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Data from: A history of phenotypic plasticity accelerates adaptation to a new environment
06-08-2011 05-31-2017
Can a history of phenotypic plasticity increase the rate of adaptation to a new environment? Theory suggests it can through two different mechanisms. Phenotypically plastic organisms can adapt rapidly to new environments through genetic assimilation, or the fluctuating environments that result in phenotypic plasticity can produce evolvable genetic architectures. In this article, I studied a model of a gene regulatory network that determined a phenotypic character in one population selected for phenotypic plasticity and a second population in a constant environment. A history of phenotypic plasticity increased the rate of adaptation in a new environment, but the amount of this increase was dependent on the strength of selection in the original environment. Phenotypic variance in the original environment predicted the adaptive capacity of the trait within, but not between, plastic and non-plastic populations. These results have implications for invasive species, and ecological studies of rapid adaptation.
Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
08-02-2011 05-31-2017
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognised as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study the sequence of eIF4E was analysed in 1090 barley landraces and non-current cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eIF4E haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 out of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest eIF4E may play a role in barley adaptation to local habitats.
Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation
07-13-2011 05-31-2017
Little is known about the genetic diversity of coho salmon in Alaska, although this area represents half of the species’ North American range. In this study, nine microsatellite loci were used to genotype 32 putative coho salmon populations from seven regions of Alaska. The primary objectives were to estimate and evaluate the degree and spatial distribution of neutral genetic diversity within and among populations of Alaskan coho salmon. Genetic analysis yielded four results that provide insight into forces influencing genetic diversity in Alaskan coho salmon and have important conservation implications: 1) significant population differentiation was found within each region; 2) the degree of differentiation (FST = 0.099) among populations was as large or larger than that reported for other Pacific salmon species in Alaska; 3) phenetic clustering of populations showed weak geographic concordance; 4) strong genetic isolation by distance was only apparent at the finest geographic scale (within a drainage). These results suggest that coho salmon populations are small relative to populations of other Pacific salmon, and the genetic diversity within and among coho salmon populations is influenced primarily by genetic drift, and not gene flow. Resource management and conservation actions affecting coho salmon in Alaska must recognize that the populations are generally small, isolated, and probably exhibit local adaptation to different spawning and freshwater rearing habitats. These factors justify managing and conserving Alaskan coho salmon at a fine geographic scale.
Data from: Effects of inversions on within- and between-species recombination and divergence
08-09-2011 05-31-2017
Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and D. persimilis, we detected one double-recombinant among 9739 progeny from F1 hybrids screened, consistent with published double crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species vs. within species. Moreover, we observed strong ‘interchromosomal effect’ (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within vs. between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible effects of inversions on interspecies gene exchange that had not been considered previously.
Data from: The risk and intensity of sperm ejection in female birds
07-19-2011 05-31-2017
The way females utilise the gametes of different males has important consequences for sexual selection, sexual conflict and intersexual coevolution in natural populations. However, patterns of sperm utilisation by females are difficult to demonstrate, and their functional significance remains unclear. Here, we experimentally study sperm ejection in the fowl, Gallus gallus domesticus, where females eject preferentially the sperm of socially subordinate males. We study two measures of sperm ejection: (i) the probability that an ejaculate is ejected ('risk'), and (ii) the proportion of semen ejected ('intensity'), and show that both measures are strongly non-random with respect to characteristics of the ejaculate, the male and the female. Sperm ejection neutralised on average 80% of an ejaculate, and while larger ejaculates suffered a higher ejection risk, smaller ejaculates suffered more intense ejection. After controlling for ejaculate volume, socially subdominant males suffered higher ejection intensity. After controlling for male and ejaculate effects, ejection risk increased and intensity declined as females mated with successive males. Collectively, these results reveal that sperm ejection risk and intensity are at least partly actively caused by female behaviour, and generate independent selective pressures on male and ejaculate phenotypes.
Data from: Data sharing by scientists: practices and perceptions
06-29-2011 05-31-2017
Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers –data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings: A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions of the barriers and enablers of data sharing. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle (collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data) but are not satisfied with long-term data preservation. Many organizations do not provide support to their researchers for data management both in the short- and long-term. If certain conditions are met (such as formal citation and sharing reprints) respondents agree they are willing to share their data. There are also significant differences and approaches in data management practices based on primary funding agency, subject discipline, age, work focus, and world region. Conclusions/Significance: Barriers to effective data sharing and preservation are deeply rooted in the practices and culture of the research process as well as the researchers themselves. New mandates for data management plans from NSF and other federal agencies and world-wide attention to the need to share and preserve data could lead to changes. Large scale programs, such as the NSF-sponsored DataNET (including projects like DataONE) will both bring attention and resources to the issue and make it easier for scientists to apply sound data management principles.
Data from: Genetic and phenotypic variation across a hybrid zone between ecologically divergent tree squirrels (Tamiasciurus)
07-19-2011 05-31-2017
A hybrid zone along an environmental gradient should contain a clinal pattern of genetic and phenotypic variation. This occurs because divergent selection in the two parental habitats is typically strong enough to overcome the homogenizing effects of gene flow across the environmental transition. We studied hybridization between two parapatric tree squirrels (Tamiasciurus spp.) across a forest gradient over which the two species vary in coloration, cranial morphology, and body size. We sampled 397 individuals at 29 locations across a 600-km transect to seek genetic evidence for hybridization; upon confirming hybridization, we examined levels of genetic admixture in relation to maintenance of phenotypic divergence despite potentially homogenizing gene flow. Applying population assignment analyses to microsatellite data, we found that T. douglasii and T. hudsonicus form two distinct genetic clusters but also hybridize, mostly within transitional forest habitat. Overall, based on this nuclear analysis, 48% of the specimens were characterized as T. douglasii, 9% as hybrids, and 43% as T. hudsonicus. Hybrids appeared to be reproductively viable, as evidenced by the presence of later-generation hybrid genotypes. Observed clines in ecologically important phenotypic traits—fur coloration and cranial morphology—were sharper than the cline of putatively neutral mtDNA, which suggests that divergent selection may maintain phenotypic distinctiveness. The relatively recent divergence of these two species (probably late Pleistocene), apparent lack of pre-zygotic isolating mechanisms, and geographic coincidence of cline centers for both genetic and phenotypic variation suggest that environmental factors play a large role in maintaining the distinctiveness of these two species across the hybrid zone.
Data from: On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison
07-13-2013 05-31-2017
Micro-organisms are known to exhibit phenotypic plasticity in response to changes in their environment. Recent studies have shown that a parasite strain can adjust its host exploitation strategies to the presence of unrelated strains, e.g. for Plasmodium chabaudi by adjusting its sex-ratio. J. Evol. Biol. 2013; 26: 1370–1378 claims to report a similar plastic response to the presence of unrelated strains in the case of siderophore-producing bacteria. I argue that she does not provide sufficient evidence to support the interpretation of the plastic response she observes (increasing siderophore production in the presence of cheaters) through a cooperator/cheater framework. I show that known plastic responses to physicochemical factors, such as siderophore or iron concentration, seem to offer a clearer and more parsimonious explanation. Finally, I also challenge the parallel she makes between the process she observes in siderophore-producing bacteria and compensation in bi-parental care models.
Data from: An interspecific comparison between morphology and swimming performance in cyprinids
07-21-2013 05-31-2017
Flow regimes are believed to be of major evolutionary significance in fish. The flow regimes inhabited by cyprinids vary extensively from still flow regimes to riptide flow regimes. To test (1) whether flow-driven swimming performance and relevant morphological differentiation are present among fish species and (2) whether evolutionary shifts between high-flow and low-flow habitats in cyprinids are associated with evolutionary tradeoffs in locomotor performance, we obtained data on both steady and unsteady swimming performance and external body shape for 19 species of cyprinids that typically occur different flow regimes (still, intermediate and riptide). We also measured the routine energy expenditure (RMR) and maximum metabolic rate (MMR) and calculated the optimal swimming speed. Our results showed that fish species from riptide groups tend to have a higher critical swimming speed (Ucrit), maximum linear velocity (Vmax) and fineness ratio (FR) than fish from the other two groups. However, there was no correlation between the reconstructed changes in the steady and unsteady swimming performance of the 19 species. According to the phylogenetically independent contrast (PIC) method, the Ucrit was actively correlated with the MMR. These results indicated that selection will favour both higher steady and unsteady swimming performance and a more streamlined body shape in environments with high water velocities. The results suggested that steady swimming performance was more sensitive to the flow regime and that for this reason, changes in body shape resulted more from selective pressure on steady swimming performance than on unsteady swimming performance. No evolutionary tradeoff was observed between steady and unsteady swimming performance, although Ucrit and MMR were found to have coevolved. However, a further analysis within each typically occur habitat group suggested that the tradeoff that may exist between steady and unsteady swimming performance may be concealed by the effect of habitat.
Data from: The role of local ecology during hybridisation at the initial stages of ecological speciation in a marine snail
05-11-2013 05-31-2017
Hybrid zones of ecologically divergent populations are ideal systems to study the interaction between natural selection and gene flow during the initial stages of speciation. Here we perform an AFLP genome scan in parallel hybrid zones between divergent ecotypes of the marine snail Littorina saxatilis, which is considered a model case for the study of ecological speciation. RB (Ridged-Banded) and SU (Smooth-Unbanded) ecotypes are adapted to different shore levels and microhabitats, although they present a sympatric distribution at the mid-shore where they meet and mate (partially assortatively). We used shell morphology, outlier and non-outlier AFLP loci from RB, SU and hybrid specimens captured in sympatry to determine the level of phenotypic and genetic introgression. We found different levels of introgression at parallel hybrid zones and non-outlier loci showed more gene flow with greater phenotypic introgression. These results were independent from the phylogeography of the studied populations, but not from the local ecological conditions. Genetic variation at outlier loci was highly correlated with phenotypic variation. In addition, we used the relationship between genetic and phenotypic variation to estimate the heritability of morphological traits and to identify potential QTLs to be confirmed in future crosses. These results suggest that ecology (exogenous selection) plays an important role in this hybrid zone. Thus, ecologically-based divergent natural selection is responsible, simultaneously, for both ecotype divergence and hybridisation. On the other hand, genetic introgression occurs only at neutral loci (non-outliers). In the future, genome-wide studies and controlled crosses would give more valuable information about this process of speciation in the face of gene flow.
Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition
01-01-1999 05-31-2017
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
Data from: Phylogenetic relationships and tempo of early diversification in Anolis lizards
01-01-1999 05-31-2017
We examine phylogenetic relationships among anoles using mitochondrial DNA sequences from the NADH dehydrogenase subunit 2 gene (ND2) and five transfer-RNA genes representing 1,455 alignable base positions and 866 phylogenetically informative characters (parsimony criterion). We also present 16 morphological characters for phylogenetic analysis. Our analyses yielded poorly-supported nodes deep in the anole tree but many well-supported nodes for more recent phylogenetic divergences. We test the hypothesis that the major clades of anoles form a hard polytomy and present a general statistical framework for testing hypothesis of simultaneous branching of lineages by using molecular sequence data. Our results suggest that rapid diversification early in the evolutionary history of anoles explains why numberous researchers have had difficulty reconstruction well-supported dichotomous phylogenetic trees for anoles.
Data from: The strength of phenotypic selection in natural populations
01-01-2001 05-31-2017
How strong is phenotypic selection on quantitative traits in the wild? We reviewed the literature from 1984 through 1997 for studies that estimated the strength of linear and quadratic selection in terms of standardized selection gradients or differentials on natural variation in quantitative traits for field populations. We tabulated 63 published studies of 62 species that reported over 2,500 estimates of linear or quadratic selection. More than 80% of the estimates were for morphological traits; there is very little data for behavioral or physiological traits. Most published selection studies were unreplicated and had sample sizes below 135 individuals, resulting in low statistical power to detect selection of the magnitude typically reported for natural populations. The absolute values of linear selection gradients |β| were exponentially distributed with an overall median of 0.16, suggesting that strong directional selection was uncommon. The values of |β| for selection on morphological and on life-history/phenological traits were significantly different: on average, selection on morphology was stronger than selection on phenology/life history. Similarly, the values of |β| for selection via aspects of survival, fecundity, and mating success were significantly different: on average, selection on mating success was stronger than on survival. Comparisons of estimated linear selection gradients and differentials suggest that indirect components of phenotypic selection were usually modest relative to direct components. The absolute values of quadratic selection gradients |γ| were exponentially distributed with an overall median of only 0.10, suggesting that quadratic selection is typically quite weak. The distribution of γ values was symmetric about 0, providing no evidence that stabilizing selection is stronger or more common than disruptive selection in nature.
Data from: The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster
01-01-2001 05-31-2017
Here we present a statistically rigorous approach to quantifying microarray expression data that allows the relative effects of multiple classes of treatment to be compared and incorporates analytical methods that are common to quantitative genetics. From the magnitude of gene effects and contributions of variance components, we find that gene expression in adult flies is affected most strongly by sex, less so by genotype and only weakly by age (for 1- and 6-wk flies); in addition, sex x genotype interactions may be present for as much as 10% of the Drosophila transcriptome. This interpretation is compromised to some extent by statistical issues relating to power and experimental design. Nevertheless, we show that changes in expression as small as 1.2-fold can be highly significant. Genotypic contributions to transcriptional variance may be of a similar magnitude to those relating to some quantitative phenotypes and should be considered when assessing the significance of experimental treatments.
Data from: The Beagle collections of Darwin's finches (Geospizinae)
01-01-1982 05-31-2017
n/a
Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae
12-30-1998 05-31-2017
A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction-site survey) were used to reconstruct the phylogenetic history of the Pickerelweed family Pontederiaceae. The chloroplast data are converging to a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from the three chloroplast data sets were identical or extremely similar in shape to each other, mostly robustly supported and there was no evidence of significant heterogeneity among them. The few topological differences seen among unrooted trees from each chloroplast data set are probably artifacts of sampling error on short branches. Despite well documented differences in rates of evolution for different characters in individual data sets, equally weighted parsimony therefore permits accurate reconstructions of chloroplast relationships in Pontederiaceae. A separate morphology-based data set yielded trees that were very different from the chloroplast trees. While there was substantial support by the morphological evidence for several major clades supported by chloroplast trees, most of the conflicting phylogenetic structure on the morphology trees was not robust. Nonetheless, several statistical tests of incongruence indicate significant heterogeneity between molecules and morphology. The source of this apparent incongruence appears to be a low ratio of phylogenetic signal to noise in the morphological data.
Data from: Incongruence between morphological data sets: an example from the evolution of endoparasitism among parasitic wasps (Hymenoptera: Braconidae)
01-01-1999 05-31-2017
Phylogenetic analyses of molecular and morphological data sets for a group of parasitic wasps (Hymenoptera: Braconidae) give strikingly different results. The molecular data indicate that the major life history transition from ectoparasitism to endoparasitism has occurred independently several times within the family while the morphological data indicate a single origin. Similar incongruent topologies are obtained if the morphological data are partitioned by either of two methods: distinguishing (1) characters of the larval stage and female reproductive system, or (2) characters selected individually by the authors prior to the analysis as likely to be mechanistically associated with endo/ectoparasitism. This result is supported by significant differences in tests of incongruence, and we propose that it is caused by convergence among morphological characters resulting from a shared life history strategy.
Data from: Effects of population structure and sex on association between serotonin receptors and Drosophila heart rate
01-01-2004 05-31-2017
As a first step toward population and quantitative genetic analysis of neurotransmitter receptors in Drosophila melanogaster, we describe the parameters of nucleotide variation in three serotonin receptors and their association with pupal heart rate. Thirteen kilobases of DNA including the complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216 highly inbred lines extracted from two North American populations in California and North Carolina. Nucleotide and amino acid polymorphism is in the normal range for Drosophila genes and proteins, and linkage disequilibrium decays rapidly such that haplotype blocks are typically only a few SNPs long. However, intron 1 of 5-HT1A consists of two haplotypes that are at significantly different frequencies in the two populations. Neither this region of the gene nor any of the common amino acid polymorphisms in the three loci associate with either heart rate or heart rate variability. A cluster of SNPs in intron 2 of 5-HT1A, including a triallelic site, do show a highly significant interaction between genotype, sex, and population. While it is likely that a combination of weak, complex selection pressures and population structure has helped shape variation in the serotonin receptors of Drosophila, much larger sampling strategies than are currently adopted in evolutionary genetics will be required to disentangle these effects.
Data from: Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms
03-01-1998 05-31-2017
To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbc L (1,428 bp), and atp B (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA rbc L atp B data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.
Data from: Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences
06-01-1998 05-31-2017
We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the *-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little-used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome evolve relatively slowly. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most-parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.