Joseph Ivan Hoffman

Joseph Ivan Hoffman
Bielefeld University · Animal Behaviour Work Group

PhD

About

328
Publications
51,666
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
5,059
Citations
Introduction
Our research focuses on the molecular ecology of natural populations and uses a combination of classical genetic markers and population genomic approaches to address a variety of questions relating to genetic diversity and its maintenance in the wild.
Additional affiliations
October 2010 - present
Bielefeld University
Position
  • Professor
October 2007 - October 2010
University of Cambridge
Position
  • PostDoc Position

Publications

Publications (328)
Article
Full-text available
Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a...
Article
Understanding the ability of animals to cope with a changing environment is critical in a world affected by anthropogenic disturbance. Individual foraging strategies may influence the coping ability of entire populations, as these strategies can be adapted to contrasting conditions, allowing populations with foraging polymorphisms to be more resili...
Article
Full-text available
Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic‐pituitary‐adrenal (HPA) axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the f...
Article
The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the ori...
Article
Full-text available
Adult survival is a key component of population dynamics, and understanding variation in and the drivers of adult survival rates and longevity is critical for ecological and evolutionary studies, as well as for conservation biology and practice. Tropical species of landbirds are often selected to have higher adult survival due to high nest predatio...
Article
Full-text available
Intraspecific variation in animal mating systems can have important implications for ecological, evolutionary and demographic processes in wild populations. For example, patterns of mating can impact social structure, dispersal, effective population size and inbreeding. However, few species have been studied in sufficient detail to elucidate mating...
Preprint
Full-text available
Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or stressors often produce an individualized response of the hypothalamic-pituitary-adrenal axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping indiv...
Article
Full-text available
Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice-associated prey and ice-free coastal breeding areas. We reconstr...
Article
Full-text available
A long-standing paradox of marine populations is chaotic genetic patchiness (CGP), temporally unstable patterns of genetic differentiation that occur below the geographic scale of effective dispersal. Several mechanisms are hypothesized to explain CGP including natural selection, spatiotemporal fluctuations in larval source populations, self-recrui...
Article
Full-text available
In species that live in family groups, such as cooperative breeders, inbreeding is usually avoided through the recognition of familiar kin. For example, individuals may avoid mating with conspecifics encountered regularly in infancy, as these likely include parents, siblings, and closely related alloparents. Other mechanisms have also been reported...
Article
Full-text available
Tracking studies of juveniles are rare compared to those of adults, and consequently little is known about the influence of intrinsic and extrinsic factors on activity during this critical life stage. We used hourly GPS data, collected from 66 Antarctic fur seal pups from birth until moulting, to investigate the explanatory power of multiple indivi...
Article
Full-text available
Mussels belonging to the Mytilus species complex (M. edulis, ME; M. galloprovincialis, MG; and M. trossulus, MT) often occur in sympatry, facilitating introgressive hybridisation. This may be further promoted by mussel aquaculture practices, with MT introgression often resulting in commercially unfavourable traits such as low meat yield and weak sh...
Article
Full-text available
Rawls argued that fairness in human societies can be achieved if decisions about the distribution of societal rewards are made from behind a veil of ignorance, which obscures the personal gains that result. Whether ignorance promotes fairness in animal societies, that is, the distribution of resources to reduce inequality, is unknown. Here we show...
Article
Full-text available
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zaloph...
Preprint
Full-text available
Intraspecific variation in animal mating systems can have important implications for ecological, evolutionary and demographic processes in wild populations. For example, patterns of mating can impact social structure, dispersal, effective population size and inbreeding. However, few species have been studied in sufficient detail to elucidate mating...
Article
Full-text available
Allee effects play an important role in the dynamics of many populations and can increase the risk of local extinction. However, some authors have questioned the weight of evidence for Allee effects in wild populations. We therefore exploited a natural experiment provided by two adjacent breeding colonies of contrasting density to investigate the p...
Preprint
Full-text available
Tracking studies of juveniles are rare compared to those of adults and consequently, little is known about the influence of intrinsic and extrinsic factors on activity during this critical life stage. We therefore collected GPS data from birth until moult from 66 Antarctic fur seal pups in two nearby but contrasting breeding colonies. The Special S...
Article
Behavioral mechanisms for avoiding inbreeding are common in the natural world and are believed to have evolved as a response to the negative consequences of inbreeding. However, despite a fundamental role in fitness, we have a limited understanding of the cues that individuals use to assess inbreeding risk, as well as the extent to which individual...
Article
Full-text available
Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publ...
Article
Full-text available
In some animal species, individuals regularly breed with relatives, including siblings and parents. Given the high fitness costs of inbreeding, evolutionary biologists have found it challenging to understand the persistence of these inbred societies in nature. One appealing but untested explanation is that early life care may create a benign enviro...
Article
Full-text available
The three mussel species comprising the Mytilus complex are widespread across Europe and readily hybridize when they occur in sympatry, resulting in a mosaic of populations with varying genomic backgrounds. Two of these species, M. edulis and M. galloprovincialis, are extensively cultivated across Europe, with annual production exceeding 230,000 to...
Article
Full-text available
The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimat...
Article
Full-text available
Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO3 crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite mu...
Article
Full-text available
Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 d...
Article
Full-text available
Eukaryotic organisms vary widely in genome size and much of this variation can be explained by differences in the abundance of repetitive elements. However, the phylogenetic distributions and turnover rates of repetitive elements are largely unknown, particularly for species with large genomes. We therefore used de novo repeat identification based...
Article
Full-text available
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetri...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
Replication studies are essential for assessing the validity of previous research findings and for probing their generality. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes...
Preprint
Full-text available
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 90K Affymetri...
Article
Full-text available
Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arcto...
Article
Full-text available
The soft-shell clam Mya arenaria is one of the most ancient invaders of European coasts and is present in many coastal ecosystems, yet little is known about its genetic structure in Europe. We collected 266 samples spanning a latitudinal cline from the Mediterranean to the North Sea and genotyped them at 12 microsatellite loci. In parallel, geometr...
Article
Full-text available
The gut microbiome is an integral part of a species’ ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups sta...
Preprint
Full-text available
The gut microbiome is an integral part of a species’ ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups sta...
Article
Full-text available
Marine encrusting communities play vital roles in benthic ecosystems and have major economic implications with regards to biofouling. However, their ability to persist under projected warming scenarios remains poorly understood and is difficult to study under realistic conditions. Here, using heated settlement panel technologies, we show that after...
Article
Full-text available
The Antarctic fur seal (Arctocephalus gazella) is an abundant Antarctic otariid. Here, we present the complete mitochondrial DNA sequence of this species, which includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and the control region for a total length of 16,156 bp. A phylogenetic analysis including all 25 publically a...
Article
Full-text available
Abstract Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity–fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral...
Article
Full-text available
Recent developments in genomics are advancing our understanding of the processes shaping population structure in wild organisms. In particular, reduced representation sequencing has facilitated the generation of dense genetic marker datasets that provide greater power for resolving population structure, investigating the role of selection and recon...
Article
Full-text available
Background The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo tran...
Article
Despite an increasing appreciation of the importance of host‐microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low s...
Article
Full-text available
Background Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it can be challenging to select the restriction enzyme that offers the best balance between the number of obtained RAD loci and dept...
Article
Full-text available
A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potenti...
Article
Full-text available
Cultivated bivalves are hugely important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium density single...
Data
R-code for “A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal.”
Article
Full-text available
Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed...