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opennotspecifiedJan 2016View details →

Figure 2 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA

Figure 2: Principal Components Analysis based on Nei's genetic distances among Porphyra umbilicalis genotypes. The genotypes as well as the individuals assayed with the genotype are given (DP =Dover Point, FS=Fort Stark, NL= Nubble Light, QH =Quoddy Head, RSP=Reid State Park, and W =Wiscasset).

opennotspecifiedJan 2016View details →

Figure 3 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA

Figure 3: Principal components analysis based on Nei's unbiased genetic distances among populations of Porphyra umbilicalis in the Gulf of Maine, USA.

opencc-zeroNov 2021View details →

R script used for: Telomeres in a spatial context: a tool for understanding ageing pattern variation in wild populations

Ageing refers to the loss of organismal functionality with age, a process that is characterised by decreased reproduction and survival probability. In natural populations, it is expected that environmental conditions influence an individual's ageing trajectory. Understanding the role of environmental heterogeneity on ageing variation could provide criticleinsights into population resilience and species distribution but remains overlooked. Telomeres, the end cap of chromosomes, are a promising integrative physiological marker of an individual's health and a possible proxy to aid the understanding of variation in ageing trajectories. Here, we review the existing information on telomere length and its dynamics in wild populations distributed across spatial scales. Despite a relative scarcity of information, there is evidence for divergence in telomere length between populations facing contrasting environments. Nonetheless, a higher spatial resolution and temporal replication is needed to fully understand the role that environmental conditions play on telomere length variation. Since most of the existing studies are correlational, future field and laboratory experiments are required. For the first time, we demonstrate the use of population telomere data to predict species habitat suitability through Species Distribution Models (SDMs). This represents a promising new research area in the study of ageing pattern variation in wild populations. Furthermore, the inclusion of telomere data in future physiological-SDMs may improve our understanding of species distribution and population resilience. However, the use of telomeres within this context could be limited if no previous knowledge on the relevance of telomeres as markers of health and survival at the species level is available. Finally, we suggest some key practical and theoretical considerations that, ideally, future studies combining biogeographic and telomere data should pay attention.

opencc-zeroDec 2021View details →

Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon

Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.

opencc-zeroDec 2021View details →

Context dependent variation in corticosterone and phenotypic divergence of Rana arvalis populations along an acidification gradient

Background Physiological processes, as immediate responses to the environment, are important mechanisms of phenotypic plasticity and can influence evolution at ecological time scales. In stressful environments, physiological stress responses of individuals are initiated and integrated via the release of hormones, such as corticosterone (CORT). In vertebrates, CORT influences energy metabolism and resource allocation to multiple fitness traits (e.g. growth and morphology) and can be an important mediator of rapid adaptation to environmental stress, such as acidification. The moor frog, Rana arvalis, shows adaptive divergence in larval life-histories and predator defense traits along an acidification gradient in Sweden. Here we take a first step to understanding the role of CORT in this adaptive divergence. We conducted a fully factorial laboratory experiment and reared tadpoles from three populations (one acidic, one neutral and one intermediate pH origin) in two pH treatments (Acid versus Neutral pH) from hatching to metamorphosis. We tested how the populations differ in tadpole CORT profiles and how CORT is associated with tadpole life-history and morphological traits. Results We found clear differences among the populations in CORT profiles across the developmental stages, but only weak effects of pH treatment on CORT. Tadpoles from the acid origin population had, on average, lower CORT levels than tadpoles from the neutral origin population, and the intermediate pH origin population had intermediate CORT levels. Overall, tadpoles with higher CORT levels developed faster and had shorter and shallower tails as well as shallower tail muscles. Conclusions Our common garden results indicate among population divergence in CORT levels, likely reflecting acidification mediated divergent selection on tadpole physiology, concomitant to selection on larval life-histories and morphology. However, CORT levels were highly environmental context dependent. Jointly these results indicate a potential role for CORT as a mediator of multi-trait divergence along environmental stress gradients in natural populations. At the same time, the population level differences and high context dependency in CORT levels suggest that snapshot assessment of CORT in nature may not be reliable bioindicators of stress.

opencc-zeroFeb 2022View details →

Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)

Loss of biodiversity is accelerating, including the loss of genetic diversity. Conservation of small, isolated populations may be important, as they can provide valuable contributions to overall genetic variation and long-term viability of species. Furthermore, such populations may play an essential role in adaptation to new environments following changes in e.g. land-use and climate. Dracocephalum ruyschiana is a threatened plant species throughout its European distribution, but 25% of the European populations are situated within Norway. Therefore, the species has its own action plan in Norway, which includes demographic monitoring. However, this monitoring does not cover genetic variation nor is the selection of monitored populations based on genetic differentiation, therefore this fundamental level of biodiversity is overlooked. We analyzed 43 sites using 96 SNPs developed for D. ruyschiana, to investigate whether the monitored populations cover the genetic variation and differentiation found within the Norwegian distribution. The results show structuring and differentiation between populations and indicate that there are at least four distinct genetic groups, of which only two are covered extensively by current demographic monitoring. We suggest that two sites representing the two other genetic groups should be included in the national monitoring program to better conserve the genetic variation found in the Norwegian population of D. ruyschiana. Overall, our results highlight the importance of an integrated, interdisciplinary framework to better monitor and conserve biodiversity at several levels.

opennotspecifiedMay 2022View details →

FIGURE. Umbellules within four populations of Sanicula orthacantha, showing the fruits characters and the variation in numbers of staminate flowers (each line represents a plant individual). The ratio of staminate flowers number/ umbellule number is given for each individual. A. China, Hubei, Xuan'en, Qizimei Mountain, H.M. Li, Y.M. Yi & Y.S. Zhang 1077 (NAS). B. China, Jiangxi, Jiujiang, Lushan, H.M. Li, Y.S. Zhang & Y. Xu 1109 (NAS). C. China, Chongqing, Nanchuan, Jinfo Shan, H.M. Li, Y.S. Zhang & X. Zhang 1141 (NAS). D. China, Sichuan, Emei Shan, H.M. Li & Y.S. Zhang 1157 (NAS). All same scale. in Taxonomic studies on the genus Sanicula (Apiaceae) from China ( ): The clarification of some morphological distinction between S. orthacantha var. orthacantha and S. orthacantha var. brevispina, with the reduction of S. petagnioides to the synonymy of the former, and S. orthacantha var. stolonifera to

FIGURE. Umbellules within four populations of Sanicula orthacantha, showing the fruits characters and the variation in numbers of staminate flowers (each line represents a plant individual). The ratio of staminate flowers number/ umbellule number is given for each individual. A. China, Hubei, Xuan'en, Qizimei Mountain, H.M. Li, Y.M. Yi & Y.S. Zhang 1077 (NAS). B. China, Jiangxi, Jiujiang, Lushan, H.M. Li, Y.S. Zhang & Y. Xu 1109 (NAS). C. China, Chongqing, Nanchuan, Jinfo Shan, H.M. Li, Y.S. Zhang & X. Zhang 1141 (NAS). D. China, Sichuan, Emei Shan, H.M. Li & Y.S. Zhang 1157 (NAS). All same scale.

opennotspecifiedMay 2022View details →

FIGURE. Umbellules within two populations of Sanicula orthacantha var. brevispina from China, Sichuan, Emei Shan, showing the fruits characters and the variation in numbers of staminate flowers (each line represents a plant individual). The ratio of staminate flowers number/ umbellule number is given for each individual. A. C.H. Li 1122 (NAS). B. H.M. Li & Y.S. Zhang 1151 (NAS). in Taxonomic studies on the genus Sanicula (Apiaceae) from China ( ): The clarification of some morphological distinction between S. orthacantha var. orthacantha and S. orthacantha var. brevispina, with the reduction of S. petagnioides to the synonymy of the former, and S. orthacantha var. stolonifera to

FIGURE. Umbellules within two populations of Sanicula orthacantha var. brevispina from China, Sichuan, Emei Shan, showing the fruits characters and the variation in numbers of staminate flowers (each line represents a plant individual). The ratio of staminate flowers number/ umbellule number is given for each individual. A. C.H. Li 1122 (NAS). B. H.M. Li & Y.S. Zhang 1151 (NAS).

opennotspecifiedMay 2022View details →

FIGURE. Individuals in two Populations of Sanicula orthacantha var. brevispina from China, Sichuan, Emei Shan, showing the variation in plant size and rhizome character (each line represents a population). A. C.H. Li 1122 (NAS). B. H.M. Li & Y.S. Zhang 1151 (NAS). in Taxonomic studies on the genus Sanicula (Apiaceae) from China ( ): The clarification of some morphological distinction between S. orthacantha var. orthacantha and S. orthacantha var. brevispina, with the reduction of S. petagnioides to the synonymy of the former, and S. orthacantha var. stolonifera to

FIGURE. Individuals in two Populations of Sanicula orthacantha var. brevispina from China, Sichuan, Emei Shan, showing the variation in plant size and rhizome character (each line represents a population). A. C.H. Li 1122 (NAS). B. H.M. Li & Y.S. Zhang 1151 (NAS).

opencc-zeroJun 2022View details →

Variations in immune parameters with age in a wild rodent population and links with survival

Recent findings suggest that immune functions do not unidirectionally deteriorate with age but that a potentially adaptive remodelling, where functions of the immune system get down regulated while others get upregulated with age could also occur. Scarce in wild populations, longitudinal studies are yet necessary to properly understand the patterns and consequences of age variations of the immune system in the wild. Meanwhile, it is challenging to understand if the observed variations in immune parameters with age are due to changes at the within-individual level or to selective (dis)appearance of individuals with peculiar immune phenotypes. Thanks to a long-term and longitudinal monitoring of a wild Alpine marmot population, we aimed to understand within- and between-individual variation in the immune phenotype with age, in order to improve our knowledge about the occurrence and the evolutionary consequences of such age-variations in the wild. To do so, we recorded the age-specific leukocyte concentration and leukocyte profile in repeatedly sampled dominant individuals. We then tested whether the potential changes with age were attributable to within-individual variations and/or selective (dis)appearance. Finally, we investigated if the leukocyte concentration and profiles were correlated to the probability of death at a given age. The leukocyte concentration was stable with age, but the relative number of lymphocytes decreased, while the relative number of neutrophils increased, over the course of an individual's life. Moreover, between individuals of the same age, individuals with fewer lymphocytes but more neutrophils were more likely to die. Therefore, selective disappearance seems to play a role in the age variations of the immune parameters in this population. Further investigations linking age variations in immune phenotype to individual fitness are needed to understand whether remodelling of the immune system with age could or could not be adaptive.

opencc-zeroDec 2014View details →

Data from: Population variation reveals independent selection towards small body size in Chinese Debao pony

Body size, one of the most important quantitative traits under evolutionary scrutiny, varies considerably among species and among populations within species. Revealing the genetic basis underlying this variation is very important, particularly in humans where there is a close relationship with diseases and in domestic animals as the selective patterns are associated with improvements in production traits. The Debao pony is a horse breed with small body size that is unique to China; however, it is unknown whether the size-related candidate genes identified in Western breeds also account for the small body size of the Debao pony. Here, we compared individual horses from the Debao population with other two Chinese horse populations using SNPs identified with the Equine SNP 65 Bead Chip. The previously reported size-related candidate gene HMGA2 showed a significant signature for selection, consistent with its role observed in human populations. More interestingly, we found a candidate gene TBX3, which had not been observed in previous studies on horse body size that displayed the highest differentiation and most significant association, and thus likely is the dominating factor for the small stature of the Debao pony. Further comparison between the Debao pony and other breeds of horses from around the world demonstrated that TBX3 was selected independently in the Debao pony, suggesting that there were multiple origins of small stature in the horse.

opennotspecifiedJul 2022View details →

FIGURE. Drosera communis (a–d): a, habit with emerging inflorescence (Parque Nacional das Sempre-Vivas, MG); b, habit with emerging inflorescence; c, variation in flower color within a population (Parque Nacional da Chapada dos Veadeiros, GO); d, habit (Paranapiacaba, SP). Drosera esmeraldae (e, f): e, habit (Puerto Inirida, Guainía, Colombia); f, flower (Gran Sabana, Bolívar, Venezuela). Drosera graminifolia (g–i): g, habit; h, detail of the leaf bases and stipules; i, flower (Serra do Caraça, MG). Photo credits: a–d, g–i by PMG; e by FR; f by AF. in A synopsis of the genus Drosera (Droseraceae) in Brazil

FIGURE. Drosera communis (a–d): a, habit with emerging inflorescence (Parque Nacional das Sempre-Vivas, MG); b, habit with emerging inflorescence; c, variation in flower color within a population (Parque Nacional da Chapada dos Veadeiros, GO); d, habit (Paranapiacaba, SP). Drosera esmeraldae (e, f): e, habit (Puerto Inirida, Guainía, Colombia); f, flower (Gran Sabana, Bolívar, Venezuela). Drosera graminifolia (g–i): g, habit; h, detail of the leaf bases and stipules; i, flower (Serra do Caraça, MG). Photo credits: a–d, g–i by PMG; e by FR; f by AF.

opencc-zeroJul 2022View details →

Spatio-temporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population

Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within-population level. Spatial and temporal environmental heterogeneity represent ecological drivers of within-population genetic variation, determining the evolutionary trajectory of populations along with random processes. Here, we focused on the effects of spatio-temporal heterogeneity on quantitative and molecular variation in a natural population of the annual plant Arabidopsis thaliana. We sampled 1,093 individuals from a Spanish A. thaliana population across an area of 7.4 ha for 10 years (2012-2021). Based on a sample of 279 maternal lines, we estimated spatio-temporal variation in life-history traits and fitness from a common garden experiment. We genotyped 884 individuals with nuclear microsatellites to estimate spatio-temporal variation in genetic diversity. We assessed spatial patterns by estimating spatial autocorrelation of traits and fine-scale genetic structure. We analyzed the relationships between phenotypic variation, geographic location and genetic relatedness, as well as the effects of environmental suitability and genetic rarity on phenotypic variation. The common garden experiment indicated that there was more temporal than spatial variation in life-history traits and fitness. Despite the differences among years, genetic distance in ecologically relevant traits (e.g. flowering time) tended to be positively correlated to genetic distance among maternal lines, whilst isolation by distance was less important. Genetic diversity exhibited significant spatial structure at short distances, which were consistent among years. Finally, genetic rarity, and not environmental suitability, accounted for genetic variation in life-history traits. Synthesis. Our study highlighted the importance of repeated sampling to detect the large amount of genetic diversity at the quantitative and molecular levels that a single A. thaliana population can harbor. Overall, population genetic attributes estimated from our long-term monitoring scheme (genetic relatedness and genetic rarity), rather than biological (dispersal) or ecological (vegetation types and environmental suitability) factors, emerged as the most important drivers of within-population structure of phenotypic variation in A. thaliana.

opencc-zeroSep 2022View details →

Data from: Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata

Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of Triodanis perfoliata, a widespread mix-mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4,705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R2 = 0.63, P = 0.01, n = 9 populations), and we found significant population structuring (FST = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environment appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that T. perfoliata experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of T. perfoliata in the US.

Fig. 3. A 50 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 3. A 50% majority rule consensus tree from MSC-bootstrap analysis of the "All individuals" dataset. Color labels as in figures 1 and 2.

Fig. 2 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 2. Maximum likelihood tree of the "All individuals" concatenated dataset generated with IQ-TREE.Topology with branch lengths in substitutions/site shown in bottom left. Black dots indicate deeper nodes with bootstrap and SH-like aLRT both under 90, otherwise deeper nodes are above 90. Support values for shallow nodes not shown.

Fig. 4 in Divergence in Body Mass, Wing Loading, and Population Structure Reveals Species-Specific and Potentially Adaptive Trait Variation Across Elevations in Montane

Fig. 4. Parameter estimates for fixed effects (β) in spatial mixed effects models (spaMM) for each species, with 95% CIs, testing the effects of Elevation (scaled), AMT (scaled), and Elevation * AMT interaction on traits; Asterisk indicates the CIs did not encompass zero. If no estimate is shown that variable was not included in the model for that species. Maps show spatial trends of trait value from interpolation of estimates for each model (filled.mapMM function in spaMM). Note, for B. vosnesenskii mass and pw-Empty, the low-AIC models were intercept plus random effect only, but for visualization, results are presented for the next best model with at least one fixed effect (seeTable 2 for model details).

Fig. 3 in Divergence in Body Mass, Wing Loading, and Population Structure Reveals Species-Specific and Potentially Adaptive Trait Variation Across Elevations in Montane

Fig. 3. Effect predictions (with 95% CI) of mass (field and empty), thorax size (ITS), forewing area, and transformed wing loading (pw-Field, pw-Empty) against (A) latitude, (B) AMT (Worldclim BIO1 variable), and (C) elevation from univariate linear mixed effects models for B. vancouverensis (blue) and B. vosnesenskii (red). Statistical analyses were conducted on log-transformed mass, ITS, and wing loading (see SuppTable S4 [online only]), but responses were back-transformed to the original scale for plotting (plot_model function in sjPlot). Lines are labeled with significance estimate of the β parameter estimated from lmerTest (*P <0.05; ***P <0.001; unlabeled = not significant, CI encompasses zero).

Fig. 1 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 1. Collection locations in western North America. Colors for S. MCCooki are based on phylogenetic group assignment (see Fig. 2). Female (left) and male (right) S. MaxiMa from Davis, CA shown in inset.

Fig. 5 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 5. Cluster analysis of unlinked SNPs using VAE and carapace length of (a) male and (b) female individuals from Davis, CA. Individuals with carapace length (a)>8.5 mm (male) and (b)>10.0 mm (female) are indicated as S. MaxiMa.