Identifying and Controlling for Variation in Canid Harvest Data

An accurate understanding of harvest trends is required for effective wildlife management. Trapper harvest data represent valuable long-term data for evaluating patterns and trends for wildlife species at broad spatiotemporal scales. Inferring accurate trends from harvest data, however, first requires identifying and controlling for confounding factors that vary independent of abundance. We investigated trends in 43 years of trapper harvest data (1976–2018) from Illinois, USA, for red fox (Vulpes vulpes), gray fox (Urocyon cinereoargenteus), and coyote (Canis latrans) while controlling for factors that may affect trapper effort, including number of effective (i.e., successful) trappers, pelt price, gasoline price, winter unemployment, and winter weather conditions. Annual trapper harvest for red and gray foxes declined and was affected by gasoline price and winter unemployment, whereas annual trapper harvest for coyotes increased and was not strongly affected by other covariates. After adjusting for pelt price, harvest of red foxes was relatively stable, but harvest of gray foxes declined and harvest of coyotes increased. Effects of covariates on harvest per successful trapper varied by species; nevertheless, we detected an increasing trend for coyotes and decreasing trends for gray foxes and red foxes. Concordance across indices for gray foxes and coyotes was consistent with hypothesized declines for gray foxes and increases for coyotes in the midwestern United States. Trends for red foxes varied depending on how we accounted for potential confounding factors and it is unclear if these trends suggest population declines or distribution shifts to urban areas with reduced trapping susceptibility. Our results highlight the importance of understanding sources of variation in harvest data and that their effects can vary across species. © 2020 The Wildlife Society.     

Survival and Cause-Specific Mortality of Red Foxes in Agricultural and Urban Areas of Illinois

Abstract: Range expansion and population increase by coyotes (Canis latrans), reduced hunting and trapping, and intensified agricultural practices in the Midwest have altered red fox (Vulpes vulpes) mortality, although relative impacts of these factors are unknown. We examined mortality causes and survival of red foxes in urban and rural agricultural areas of Illinois, using radio telemetry data from 335 foxes (Nov 1996 to May 2002). We used Akaike's Information Criterion to evaluate six survival models for foxes reflecting 1) environmental effects, 2) intrinsic effects, 3) temporal effects, 4) behavioral effects, 5) social effects, and 6) a global model. Environmental and intrinsic models of survival were optimal for adult foxes. Adult foxes with low (0-20%) and high (80-100%) percentages of row crops in their home ranges had higher survival than adults with moderate percentages (40-70%). Heavier adults at capture also survived better. A global model (all covariates) was optimal for juvenile foxes. Higher juvenile survival associated with larger litters, lower body fat, and reduced dispersal time. Yearly survival ranged from 0.18 for rural male juveniles to 0.44 for rural female adults. Adult survival rates (0.35) were 11% higher than juvenile survival rates (0.24). Yearly survival varied for urban foxes due to cyclic outbreaks of sarcoptic mange (Sarcoptes scabei). Thus, summer survival (May-Sep) of urban juveniles ranged from 0.10 (mange present) to 0.83 (no mange recorded). Mange was the most common (45% of all fatalities) source of mortality for urban foxes, followed by road kill (31%). We recorded only 4 mange fatalities (2%) for rural foxes. Rural foxes experienced low hunting mortality (7%) and equivalent road kill and coyote predation fatalities (40% each). Sources of mortality for midwestern foxes have dramatically changed since the 1970s when hunting was the major cause of mortality. Coyote predation has effectively replaced hunting mortality, and cyclic patterns of mange outbreaks in urban fox populations might indicate a dynamic source or sink relationship to surrounding rural fox populations. Absent mange, urban areas might provide refugia for red foxes where coyote populations persist at high densities in rural areas. Managers of sympatric urban and rural wildlife populations must understand survival dynamics influencing the population at the landscape level.     

Field Sedation of Coyotes,Red Foxes,and Raccoons With Medetomidine and Atipamezole

Abstract: We chemically restrained free-ranging coyotes (Canis latrans), red foxes (Vulpes vulpes), and raccoons (Procyon lotor) using medetomidine antagonized by atipamezole. All coyotes and 80% of red foxes were sedated with mean ± standard deviation doses of 0.12 ± 0.02 mg/kg and 0.14 ± 0.02 mg/kg medetomidine, respectively. Seventy-seven percent of raccoons were sedated with 0.21 ± 0.05 mg/kg medetomidine. In all species we observed occasional movement, muscle rigidity, and partial-arousal during sedation. Animals were alert within 4.3–8.6 ± 3.5–8.4 min following atipamezole at 0.4 mg/kg. Medetomidine and atipamezole provided safe handling in most animals and rapid recovery without use of a controlled substance. At these doses, biologists in the field should be prepared to administer a supplementary dose of medetomidine to some animals depending on ambient conditions and the objectives of the restraint event.     

Characterization of 59 canine single nucleotide polymorphisms in the Italian wolf (Canis lupus) population

We characterized 59 canine single nucleotide polymorphisms (SNPs) in the endangered Italian wolf (Canis lupus) population, which were discovered by resequencing sequence‐tagged‐site (STS) DNA sequences that are known to contain SNPs in domestic dogs. Dog SNPs were usually found also in wolves. Additional SNPs unique in dogs or wolves were discovered, which is important for detecting hybrids between dogs and wolves. We developed new primer sets and analysed 15 SNPs by Pyrosequencing. The characterized SNPs will provide an important addition to the genetic markers that are currently available for studying wild populations of canids.     

Association between temperament related traits and single nucleotide polymorphisms in the serotonin and oxytocin systems in Merino sheep

Animal temperament is defined as the consistent behavioral and physiological differences that are seen between individuals in response to the same stressor. Neurotransmitter systems, like serotonin and oxytocin in the central nervous system, underlie variation in behavioral traits in humans and other animals. Variations like single nucleotide polymorphisms (SNPs) in the genes for tryptophan 5-hydroxylase (TPH2), the serotonin transporter (SLC6A4), the serotonin receptor (HTR2A), and the oxytocin receptor (OXTR) are associated with behavioral phenotype in humans. Thus, the objective of this study was to identify SNPs in those genes and to test if those variations are associated with the temperament in Merino sheep. Using ewes from the University of Western Australia temperament flock, which has been selected on emotional reactivity for more than 20 generations, eight SNPs (rs107856757, rs107856818, rs107856856 and rs107857156 in TPH2, rs20917091 in SLC6A4, rs17196799 and rs17193181 in HTR2A, and rs17664565 in OXTR) were found to be distributed differently between calm and nervous sheep. These eight SNPs were then genotyped in 260 sheep from a flock that has never been selected on emotional reactivity, followed by the estimation of the behavioral traits of those 260 sheep using an arena test and an isolation box test. We found that several SNPs in TPH2 (rs107856757, rs107856818, rs107856856 and rs107857156) were in strong linkage disequilibrium, and all were associated with behavioral phenotype in the nonselected sheep. Similarly, rs17196799 in HTR2A was also associated with the behavioral phenotype.     

The use of nuclear and mitochondrial single nucleotide polymorphisms to identify cryptic species

There is growing interest in the use of single nucleotide polymorphisms for evolutionary and population genetics. We tested the efficacy of one of the available single nucleotide polymorphism techniques, single-base extension, in distinguishing four cryptic species of Microtus. Sequence data were available for these species at nuclear and mitochondrial loci and their identity could be independently confirmed using karyotypes. We found that the development and optimization of single nucleotide polymorphisms required extensive effort, and that the method accurately identified the correct nucleotide at single nucleotide polymorphism sites approximately 90% of the time at the conserved nuclear locus. Correct identification rates were much lower at the highly variable mitochondrial locus.     

Development of new nuclear markers and characterization of single nucleotide polymorphisms in kelp gull (Larus dominicanus)

The present study seeks to develop nuclear markers for the kelp gull (Larus dominicanus). We hereby report the characterization of 12 independent nuclear introns, where 104 single nucleotide polymorphisms (SNPs) in 8138 sequenced base pairs were observed. These SNP markers are the first to be designed for genotyping a gull species. The markers will provide useful tools for understanding which processes act or acted upon kelp gulls to cause their low genetic variability in mitochondrial DNA. In addition, these markers open a new opportunity for population genetic and evolutionary studies in the Laridae group.     

Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large‐scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual‐based structuring algorithms discern geographical structuring. Model‐based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.     

Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery

The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next‐generation sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127 041 single‐nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.     

Sequence context at human single nucleotide polymorphisms: overrepresentation of CpG dinucleotide at polymorphic sites and suppression of variation in CpG islands

Human polymorphisms originate as mutations, and the influence of context on mutagenesis should be reflected in the distribution of sequences surrounding single nucleotide polymorphisms (SNPs). We have performed a computational survey of nearly two million human SNPs to determine if sequence-dependent hotspots for polymorphism exist in the human genome. Here we show that sequences containing CpG dinucleotides, which occur at low frequencies in the human genome, are 6.7-fold more abundant at polymorphic sites than expected. In contrast, polymorphisms in CpG sequences located within CpG islands, important regulatory regions that modulate gene expression, are 6.8-fold less prevalent than expected. The distribution of polymorphic alleles at CpGs in CpG islands is also significantly different from that in non-island regions. These data strongly support a role for 5-methylcytosine deamination in the generation of human variation, and suggest that variation at CpGs in islands is suppressed.     

Identification of single nucleotide polymorphisms in the bovine follicle‐stimulating hormone receptor and effects of genotypes on superovulatory response traits

In dairy cows, there is evidence that failure to respond to superovulation protocols is a heritable trait. In women, genotyping for the p.N680S single nucleotide polymorphism (SNP) in the follicle‐stimulating hormone receptor (FSHR) gene may help identify poor responders before ovarian stimulation is initiated. Our objectives were to identify SNPs in the coding region of the bovine FSHR gene and to investigate the effect of FSHR genotypes on superovulatory response in Holstein cattle. Sequencing of FSHR exons 1–10 revealed seven SNPs. Three were non‐synonymous mutations (c.337C>G, c.871A>G and c.1973C>G). SNP c.337C>G encodes for a proline‐to‐alanine (p.Pro113Ala) amino acid replacement in the extracellular ligand‐binding domain of the receptor. PCR‐RFLP analyses showed that homozygous GG Holstein cows present a higher percentage of viable embryos, whereas GG and CG animals have less unfertilised oocytes. SNP c.871A>G results in an isoleucine‐to‐valine (p.Ile291Val) modification, and homozygous AA animals present lower embryo yield after superovulatory treatments. SNP c.1973C>G corresponds to a threonine‐to‐serine (p.The658Ser) modification in the intracellular carboxyl‐terminal domain of the FSHR protein, and homozygous GG Holstein cows were associated with a lower embryo yield and a higher percentage of unfertilised oocytes. Our results suggest that specific alleles of the bovine FSHR gene are associated with variations in embryo yield and in the number of unfertilised oocytes.     

Multiple-strand displacement and identification of single nucleotide polymorphisms as markers of genotypic variation of Pasteuria penetrans biotypes infecting root-knot nematodes

Pasteuria species are endospore-forming obligate bacterial parasites of soil-inhabiting nematodes and water-inhabiting cladocerans, e.g. water fleas, and are closely related to Bacillus spp. by 16S rRNA gene sequence. As naturally occurring bacteria, biotypes of Pasteuria penetrans are attractive candidates for the biocontrol of various Meloidogyne spp. (root-knot nematodes). Failure to culture these bacteria outside their hosts has prevented isolation of genomic DNA in quantities sufficient for identification of genes associated with host recognition and virulence. We have applied multiple-strand displacement amplification (MDA) to generate DNA for comparative genomics of biotypes exhibiting different host preferences. Using the genome of Bacillus subtilis as a paradigm, MDA allowed quantitative detection and sequencing of 12 marker genes from 2000 cells. Meloidogyne spp. infected with P. penetrans P20 or B4 contained single nucleotide polymorphisms (SNPs) in the spoIIAB gene that did not change the amino acid sequence, or that substituted amino acids with similar chemical properties. Individual nematodes infected with P. penetrans P20 or B4 contained SNPs in the spoIIAB gene sequenced in MDA-generated products. Detection of SNPs in the spoIIAB gene in a nematode indicates infection by more than one genotype, supporting the need to sequence genomes of Pasteuria spp. derived from single spore isolates.     

PRIMER NOTE. Using the incomplete genome of the ectomycorrhizal fungus Amanita bisporigera to identify molecular polymorphisms in the related Amanita phalloides

We describe the cross‐genomic isolation of 13 single nucleotide polymorphisms (SNPs) and one variable microsatellite from five loci for the death cap mushroom Amanita phalloides. Microsatellite repeats were identified by searching the partial Amanita bisporigera genome. Flanking primers were designed for 25 of these microsatellite loci and tested for cross‐amplification in A. phalloides. One locus contained an interrupted, compound microsatellite, and four loci contained one to six SNPs. These results demonstrate the usefulness of even an incomplete genome to identify molecular markers for population studies in nonmodel organisms.     

延边朝鲜族和汉族脂联素启动子SNPs与原发性高血压的相关性

为了探讨延边朝鲜族和汉族脂联素基因启动子单核苷酸多态性(SNPs)与原发性高血压(EH)的关系, 文章采用PCR产物直接测序方法检测了220例EH患者和268例对照个体的脂联素启动子5个SNPs位点: -11426A>G(rs16861194)、-11391G>A(rs17300539)、-11377C>G(rs62620185)、-11156insCA(rs60806105)、-11043C>T(rs76786086), 氧化酶法测定空腹血糖、甘油三酯、总胆固醇、低密度脂蛋白、高密度脂蛋白, 酶联免疫吸附法(ELISA)测定血浆脂联素和胰岛素。结果显示: (1) -11426A>G、-11377C>G 和-11156insCA 3个位点具有多态性, 且它们的基因型频率分布符合Hardy-Weinberg平衡定律(P>0.05), -11391G>A和-11043C>T位点无多态性; (2) -11426A>G和-11156insCA呈完全连锁不平衡(D’=1; r2=1); (3) -11426G基因频率比较, 朝鲜族(21.10%)高于汉族(12.05%), 汉族EH组高于对照组; -11377C>G的基因型和基因频率在朝鲜族和汉族间及同一民族内EH组和对照组间比较均无统计学意义(P>0.05); (4)单倍型?11426G -11377C的频率, 汉族EH组高于对照组(P<0.05), 朝鲜族EH组和对照组比较无统计学意义(P>0.05); (5)EH组的血浆脂联素水平明显低于对照组(P<0.001)。据此得出结论: (1)首次发现?11426A>G和?11156insCA呈完全连锁不平衡, -11426 A>G的多态性在朝鲜族和汉族中存在民族差异; (2) -11426 G和-11426G -11377C是延边汉族EH的危险因子和危险单倍型, 但不是朝鲜族的; (3)低血浆脂联素是延边朝鲜族和汉族EH的重要危险因素; (4)血浆脂联素水平与-11426A>G基因型无关。     

Frequency distribution of single nucleotide polymorphisms in P-selectin gene in Chinese Tibetan and Han populations

Background

Chinese Tibetans have a series of distinctive physiological traits which enable them to tolerate the extreme environment of the Tibetan plateau. P-selectin gene has been proved to be highly polymorphic in Europeans and Americans. Nevertheless, studies on either the frequency distributions of single nucleotide polymorphisms (SNPs) or haplotype diversity and linkage disequilibrium of P-selectin gene in Chinese Tibetan population are still unavailable.

Methods

The frequency distributions of 3 SNPs in P-selectin gene promoter (− 2123C/G, − 1969A/G, − 1817T/C) and 3 SNPs in exon region (Ser290Asn, Val599Leu, Thr715Pro) were investigated by real-time PCR and high-resolution melting method among 314 Chinese Tibetans and 328 age- and sex-matched Han people.

Results

The frequencies of the − 2123G and − 1817T alleles among the Tibetan population had no significant differences from those of the Han population. Among the Tibetan population, the G allele frequency of − 1969A/G and Ser290Asn were both higher than those of the Han population. Val599Leu and Thr715Pro did not show any polymorphism in the two populations. In the Tibetan population, − 2123C/G, − 1969A/G, − 1817T/C and Ser290Asn were in tight linkage disequilibrium with each other.

Conclusions

The frequency distributions of − 1969A/G and Ser290Asn polymorphisms in the Tibetan population were different from those in the Han population.     

Single nucleotide polymorphisms in the mitochondrial control region are associated with metabolic phenotypes and oxidative stress

Objective

To identify the mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) in the control region and elucidate their role in metabolic phenotypes and oxidative stress.

Methods

A total of 861 nondiabetic subjects were enrolled, including 250 impaired fasting glucose (IFG) and 370 obese subjects (body mass index [BMI] > 25 kg/m²). Antioxidant status presented as total free thiol level was determined from serum samples. DNA was extracted from peripheral blood leucocytes, and the sequences were analyzed using the DNASTAR software. SNPs were identified by comparison with the Cambridge Reference Sequence.

Results

After adjusting odds ratios for age, sex, and BMI, the selected independently significant SNPs indicated 4 susceptible SNPs: SNP-16126C and SNP-16261T, which were related to abdominal obesity (P = 0.009; 0.06); SNP-16390A, related to hypertension (HTN) (P = 0.007); and SNP-16092C, related to decreased antioxidant capacity (P = 0.015). In the obese subgroup, 3 susceptible SNPs included SNP-16189C and SNP-16260T, which showed significantly higher IFG prevalence (P = 0.016 and 0.024, respectively), and SNP-16519C, which was significantly higher in the HTN group (P = 0.036). As to protective SNPs, 5 protective SNPs were identified in all subjects but only one SNP-16093C is consistent in obese group, which showed a significantly lower prevalence in patients with abdominal obesity and was associated with a higher antioxidant status (P < 0.001).

Conclusion

SNPs in the mtDNA control region are associated with metabolic phenotypes and oxidative stress markers. Some SNPs are relating to the interaction between obesity and genetic factors. The beneficial effects of these protective SNPs were insignificant and some susceptible SNPs became dominant within the obese subgroup. Subjects harboring these SNPs should avoid excessive weight gain.