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opencc-by-4.0Apr 2017View details →

Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)

This dataset provides the raw data for the population genetic analyses for the article: "Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)" by Benoit Pujol; Juliette Archambeau; Aurore Bontemps; Mylène Lascoste; Sara Marin; and Alexandre Meunier found in the journal "Botany Letters", Vol 164 pp. 111-119 (DOI: 10.1080/23818107.2017.1310056). Link to journal open access article: http://www.tandfonline.com/doi/pdf/10.1080/23818107.2017.1310056 Link to Zenodo article reporsitory: https://zenodo.org/record/801169 The datafile includes three data sheets: Data, which contains for each plant : the name of the population, the name of the sampled individual, the subspecies, the latitude of the population, the longitude of the population, the altitudinal elevation of the population in meters, and the microsatellite genotype of each plant. Genotype data is recorded by locus (two columns for the two alleles at one locus). Locus name is found as the title of the column. The record for each allele is its allele size. valleys 1 and valleys 2, which contains the association between populations and valleys following the two scenarios that we analyzed in the paper. Microsatelite loci were developed during previous work: see the following paper for more details: Debout, G., E. Lhuillier, P.-J. Malé, B. Pujol, and C. Thébaud. 2012. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum majus subspecies (Plantaginaceae) using pyrosequencing technology. Conservation Genetics Resources 4:75-79.

opencc-zeroOct 2022View details →

Data and analysis from: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

An important challenge in ecology is to understand variation in species' maximum intrinsic rate of population increase, 𝑟𝑚𝑎𝑥, not least because 𝑟𝑚𝑎𝑥 underpins our understanding of the limits of fishing, recovery potential, and ultimately extinction risk. Across many vertebrate species, terrestrial and aquatic, body mass and environmental temperature are important correlates of 𝑟𝑚𝑎𝑥. In sharks and rays, specifically, 𝑟𝑚𝑎𝑥 is known be lower in larger species, but also in deep-sea ones. We use an information-theoretic approach that accounts for phylogenetic relatedness to evaluate the relative importance of body mass, temperature and depth on 𝑟𝑚𝑎𝑥. We show that both temperature and depth have separate effects on shark and ray 𝑟𝑚𝑎𝑥 estimates, such that species living in deeper waters have lower 𝑟𝑚𝑎𝑥. Furthermore, temperature also correlates with changes in the mass scaling coefficient, suggesting that as body size increases, decreases in 𝑟𝑚𝑎𝑥 are much steeper for species in warmer waters. These findings suggest that there are (as-yet understood) depth-related processes that limit the maximum rate at which populations can grow in deep sea sharks and rays. While the deep ocean is associated with colder temperatures, other factors that are independent of temperature, such as food availability and physiological constraints, may influence the low 𝑟𝑚𝑎𝑥 observed in deep sea sharks and rays. Our study lays the foundation for predicting the intrinsic limit of fishing, recovery potential, and extinction risk species based on easily accessible environmental information such as temperature and depth, particularly for data-poor species. This repository contains the data and a minimum working example of the model-fitting process used for the article "Body mass, temperature, and depth shape productivity in sharks and rays", which is currently in press at Ecology and Evolution.

opencc-zeroOct 2022View details →

Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation

Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

opencc-zeroJun 2024View details →

Data from: Effects of age, breeding strategy, population density, and number of neighbors on territory size and shape in Savannah Sparrows

The size and shape of an animal's breeding territory are dynamic features influenced by multiple intrinsic and extrinsic factors and can have important implications for survival and reproduction. Quantitative studies of variation in these territory features can generate deeper insights into animal ecology and behavior. We explored the effect of age, breeding strategy, population density, and number of neighbors on the size and shape of breeding territories in an island population of Savannah Sparrows (Passerculus sandwichensis). Our dataset consisted of 407 breeding territories belonging to 225 males sampled over 11 years. We compared territory sizes to the age of the male territorial holder, the male's reproductive strategy (monogamy vs. polygyny), the number of birds in the study population (population density), and the number of immediate territorial neighbors (local density). We found substantial variation in territory size, with territories ranging over two orders of magnitude from 57 to 5727 m2 (0.0057 to 0.57 ha). Older males had larger territories, polygynous males had larger territories, territories were smaller in years with higher population density, and larger territories were associated with more immediate territorial neighbors. We also found substantial variation in territory shape, from near-circular to irregularly-shaped territories. Males with more neighbors had irregularly shaped territories, but the shape did not vary with male age, breeding strategy, or population density. For males that lived two years or longer, we found strong consistent individual differences in territory size across years, but weaker individual differences in territory shape, suggesting that size has high repeatability whereas shape has low repeatability. Our work provides evidence that songbird territories are highly dynamic and that their size and shape reflect both intrinsic factors (age and number of breeding partners) and extrinsic factors (population density and number of territorial neighbors).

opencc-by-4.0Dec 2005View details →

Fig. 3 in Repeatability Analysis Of Egg Shape In A Wild Tree Sparrow (Passer Montanus) Population: A Sensitive Method For Egg Shape Description

Fig. 3. The effect of egg-photographing on the description of outline. Panel a shows ten outlines described following the photos of ten randomly chosen eggs, panel b shows ten outlines described fol-

Fig. 8 in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals

Fig. 8. Geometric Morphometric Analysis applied to O. hatcheri individuals. Left: plot of DF3 vs. DF2 showing means and 95% confidence intervals by sampling sites (locality labels as in Fig. 1) NIHL (white triangle), CDP (black circle), 7: PELE (gray square), PDA (black triangle), MITO (black diamond), CARI (white square), EPU (black and white diamond), RIV (gray circle), ROS (white diamond), AME (black square), CHU (gray diamond), MUS (gray triangle), LBA (white circle), and PUY (white triangle). Right: deformation grids correspond to a relative warps analysis involving only CDP, PDA, and NIHL and PUY. Arrowheads indicate displacement of landmarks relative to consensus. Shaded area remarks relative position of landmarks 5 (anterior insertion of the first dorsal fin) and 12 (distal tip of the pelvic fin onto fish body).

Fig. 6 in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals

Fig. 6. Probability for taxonomically identified Odontesthes hatcheri individuals of being O. hatcheri (left) and probability of taxonomically identified O. bonariensis individuals of being O. bonariensis (right). Number of fish, median, quartiles, and data outside 10 and 90th percentile are indicated. Water bodies are named as in Fig. 1.

Fig. 5 in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals

Fig. 5. Morphometric differences between species. DF1 and residual DF2 (of the regression of DF2 versus Standard length) vs. Standard length (SL). Odontesthes bonariensis (white circle), O. hatcheri (black circle), and presumptive hybrids (gray circle).

Fig. 4 in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals

Fig. 4. Geometric Morphometric Analysis applied to Odontesthes individuals. RW2 versus RW1 and deformation grids (tied to group means) for Odontesthes bonariensis (white circle), O. hatcheri (black circle) and presumptive hybrids (gray circle). Arrowheads indicate displacement of landmarks relative to consensus. Shaded area shows relative position of landmarks 5 (anterior insertion of the first dorsal fin) and 12 (distal tip of the pelvic fin onto fish body).

Fig. 1 in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals

Fig. 1. Distribution of O. hatcheri (light gray) and O. bonariensis (dark gray) described by Dyer (2006) and sampling localities: ULLM, Ullum Reservoir; CARZ, Carrizal Reservoir; NIHL, Nihuil Reservoir; D, Lake San Lorenzo; URRE, Lake Urre Lauquen; CDP, Casa de Piedra Reservoir; PELE, Lake Pellegrini; PDA, Piedra del Aguila Reservoir; MITO, Lake Morenito; CARI, Lake Carilafquen; EPU, Lake Epuyén; RIV, Lake Rivadavia; ROS, Lake Rosario; AME, Florentino Ameghino Reservoir; CHU, Chubut River at Los Altares; MUS, Lake Musters; LBA, Lake Buenos Aires; PUY, Lake Pueyrredón. White triangles show the location of the three hatcheries (Estación Hidrobiológica de Chascomús 35º36'S, 58º01'W, Estación de Piscicultura de Embalse 32º13'S, 64º29'W, and Estación de Piscicultura Río Limay 38º59'S, 68º14'W), sources of stocking practices.

FIGURE 1 in Discriminating Scleromystax barbatus (Siluriformes: Callichthyidae) populations from Atlantic Rainforest streams employing otolith shape

FIGURE 1 | Locations where Scleromystax barbatus populations were sampled in clear-water streams of the coastal Atlantic Rainforest biome. Red symbols represent the southern locations (VR, GR, DM, CU, and PE) and blue symbols indicate the southeastern locations (AR, PM, and AE).

FIGURE 4 in Discriminating Scleromystax barbatus (Siluriformes: Callichthyidae) populations from Atlantic Rainforest streams employing otolith shape

FIGURE 4 | Otolith shapes of males and females of Scleromystax barbatus from southern and southeastern regions in the Atlantic Rainforest biome employing a Canonical Analysis of Principal Coordinates (CAP) applied to Fourier (above) and Wavelet (below) coefficients. Bold letters represent the mean canonical coordinates surrounding the standard error for each population. Lines represent the groups: SeFe (Females from the southeastern region), SeMa (Males from the southeastern region), SFe (Females from the southern region), SMa (Males from the southeastern region).

FIGURE 3 in Discriminating Scleromystax barbatus (Siluriformes: Callichthyidae) populations from Atlantic Rainforest streams employing otolith shape

FIGURE 3 | Mean otolith shape based on the Fourier (above) and Wavelet (below) reconstructions for males and females of Scleromystax barbatus from southern and southeastern regions in the Atlantic Rainforest biome. Lines represent the groups: SeFe (Females from the southeastern region), SeMa (Males from the southeastern region), SFe (Females from the southern region), SMa (Males from the southeastern region).

FIGURE 2 in Discriminating Scleromystax barbatus (Siluriformes: Callichthyidae) populations from Atlantic Rainforest streams employing otolith shape

FIGURE 2 | Ventral view of the left lapillus otoliths of Scleromystax barbatus from streams in the southern (VR, GR, DM, CU, and PE) and southeastern (AR, PM, and AE) regions of the Atlantic Rainforest biome. A (Anterior), M (Medial).

opencc-zeroJan 2023View details →

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (Ne) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate Ne variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of Ne through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in Ne. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. Ne fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large Ne. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in Ne dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.

opencc-zeroApr 2023View details →

Temperature adaptation and its impact on the shape of performance curves in Drosophila populations

Understanding how species adapt to different temperatures is crucial to predict their response to global warming, and thermal performance curves (TPCs) have been employed recurrently to study this topic. Nevertheless, fundamental questions regarding how thermodynamic constraints and evolution interact to shape TPCs in lineages inhabiting different environments remain unanswered. Here, we study Drosophila simulans along a latitudinal gradient spanning 3,000 km to test opposing hypotheses based on thermodynamic constraints ('hotter-is-better') versus biochemical adaptation ('jack-of-all-temperatures') as primary determinants of TPCs variation across populations. We compare thermal responses in metabolic rate and the egg-to-adult survival as descriptors of organismal performance and fitness, respectively, and show that different descriptors of TPCs vary in tandem with mean environmental temperatures, providing strong support to hotter-is-better. Thermodynamic constraints also resulted in a strong negative association between maximum performance and thermal breadth. Lastly, we show that descriptors of TPCs for metabolism and egg-to-adult survival are highly correlated, providing evidence of coadaptation and that curves for egg-to-adult survival are systematically narrower and displaced towards lower temperatures. Taken together, results support the pervasive role of thermodynamics constraining thermal responses in Drosophila populations along a latitudinal gradient, that are only partly compensated by evolutionary adaptation.

opencc-zeroJun 2023View details →

Data from: Additive genetic and environmental variation interact to shape the dynamics of seasonal migration in a wild bird population

Dissecting joint micro-evolutionary and plastic responses to environmental perturbations requires quantifying interacting components of genetic and environmental variation underlying expression of key traits. This ambition is particularly challenging for phenotypically discrete traits where multiscale decompositions are required to reveal non-linear transformations of underlying genetic and environmental variation into phenotypic variation, and when effects must be estimated from incomplete field observations. We devised a joint multistate capture-recapture and quantitative genetic animal model and fitted this model to full-annual-cycle resighting data from partially-migratory European shags (Gulosus aristotelis) to estimate key components of genetic, environmental and phenotypic variance in the ecologically critical discrete trait of seasonal migration versus residence. We demonstrate non-negligible additive genetic variance in latent liability for migration, resulting in detectable micro-evolutionary responses following two episodes of strong survival selection. Further, liability-scale additive genetic effects interacted with substantial permanent individual and temporary environmental effects to generate complex non-additive effects on expressed phenotypes, causing substantial intrinsic gene-by-environment interaction variance on the phenotypic scale. Our analyses therefore reveal how temporal dynamics of partial seasonal migration arise from combinations of instantaneous micro-evolution and within-individual phenotypic consistency, and highlight how intrinsic phenotypic plasticity could expose genetic variation underlying discrete traits to complex forms of selection.

opencc-by-4.0Jul 2023View details →

Data and codes from "How does dispersal shape the genetic structure of animal populations in European cities? A simulation approach"

Codes and data used for "Savary et al. How does dispersal shape the genetic structure of animal populations in European cities? A simulation approach".