Influence of life-history variation on the genetic structure of two sympatric salamander taxa

Life-history characteristics are an important determinant of a species' dispersal abilities. We predict that variation in life history can influence population-level genetic patterns. To test this prediction, we estimate population-level genetic structure for two sympatric species of stream-breeding salamander. The Cope's giant salamander ( Dicamptodon copei ) rarely metamorphoses into a terrestrial adult, thereby limiting overland dispersal and potentially gene flow. In contrast, the Pacific giant salamander ( D. tenebrosus ) commonly metamorphoses, which is expected to facilitate overland dispersal and gene flow. Three sets of analyses based on microsatellite data support these hypotheses, showing that D . tenebrosus displays minimal population-level genetic structuring and no pattern of isolation by distance, whereas D . copei displays a high degree of population-level genetic structure and significant isolation by distance. Specifically, nearly all pairwise F _ST values were significantly different from 0 between populations of D. copei , with fewer than half the pairwise F _ST values significant from 0 in D. tenebrosus . Additionally, S tructure analyses indicated eight genetic clusters for D. copei but only one genetic cluster for D. tenebrosus . Finally, Mantel tests showed significant correlations between stream and overland distance with genetic distance for D. copei but no significant correlations of either landscape feature for D. tenebrosus at the scale of the study. These results provide a case study of the link between life-history variation and population genetic patterns while controlling for phylogeny and environmental variation.     

Stochastic population dynamics and life-history variation in marine fish species

Abstract We examined whether differences in life-history characteristics can explain interspecific variation in stochastic population dynamics in nine marine fish species living in the Barents Sea system. After observation errors in population estimates were accounted for, temporal variability in natural mortality rate, annual recruitment, and population growth rate was negatively related to generation time. Mean natural mortality rate, annual recruitment, and population growth rate were lower in long-lived species than in short-lived species. Thus, important species-specific characteristics of the population dynamics were related to the species position along the slow-fast continuum of life-history variation. These relationships were further associated with interspecific differences in ecology: species at the fast end were mainly pelagic, with short generation times and high natural mortality, annual recruitment, and population growth rates, and also showed high temporal variability in those demographic traits. In contrast, species at the slow end were long-lived, deepwater species with low rates and reduced temporal variability in the same demographic traits. These interspecific relationships show that the life-history characteristics of a species can predict basic features of interspecific variation in population dynamical characteristics of marine fish, which should have implications for the choice of harvest strategy to facilitate sustainable yields.     

Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom

A common pattern found in phylogeny-based empirical studies of diversification is a decrease in the rate of lineage accumulation toward the present. This early-burst pattern of cladogenesis is often interpreted as a signal of adaptive radiation or density-dependent processes of diversification. However, incomplete taxonomic sampling is also known to artifactually produce patterns of rapid initial diversification. The Monte Carlo constant rates (MCCR) test, based upon Pybus and Harvey's gamma (γ)-statistic, is commonly used to accommodate incomplete sampling, but this test assumes that missing taxa have been randomly pruned from the phylogeny. Here we use simulations to show that preferentially sampling disparate lineages within a clade can produce severely inflated type-I error rates of the MCCR test, especially when taxon sampling drops below 75%. We first propose two corrections for the standard MCCR test, the proportionally deeper splits that assumes missing taxa are more likely to be recently diverged, and the deepest splits only MCCR that assumes that all missing taxa are the youngest lineages in the clade, and assess their statistical properties. We then extend these two tests into a generalized form that allows the degree of nonrandom sampling (NRS)to be controlled by a scaling parameter, α. This generalized test is then applied to two recent studies. This new test allows systematists to account for nonrandom taxonomic sampling when assessing temporal patterns of lineage diversification in empirical trees. Given the dramatic affect NRS can have on the behavior of the MCCR test, we argue that evaluating the sensitivity of this test to NRS should become the norm when investigating patterns of cladogenesis in incompletely sampled phylogenies.     

Evolutionary rates for multivariate traits: the role of selection and genetic variation

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders'' equation (), which predicts evolutionary change for a suite of phenotypic traits () as a product of directional selection acting on them (β) and the genetic variance–covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.     

Early life-history dynamics of Caribbean coral species on artificial substratum: the importance of competition, growth and variation in life-history strategy

The development of a coral community was monitored for 6 years (1998–2004) on 46 m² of artificial settlement substrate in Curaçao, Netherlands Antilles. Growth and survival of recruits (n=1385) belonging to 16 different species were quantified in relation to characteristics of the benthic community developing around them. The early life history dynamics (i.e. growth rate, growth strategy and survival) of corals differed among species although these differences were small for species occupying similar habitats (i.e. underside versus topside of substratum). In contrast to recruit survival, juvenile growth rates were highly variable and unrelated to benthic community structure, at least at the scale of this study. Competing benthic organisms affected coral recruitment success through space preemption (mainly by macroalgae) or recruit overgrowth (mainly by sponges). The results highlight the small spatial scale (mm–cm) at which the processes responsible for recruitment success or failure occur and emphasize the need to include such small-scale observations in studies of coral early life-phase dynamics.     

To compete or defend: linking functional trait variation with life-history tradeoffs in a foundation tree species

Oecologia - Although chemical deterrents to herbivory often exact costs in terms of plant growth, the manner in which those costs arise, and their physiological relationship to other functional...     

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.     

Latitudinal variation of life-history traits of an exotic and a native impatiens species in Europe

Understanding the responses of invasive and native populations to environmental change is crucial for reliable predictions of invasions in the face of global change. While comparisons of responses across invasive species with different life histories have been performed before, comparing functional traits of congeneric native and invasive species may help to reveal driving factors associated with invasion. Here we compared morphological functional trait patterns of an invasive species (Impatiens parviflora) with its congeneric native species (I. noli-tangere) along an approximately 1600 km European latitudinal gradient from France (49°34′N) to Norway (63°40′N). Soil nitrogen was recorded during six weeks of the growing season, and light, soil moisture, and nutrient availability were estimated for each sampled population using community weighted means of indicator values for co-occurring species. Temperature data were gathered from nearby weather stations.Both the native and invasive species are taller at higher latitudes and this response is strongest in the invasive species. Seed mass and number of seeds per capsule increase in I. noli-tangere but decrease in I. parviflora towards higher latitudes. Surprisingly, plant height in the invasive I. parviflora decreases with increasing soil nitrogen availability. The latitudinal pattern in seed mass is positively related to temperature in I. noli-tangere and negatively in I. parviflora. Leaf area of both species decreases with increasing Ellenberg indicator values for nitrogen and light but increases with increasing soil moisture. Soil nitrogen concentrations and Ellenberg indicator values for nitrogen have significant positive (I. noli-tangere) and negative (I. parviflora) effects on the number of seeds per capsule. Our results show that the native I. noli-tangere has efficient reproduction at its range edge while the invasive I. parviflora shows a marked decrease in seed size and seed number per capsule. These patterns are unrelated to the growth and obtained size of the plants: even low soil nitrogen availability in the north seemed not to limit plant growth and size. Our results suggest that the invasive I. parviflora tends to become more invasive at lower latitudes by producing heavier seeds and more seeds per capsule.     

Phylogenetic evidence for pollinator-driven diversification of angiosperms

Since Darwin, the diversity of flowers has been attributed to selection by pollinators. Although pollinators commonly act as selective agents on floral traits, determining the extent to which they have influenced angiosperm diversification requires a historical perspective. Here we review recent studies that combine species-level phylogenies with pollinator data and show that pollinator shifts are common, being associated with at least a quarter of documented divergence events. However, shift frequency and directionality vary extensively, owing to variation in intrinsic factors such as floral features and phylogenetic history, as well as extrinsic factors such as interactions with local pollinator assemblages. Despite technical advances, phylogenies remain limited in their power to distinguish among various pollinator-driven evolutionary processes.     

SYMMETREE: whole-tree analysis of differential diversification rates

SymmeTREE implements several tests of differential diversification rates that exploit information on the topological distribution of species diversity throughout entire trees to address two general questions: (1) Has a given tree experienced significant variation in diversification rates among its branches? and (2) If so, along which branches have significant shifts in diversification rate occurred? These explicitly model-based methods are robust to uncertainty in estimates of branch length/duration and can accommodate incompletely resolved trees and other forms of phylogenetic uncertainty. AVAILABILITY: http://www.phylodiversity.net/bmoore/software.html CONTACT: brian.moore@yale.edu.     

Craniofacial variation in Homo habilis: an analysis of the evidence for multiple species

The question of heterogeneity in the Homo habilis sample continues to be controversial. Various lines of evidence have been used to reject the null hypothesis of intraspecific variation. This evidence derives from analyses of endocranial volume variation, probability estimates of sexual dimorphism, facial variation, cranial angles, CV analysis of craniofacial variation, the multivariate pattern of sexual dimorphism, the pattern of variability (CV) profiles, distance data using exact randomization methods, and various kinds of quantitative ordinations of fossils. Although consensus is lacking as to how the H. habilis sample is to be split, there is a growing perception that the degree of variation among the fossils is too great and the pattern of variation is too different to be explained by intraspecific variation. This has resulted in the recognition of new species such as "Homo rudolfensis." The present study critically examines the evidence commonly cited as the basis for recognizing multiple species in the extended H. habilis hypodigm. Reanalysis and reinterpretation of these data indicates that: (1) the degree of variation in the H. habilis sample is typical of modern hominoids, and (2) the pattern of variation among specimens of the H. habilis sample is consistent with intraspecific variation. Thus, at present, there is no sound basis to reject the null hypothesis of intraspecific variation as an adequate explanation of the morphological variation seen among specimens of the extended H. habilis sample. If multiple species are indeed represented, then their presence has not yet been satisfactorily demonstrated.     

Energy budgets, growth rates, and thermal constraints: toward an integrative approach to the study of life-history variation

Variation in thermal constraints on activity has been hypothesized to be an important ecological source of geographic variation in growth rates of juvenile eastern fence lizards Sceloporus undulatus. However, most of the evidence to support this hypothesis is either inferential or indirect. In this study, I quantitatively compared thermal constraints on activity and their relationship to growth rates of free-ranging juvenile fence lizards from two extremes of the range of variation in growth rate (Nebraska and New Jersey) used in a reciprocal transplant experiment. I also examined energy allocation made to growth and storage by yearling lizards. Reduced growth rates in New Jersey of normally fast-growing hatchlings from Nebraska were associated with a more stringent thermal constraint on activity corresponding to a 2-3-h shorter predicted daily activity period in New Jersey compared to Nebraska. The thermal constraint on activity was particularly strong (24% less time available in New Jersey compared to Nebraska) during the period when hatchling lizards emerge (August-October). An 8% reduction in total activity time available over the course of a single year was associated with a 7% reduction in the total amount of energy accumulated by lizards in New Jersey. Differences in the total amount of energy available for allocation were also accompanied by differences in how energy was allocated. Lizards from New Jersey had an allocatable energy pool of approximately 40.34 kJ (88% to growth, 12% to storage, and 0% to reproduction). Lizards from Nebraska had an allocatable pool of 43.44 kJ (22% to growth, 18% to storage, and 60% to reproduction). This study joins others in advocating and illustrating an integrative approach to determining the causes and consequences of life-history variation by combining experimental, comparative, and phylogenetic methods in a single system.     

Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates.

This report describes the sequencing in the Escherichia coli B genome of 36 randomly chosen regions that are present in most or all of the fully sequenced E. coli genomes. The phylogenetic relationships among E. coli strains were examined, and evidence for the horizontal gene transfer and variation in mutation rates was determined. The overall phylogenetic tree indicated that E. coli B and K-12 are the most closely related strains, with E. coli O157:H7 being more distantly related, Shigella flexneri 2a even more, and E. coli CFT073 the most distant strain. Within the B, K-12, and O157:H7 clusters, several regions supported alternative topologies. While horizontal transfer may explain these phylogenetic incongruities, faster evolution at synonymous sites along the O157:H7 lineage was also identified. Further interpretation of these results is confounded by an association among genes showing more rapid evolution and results supporting horizontal transfer. Using genes supporting the B and K-12 clusters, an estimate of the genomic mutation rate from a long-term experiment with E. coli B, and an estimate of 200 generations per year, it was estimated that B and K-12 diverged several hundred thousand years ago, while O157:H7 split off from their common ancestor about 1.5-2 million years ago.     

Complex selection on life-history traits and the maintenance of variation in exaggerated rostrum length in acorn weevils

Trophic interactions can trigger the development of exaggerated specialized characters and promote morphological diversification. For example, acorn weevils (genus Curculio) present strikingly long rostrums, which are used by females to perforate oviposition holes through the seed coat. Species exhibiting longer rostrums are known to exploit larger acorns, and therefore rostrum length is thought to be subject to selection to match the preferred acorn type. However, rostrum length is strongly correlated with body size, and morphological divergence could result from either selection on rostrum length for optimal food exploitation or from other pressures acting on body size. We collected infested acorns at oak forests where the large Curculio elephas and the small-bodied Curculio glandium co-occur. There were no interspecific differences in adult female body size to rostrum length allometric relationships, and rostrum length is equally correlated with body size in either species. MtDNA-based species identification showed that C. glandium larvae were present within acorns of all sizes, whereas C. elephas larvae were restricted to acorns above a minimum size, irrespective of oak species. Hence, exploitation of large acorns can hardly have triggered rostrum enlargement, as the small sized C. glandium adults (with short rostrums) could perforate and oviposit in both small and large acorns. Rather, increased rostrum length is probably a by-product of the larger body sizes of individuals emerging from bigger acorns, which allow increased larval size and enhance larval survival likelihood. Summarizing, when exaggerated feeding traits co-vary with other body features, interspecific morphological variability may result from contrasting selective pressures acting on these correlated characters.     

Population and life-history consequences of within-cohort individual variation

The consequences of within-cohort (i.e., among-individual) variation for population dynamics are poorly understood, in particular for the case where life history is density dependent. We develop a physiologically structured population model that incorporates individual variation among and within cohorts and allows us to explore the intertwined relationship between individual life history and population dynamics. Our model is parameterized for the lizard Zootoca vivipara and reproduces well the species' dynamics and life history. We explore two common mechanisms that generate within-cohort variation: variability in food intake and variability in birth date. Predicted population dynamics are inherently very stable and do not qualitatively change when either of these sources of individual variation is introduced. However, increased within-cohort variation in food intake leads to changes in morphology, with longer but skinnier individuals, even though mean food intake does not change. Morphological changes result from a seemingly universal nonlinear relationship between growth and resource availability but may become apparent only in environments with strongly fluctuating resources. Overall, our results highlight the importance of using a mechanistic framework to gain insights into how different sources of intraspecific variability translate into life-history and population-dynamic changes.     

Parasites and host life-history traits: implications for community ecology and species co-existence

Most of the evidence for a key role of parasites in structuring communities is based on the idea of a differential susceptibility of host species to infection and its consequences. Recent advances in community ecology suggest that life-history traits of free-living species can be an important determinant of their co-existence within communities. On the other hand, parasites have the potential to indirectly alter the life-history traits of their hosts, such as developmental time or dispersal. We discuss the idea that these indirect effects could influence the structure of free-living and parasite communities. We explore this idea in relation to related concepts including 'parasitic arbitration' and engineering processes.     

Sequence variation in human succinate dehydrogenase genes: evidence for long-term balancing selection on SDHA

Background  

Balancing selection operating for long evolutionary periods at a locus is characterized by the maintenance of distinct alleles because of a heterozygote or rare-allele advantage. The loci under balancing selection are distinguished by their unusually high polymorphism levels. In this report, we provide statistical and comparative genetic evidence suggesting that the SDHA gene is under long-term balancing selection. SDHA encodes the major catalytical subunit (flavoprotein, Fp) of the succinate dehydrogenase enzyme complex (SDH; mitochondrial complex II). The inhibition of Fp by homozygous SDHA mutations or by 3-nitropropionic acid poisoning causes central nervous system pathologies. In contrast, heterozygous mutations in SDHB, SDHC, and SDHD, the other SDH subunit genes, cause hereditary paraganglioma (PGL) tumors, which show constitutive activation of pathways induced by oxygen deprivation (hypoxia).     

Clonal variation in life-history traits and feeding rates in the gastropod, Potamopyrgus antipodarum: performance across a salinity gradient

1. Parthenogenetic species are often geographically more widely distributed than their sexual relatives. This success in colonizing can be explained either by dispersal of one or a few clones of wide physiological tolerance or by the distribution of many locally adapted clones.
2. Here we compare the influence of salinity on reproductive output, feeding rate, growth rate and size at birth between two genotypes of Potamopyrgus antipodarum to address the questions (i) Do these traits vary in response to changing salinity? (ii) Does the response to a salinity gradient differ between genotypes? (iii) Can the patterns of variation, in relation to salinity, contribute to explaining the geographical distribution of P. antipodarum in Europe?
3. Our results demonstrate that genetic variation among populations of P. antipodarum is reflected in differences in life-history traits and feeding rates in response to a salinity gradient. The phenotypic differences between the genotypes are consistent with the geographical distribution of P. antipodarum clones in Europe.
4. The overall response to salinity of both genotypes of P. antipodarum suggests an optimum at ≈ 5‰ S; however, both genotypes showed a broad salinity tolerance and were able to feed, grow and reproduce over the entire salinity range tested (0–15‰ S). The broad environmental tolerance of both genotypes together with their widespread geographical distribution across Europe provide evidence consistent with the general-purpose genotype hypothesis.     

Gradients of life-history variation: an intercontinental comparison of fishes

Multivariate analysis identified atwo-dimensional continuum of life-historyvariation among 301 fish species from Europe,North America, South America and the Atlanticand Pacific coasts of North America. The firstaxis was associated with larger body size,higher fecundity, delayed maturation, fewerreproductive events, and shorter breedingseason on one end and small size, lowfecundity, early maturity, multiplereproductive events per year, and prolongedbreeding season on the other. The second axiscontrasted fishes having larger eggs and moreparental care against fishes with the oppositesuite of traits.Phylogenetic affiliations of species wereapparent in the general patterns of ordinationof species within orders, indicatingevolutionary divergences in life-historypatterns. In fact, partitioning the variance oflife-history traits showed that taxonomic orderand latitude were the most important factorsand geographic region and habitat the least.Despite phylogenetic constraints, basiclife-history patterns showed consistencybetween distantly geographical regions,latitudinal ranges and basic adult habitats,indicating convergences in life-historypatterns. Although the basic life-historypatterns seemed repeatable among distantlyrelated taxa, geographical and latitudinalaffiliations were apparent. Species from SouthAmerica are skewed toward the opportunisticendpoint, whereas North American marine speciesare skewed toward the periodic endpoint of thetrilateral continuum model. Most of the fishspecies from South American data set came fromfluctuating environments, so an opportunisticstrategy of early maturation and continuousspawning permits efficient recolonization ofhabitats over small spatial scales. Incontrast, most species in the North Americanand European data sets came from seasonalhabitats that are nonetheless more hydrologicalstable, so a periodic strategy of delayingmaturation to attain large clutches enhancesadult survivorship during suboptimalenvironmental conditions and recruitment whenearly life stages encounter suitableenvironmental conditions. Similarly,latitudinal affiliations were also observed:opportunistic strategists more common intropical latitudes and periodic strategistsmore common in temperate and Arctic latitudes.     

Interpretation of variation across marker loci as evidence of selection

Population structure and history have similar effects on the genetic diversity at all neutral loci. However, some marker loci may also have been strongly influenced by natural selection. Selection shapes genetic diversity in a locus-specific manner. If we could identify those loci that have responded to selection during the divergence of populations, then we may obtain better estimates of the parameters of population history by excluding these loci. Previous attempts were made to identify outlier loci from the distribution of sample statistics under neutral models of population structure and history. Unfortunately these methods depend on assumptions about population structure and history that usually cannot be verified. In this article, we define new population-specific parameters of population divergence and construct sample statistics that are estimators of these parameters. We then use the joint distribution of these estimators to identify outlier loci that may be subject to selection. We found that outlier loci are easier to recognize when this joint distribution is conditioned on the total number of allelic states represented in the pooled sample at each locus. This is so because the conditional distribution is less sensitive to the values of nuisance parameters.