Peter J. Van Coeverden de Groot

Queen's University

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Peter T. Boag

Queen's University

Alfred L. Roca

University of Illinois Urbana-Champaign

John M. Casselman

Queen's University

Murray D. Wiegand

University of Winnipeg

Robert Montgomerie

Queen's University

Yasuko Ishida

University of Illinois Urbana-Champaign

Paul A. Venturelli

Ball State University

C. Scott

Queen's University

Cheryl A. Murphy

Michigan State University

Markus Dyck

Government of Nunavut

Cooperative Institutions

Queen's University

University of Copenhagen

University of Toronto

American Museum of Natural History

Institut de Génétique, Environnement et Protection des Plantes

Centre National de la Recherche Scientifique

University of Illinois Urbana-Champaign

Université de Rennes

Natural History Museum Aarhus

University of Guelph

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Distinguishing Forest and Savanna African Elephants Using Short Nuclear DNA Sequences

Journal of Heredity (2011)

Yasuko Ishida Yirmed Demeke Peter J. Van Coeverden de Groot Nicholas J. Georgiadis Keith Leggett

A more complete description of African elephant phylogeography would require a method that distinguishes forest and savanna elephants using DNA from low-quality samples. Although mitochondrial DNA is often the marker of choice for species identification, the unusual cytonuclear patterns in African elephants make nuclear markers more reliable. We therefore designed and utilized genetic markers for short nuclear DNA regions that contain fixed nucleotide differences between forest and savanna elephants. We used M13 forward and reverse sequences to increase the total length of PCR amplicons and to improve the quality of sequences for the target DNA. We successfully sequenced fragments of nuclear genes from dung samples of known savanna and forest elephants in the Democratic Republic of Congo, Ethiopia, and Namibia. Elephants at previously unexamined locations were found to have nucleotide character states consistent with their status as savanna or forest elephants. Using these and results from previous studies, we estimated that the short-amplicon nuclear markers could distinguish forest from savanna African elephants with more than 99% accuracy. Nuclear genotyping of museum, dung, or ivory samples will provide better-informed conservation management of Africa's elephants.

African elephant

Nuclear DNA

Amplicon

Nuclear gene

10.1093/jhered/esr073

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Citations (27)

Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus

Molecular Ecology (2006)

JOSEPH W. BROWN Peter J. Van Coeverden de Groot Tim P. Birt Gilles Seutin Peter T. Boag

Peregrinus

Population bottleneck

Variation (astronomy)

10.1111/j.1365-294x.2006.03151.x

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Citations (4)

An assessment of microplastics in fecal samples from polar bears (<i>Ursus maritimus</i>) in Canada’s North

Arctic Science (2024)

P.U. Iyare H.L. Vanderlip Márcia Kelly Reis Dias Jennifer F. Provencher Shan Zou

We assessed the potential for plastic ingestion in polar bears ( Ursus maritimus (Phipps (1774))) using fecal analysis. Two method studies ensured our protocols could effectively recover and identify plastics in feces. First, microplastics (film, foam, or fragments) were intentionally introduced into a model organic matrix. Recovery rates (mean ± standard deviation) averaged 95.8 ± 14.7% ( n = 18) and were significantly affected by microplastic morphology but not digestion status. Second, microplastic fragments of polypropylene, polyethylene terephthalate, and polystyrene were intentionally introduced to polar bear feces. Recovery rates averaged 79.3 ± 21.6% ( n = 8) and Raman microscopy successfully identified all three polymers in 87.5% of samples. The main study then investigated the presence of microplastics in hunter-collected polar bear feces in the Canadian Arctic. Feces from the colons of hunted bears ( n = 15) and field scat ( n = 15) were collected through collaboration with Inuit communities. Polypropylene, polyethylene, and/or polyethylene terephthalate were detected in the feces of eight bears. Concentrations of microplastics in feces were, on average, less than 1 particle/g dry weight feces and at or near detection limits. Overall, this work suggests microplastic ingestion by Canadian polar bears may be low and demonstrates the utility of fecal sampling for community-based monitoring programs.

Ursus maritimus

10.1139/as-2023-0060

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Dinucleotide microsatellite primers designed for a critically endangered primate, the black lion tamarin (Leontopithecus chrysopygus)

Molecular Ecology Notes (2005)

Beatriz Perez‐Sweeney Cláudio Valladares‐Pádua Andrew S. Burrell Anthony Di Fiore Jessica Satkoski

Abstract Black lion tamarin (BLT) monkeys ( Leontopithecus chrysopygus ) have suffered a severe reduction in their natural range and are consequently critically endangered. Because allozyme data showed very low levels of variation, it was not clear if these monkeys had much genetic diversity. We designed microsatellite primers for BLTs, and from them we identified nine polymorphic loci, seven of which were tested on golden lion tamarins (GLTs) ( Leontopithecus rosalia ). All of the seven polymorphic loci and two other monomorphic BLT loci were polymorphic in GLTs. The microsatellite markers identified here are directly applicable to ongoing lion tamarin population and conservation genetics studies.

10.1111/j.1471-8286.2005.00875.x

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Citations (27)

Low MHC variation in the polar bear: implications in the face of Arctic warming?

Animal Conservation (2013)

Diana S. Weber Peter J. Van Coeverden de Groot E. Peacock Mark D. Schrenzel D. A. Perez

Abstract Animals in the A rctic have low pathogen diversity but with rapid climate warming, this is expected to change. One insidious consequence of climate change is exposure of A rctic species to new pathogens derived from more southern species expanding their range northward. To assess potential vulnerability of polar bears to disease exposure, we examined genetic variation in major histocompatibility complex ( MHC ) loci (part of immune system) in C anadian polar bears and found low genetic diversity, consistent with long‐standing exposure to low pathogen/parasite loads. All polar bears surveyed showed maximum linkage disequilibrium between DRB / DQB loci and 12% of individuals had a duplicated DQB gene haplotype. These results may reflect balancing selection at these loci, a response to an earlier immune‐challenge and/or be artifacts of polar bear‐brown bear divergence. Consistent with the latter, we found one DQA allele in polar bears that was also a brown bear DQA allele. The reported low MHC diversity and high linkage disequilibrium may have serious implications for polar bear resistance to new pathogens, which would be maladaptive to species in an environment undergoing rapid climate change, such as the A rctic.

Linkage Disequilibrium

Disequilibrium

Balancing selection

10.1111/acv.12045

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Citations (27)

Population genomics of the muskox' resilience in the near absence of genetic variation

Molecular Ecology (2023)

Patrícia Pečnerová Edana Lord Genís Garcia‐Erill Kristian Hanghøj Malthe Sebro Rasmussen

Abstract Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox ( Ovibos moschatus ), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present‐day individuals representing the current native range of both muskox subspecies, the white‐faced and the barren‐ground muskox ( O. moschatus wardi and O. moschatus moschatus ) and a ~21,000‐year‐old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post‐glacial re‐colonizations. In particular, the white‐faced muskox has the lowest genome‐wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long‐term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.

Extinction (optical mineralogy)

Effective population size

Population bottleneck

Population genomics

10.1111/mec.17205

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Citations (9)

Distinct intestinal microbial communities of two sympatric anadromous Arctic salmonids and the effects of migration and feeding

Arctic Science (2020)

Geraint Element Katja Engel Josh D. Neufeld John M. Casselman Peter J. Van Coeverden de Groot

Although intestinal microbial communities from anadromous Arctic char (Salvelinus alpinus (Linnaeus, 1758)) in Kitikmeot, Nunavut, Canada, differ depending on the timing and location of capture, determinants of gut microbiota in other wild Arctic salmonids are largely unknown. Using high-throughput 16S rRNA gene sequence data, we compared intestinal microbiota from Arctic char to those from a related and sympatric salmonid, lake whitefish (Coregonus clupeaformis (Mitchill, 1818)). Shifts in lake whitefish gut microbial community composition were observed between brackish water and freshwater, similar to impacts of salinity reported previously for Arctic char. Despite these similarities, gut community profiles for the two salmonids differed, with whitefish having higher diversities and increased proportions of taxa affiliated with potential pathogens. Geography seemed to have a greater impact on freshwater whitefish gut microbiota than on corresponding Arctic char. Additionally, microbiota diversity was significantly more affected by feeding behavior in whitefish compared with sympatric Arctic char. As sampled whitefish were at their northern range limits and grew slowly, we speculate that they, and their microbial consortia, could be more vulnerable to certain abiotic and biotic factors than Arctic char, which are well adapted to conditions found in these high latitude environments and have the most northern distribution of any freshwater fish.

Arctic char

Coregonus clupeaformis

Coregonus

10.1139/as-2020-0011

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Citations (14)

Pilot study: Catches of North Sea cod by recreational fishermen in the Netherlands

O.A. van Keeken H.J.A. Dijkman Dulkes Peter J. Van Coeverden de Groot

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Maternal influences on population dynamics: evidence from an exploited freshwater fish

Ecology (2010)

Paul A. Venturelli Cheryl A. Murphy Brian J. Shuter Thomas A. Johnston Peter J. Van Coeverden de Groot

We used a field experiment, population modeling, and an analysis of 30 years of data from walleye (Sander vitreus; a freshwater fish) in Lake Erie to show that maternal influences on offspring survival can affect population dynamics. We first demonstrate experimentally that the survival of juvenile walleye increases with egg size (and, to a lesser degree, female energy reserves). Because egg size in this species tends to increase with maternal age, we then model these maternal influences on offspring survival as a function of maternal age to show that adult age structure can affect the maximum rate at which a population can produce new adults. Consistent with this hypothesis, we present empirical evidence that the maximum reproductive rate of an exploited population of walleye was approximately twice as high when older females were abundant as compared to when they were relatively scarce. Taken together, these results indicate that age- or size-based maternal influences on offspring survival can be an important mechanism driving population dynamics and that exploited populations could benefit from management strategies that protect, rather than target, reproductively valuable individuals.

Juvenile fish

Affect

Fresh water fish

10.1890/09-1218.1

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Citations (112)

Conservation genetics of the black rhinoceros, Diceros bicornis bicornis, in Namibia

Conservation Genetics (2011)

Peter J. Van Coeverden de Groot Andrea S. Putnam Peter Erb C. Scott Don J. Melnick

Rhinoceros

Subspecies

Population bottleneck

10.1007/s10592-011-0185-1

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Citations (16)