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openCC (other)Mar 2024View details →

Growth, development, activity, and survival of wood frog tadpoles from different populations in eastern NY in 2022.

These data were collected as two lab experiments that examined larval (i.e., tadpole) wood frog populations. The first was a time-to-death experiment in which we exposed individuals tadpoles to either a control or lethal concentrations of NaCl. The second was a growth and development experiment in which we raised tadpoles from the same populations in a sublethal concentration of NaCl for several weeks to examine their growth and development (i.e. Gosner developmental stage).

openCC (other)Jun 2024View details →

Relyea, R. A. 2002. Local population differences in phenotypic plasticity: Predator-induced changes in wood frog tadpoles. Ecological Monographs 72:77-93

Taxa that are divided into separate populations with low levels of interpopulation dispersal have the potential to evolve genetically based differences in their phenotypes and the plasticity of those phenotypes. These differences can be due to random processes, including genetic drift and founder effects, or they can be the result of different selection pressures among populations. I investigated population-level differences in predator- induced phenotypic plasticity in eight populations of larval wood frogs (Rana sylvatica) over a small geographic scale (interpopulation distances of 0.3–8 km). Using a common-garden experiment containing predator and no-predator environments, I found population differences in behavior, morphology, and life history. These responses exhibited a habitat-related pattern: the four populations from closed-canopy ponds did not differ from each other in any of their phenotypes whereas the four populations from opencanopy ponds did differ from each other in these traits. This phenotypic pattern matches the pattern of competitors and predators found in these two types of ponds. Based on two years of pond surveys, the four closed-canopy ponds contained very similar competitor and predator assemblages while the assemblages of the four open-canopy ponds were more diverse and highly variable among open-canopy ponds. When combined with past studies, which demonstrate that predators and competitors select for alternative behavioral and morphological traits, these patterns suggest that the population differences may have arisen via natural selection and not via random mutation or drift. In a second experiment, I cross-transplanted two of the populations into each other’s ponds to determine if the populations were locally adapted to the conditions of their native pond (using low and high competition crossed with the presence or absence of a lethal predator). The populations continued to exhibit phenotypic differences, and one of the two populations t

openCC (other)Aug 2024View details →

Blarina brevicauda populations in three different habitats in east-central Illinois, 1972 to 1997.

The population demography of the northern short-tailed shrew, Blarina brevicauda, was monitored monthly from 1972-1997 in bluegrass, alfalfa, and tallgrass prairie habitats in east-central Illinois. Blarina brevicauda were incidentally collected as part of a 25-year prairie vole (Microtus ochrogaster) and meadow vole (M. pennsylvanicus) trapping study. The study sites were located in the University of Illinois Biological Research Area (Phillips Tract) and Trelease Prairie. Animals were trapped with wooden multiple-capture live-traps. Over the span of 25 years, three 3-day trapping sessions monthly were conducted to cover the three habitats. All live shrews were toe-clipped at first capture for individual identification. Animals known to be present on study site, but not captured, were included in totals for that month. While trap mortality of shrews was high in this study (40%), the data obtained were sufficient for analysis of many aspects of the demography of the species.

openCC0Jul 2021View details →

CBP01 Variable distance line-transect sampling of bird population numbers in different habitats on Konza Prairie (Reformatted to a Darwin Core Archive)

This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/339/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-knz/26/11. The abstract below was extracted from the Level 0 data package and is included for context: Records of bird species based on line transect sampling, giving perpendicular distance of sighting from the transect line on 16 separate transects. Bird surveys were conducted 2-4 times per year in January, April, June, and October for a 29-year period from 1981 to 2009. Transects were designed to determine bird communities and population numbers associated with tallgrass prairie habitats with different experimental treatments (fire frequency, grazed by bison vs. ungrazed), riparian habitats on forest edge, and gallery forests dominated by oak woodland.

opencc-zeroDec 2019View details →

Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)

Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically-important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed (Centaurea diffusa Lam. [Asteraceae]). To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and the one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.

opencc-zeroDec 2016View details →

Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host

Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.

opencc-by-4.0Dec 2021View details →

Figure 3 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 3. – Projection of Procrustes coordinates and scores of canonical variate on Aphanius fasciatus shape analysis (A) and comparative transformation grids (B). LM: Mellah lagoon, M: Mellah marsh, BZ: Lagoon of Bizerte, LA: Ayata Lake.

opencc-by-4.0Dec 2021View details →

Figure 2 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 2. – Landmarks distribution on fish body of Aphanius fasciatus. 1: Eye position, 2: Dorsal opercular limit, 3: Beginning of dorsal fin, 4: End of dorsal fin, 5: Dorsal limit of caudal peduncle, 6: Median limit of caudal peduncle, 7: Ventral limit of caudal peduncle, 8: End of anal fin, 9: Beginning of anal fin, 10: Pelvic fin insertion, 11: Ventral opercula limit, 12: Dorsal limit of pectoral fin, 13: Ventral limit of pectoral fin, 14: Mouth.

opencc-by-4.0Dec 2021View details →

Figure 1 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 1. – Map of the west Mediterranean basin with North African sample sites. 1: Mellah lagoon (LM), 2: Mellah marsh (M), 3: Lagoon of Bizerte (BZ), 4: Ayata Lake (LA).

opencc-zeroFeb 2024View details →

Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection

Phylogenetic reconstruction and introgression detection rely on an assumption about the probability distribution of gene tree topologies. Recently, evidence has emerged that population size differences can affect the probability distribution of gene tree topologies in the presence of purifying selection. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can lead to biases in phylogenetic inference. We also provide evidence that in the presence of purifying selection, population size differences can cause statistics used for introgression detection to exhibit patterns resembling those caused by introgression. In addition, we present a theoretical analysis showing that the occurrence of population size–dependent gene tree distributions is an inherent consequence of purifying selection. Our work underscores the importance of considering the potential confounding effect of purifying selection on phylogenetic inference and introgression detection.

opencc-by-4.0Dec 2023View details →

Fat oxidation rates and cardiorespiratory responses during exercise in different subject populations with post-acute sequelae of SARS-CoV-2 infection: a comparison with normative percentile values

INTRODUCTION: Post-acute sequelae of SARS-CoV-2 infection (PASC) presents a spectrum of symptoms following acute COVID-19, with exercise intolerance being a prevalent manifestation likely linked to disrupted oxygen metabolism and mitochondrial function. This study aims to assess maximal fat oxidation (MFO) and exercise intensity at MFO (FATmax) in distinct PASC subject groups and compare these findings with normative data. METHODS: Eight male subjects with PASC were involved in this study. The participants were divided in two groups: “endurance-trained” subjects (V̇O2max > 55 ml/min/kg) and “recreationally-active” subjects (V̇O2max < 55 ml/min/kg). Each subject performed a graded exercise test until maximal oxygen consumption (V̇O2max) to measure fat oxidation. Subsequently, MFO was assessed and FATmax calculated as the ratio between V̇O2 at MFO and V̇O2max. RESULTS: The MFO and FATmax of “endurance-trained” subjects were 0.85, 0.89, 0.71 and 0.42, and 68%, 69%, 64% and 53%, respectively. Three out of four subjects showed both MFO and FATmax values placed over the 80th percentile of normative data. The MFO and FATmax of “recreationally-active” subjects were 0.34, 0.27, 0.35 and 0.38, and 47%, 39%, 43% and 41%, respectively. All MFO and FATmax values of those subjects placed below the 20th percentile or between the 20th and 40th percentile. DISCUSSION: Significant differences in MFO and FATmax values between 'endurance-trained' and “recreationally-active” subjects suggest that specific endurance training, rather than simply an active lifestyle, may provide protective effects against alterations in mitochondrial function during exercise in subjects with PASC.

opencc-zeroApr 2024View details →

Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?

When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot's pipit populations, between subspecies across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million – ca. 8,000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism, and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism, and immune defence.