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55 results for “mammal genetics”
Varying genetic imprints of roads and human density in North American mammal populations
<p>Road networks and human density are major factors contributing to habitat fragmentation and loss, isolation of wildlife populations and reduced genetic diversity. Terrestrial mammals are particularly sensitive to road networks and encroachment by human populations. However, there are limited assessments of the impacts of road networks and human density on population-specific nuclear genetic diversity, and it remains unclear how these impacts are modulated by life history traits. Using generalized linear mixed models and microsatellite data from 1444 North American terrestrial mammal populations we show that taxa with large home range sizes, dense populations, and large body sizes had reduced nuclear genetic diversity with increasing road impacts and human density, but the overall influence of life history traits was generally weak. Instead, we observed a high degree of genus-specific variation in genetic responses to road impacts and human density. Human density negatively affected allelic diversity or heterozygosity more than road networks (13 versus 5-7 of 25 assessed genera, respectively); increased road networks and human density also positively affected allelic diversity and heterozygosity in 15 and 6-9 genera, respectively. Large bodied, human-averse species were generally more negatively impacted than small, urban-adapted species. Genus-specific responses to habitat fragmentation by ongoing road development and human encroachment likely depend on the specific capability to (i) navigate roads as either barriers or movement corridors, and (ii) exploit resource-rich urban environments. The non-uniform genetic response to roads and human density highlights the need to implement efforts to mitigate the risk of vehicular collisions, while also facilitating gene flow between populations of particularly vulnerable taxa.</p>
Figure 3 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species
Figure 3. Published values of percent divergence between cetacean subspecies (black bars), species (white bars), and taxa of uncertain taxonomic status (gray bars). Values are based on mtDNA control region sequence data. Not all values represent net sequence divergence. See Table 1 for list of papers corresponding to each value. Since completing this work, Sousa species have been supported ((Mendez et al. 2013) and Inia subspecies changed.
Figure 1 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species
Figure 1. Sample sizes used in publications of molecular genetic studies of marine mammals at different taxonomic levels. Graphs present the proportion of studies at each taxonomic level that fall into each sample size category. (A) minimum total sample size per focal taxon; (B) maximum sample size per single sampling locality. Papers were categorized as examining taxonomic questions at: species = subspecies/species boundary; subspecies = population/subspecies boundary; uncertain = taxonomic boundary uncertain (see text).
Figure 2 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species
Figure 2. Types of molecular genetic data used in published studies examining questions at the species-level, subspecies-level, or undefined taxonomic level for marine mammals. Note that studies may have used more than one data type. Mitochondrial DNA sequence data (MtDNASeq), nuclear DNA sequence data (NuSeq), microsatellites (Msats), morphological data (Morph).
Data from: Genetic diversity in a long-lived mammal is explained by the past's demographic shadow and current connectivity
<p>Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can however change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of <i>Rhinolophus hipposideros,</i> a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. We present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony sizes, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.</p>
Contributions of genetic and non-genetic sources to variation in cooperative behaviour in a cooperative mammal
<p>The evolution of cooperative behaviour is a major area of research among evolutionary biologists and behavioural ecologists, yet there are few estimates of its heritability or of its evolutionary potential and long-term studies of identifiable individuals are required to disentangle genetic and non-genetic components of cooperative behaviour. Here we use long-term data on over 1800 individually recognisable wild meerkats (<i>Suricata suricatta</i>) collected over 30 years and a multi-generational genetic pedigree to partition phenotypic variation in three cooperative behaviours (babysitting, pup feeding and sentinel behaviour) into individual, additive genetic and other sources, and to assess their repeatability and heritability. In addition to strong effects of sex, age and dominance status, we found significant repeatability in individual contributions to all three types of cooperative behaviour both within and across breeding seasons. Like most other studies of the heritability of social behaviour, we found that the heritability of cooperative behaviour was low. However, our analysis suggests that a substantial component of the repeatable individual differences in cooperative behaviour that we observed was a consequence of additive genetic variation. Our results consequently indicate that cooperative behaviour can respond to selection, and suggest scope for further exploration of the genetic basis of social behaviour.</p>
Data from: Genetic diversity in a long-lived mammal is explained by the past’s demographic shadow and current connectivity
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Varying genetic imprints of roads and human density in North American mammal populations
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Contributions of genetic and non-genetic sources to variation in cooperative behaviour in a cooperative mammal
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Data from: The coevolution of male and female genitalia in a mammal: a quantitative genetic insight
<p>Male genitalia are among the most phenotypically diverse morphological traits, and sexual selection is widely accepted as being responsible for their evolutionary divergence. Studies of house mice suggest that the shape of the baculum (penis bone) affects male reproductive fitness and experimentally imposed postmating sexual selection has been shown to drive divergence in baculum shape across generations. Much less is known of the morphology of female genitalia and its coevolution with male genitalia. In light of this, we used a paternal half-sibling design to explore patterns of additive genetic variation and covariation underlying baculum shape and female vaginal tract size in house mice (Mus musculus domesticus). We applied a landmark-based morphometrics approach to measure baculum size and shape in males and the length of the vaginal tract and width of the cervix in females. Our results reveal significant additive genetic variation in house mouse baculum morphology and cervix width, as well as evidence for genetic covariation between male and female genital measures. Our data thereby provide novel insight into the potential for the coevolutionary divergence of male and female genital traits in a mammal. </p>
Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal
<p>The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture and daylight. Muskoxen (<i>Ovibos moschatus</i>) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters.<a name="_Hlk534564036"> These clusters are defined by Arctic Mainland and Island populations, including; 1) two mainland sampling locations of the Northwest Territories and Nunavut; and 2) four locations of Victoria Island. </a>Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.</p>
Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples
<p>Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Though many DNA sequencing approaches still require high quality and quantity of DNA obtained from traditional sources (e.g. blood and tissue), rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have improved our ability to make use of degraded and less concentrated DNA commonly obtained from non-invasive and archival samples. Here, we developed a multi-purpose GT-seq panel (307 single nucleotide polymorphisms) for a climate sentinel mammal (the American pika, <em>Ochotona princeps</em>) for use as a genetic tool for monitoring populations in the Canadian Rocky Mountains. We optimized the panel using contemporary tissue samples (n = 77) and subsequently applied it to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) to evaluate its effectiveness at identifying individuals and sex, estimating relatedness, and inferring population structure. The panel demonstrated high efficacy with contemporary and archival tissue samples (94.7% and 90.5% genotyping success, respectively) and negligible genotyping error (0.001% and 0.0%, respectively). Despite relatively high genotyping success for fecal pellet samples (79.7%), high genotyping error (28.4%) limited its power as a monitoring tool to assess genetic variation using non-invasive samples and highlighted the need for further optimization around sample and data collection.</p>
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
<p><span>Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (<em>Galemys</em> <em>pyrenaicus</em>). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.</span></p>
Data from: Host genetic diversity and body condition influence parasite resistance and clearance in a wild marine mammal population
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Data from: The coevolution of male and female genitalia in a mammal: a quantitative genetic insight
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Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
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Geography, seasonality, and host‐associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal
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Data from: Assessing the effects of land‑use intensity on small mammal community composition and genetic variation in Myodesglareolus and Microtus arvalis across grassland and forest habitats
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Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples
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Estimation of environmental, genetic and parental age at conception effects on telomere length in a wild mammal
<p class="MsoNoSpacing">Understanding individual variation in fitness-related traits requires separating the environmental and genetic determinants. Telomeres are protective caps at the ends of chromosomes that are thought to be a biomarker of senescence as their length predicts mortality risk and reflect the physiological consequences of environmental conditions. The relative contribution of genetic and environmental factors to individual variation in telomere length is however unclear, yet important for understanding its evolutionary dynamics. In particular, the evidence for transgenerational effects, in terms of parental age at conception, on telomere length is mixed. Here, we investigate the heritability of telomere length, using the 'animal model', and parental age at conception effects on offspring telomere length in a wild population of European badgers (<i>Meles meles</i>). While we found no heritability of telomere length and low evolvability (<0.001), our power to detect heritability was low and a repeatability of 2% across individual lifetimes provides a low upper limit to ordinary narrow-sense heritability. However, year (25%) and cohort (3%) explained greater proportions of the phenotypic variance in telomere length. There was no support for cross-sectional or within-individual parental age at conception effects on offspring telomere length. Our results indicate a lack of transgenerational effects through parental age at conception and a low potential for evolutionary change in telomere length in this population. Instead, we provide evidence that individual variation in telomere length is largely driven by environmental variation in this wild mammal.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.