Genomic Evidence for the Purging of Deleterious Genetic Variation in the Endangered North Atlantic Right Whale.

The reduced genetic diversity and frequent inbreeding associated with small population size may underpin the accumulation and expression of deleterious mutations (mutation load) in some declining populations. However, demographic perturbations and inbreeding coupled with purifying selection can also purge declining populations of deleterious mutations, leading to intriguing recoveries. To better understand the links between deleterious genetic variation and population status, we assess patterns of genetic diversity, inbreeding, and mutation load across the genomes of three species of whale with different demographic histories and recoveries following the end of commercial whaling in the 1980s.

Effects of inbreeding on reproductive success in endangered North Atlantic right whales.

Only approximately 356 North Atlantic right whales () remain. With extremely low levels of genetic diversity, limited options for mates, and variation in reproductive success across females, there is concern regarding the potential for genetic limitations of population growth from inbreeding depression. In this study, we quantified reproductive success of female North Atlantic right whales with a modified de-lifing approach using reproductive history information collected over decades of field observations.

A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales.

Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E.

An example of DNA methylation as a means to quantify stress in wildlife using killer whales.

The cumulative effects of non-lethal stressors on the health of biodiversity are a primary concern for conservation, yet difficulties remain regarding their quantification. In mammals, many stressors are processed through a common stress-response pathway, and therefore epigenetic changes in genes of this pathway may provide a powerful tool for quantifying cumulative effects. As a preliminary assessment of this approach, we investigated epigenetic manifestations of stress in two killer whale populations with different levels of exposure to anthropogenic stressors.

Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground.

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds.

Kinship influences sperm whale social organization within, but generally not among, social units.

Sperm whales have a multi-level social structure based upon long-term, cooperative social units. What role kinship plays in structuring this society is poorly understood. We combined extensive association data (518 days, during 2005-2016) and genetic data (18 microsatellites and 346 bp mitochondrial DNA (mtDNA) control region sequences) for 65 individuals from 12 social units from the Eastern Caribbean to examine patterns of kinship and social behaviour.

What factors shape genetic diversity in cetaceans?

Understanding what factors drive patterns of genetic diversity is a central aspect of many biological questions, ranging from the inference of historical demography to assessing the evolutionary potential of a species. However, as a larger number of datasets have become available, it is becoming clear that the relationship between the characteristics of a species and its genetic diversity is more complex than previously assumed. This may be particularly true for cetaceans, due to their relatively long lifespans, long generation times, complex social structures, and extensive ranges.

Conservation genetics of the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi): River valleys are critical features for snakes at northern range limits.

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan.

Gamete compatibility genes in mammals: candidates, applications and a potential path forward.

Fertilization represents a critical stage in biology, where successful alleles of a previous generation are shuffled into new arrangements and subjected to the forces of selection in the next generation. Although much research has been conducted on how variation in morphological and behavioural traits lead to variation in fertilization patterns, surprisingly little is known about fertilization at a molecular level, and specifically about how genes expressed on the sperm and egg themselves influence fertilization patterns. In mammals, several genes have been identified whose products are expressed on either the sperm or the egg, and which influence the fertilization process, but the specific mechanisms are not yet known.

Cultural Hitchhiking in the Matrilineal Whales.

Five species of whale with matrilineal social systems (daughters remain with mothers) have remarkably low levels of mitochondrial DNA diversity. Non-heritable matriline-level demography could reduce genetic diversity but the required conditions are not consistent with the natural histories of the matrilineal whales. The diversity of nuclear microsatellites is little reduced in the matrilineal whales arguing against bottlenecks.

A note on the use of multiple linear regression in molecular ecology.

Multiple linear regression analyses (also often referred to as generalized linear models--GLMs, or generalized linear mixed models--GLMMs) are widely used in the analysis of data in molecular ecology, often to assess the relative effects of genetic characteristics on individual fitness or traits, or how environmental characteristics influence patterns of genetic differentiation. However, the coefficients resulting from multiple regression analyses are sometimes misinterpreted, which can lead to incorrect interpretations and conclusions within individual studies, and can propagate to wider-spread errors in the general understanding of a topic. The primary issue revolves around the interpretation of coefficients for independent variables when interaction terms are also included in the analyses.

Small Ne of the Isolated and Unmanaged Horse Population on Sable Island.

For small, isolated populations 2 common conservation concerns relate to genetic threats: inbreeding and negative consequences associated with loss of genetic diversity due to drift. Mitigating these threats often involves conservation actions that can be controversial, such as translocations or captive breeding programs. Although such actions have been successful in some situations, in others they have had undesirable outcomes.

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus).

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species.

related: an R package for analysing pairwise relatedness from codominant molecular markers.

Analyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system.

Assessment of the extirpated Maritimes walrus using morphological and ancient DNA analysis.

Species biogeography is a result of complex events and factors associated with climate change, ecological interactions, anthropogenic impacts, physical geography, and evolution. To understand the contemporary biogeography of a species, it is necessary to understand its history. Specimens from areas of localized extinction are important, as extirpation of species from these areas may represent the loss of unique adaptations and a distinctive evolutionary trajectory.

STORM: software for testing hypotheses of relatedness and mating patterns.

Storm is a software package that allows users to test a variety of hypotheses regarding patterns of relatedness and patterns of mate choice and/or mate compatibility within a population. These functions are based on four main calculations that can be conducted either independently or in the hypothesis-testing framework: internal relatedness; homozygosity by loci; pairwise relatedness; and a new metric called allele inheritance, which calculates the proportion of loci at which an offspring inherits a paternal allele different from that inherited from its mother. STORM allows users to test four hypotheses based on these calculations and Monte Carlo simulations: (i) are individuals within observed associations or groupings more/less related than expected; (ii) do observed offspring have more/less genetic variability (based on internal relatedness or homozygosity by loci) than expected from the gene pool; (iii) are observed mating pairs more/less related than expected if mating is random with respect to relatedness; and (iv) do observed offspring inherit paternal alleles different from those inherited from the mother more/less often than expected based on Mendelian inheritance.

Increased efficiency of genetic profiling through quantity and quality assessment of fluorescently labeled oligonucleotide primers.

Optimizing the amount of primer to use in PCR amplification is one of the most important steps when developing protocols for genetic profiling, where subtle changes in primer concentration result in major impacts on the amount of desired product that is amplified. However; there are frequently discrepancies between the reported and actual quantity of primers delivered by suppliers, resulting in a need for re-optimization of conditions between primer orders and limiting the ability to standardize conditions between laboratories. To increase the consistency of genetic profiling protocols, we have developed a simple method to assess the quantity and quality of fluorescently labeled primers and therefore standardize reaction conditions through time and across laboratories.