Biology subjects

Tallman, R. F.

Publications and source records attributed to Tallman, R. F..

3 recordsLinked to original sources

bioRxiv2024

Estimating survival of an anadromous salmonid using Bayesian hierarchical models applied to acoustic telemetry, biological, and environmental data

Hierarchical modelling is frequently used to model ecological processes because of its ability to handle complex ecological phenomena by decomposing them into naturally explainable sub-models. Hierarchical Bayesian approaches have gained widespread use in health, social, and environmental sciences, including in the estimation of demo-graphic parameters such as survival. In this study, we combine Bayesian hierarchical models with acoustic telemetry data to estimate survival probabilities for high-latitude populations of an anadromous salmonid, the Arctic char (Salvelinus alpinus), while in-corporating environmental and biological covariates to assess their impact on survival. The model we present here can also account for temporally varying detection probabilities due to changes to the acoustic receiver array design and seasonal variation in the detection probabilities related to environmental conditions (e.g., ice vs. no ice). As previously documented in this species, survival was high (> 0.87) and we found that the covariates pertaining to sea ice coverage and Fultons condition factor impacted the survival probabilities. Contrary to our expectations, high-condition fish had lower survival rates. Survival was also considerably lower during the summer (open-water) compared to winter (ice-covered) seasons. While the biological explanations and implications of these findings require further exploration, they nonetheless demonstrate the utility of this approach. Specifically, we present a hierarchical Bayesian model that can consider environmental and biological covariates while accounting for varying detection probabilities, a major concern of acoustic telemetry studies. The model can be easily adapted for other taxa with similar life histories where mark recapture data are available and can be extended to include additional environmental (e.g., salinity) and biological parameters (e.g., sex).

ecology↗

bioRxiv2017

Migration Harshness Drives Habitat Choice And Local Adaptation In Anadromous Arctic Char: Evidence From Integrating Population Genomics And Acoustic Telemetry

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise FST = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian Computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in non-breeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in non-model organisms in logistically challenging environments such as the Arctic.

evolutionary biology↗

bioRxiv2016

Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Using massively parallel sequencing data from two species with different life history traits -- American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus) -- we highlighted how an unbalanced sex ratio in the samples combined with a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Multivariate analyses revealed two genetic clusters that separated males and females instead of showing the expected pattern of genetic differentiation among ecologically divergent (inshore vs. offshore in lobster) or geographically distant (east vs. west in Arctic Char) sampling locations. We created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia for lobster, and that Fst values were overestimated for Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to nonsignificant genetic structure (lobster) and a more accurate estimation of Fst (Arctic Char). We further characterized the putative functions of sex-linked markers. Given that only 9.6% of all marine/diadromous population genomic studies to date reported sex information, we urge researchers to collect and consider individual sex information. In summary, we argue that sex information is useful to (i) control sex ratio in sampling, (ii) overcome \"sex-ratio bias\" that can lead to spurious genetic differentiation signals and (iii) fill knowledge gaps regarding sex determining systems.

genomics↗