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opennotspecifiedJul 2016View details →

FIGURE 3 in Morphological variations among populations of Monochoria vaginalis s.l. (Pontederiaceae) in Thailand

FIGURE 3. UPGMA clustering of each population (number of OTUs) based on Gower General Similarity Coefficient calculated between means of 22 quantitative and 12 qualitative characters of M. vaginalis s.l. in Thailand. MV 1 and MV 2 represent the morphological forms of each population.

opencc-by-4.0Sep 2024View details →

Seasonal and between-population variation in heat tolerance and cooling efficiency in a Mediterranean songbird

Data collection This database contains physiological data on thermoregulation in response to heat -- heat tolerance limit (HTL), body temperature (Tb), resting metabolic rate (RMR), evaporative water loss (EWL) and evaporative cooling efficiency (EHL/MHP) -- collected during winter and summer in two populations on Great tits Parus major submitted to different thermal environments (one from a montane, more thermally stable site; and the other from a lowland, warmer and more thermally heterogeneous site) in southwestern Iberia. Physiological data were collected by using open flow through respirometry (see Material and Methods for detailed protocols).  Statistical analyses  We evaluated seasonal and between population differences to asses the degree of phenotypical flexibility in those physiological thermoregulatory traits both above and below thermoneutrlaity. See detailed analyses below:  We conducted all statistical analyses in R 4.1.2 (R Core Team, 2021). We used the segmented package (Muggeo, 2009) to determine inflection points in Tb, RMR, EWL, and EHL/MHP for each site and season. Then, the data were split based on inflection points for subsequent analyses below and above thermoneutrality (as in Whitfield et al., 2015). Linear and linear mixed-effects models were fitted to the data by using the lme4 package (Bates et al., 2015). We used the emmeans package (Lenth, 2022) to perform post-hoc pairwise contrasts between groups, and visually checked model assumptions in model residuals. First, to assess seasonal and between-population variation in heat tolerance, we fitted a linear model with HTL (please see Heat Tolerance Limits sheet on dataset) as response variable and body mass, site, season, and the site×season interaction as predictors. Then, we fitted linear models to each thermoregulatory trait (namely Tb, RMR, EWL and EHL/MHP; please see Physiological Data sheet on dataset), using a single Tair stage per individual within (Tair ~ 30 ºC) and above thermoneutral zone (Tair ~ 37 ºC) of Great tits (as inflection points of all variables were below this last Tair stage), including body mass, site, season, and the site×season interaction as predictor variables. Second, for summer measurements, we fitted linear mixed-effects models to evaluate population variation in the slopes of Tb, RMR, EWL and EHL/MHP against Tair above thermoneutrality, as we could obtain several measurements per individual above inflection points for each trait during this season. Initial models included Tair, body mass, site, and the Tair×site interaction as predictor variables, with ring as a random effect. When site emerged as a significant predictor, we additionally fitted separate population-specific models to calculate the slopes and y-intercepts of each thermoregulatory trait in response to Tair.

FIG. 1 in Temperature and Development Drive Variation in Oral Morphology among Tailed Frog (Ascaphus spp.) Populations

FIG. 1. Pinned specimen of Ascaphus montanus (specimen ID WCF08228 from Lost Horse Creek, MT) showing labeled oral morphology, including labial tooth rows. Rows are numbered from anterior to posterior. The A2, A3, and P1 rows are biserial (i.e., have two rows of teeth), as demonstrated by the labeled P1 row. The labial tooth row formula (see Methods) for this specimen is 3/9(1), where (1) indicates the medial gap in the P1 row.

FIG. 2 in Temperature and Development Drive Variation in Oral Morphology among Tailed Frog (Ascaphus spp.) Populations

FIG. 2. Sampling locations for Ascaphus truei (left) and Ascaphus montanus (right). Inset maps show estimated range boundaries for A. truei (in green) and A. montanus (in blue). Range maps from NatureServe & IUCN (2012).

FIG. 4 in Temperature and Development Drive Variation in Oral Morphology among Tailed Frog (Ascaphus spp.) Populations

FIG. 4. From the results of the species-specific GLMs, we predicted relationships (shown with 1.96*SE confidence intervals) between P2 tooth counts and developmental stage at each temperature point sampled (annual average stream temperature). Raw data points are also shown on these plots.

FIG. 3 in Temperature and Development Drive Variation in Oral Morphology among Tailed Frog (Ascaphus spp.) Populations

FIG. 3. Ascaphus truei tadpoles had higher overall counts of labial teeth in the P2 row than A. montanus tadpoles. Within both species, populations (here shown as different colored boxplots) varied in their P2 tooth counts.

opencc-zeroDec 2014View details →

Data from: Drift, not selection, shapes toll-like receptor variation among oceanic island populations

Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analyzed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here we focused on diversity at toll-like receptor (TLR) loci, which play a key role in the vertebrate innate immune system and, therefore, are expected to be under pathogen-mediated selection. We assessed TLR variation within and among 13 island populations (grouped into three archipelagos) of Berthelot's pipit, Anthus berthelotii, for which detailed population history has previously been ascertained. We also compared the variation observed with that found in its widespread sister species, the tawny pipit, Anthus campestris. We found strong evidence for positive selection at specific codons in TLR1LA, TLR3 and TLR4. Despite this, we found that at the allele frequency level, demographic history has played the major role in shaping patterns of TLR variation in Berthelot's pipit. Levels of diversity and differentiation within and across archipelagos at all TLR loci corresponded very closely with neutral microsatellite variation, and with the severity of the bottlenecks that occurred during colonization. Our study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales.

opencc-zeroDec 2010View details →

Data from: Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations

Currently there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during four years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life-cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only one year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were very low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programs into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.

opencc-zeroDec 2017View details →

Data from: Geographic variation in larval metabolic rate between northern and southern populations of the invasive gypsy moth

Thermal regimes can diverge considerably across the geographic range of a species, and accordingly, populations can vary in their response to changing environmental conditions. Both local adaptation and acclimatization are important mechanisms for ectotherms to maintain homeostasis as environments become thermally stressful, which organisms often experience at their geographic range limits. The spatial spread of the gypsy moth (Lymantria dispar L.) after introduction to North America provides an exemplary system for studying population variation in physiological traits given the gradient of climates encompassed by its current invasive range. This study quantifies differences in resting metabolic rate (RMR) across temperature for four populations of gypsy moth, two from the northern and two from southern regions of their introduced range in North America. Gypsy moth larvae were reared at high and low thermal regimes, then metabolic activity was monitored at four temperatures using stop-flow respirometry to test for an acclimation response. For all populations, there was a significant increase in RMR as respirometry test temperature increased. Contrary to our expectations, we did not find evidence for metabolic adaptation to colder environments based on our comparisons between northern and southern populations. We also found no evidence for an acclimation response of RMR to rearing temperature for three of the four pairwise comparisons examined. Understanding the thermal sensitivity of metabolic rate in gypsy moth, and understanding the potential for changes in physiology at range extremes, is critical for estimating continued spatial spread of this invasive species both under current and potential future climatic constraints.

opencc-zeroDec 2017View details →

Data from: Regional and local patterns of genetic variation and structure in yellow-necked mice − the roles of geographic distance, population abundance and winter severity

The goal of this study, conducted in seven large woodlands and three areas with small woodlots in north-eastern Poland in 2004-2008, was to infer genetic structure in yellow-necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harboured two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine-scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.

opencc-zeroDec 2009View details →

Data from: Inter-population variation in mating system and late-stage inbreeding depression in Magnolia stellata

Inbreeding has the potential to cause evolutionary changes in populations, although these changes are likely to drive populations to extinction through inbreeding depression and reductions in genetic diversity. We investigated the mating system and late-stage inbreeding depression (δ) in 10 populations of Magnolia stellata using nine microsatellite markers and evaluated the effects of population size and the degree of population isolation through inbreeding and inbreeding depression on the persistence of populations. The outcrossing rates were very similar (~0.7) among populations, but the correlations of paternity, fractions of biparental inbreeding and inbreeding coefficients at the seed stage (FS) varied among populations, suggesting that the level of outcrossing was similar among populations, while the quality of it was not. A significant negative correlation was detected between FS and population size. The average value of δ was 0.709, and the values in six of the 10 populations were significant. The values of δ differed among populations, although clear relationships with population size and the degree of population isolation were not detected. However, in one population, which was very small and located in the edge of the species' range, we obtained a very low value of δ (-0.096), which may be indicative of purging or the fixation of deleterious alleles. Existing M. stellata populations that are small (and thus might be expected to have higher frequencies of inbreeding) and have large values of δ may be in danger of declining, even if the populations are located within the central region of the species range.

opencc-zeroDec 2017View details →

Data from: Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations

Intraspecific trait variation within natural populations (i.e. intra‐population trait variation, IPTV) is the basic source for selection and can have significant ecological consequences. Higher IPTV may increase a population's niche breath and benefit interspecies competition under a resource‐limited environment, thus affecting the ability of a species to move into novel habitats. However, the reciprocal influences of variation in environmental conditions and phenotypic trait expression in spreading plant populations are not clearly defined. We propose that during invasion, IPTV and its relative change in response to key resource enrichment may increase with the resource deficit of invaded sites, and that this relationship may facilitate plant invasions into resource‐limited environments. We analyzed the invasion trend, IPTV and its response to water enrichment, and moisture variability among populations of an annual grass Brachypodium hybridum in California, United States. We incorporated a genotyping‐by‐sequencing approach, a common garden experiment that had two water level treatments, and public plant and climate databases. Our hypothesis was supported by the observation that for populations that invaded sites with higher spring moisture deficit, both their seed biomass IPTV (for the water‐enriched treatment only) and relative change of the IPTV across water treatments were larger when examined in the common garden experiment. A generally north to south spreading direction was found in these B. hybridum populations, towards a drier and warmer climate exhibiting higher moisture deficit for plant growth. Our results suggest a role for interactions between IPTV (rather than trait means) and environmental resource availability in promoting plant invasions, providing new insights into the significance of IPTV in shaping plant geographic distributions.

opencc-zeroDec 2010View details →

Data from: Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima

Natural selection, random processes, and gene flow are known to generate sex ratio variations among sexually polymorphic plant populations. In gynodioecious species, in which hermaphrodites and females coexist, the relative effect of these processes on the maintenance of sex polymorphism is still up for debate. The aim of this study was to document sex ratio and cytonuclear genetic variation at a very local scale in wind-pollinated gynodioecious Beta vulgaris ssp. maritima, and attempt to elucidate which processes explained the observed variation. The study sites were characterized by geographically distinct patches of individuals and appeared to be dynamic entities, with recurrent establishment of distinct haplotypes through independent founder events. Along with substantial variation in sex ratio and unexpectedly low gene flow within study sites, our results showed a high genetic differentiation among a mosaic of genetically distinct demes, with isolation by distance or abrupt genetic discontinuities taking place within a few tens of meters. Overall, random founder events with restricted gene flow could be primary determinants of sex structure, by promoting the clumping of sex-determining genes. Such high levels of sex structure provide a landscape for differential selection acting on sex-determining genes, which could modify the conditions of maintenance of gynodioecy in structured populations.

opencc-zeroDec 2014View details →

Data from: Comparative population genomics of latitudinal variation in D. simulans and D. melanogaster

Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and D. melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple timepoints over two years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, we find that clinally varying loci in D. simulans are less stable over multiple years than comparable clines in D. melanogaster. D. simulans shows a significantly weaker pattern of isolation by distance than D. melanogaster and we find evidence for a strong contribution of annual re-migration to D. simulans population genetic structure. While population bottlenecks and migration can plausibly explain the differences in amount and stability of clinal variation between the two species, we also observe a significant enrichment of shared clinal genes, suggesting that the selective forces associated with climate are acting on the same genes and phenotypes in D. simulans and D. melanogaster.

opencc-zeroAug 2021View details →

Geographic variation in dispersal of western burrowing owl (Athene cunicularia hypugaea) populations

Dispersal is one of the key elements of species' metapopulation dynamics and, hence, influences global conservation status. Furthermore, determining the geographic variation in magnitude and direction of dispersal throughout a species' distribution may expand our understanding of the causes of population declines in species of conservation concern. For instance, western burrowing owl (Athene cunicularia hypugaea) populations have declined at the northern and eastern edge of their breeding distribution during the 20th century. In the same period, large areas of thornscrub that did not support breeding owls were converted to irrigated agriculture in the southern edge of the subspecies' breeding distribution in northwestern Mexico. These farmlands now support some of the highest breeding densities of owls. We tested the hypothesis that owls that colonized this recently created habitat originated from declining migratory populations from the northern portion of the subspecies' range. We used stable isotopes 2H, 13C, and 15N in owl feathers to infer breeding dispersal patterns throughout the subspecies' breeding range. Populations near the northern edge of the subspecies' breeding range had immigrants that dispersed over larger distances than immigrants at low and mid latitude populations. However, agricultural populations in northwestern Mexico disrupted this latitudinal pattern, attracting owls from more distant locations. We also found immigrants originated from further distances in declining populations than increasing populations. Stable isotopes provided no evidence of contemporaneous breeding dispersal from Canadian populations to northwestern Mexico but suggest that agricultural areas in the southern edge of the subspecies' distribution have altered the continental dispersal pattern.

Figure 2 in Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) in Shandong and Liaodong peninsulas, China

Figure 2. Maximum-parsimony (MP) tree of the unique haplotypes. Numbers at nodes represent bootstrap values (> 50) as a measure of support.

Figure 4 in Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) in Shandong and Liaodong peninsulas, China

Figure 4. Mismatch curve of nucleotide pairwise based on 16S sequences. Exp, expected value; Obs, observed value.

Figure 3 in Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) in Shandong and Liaodong peninsulas, China

Figure 3. Maximum-likelihood (ML) tree of the unique haplotypes. Bootstrap values (> 50) are shown on the nodes; Bayesian inference (BI) tree based on the analysis of the unique haplotypes. Posterior probability values (> 0.5) are shown.

Figure 5 in Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) in Shandong and Liaodong peninsulas, China

Figure 5. Mismatch curve of nucleotide pairwise based on 28S sequences. Exp, expected value; Obs, observed value.