Nicholas W. Jeffery

Bedford Institute of Oceanography · Fisheries and Oceans Canada

The study of genome size diversity is an ever-expanding field that is highly relevant in today's world of rapid and efficient DNA sequencing. Animal genome sizes range from 0.02 to 132.83 pg but the majority of animal genomes are small, with the most of these genome sizes being less than 5 pg. Animals with large genomes (> 10 pg) are scattered with...

The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has...

Advances in genetic sequencing technologies and techniques have made large, genome-wide datasets comprised of hundreds or even thousands of individuals and loci the norm rather than the exception even for non-model organisms. While such data presents new opportunities for evaluating population structure and demographic processes, the large size of...

Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia fro...

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, repr...

Context Prioritizing regions that facilitate connectivity among populations is an essential principle for conservation planning. However, the lack of conspicuous geographical and environmental features that constrain dispersal and gene flow throughout life history challenges the characterization of dispersal pathways within a three-dimensional mari...

Marine Protected Areas require comprehensive monitoring to ensure objectives are achieved; however, monitoring natural ecosystems at scale is challenged by the biodiversity it aims to measure. Environmental DNA (eDNA) metabarcoding holds promise to address this monitoring challenge. We conducted paired sampling at 54 sites for fish and invertebrate...

A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. Ho...

A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. Ho...

Context Prioritizing regions that facilitate connectivity among populations is an essential principle for conservation planning. However, the lack of conspicuous geographical and environmental features that constrain dispersal and geneflow throughout life history challenges the characterization of dispersal pathways within a three-dimensional marin...

A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. Ho...

A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and...

Marine Protected Areas (MPAs) have been adopted globally as a tool to combat biodiversity loss and restore marine ecosystems. Successful application of MPAs will be predicated on the ability to monitor biodiversity in a synoptic and non-invasive manner. Environmental DNA (eDNA) methods have important advantages over traditional biodiversity survey...

Marine classification schemes based on abiotic surrogates often inform regional marine conservation planning in lieu of detailed biological data. However, these schemes may poorly represent ecologically relevant biological patterns required for effective design and management strategies. We used a community-level modeling approach to characterize a...

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. It is an especially effective approach for investigating the marine microbiome. To mature marine microbiome rese...

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. To achieve a global ocean biomolecular observing network (OBON) for the UN Decade of Ocean Science for Sustainab...

Significance Despite great progress in uncovering the genomic underpinnings of advanced forms of social organization like eusociality, much less is known about how eusociality feeds back to drive genome evolution. Using snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size, we show that eus...

Canada has committed to developing effective and representative marine conservation networks. Guidance for the development of these networks focuses on core design features, including the incorporation of ecologically and biologically significant areas, ecological representation, replication, connectivity, and adequacy/viability. Network planning u...

The Biophysical and Ecological Overview of the Eastern Shore Islands Area of Interest (AOI) summarizes what is known about key physical and biological components of the Eastern Shore Islands ecosystem. These key attributes and description of their ecosystem function can be used to inform the development of Conservation Objectives and management mea...

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such quantifying diversity is central to combatting ongoing wide spread reductions in biodiversity. With the advent of next‐generation sequencing, several methods now exist for resolving fine‐scale population structure, but...

The impacts of climate change and the socioecological challenges they present are ubiquitous and increasingly severe. Practical efforts to operationalize climate-responsive design and management in the global network of marine protected areas (MPAs) are required to ensure long-term effectiveness for safeguarding marine biodiversity and ecosystem se...

Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct cha...

In 2010, the Conference of the Parties of the Convention on Biological Diversity agreed on the Strategic Plan for Biodiversity 2011-2020 in Aichi Prefecture, Japan. As this plan approaches its end, we discussed whether marine biodiversity and prediction studies were nearing the Aichi Targets during the 4th World Conference on Marine Biodiversity he...

Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreedi...

Hybridization between wild and escaped cultured Atlantic salmon (Salmo salar) can threaten the stability and persistence of locally adapted wild populations. Here we describe the development and validation of a genomic-based approach to quantify recent hybridization between escapee and wild salmon in the western Atlantic. Based on genome-wide singl...

Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genet...

In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus) has been characterized by a latitudinal genetic cline with a breakpoint between northern and southern genetic clusters occurring at ~45°N along eastern Nova Scotia, Canada. Using 96 diagnostic single-nucleotide polymorphisms (SNPs) capable of discriminating between northern and...

The spatial genetic structure of most species in the open marine environment remains largely unresolved. This information gap creates uncertainty in the sustainable management, recovery, and associated resilience of marine communities and our capacity to extrapolate beyond the few species for which such information exists. We document a previously...

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools a...

In animals, genome size is correlated with many traits that also vary with latitude, such as body size and developmental rate. Crustaceans have highly variable genome sizes (ranging nearly 650-fold), and some polar crustaceans have exceptionally large genomes. Here, we investigate whether genome size is positively correlated with latitude across 27...

Genetic-environment associations are increasingly revealed through population genomic data and can occur through a number of processes, including secondary contact, divergent natural selection, or isolation-by-distance. Here we investigate the influence of the environment, including seasonal temperature and salinity, on the population structure of...

The escape of Atlantic salmon (Salmo salar) from aquaculture facilities can result in both negative genetic and ecological interactions with wild populations, yet the ability to predict the associated risk to wild populations has remained elusive. Here we assess the potential of a spatiotemporal database of aquaculture facility locations, productio...

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American...

The ability to detect and characterize hybridization in nature has long been of interest to many fields of biology and often has direct implications for wildlife management and conservation. The capacity to identify the presence of hybridization, and quantify the numbers of individuals belonging to different hybrid classes, permits inference on the...

Within animals a positive correlation between genome size and body size has been detected in several taxa but not in others, such that it remains unknown how pervasive this pattern may be. Here we provide another example of a positive relationship in a group of crustaceans whose genome sizes have not previously been investigated. We analyze genome...

Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolu...

Within animals a positive correlation between genome size and body size has been detected in several taxa but not in others, such that it remains unknown how pervasive this pattern may be. Here we provide another example of a positive relationship, in a group of crustaceans whose genome sizes have not previously been investigated. We analyze genome...

Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a la...

Hybridization among populations and species is a central theme in many areas of biology, and the study of hybridization has direct applicability to testing hypotheses about evolution, speciation, and genetic recombination, as well as having conservation, legal and regulatory implications. Yet, despite being a topic of considerable interest, the ide...

Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scall...

Heterochromatin distribution and chromosomal rearrangements have been proposed as the main sources of karyotype differences among species of Neotropical primates. This variability suggests that there could be differences at other smaller-scale levels of DNA organization as well. In particular, quantitative differences between genomes result from ga...

Crustaceans are enormously diverse both phylogenetically and ecologically, but they remain substantially underrepresented in the existing genome size database. An expansion of this dataset could be facilitated if it were possible to obtain genome size estimates from ethanol-preserved specimens. In this study, two tests were performed in order to as...

Ribbon worms (phylum Nemertea) are among several animal groups that have been overlooked in past studies of genome-size diversity. Here, we report genome-size estimates for eight species of nemerteans, including representatives of the major lineages in the phylum. Genome sizes in these species ranged more than fivefold, and there was some indicatio...

The phyla known as early-branching lineages of animals have become the subject of increasing interest from the perspectives of genomics and evolutionary biology. Unfortunately, data on even the most fundamental properties of their genomes, such as genome size, remain very scarce. In this study, genome size estimates are reported for 75 species of s...

Background Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biod...

The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow c...

Krill (family Euphausiidae) represent some of the most abundant organisms in the both northern and southern oceanic environments and provide food for various animals including humans. Despite their importance, little is known about krill from a genomic standpoint, even with regard to basic properties such as total genome size. This study provides g...

List of species found in Churchill from the literature versus the species revealed by DNA barcoding. The results of our study show a large increase in the number of species compared to the number found in published literature on Churchill branchiopods. The type of habitat where each species was found is also listed. References are listed for both t...

Summary of COI divergence patterns for all species with a sequence length >350 bp. The mean and maximum intraspecific divergence found in all species which were successfully sequenced. The distance to the nearest neighbour is also provided, along with the sample size. (DOCX)