Biology subjects

Hoffman, J. I.

Publications and source records attributed to Hoffman, J. I..

4 recordsLinked to original sources

bioRxiv2018

Recent demographic histories and genetic diversity across pinnipeds are shaped by anthropogenic interactions and mediated by ecology and life-history

A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and negatively impact population viability and adaptive potential. In an era of unprecedented biodiversity loss and climate change, understanding both the determinants and consequences of bottlenecks in wild populations is therefore an increasingly important challenge. However, as most studies have focused on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we used a comparative approach by integrating genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to elucidate the consequences of large-scale commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong genetic signatures of recent population declines, with estimated bottleneck effective population sizes reflecting just a few tens of surviving individuals in the most extreme cases. Bottleneck strength was strongly associated with both breeding habitat and mating system variation, and together with global abundance explained a large proportion of the variation in genetic diversity across species. Overall, there was no relationship between bottleneck intensity and IUCN status, although three of the four most heavily bottlenecked species are currently endangered. Our study reveals an unforeseen interplay between anthropogenic exploitation, ecology, life history and demographic declines, sheds new light on the determinants of genetic diversity, and is consistent with the notion that both genetic and demographic factors influence population viability.

evolutionary biology↗

bioRxiv2017

Demographic causes of adult sex ratio variation and their consequences for parental cooperation

The adult sex ratio (ASR) is a fundamental concept in population biology, sexual selection, and social evolution. However, it remains unclear which demographic processes generate ASR variation and how biases in ASR in turn affect social behaviour. Here, we evaluate the demographic mechanisms shaping ASR and their consequences for parental cooperation using detailed survival, fecundity, and behavioural data on 6,119 individuals from six wild shorebird populations exhibiting flexible parental strategies. We show that these closely related populations express strikingly different ASRs, despite having similar ecologies and life histories, and that ASR variation is largely driven by sex differences in the apparent survival of juveniles. Furthermore, families in populations with biased ASRs were predominantly tended by a single parent, suggesting that parental cooperation breaks down with unbalanced sex ratios. Taken together, our results indicate that sex biases emerging during early life have profound consequences for social behaviour.

ecology↗

bioRxiv2017

Adult sex ratio bias in snowy plovers is driven by sex-specific early survival: implications for mating systems and population growth

Adult sex ratio (ASR) is a central concept in population biology and a key factor in sexual selection, yet why do most demographic models ignore sex-biases? Vital rates often vary between the sexes and across life history, but their relative contributions to ASR variation remain poorly understood--an essential step to evaluate sex ratio theories in the wild and inform conservation. Here we combine structured two-sex population models with individual-based mark-recapture data from an intensively monitored polygamous population of snowy plovers. We show that a strongly male-biased ASR is primarily driven by sex-specific survival of juveniles, rather than adults or dependent offspring. This provides empirical support for theories of unbiased sex allocation when sex-differences in survival arise after the period of parental investment. Importantly, a conventional model ignoring sex-biases significantly overestimated population viability. We suggest that sex-specific population models are essential to understand the population dynamics of sexual organisms: reproduction and population growth is most sensitive to perturbations in survival of the limiting sex. Overall, our study suggests that sex-biased early survival may contribute towards mating system evolution and population persistence, with implications for both sexual selection theory and biodiversity conservation.\n\nSIGNIFICANCE STATEMENTSex biases are widespread in nature and represent a fundamental component of sexual selection and population biology--but at which point in life history do these biases emerge? Here we report a detailed individual-based demographic analysis of an intensively studied wild bird population to evaluate the origins of sex biases and their consequences on mating strategies and population dynamics. We document a strongly male-biased adult sex ratio, which is consistent with behavioral observations of female-biased polygamy. Notably, sex-biased juvenile, rather than adult survival, contributed most to the adult sex ratio. Sex-biases also strongly influenced population viability, which was significantly overestimated when sex ratio and mating system were ignored. Our study therefore has implications for both sexual selection theory and biodiversity conservation.

ecology↗

bioRxiv2017

GCalignR: An R package for aligning Gas-Chromatography data

Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, gas chromatography (GC) in combination with either mass spectrometry (MS) or flame ionisation detection (FID) are commonly used to characterise complex chemical samples. Both GC-FID and GC-MS generate chromatograms comprising peaks that are separated according to their retention times and which represent different substances. Across chromatograms of different samples, homologous substances are expected to elute at similar retention times. However, random and often unavoidable experimental variation introduces noise, making the alignment of homologous peaks challenging, particularly with GC-FID data where mass spectral data are lacking. Here we present GCalignR, a user-friendly R package for aligning GC-FID data based on retention times. The package also implements dynamic visualisations to facilitate inspection and fine-tuning of the resulting alignments, and can be integrated within a broader workflow in R to facilitate downstream multivariate analyses. We demonstrate an example workflow using empirical data from Antarctic fur seals and explore the impact of user-defined parameter values by calculating alignment error rates for multiple datasets. The resulting alignments had low error rates for most of the explored parameter space and we could also show that GCalignR performed equally well or better than other available software. We hope that GCalignR will help to simplify the processing of chemical datasets and improve the standardization and reproducibility of chemical analyses in studies of animal chemical communication and related fields.

animal behavior and cognition↗