Variation In Mammals Research Articles

Rocky rule: the idiosyncrasy of spatial and temporal size variation in mammals

Abstract Mammals are predicted to vary in body size following Bergmann’s rule, with individuals found at higher latitudes in colder temperatures being larger in size compared to conspecifics occurring at lower latitudes in warmer temperatures. Body size is similarly expected to vary temporally, with a decrease in size through time due to recent climate warming. While Bergmann’s rule is well-supported in mammals, there is increasing evidence of exceptions to the rule. Here, we present patterns of size variation in 17 North American mammal species using five morphological traits (condylobasal skull length, skull width, maxillary toothrow length, body weight, and head-and-body length) to determine if size varies predictably for each species in space and time. We found little support for a widespread Bergmannian pattern for these species at a broad spatial scale (across North America) and a contemporary temporal scale (the past 120 years). The effects of latitude or year on each trait were highly variable with three types of responses: an increase, a decrease, or no change in size across space or through time. Spatial size trends were detected more often than temporal size trends, as the temperature range was significantly larger in space than through time. Body weight (the most variable trait) and head-and-body length were more likely to conform to Bergmann’s rule than craniodental measurements. We did not detect any changes in size variability with latitude, and our study species either increased or decreased in size variability over time. Our findings demonstrate that size variation in mammals is highly context-dependent. As such, caution is needed when using rules of body size variation to predict the future response of species to climate warning while valid in theory, it is likely too simplistic of an approach.

Remote monitoring of short‐term body mass variation in savanna ungulates

AbstractLarge herbivores in seasonal environments often experience mass variation due to temporal changes in the availability of critical resources like water and forage, as well as due to breeding events. Yet the documentation of mass variation in mammals of highly seasonal savanna habitats, which host the highest densities of grazing ungulates globally, has rarely been explored. Here, we showcase a method to evaluate seasonal mass variation in bovids. Our method used mineral‐baited scales and camera traps to enable us to track the body mass of three species through a period of wet and dry seasons in a South African savanna ecosystem. To illustrate one potential application of the method, we related body mass data to time, weather and resource availability. This showed that individuals altered their body masses markedly between seasons with, for example, female Kudu (Tragelaphus strepsiceros) gaining, on average, >21 kg over the 15‐week wet‐season period in 1 year. These changes were positively related to factors such as vegetation productivity (assessed using NDVI) and the frequency of rains. This method enables easy, non‐lethal and non‐invasive acquisition of mass data. The equipment is easy to deploy concurrently over large areas. Monitoring by this method has a variety of possible applications, potentially providing a useful early‐warning indicator of body condition to inform management, or providing information about ecological states, such as parturition or the reproductive effort of males. Given the longer and harsher dry seasons experienced in many arid systems in recent decades, and projected in future, this method may provide a straightforward means of monitoring long‐term body condition in animals as a result of environmental change.

Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks

Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome of 10 long-haired Tianzhu white yaks (LTWY) and 10 normal-haired Tianzhu white yaks (NTWY), and analyzed the differences of CNV in the genome of LTWYs and NTWYs. A total of 110268 CNVs were identified, 2006 CNVRs were defined, and the distribution map of these CNVRs on chromosomes was constructed. The comparison of LTWYs and NTWYs identified 80 differential CNVR-harbored genes, which were enriched in lipid metabolism, cell migration and other functions. Notably, some differential genes were identified as associated with hair growth and hair-follicle development (e.g., ASTN2, ATM, COL22A1, GK5, SLIT3, PM20D1, and SGCZ). In general, we present the first genome-wide analysis of CNV in LTWYs and NTWYs. Our results can provide new insights into the phenotypic variation of different hair lengths in Tianzhu white yaks.

Non-Invasive Assessment of Mild Stress-Induced Hyperthermia by Infrared Thermography in Laboratory Mice.

Simple SummaryStressful events can trigger body temperature variations in mammals. The most commonly used methods for measuring temperature in laboratory mice are stressful and invasive in nature, and can themselves cause stress-induced hyperthermia (SIH). This raises concerns regarding both animal welfare and research output. Infrared thermography (IRT) offers a non-invasive alternative, if proven to accurately identify SIH. We exposed mice to mild handling-induced stress, by either tail-picking or the reportedly less-impactful tunnel-handling technique. Temperature was measured by reading microchip devices (PIT-tags) implanted subcutaneously (Tsc), and by a thermal camera to measure mean body surface temperature (Tbody) and mean tail surface temperature (Ttail). As expected, during acute stress exposure, both Tsc and Tbody increased, while Ttail decreased. No differences in stress-induced hyperthermia were found between the two handling techniques. This suggests that such differences may not be detectable in the context of co-occurring stressful events, such as opening of the cage lid, exposure to light, or presence of the handler. Within the same cage, animals handled last consistently showed higher body temperatures than those handled first, raising the issue of minding the order by which animals are tested. Our results suggest IRT offers a reliable non-invasive method for assessing SIH in laboratory rodents.Stress-induced hyperthermia (SIH) is a physiological response to acute stressors in mammals, shown as an increase in core body temperature, with redirection of blood flow from the periphery to vital organs. Typical temperature assessment methods for rodents are invasive and can themselves elicit SIH, affecting the readout. Infrared thermography (IRT) is a promising non-invasive alternative, if shown to accurately identify and quantify SIH. We used in-house developed software ThermoLabAnimal 2.0 to automatically detect and segment different body regions, to assess mean body (Tbody) and mean tail (Ttail) surface temperatures by IRT, along with temperature (Tsc) assessed by reading of subcutaneously implanted PIT-tags, during handling-induced stress of pair-housed C57BL/6J and BALB/cByJ mice of both sexes (N = 68). SIH was assessed during 10 days of daily handling (DH) performed twice per day, weekly voluntary interaction tests (VIT) and an elevated plus maze (EPM) at the end. To assess the discrimination value of IRT, we compared SIH between tail-picked and tunnel-handled animals, and between mice receiving an anxiolytic drug or vehicle prior to the EPM. During a 30 to 60 second stress exposure, Tsc and Tbody increased significantly (p < 0.001), while Ttail (p < 0.01) decreased. We did not find handling-related differences. Within each cage, mice tested last consistently showed significantly higher (p < 0.001) Tsc and Tbody and lower (p < 0.001) Ttail than mice tested first, possibly due to higher anticipatory stress in the latter. Diazepam-treated mice showed lower Tbody and Tsc, consistent with reduced anxiety. In conclusion, our results suggest that IRT can identify and quantify stress in mice, either as a stand-alone parameter or complementary to other methods.

Reconstruction of evolutionary changes in fat and toxin consumption reveals associations with gene losses in mammals: A case study for the lipase inhibitor PNLIPRP1 and the xenobiotic receptor NR1I3.

The inactivation of ancestral protein-coding genes (gene loss) can be associated with phenotypic modifications. Within placental mammals, repeated losses of PNLIPRP1 (gene inhibiting fat digestion) occurred preferentially in strictly herbivorous species, whereas repeated NR1I3 losses (gene involved in detoxification) occurred preferentially in strictly carnivorous species. It was hypothesized that lower fat contents of herbivorous diets and lower toxin contents of carnivorous diets cause relaxed selection pressure on these genes, resulting in the accumulation of mutations and ultimately to convergent gene losses. However, because herbivorous and carnivorous diets differ vastly in their composition, a fine-grained analysis is required for hypothesis testing. We generated a trait matrix recording diet and semi-quantitative estimates of fat and toxin consumption for 52 placental species. By including data from 31 fossil taxa, we reconstructed the ancestral diets in major lineages (grundplan reconstruction). We found support that PNLIPRP1 loss is primarily associated with low levels of fat intake and not simply with herbivory/carnivory. In particular, PNLIPRP1 loss also occurred in carnivorous lineages feeding on a fat-poor diet, suggesting that the loss of this gene may be beneficial for occupying ecological niches characterized by fat-poor food resources. Similarly, we demonstrated that carnivorous species are indeed less exposed to diet-related toxins, suggesting that the loss of NR1I3 and related genes (NR1I2 and UGT1A6) resulted from relaxed selection pressure. This study illustrates the need of detailed phenotype studies to obtain a deeper understanding of factors underlying gene losses and to progress in understanding genomic causes of phenotypic variation in mammals.

Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation.

Although each Mendelian Disorder of the Epigenetic Machinery (MDEM) has a different causative gene, there are shared disease manifestations. We hypothesize that this phenotypic convergence is a consequence of shared epigenetic alterations. To identify such shared alterations, we interrogate chromatin (ATAC-seq) and expression (RNA-seq) states in B cells from three MDEM mouse models (Kabuki [KS] type 1 and 2 and Rubinstein-Taybi type 1 [RT1] syndromes). We develop a new approach for the overlap analysis and find extensive overlap primarily localized in gene promoters. We show that disruption of chromatin accessibility at promoters often disrupts downstream gene expression, and identify 587 loci and 264 genes with shared disruption across all three MDEMs. Subtle expression alterations of multiple, IgA-relevant genes, collectively contribute to IgA deficiency in KS1 and RT1, but not in KS2. We propose that the joint study of MDEMs offers a principled approach for systematically mapping functional epigenetic variation in mammals.

Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel.

Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat coloration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage color moults across regions with varying winter snow. Whole-genome sequence data were obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris coloration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200-kb genomic region to coloration morph, which was validated by genotyping museum specimens from intermorph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change cosegregating with coloration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favored winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter color variation in mammals and that seasonal camouflage can be modulated by changes at single key genes.

Diel niche variation in mammals associated with expanded trait space

Mammalian life shows huge diversity, but most groups remain nocturnal in their activity pattern. A key unresolved question is whether mammal species that have diversified into different diel niches occupy unique regions of functional trait space. For 5,104 extant mammals we show here that daytime-active species (cathemeral or diurnal) evolved trait combinations along different gradients from those of nocturnal and crepuscular species. Hypervolumes of five major functional traits (body mass, litter size, diet, foraging strata, habitat breadth) reveal that 30% of diurnal trait space is unique, compared to 55% of nocturnal trait space. Almost half of trait space (44%) of species with apparently obligate diel niches is shared with those that can switch, suggesting that more species than currently realised may be somewhat flexible in their activity patterns. Increasingly, conservation measures have focused on protecting functionally unique species; for mammals, protecting functional distinctiveness requires a focus across diel niches.

Geometric morphometrics of mandibular shape in the dwarf fat-tailed jerboa: relevancy for trinomial taxonomy

Abstract We explore the pattern of spatial variation in mandibular morphology in relation to subspecific taxonomy in the dwarf fat-tailed jerboa, Pygeretmus pumilio. The unguided k-means clustering on mandible shape scores, partitioned populations into two clusters, corresponding to western and eastern populations. These clusters nearly perfectly matched the two subspecies groups (pumilio and potanini groups) recognized in an independent study based on the morphology of the glans penis. The mandible, although under environmental pressure, has retained a sufficient amount of taxonomic information to retrieve grouping closely resembling the one derived from a sexually selective trait. We recommend morphometrics of the mandible as a routine step in addressing variations in mammals at species and subspecies levels. We also stress the advantage of unsupervised k-clustering in testing null expectation in subspecies taxonomies. However, the power of this approach has its limitations and in our analysis, the k-clustering failed to retrieve subspecies in the potanini group.

Unusual tertiary pairs in eukaryotic tRNAAla

tRNA molecules have well-defined sequence conservations that reflect the conserved tertiary pairs maintaining their architecture and functions during the translation processes. An analysis of aligned tRNA sequences present in the GtRNAdb database (the Lowe Laboratory, University of California, Santa Cruz) led to surprising conservations on some cytosolic tRNAs specific for alanine compared to other tRNA species, including tRNAs specific for glycine. First, besides the well-known G3oU70 base pair in the amino acid stem, there is the frequent occurrence of a second wobble pair at G30oU40, a pair generally observed as a Watson–Crick pair throughout phylogeny. Second, the tertiary pair R15/Y48 occurs as a purine–purine R15/A48 pair. Finally, the conserved T54/A58 pair maintaining the fold of the T-loop is observed as a purine–purine A54/A58 pair. The R15/A48 and A54/A58 pairs always occur together. The G30oU40 pair occurs alone or together with these other two pairs. The pairing variations are observed to a variable extent depending on phylogeny. Among eukaryotes, insects display all variations simultaneously, whereas mammals present either the G30oU40 pair or both R15/A48 and A54/A58. tRNAs with the anticodon 34A(I)GC36 are the most prone to display all those pair variations in mammals and insects. tRNAs with anticodon Y34GC36 have preferentially G30oU40 only. These unusual pairs are not observed in bacterial, nor archaeal, tRNAs, probably because of the avoidance of A34-containing anticodons in four-codon boxes. Among eukaryotes, these unusual pairing features were not observed in fungi and nematodes. These unusual structural features may affect, besides aminoacylation, transcription rates (e.g., 54/58) or ribosomal translocation (30/40).

Gene expression correlates of social evolution in coral reef butterflyfishes.

Animals display remarkable variation in social behaviour. However, outside of rodents, little is known about the neural mechanisms of social variation, and whether they are shared across species and sexes, limiting our understanding of how sociality evolves. Using coral reef butterflyfishes, we examined gene expression correlates of social variation (i.e. pair bonding versus solitary living) within and between species and sexes. In several brain regions, we quantified gene expression of receptors important for social variation in mammals: oxytocin (OTR), arginine vasopressin (V1aR), dopamine (D1R, D2R) and mu-opioid (MOR). We found that social variation across individuals of the oval butterflyfish, Chaetodon lunulatus, is linked to differences in OTR,V1aR, D1R, D2R and MOR gene expression within several forebrain regions in a sexually dimorphic manner. However, this contrasted with social variation among six species representing a single evolutionary transition from pair-bonded to solitary living. Here, OTR expression within the supracommissural part of the ventral telencephalon was higher in pair-bonded than solitary species, specifically in males. These results contribute to the emerging idea that nonapeptide, dopamine and opioid signalling is a central theme to the evolution of sociality across individuals, although the precise mechanism may be flexible across sexes and species.

Employing statistical learning to derive species‐level genetic diversity for mammalian species

Abstract The patterns of genetic diversity in several genomic regions have been used in mammalian systematics for decades. For instance, when studying closely related species, it is generally assumed that the mitochondrial cytochrome b gene (cytb) exhibits significant information that can be used for differentiation between intraspecies and interspecies variation in mammals. Because of sampling limitations, early analyses of this proposition were conducted mainly on rodents and bats. Currently, more than 57000 cytb sequences are available covering all major lineages of mammals, and sequencing of several individuals per species is common practice in molecular systematics. We were thus prompted to carry out a large‐scale analysis of the utility of cytb genetic variation as a predictor of whether a pair of sequences came from within‐species or between‐species comparisons. Using predetermined species‐level assignments, we employed standard methods from statistical learning to calculate the cut‐off values able to classify genetic distances in either intraspecies or interspecies categories; we then measured the performance of such statistical classifiers to predict the species‐level taxonomic rank as defined by experts. Depending on the classifier, our results showed that when adopting cytb distance cut‐off values of 7.3% and 5.5% for small mammals (Metatheria, Rodentia, Chiroptera, and Eulipotyphla) and 4.3% and 3% for medium‐sized to large mammals (Primates, Carnivora, and Artiodactyla), the frequency of incorrect assignment of within‐species divergences to the between‐species category (type I error) varied from 7 to 11%. In order to avoid over‐splitting by future researchers, we calculated cut‐off values using a more conservative evaluation and provided a list of mammalian species that are likely to consist of complexes of cryptic species. We show that our supervised method can provide practical guidelines to improve the performance of unsupervised algorithms for species delimitation. Finally, we discuss limitations of large‐scale approaches (e.g. effects of misclassification in databases and the need for case‐by‐case evaluation of cryptic species complexes) and their consequences for conservation policies.

Chromosomal Differentiation in Genetically Isolated Populations of the Marsh-Specialist Crocidura suaveolens (Mammalia: Soricidae).

The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence.

Chromatin interaction maps reveal genetic regulation for quantitative traits in maize

Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. Collectively, these maps provide a high-resolution view of 3D maize genome architecture, and its role in gene expression and phenotypic variation.

Mapping of the binding sites of human diamine oxidase (DAO) monoclonal antibodies

ObjectiveRecently we characterized five mouse monoclonal antibodies that allow the specific and sensitive detection of human diamine oxidase (DAO). To understand differences in binding characteristics and recognition of enzyme variants, we mapped the antibody binding sites.MethodsFragments of human DAO were expressed as glutathione-S-transferase fusion proteins that were used for testing antibody binding on immunoblots. Combined information from species cross-reactivity, sequence comparison and binding site-prediction software were used to localize the epitope recognized by each antibody.ResultsAll five monoclonal DAO antibodies bound to linear epitopes between the N3 and enzymatic domains of the 732 amino acid protein. The binding sites could be mapped onto amino acid regions V262-E278 and P279-R288, respectively, which exhibit considerable sequence variation in mammals explaining the fact that the human DAO antibodies do not cross-react with DAO from other species. The antibodies efficiently bind only denatured human DAO but not the native protein.ConclusionsCharacterization of the binding sites of the DAO antibodies revealed that the antibodies bind two adjacent epitopes and exhibit similar binding characteristics and species cross-reactivity. As the epitopes do not overlap any of the amino acid substitutions described for clinically significant DAO gene polymorphisms, our antibodies will also be useful for analyses of the mutant DAO proteins.

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

Noncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of three liver-specific transcription factors between crosses of two inbred mouse strains to elucidate the regulatory mechanisms underlying transcription factor binding variations in mammals. Our results highlight the pre-eminence of cis-acting variants on transcription factor occupancy divergence. Transcription factor binding differences linked to cis-acting variants generally exhibit additive inheritance, while those linked to trans-acting variants are most often dominantly inherited. Cis-acting variants lead to local coordination of transcription factor occupancies that decay with distance; distal coordination is also observed and may be modulated by long-range chromatin contacts. Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states.

Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals.

The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species. Here, I use cytogenetic methods for in situ imaging of crossovers in karyotypically diverse house mice (Mus musculus domesticus) and voles (genus Microtus) to test how chromosome number and configuration constrain the distribution of crossovers in a genome. I show that the global distribution of crossovers in house mice is thresholded by a minimum of one crossover per chromosome arm, whereas the crossover landscape in voles is defined by a more relaxed requirement of one crossover per chromosome. I extend these findings in an evolutionary metaanalysis of published recombination and karyotype data for 112 mammalian species and demonstrate that the physical scale of the genomic crossover distribution has undergone multiple independent shifts from one crossover per chromosome arm to one per chromosome during mammalian evolution. Together, these results indicate that the chromosomal scale constraint on crossover rates is itself a trait that evolves among species, a finding that casts light on an important source of crossover rate variation in mammals.

Left, right or both? Estimating and improving accuracy of one-side-only geometric morphometric analyses of cranial variation

Procrustes-based geometric morphometric analyses of bilaterally symmetric structures are often performed using only one side. This is particularly common in studies of cranial variation in mammals and other vertebrates. When one is not interested in quantifying asymmetry, landmarking one side, instead of both, reduces the number of variables as well as the time and costs of data collection. It is assumed that the loss of information in the other half, on which landmarks are not digitized, is negligible, but this has seldom been tested. Using 10 samples of mammalian crania and a total of more than 500 specimens, and five different landmark configurations, I demonstrate that this assumption is indeed easily met for size. For shape, in contrast, one-side landmarking has potentially more severe consequences on the estimates of similarity relationships in a sample. In this respect, microevolutionary analyses of small differences are particularly affected, whereas macroevolutionary studies are fairly robust. In almost all instances, however, a simple preliminary operation improves accuracy by making one-side-only shape data more similar to those obtained by landmarking both sides. The same operation also makes estimates of allometry more accurate and improves the visualization. This operation consists in estimating the missing side by a mirror reflection of bilateral landmarks. In the Supporting Information, I exemplify how this can be easily done using free user-friendly software. I also provide an example data set for readers to repeat and learn the steps of this simple procedure.

Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries).

Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals.

The Relationship between MC1R Mutation and Plumage Color Variation in Pigeons.

The polymorphisms of MC1R gene play a crucial role in coat color variation in mammals; however, the relationship is still unclear in pigeons. In this study, we sequenced 741 bp fragment of the MC1R for 39 individuals with five plumage color patterns (gray plumage, n = 12; black plumage, n = 9; white plumage, n = 3; spotted plumage, n = 12; red plumage, n = 3). A total of three single nucleotide polymorphisms (SNPs) were detected, including G199A, G225A, and A466G, which subsequently determined four haplotypes (H1–H4). Among them, H1 is the predominant haplotype. Association analysis revealed that H1 and H3 were significantly associated with the black plumage trait (P < 0.05), while the H4 was significantly associated with gray plumage trait (P < 0.05). Furthermore, only diplotype H1H1 was significantly associated with black and gray traits of pigeons. Collectively, our study suggested an association between genetic variation of MC1R and plumage color in pigeon.