific stocks of Dall's porpoise. The lack of a strong phylogeographic orientation of mtDNA haplotypes within the Dall's porpoise is similar to the pattern reported in other vertebrates such as coyotes, blackbirds, chickadees, marine catfish, and catadromous eels. Like Dall's porpoise, these species are broadly distributed, and have large populations linked by moderate to high levels of gene flow. However, the more complex, deeply branched phylogenetic network of mtDNA haplotypes within Dall's porpoise, relative to these other vertebrates, suggests important differences between these species in the forces shaping mtDNA variation. One such force is the effective size of female populations, which appears to have been comparatively large and stable in Dall's porpoise.     

Rates of projected climate change dramatically exceed past rates of climatic niche evolution among vertebrate species

A key question in predicting responses to anthropogenic climate change is: how quickly can species adapt to different climatic conditions? Here, we take a phylogenetic approach to this question. We use 17 time‐calibrated phylogenies representing the major tetrapod clades (amphibians, birds, crocodilians, mammals, squamates, turtles) and climatic data from distributions of > 500 extant species. We estimate rates of change based on differences in climatic variables between sister species and estimated times of their splitting. We compare these rates to predicted rates of climate change from 2000 to 2100. Our results are striking: matching projected changes for 2100 would require rates of niche evolution that are > 10 000 times faster than rates typically observed among species, for most variables and clades. Despite many caveats, our results suggest that adaptation to projected changes in the next 100 years would require rates that are largely unprecedented based on observed rates among vertebrate species.     

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision‐making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = ?0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.     

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation*

Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification among clades. However, why the climatic niche evolves more rapidly in some clades than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in available climatic niche space. Here, we explore the relationships among life-history variation, climatic niche breadth, and rates of climatic niche evolution. We reconstruct a phylogeny for the genus Desmognathus, an adaptive radiation of salamanders distributed across eastern North America, based on nuclear and mitochondrial genes. Using this phylogeny, we estimate rates of climatic niche evolution for species with long, short, and no aquatic larval stage. Rates of climatic niche evolution are unrelated to the mean climatic niche breadth of species with different life histories. Instead, we find that the evolution of a short larval period promotes greater exploration of climatic space, leading to increased rates of climatic niche evolution across species having this trait. We propose that morphological and physiological differences associated with variation in larval stage length underlie the heterogeneous ability of lineages to explore climatic niche space. Rapid rates of climatic niche evolution among species with short larval periods were an important dimension of the clade's adaptive radiation and likely contributed to the rapid rate of lineage accumulation following the evolution of an aquatic life history in this clade. Our results show how variation in a key life-history trait can constrain or promote divergence of the climatic niche, leading to variation in rates of climatic niche evolution among species.     

Patterns,trends, and rates of evolution within the Actinistia

Synopsis The interrelationships of 31 actinistian species (including Latimeria chalumnae) are analyzed based on a cladistic analysis of 75 osteological characters. Inference of evolutionary trends (e.g., modification of body shape and skull morphology) from the phylogenetic patterns demonstrates that the morphology of actinistians is less conservative than has been proposed previously. This empirical cladistic approach supports two distinct tempos of evolution during an evolutionary history of 380 million years. Along a phylogenetic pathway originating with a Devonian stem-species and ending with the living Latimeria chalumnae (including 101 morphological changes and 18 cladogenetic events), the first tempo occurred during the Devonian — Permian periods as a decreasing rate of morphological changes, which was followed by a stabilizing tempo during the Permian — Recent periods. The decreasing tempo is characterized by a sequence of gradual versus quantum temporal changes and low versus faster rates, whereas the stabilizing tempo primarily is gradual and low. In contrast to a common assumption, no significant correlation was found between the rates of morphological evolution and the temporal diversity of species.     

Conservation and variation of nucleotide sequences within related bacterial genomes: enterobacteria

We have assessed the degree of relatedness of several portions of the Escherichia coli genome to the corresponding portions of the genomes of representative enteric bacteria, using the Southern transfer and hybridization technique (E. Southern, J. Mol. Biol. 98:503-517, 1975). The degree of relatedness varied among the regions examined. Judging both by the relative amounts of deoxyribonucleic acid in the various enteric genomes that are highly homologous and by the conservation of positions of restriction enzyme cleavage sites in these regions, the enteric genomes have diverged to greater extents in some parts of the genomes than in others. Portions of the genomes (including the tnaA and thyA genes, the trp operon, and one other unassigned segment) appear to have evolved in concert with the genome as a whole. By contrast, the lacZ gene and portions of the genome that are homologous to phage lambda vary more widely, perhaps reflecting a separate evolutionary origin for these segments of deoxyribonucleic acid.     

Environmental gradients and grassland trait variation: Insight into the effects of climate change

The research aim was to understand how variation of temperature and water availability drives trait assemblage of seminatural grasslands in sub-Mediterranean climate, where climate change is expected to intensify summer aridity. In the central Italy, we recorded species abundance and elevation, slope aspect and angle in 129 plots. The traits we analysed were life span, growth form, clonality, belowground organs, leaf traits, plant height, seed mass, and palatability. We used Ellenberg's indicators as a proxy to assess air temperature and soil moisture gradients. From productive to harsh conditions, we observed a shift from tolerance to avoidance strategies, and a change in resource allocation strategies to face competition and stress or that maximize exploitation of patchily distributed soil resource niches. In addition, we found that the increase of temperature and water scarcity leads to the establishment of regeneration strategies that enable plants to cope with the unpredictability of changes in stress intensity and duration. Since the dry habitats of higher elevations are also constrained by winter cold stress, we argue that, within the sub-Mediterranean bioclimate, climate change will likely lead to a variation in dominance inside plant communities rather than a shift upwards of species ranges. At higher elevations, drought-adaptive traits might become more abundant on south-facing slopes that are less stressed by winter low temperatures; traits related to productive conditions and cold stress would be replaced on north-facing slopes by those adapted to overcome both the drought and the cold stresses.     

Environmental influences on the evolution of growth and developmental rates in passerines

Abstract.— The reasons why growth and developmental rates vary widely among species have remained unclear. Previous examinations of possible environmental influences on growth rates of birds yielded few correlations, leading to suggestions that young may be growing at maximum rates allowed within physiological constraints. However, estimations of growth rates can be confounded by variation in relative developmental stage at fledging. Here, we re-estimate growth rates to control for developmental stage. We used these data to examine the potential covariation of growth and development with environmental variation across a sample of 115 North American passerines. Contrary to previous results, we found that growth rates of altricial nestlings were strongly positively correlated to daily nest predation rates, even after controlling for adult body mass and phylogeny. In addition, nestlings of species under stronger predation pressure remained in the nest for a shorter period, and they left the nest at lower body mass relative to adult body mass. Thus, nestlings both grew faster and left the nest at an earlier developmental stage in species with higher risk of predation. Growth patterns were also related to food, clutch size, and latitude. These results support a view that growth and developmental rates of altricial nestlings are strongly influenced by the environmental conditions experienced by species, and they generally lend support to an adaptive view of interspecific variation in growth and developmental rates.     

Extensive mtDNA variation within the yellow-pine chipmunk,Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America

The yellow-pine chipmunk, Tamias amoenus, is common in xerophytic forests throughout much of northwest North America. We analyzed cytochrome b sequence variation from 155 individuals representing 57 localities across the distribution of T. amoenus including 10 additional species of Tamias. Maximum likelihood and parsimony tree estimation methods were used in conjunction with nested clade analysis to infer both deep and population-level processes. Our results indicate that two currently recognized subspecies of T. amoenus (T. a. canicaudus and T. a. cratericus) are not nested within other samples of T. amoenus. Maximum uncorrected levels of intraspecific sequence divergence within remaining samples of T. amoenus are >7%. Substantial geographic variation is characterized by 12 well-supported clades that correspond to distinct mountain ranges, but do not necessarily follow existing subspecific taxonomy. Significant association between geography and genealogy was detected within many of these clades and can be attributed to different population-level processes including past fragmentation, recent range expansion, and isolation by distance.