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opencc-zeroJul 2019View details →

Data from: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions

The cochlea and semicircular canals of the inner ear are vital neurosensory devices. There are associations between the anatomy of these sensorineural structures, their function, and the function of related biological systems, e.g., hearing ability, gaze stabilization, locomotor agility, and posture. The endosseous labyrinth is frequently used as a proxy to infer the performance of the hearing and vestibular systems, locomotor abilities, and ecology of extinct species. Such fossil inferences are often based on single specimens or even a single ear, representing an entire species. To address whether a single ear is representative of a population, we used geometric morphometrics to quantitatively assess the variation in shape and symmetry in a sample of endosseous labyrinths of wild turkeys Meleagris gallopavo of southern Ohio. We predicted that ears would be symmetrical both within individuals and across the sample; that labyrinth shape and size would covary; that labyrinth shape would vary with the size of the brain, measured as width of the endocranium at the cerebellum; and that labyrinths would be morphologically integrated. To test these predictions, we microCT-scanned the heads of 26 cadaveric turkeys, digitally segmented their endosseous labyrinths in Avizo, and assigned 15 manual landmarks and 20 sliding semilandmarks to each digital model. Following Procrustes alignment, we conducted an analysis of bilateral symmetry, a Procrustes regression analysis for allometry and other covariates including side and replicate, and analyses of global integration and modularity. Based on Procrustes distances, no individual's left and right ears were clearly different from each other. When comparing the ears of different specimens, statistically clear differences in shape were found in only 66 of more than 1300 contrasts. Moreover, effects of both directional and fluctuating asymmetry were very small—generally, two orders of magnitude smaller than the variance explained by individual variation. Statistical tests disagreed on whether these asymmetric effects crossed the threshold of significance, possibly due to non-isotropic variation among landmarks. Regardless, labyrinths appeared to primarily vary in shape symmetrically. Neither labyrinth size nor endocranial width was correlated with labyrinth shape, contrary to our expectations. Finally, labyrinths were found to be moderately integrated in a global sense, but four weakly separated modules—the three semicircular canals and cochlea—were recovered using a maximum-likelihood analysis. The results show that both fluctuating and directional asymmetry play a larger role in shape variation than expected—but nonetheless, endosseous labyrinths are symmetrical within individuals and at the level of the population, and their shape varies symmetrically. Thus, inferences about populations, and very possibly species, may be confidently made when only a single specimen, or even a single ear, is available for study.

Fig. 8 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 8. Asymmetrically reduced lower mandible of specimen LPB006.

Fig. 1 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 1. Multilimbed embryo (LPB001) that also displays numerous deformities of the head. Ventral

Fig. 6 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 6. Symmetrically reduced mandibles of specimen LPB004.

Fig. 4. X in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 4. Xray of LPB002 showing that there is but a single vertebral column.

Fig. 7 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 7. Clubbed feet of specimen LPB005.

Fig. 2. X in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 2. Xray of LPB001 showing duplication of vertebral structures.

Fig. 5 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 5. Externalized eye of specimen LPB003.

Fig. 12 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 12. Externalized brain of specimen LPB010 that is missing several bones of the skull.

Fig. 10 in Developmental Abnormalities in Wild Populations of Birds: Examples from Lesser Snow Geese (Chen caerulescens caerulescens)

Fig. 10. Skull abnormalities of specimen LPB008.

opencc-by-4.0Nov 2022View details →

Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population

This repository holds the datasets and R code files needed to run the models in: Brandell et al., 2022. Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population. PLOS ONE. Excel files have associated KEYs for each data column; CSVs are analyzed with their associated R code.

opencc-by-4.0Dec 2022View details →

Supplementary materials. Publication "Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations" by Bouilloud et al.

Supplementary information Supplementary Figure S1. Maps showing the sampling area (left) and localities (right) in France. Forests are indicated in green and water in blue. The four sampling localities are represented with a colored polygon. The arrow indicates the North.   Supplementary Figure S2. Composition of the gut bacteriota. The relative abundance of six phyla representing 99% of the total composition is represented. Individuals are grouped by sampling localities, which are ordered from North to South. (A) Bar graph shows individual variation in phyla composition (phylum=color). (B) Box and whisker plots represent median and interquartile values for each phylum. Black dots correspond to mean values, and colored dots correspond to individuals.   Supplementary Figure S3. Variations of alpha diversity with individual factors, for the gut bacteriota (family level), pathogenic bacteria and gastro-intestinal helminths of bank voles. Alpha diversity is estimated using the specific richness (A, B and C) and the Shannon index (D, E and F). In graphs C and F, the blue line corresponds to the linear regression line.   Supplementary Figure S4. Relationships between the composition of the gut bacteriota, pathogenic bacteria and gastro-intestinal helminth communities: The db-RDA triplot shows the structure of the gut bacteriota at the phylum level and the correlations with the intra-host parasite communities. The arrows correspond to the significant explanatory variables. Each point corresponds to an individual, and the colors correspond to the different sampling localities.   Supplementary Table S1. Variation of the Firmicutes/Bacteroidetes ratio with localities and individual factors.   Supplementary Table S2. Alpha diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles.   Supplementary Table S3. Beta diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles

opencc-zeroApr 2023View details →

Adaptive significance of affiliative behaviour differs between sexes in a wild reptile population

In recent years, we have begun to appreciate that social behaviours might exhibit repeatable among-individual variation. Such behavioural traits may even covary and have critical evolutionary implications. Importantly, some social behaviours such as aggressiveness have been shown to provide fitness benefits, including higher reproductive success and survival. However, fitness consequences of affiliative behaviours, especially between or among sexes, can be more challenging to establish. Using a longitudinal behavioural dataset (2014-2021) collected on eastern water dragons (Intellagama lesueurii), we investigated whether various aspects of affiliative behaviour (1) were repeatable across years, (2) covaried with each other at the among-individual level, and (3) influenced individuals' fitness. In particular, we considered affiliative behaviours towards opposite-sex and same-sex conspecifics separately. We found that social traits were repeatable and covaried with each other similarly for both sexes. More notably, we found that male reproductive success was positively correlated with the number of female associates and the proportion of time spent with females, whilst females' reproductive success was not correlated with any of the measured social behaviour metrics. Overall, these findings suggest that selection may be acting differently on social behaviour of male and female eastern water dragons.

opencc-zeroApr 2023View details →

Genotype data for wild lupin populations from central Michigan

Habitat degradation can have significant effects on native species inhabiting natural ecosystems. Within oak barrens and oak-pine barrens ecosystems, there is a complex interspecies interaction between the federally endangered Karner blue butterfly (Lycaeides melissa samuelis) and its obligate host plant, wild lupine (Lupinus perennis L.). Recruitment of wild lupine is critical for maintaining butterfly populations; however, this recruitment can be impeded by habitat fragmentation. Reduced recruitment can result in low genetic diversity in isolated populations, limiting its adaptive potential to respond to environmental change. This study was aimed at understanding the genetic diversity and population structure of wild lupine populations throughout central and west Michigan. We identified significant population structure across most of the populations sampled, with only two sites not significantly different from each other. No sites within our study area displayed statistically significant levels of inbreeding. There are also at least two genetic clusters of wild lupine present within our study region, although there is significant overlap among these groups, indicating that genetic differentiation among clusters may be limited.

opencc-zeroJul 2023View details →

Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds

Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.

opencc-zeroSep 2023View details →

Contaminated sediment in the Detroit River selects for evolved CYP1A and p53 responses in wild brown bullhead (Ameiurus nebulosus) populations

<div> <div> In a previous study, adaptive responses to a single polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), were identified in brown bullhead (Ameiurus nebulosus) captured from contaminated sites across the Great Lakes. The tumor suppressor p53 and phase I toxin metabolizing CYP1A genes showed a protective and refractory response, respectively, up to the F1 generation (Williams and Hubberstey, 2014). As an extension to the first study, bullhead were exposed to sediment collected from sites along the Detroit River to see if these adaptive responses are attainable when fish from a contaminated site are exposed to a mixture of contaminants, instead of a single compound. p53 and CYP1A proteins were measured in both studies with the addition of phase II glutathione-s-transferase (GST) activity in the second. Three treatment groups were measured: acute (treated immediately), cleared (depurated for three months and subsequent treatment), and farm raised F1 offspring. All three treatment groups were exposed to clean and contaminated sediment for 24 and 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed an initial elevated p53 response that was not reached in cleared fish exposed to contaminated sediment. Instead, cleared and F1 bullhead from clean and contaminated sites had overlapping p53 expression patterns in response to contaminated sediment by 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed refractory CYP1A expression, which disappeared in cleared fish and whose F1 refractory response overlapped with clean site F1 offspring. Decreasing GST activity was evident in both clean and contaminated fish over time, with clean site fish responding to contaminated sediment more deliberately. By 96 hours, the response patterns of F1 offspring from clean and contaminated sites to clean and contaminated sediment exposures were similar. </div> <div> Because p53, CYP1A and GST activity responses to contaminated sediment dosing overlapped in clean and contaminated farm-raised F1 offspring, these results suggest that contaminated fish have acclimated to the contaminants present in their environments by reaching a tolerance threshold and no evidence of adaptation was detected in these biomarkers. </div> </div>

publicApr 2023View details →

More people, more cats, more parasites: Human population density and temperature variation predict the prevalence of Toxoplasma gondii oocyst shedding in free-ranging domestic and wild felids

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publicMar 2023View details →

Data for: Differential genotype response to increased resource abundance helps explain parallel evolution of Daphnia populations in the wild

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publicOct 2025View details →

Amblema plicata microsatellite data from wild and hatchery produced populations

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