The Heart of Silk Road “Xinjiang,” Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy–Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

Wild boar behaviour during live-trap capture in a corral-style trap: implications for animal welfare

Background Wildlife traps are used in many countries without evaluation of their effect on animal welfare. Trap-capture of wild animals should minimise negative effects on animal welfare, irrespective of whether the animals are trapped for hunting, research, or management purposes. Live-trap capture of wild boar (Sus scrofa) followed by killing inside the trap by gunshot is a recently introduced but disputed hunting method in Sweden. Approval of trap constructions is based on gross necropsy findings of 20 trapped and shot wild boars. For improved animal welfare evaluation, our aim was to study wild boar behaviour during live-trapping in a 16 m2 square corral-style trap. Behavioural assessments were conducted after filming 12 capture events of in total 38 wild boars (five adults, 20 subadults, 13 piglets). Selected behavioural traits were compared with pathological changes (trap-related lesions) found at necropsy of the 20 subadults, to determine if these variables were useful proxies of capture-induced stress in wild boar. Results The wild boars spent less time resting in the evening than in the night and morning. Using Friedman’s ANOVA, there was an overall difference in the time spent foraging. However, we only found a difference between the evening and morning in the Wilcoxon matched pairs test after the Sequential Bonferroni correction, where the wild boars spent more time foraging in the evening than in the morning. Single captured individuals showed more escape behaviours and reacted more strongly to external stimuli than individuals captured in a group. It was more common for animals to charge against the mesh walls of the trap upon human approach compared to upon initial capture when the trap door closed. Trap-related pathological findings due to trauma were documented in 13 of the 20 subadults that were necropsied. Behavioural alterations indicative of capture-induced stress (e.g. charging into the trap walls) were documented in trapped wild boars with no or minor physical injuries (e.g. skin abrasions, subcutaneous haemorrhage). Conclusions Behavioural assessment provided valuable information for determination of capture-induced stress in wild boar when evaluating live-trapping in a corral-style trap, whereas pathological evaluation through necropsy did not fully reflect the animal welfare aspects of live-trapping. We emphasize the inclusion of species-specific behavioural data assessment for evaluation of capture-related stress during live-trapping and for testing of new trap constructions before approval.

Fear expressions of dogs during New Year fireworks: a video analysis

A high proportion of pet dogs show fear-related behavioural problems, with noise fears being most prevalent. Nonetheless, few studies have objectively evaluated fear expression in this species. Using owner-provided video recordings, we coded behavioural expressions of pet dogs during a real-life firework situation at New Year’s Eve and compared them to behaviour of the same dogs on a different evening without fireworks (control condition), using Wilcoxon signed ranks tests. A backwards-directed ear position, measured at the base of the ear, was most strongly associated with the fireworks condition (effect size: Cohen’s d = 0.69). Durations of locomotion (d = 0.54) and panting (d = 0.45) were also higher during fireworks than during the control condition. Vocalisations (d = 0.40), blinking (d = 0.37), and hiding (d = 0.37) were increased during fireworks, but this was not significant after sequential Bonferroni correction. This could possibly be attributed to the high inter-individual variability in the frequency of blinking and the majority of subjects not vocalising or hiding at all. Thus, individual differences must be taken into account when aiming to assess an individual’s level of fear, as relevant measures may not be the same for all individuals. Firework exposure was not associated with an elevated rate of other so-called ‘stress signals’, lip licking and yawning.

Temporal stability of genetic diversity revealed by microsatellite markers in restocked populations of Caspian roach, Rutilus caspicus (Yakovlev, 1870)

Rutilus caspicus is considered one of the most important bony fish with high economic value in the Caspian Sea. Since the population size of Caspian roach has decreased during recent decades, restocking of the populations is done through releasing hatchery-produced larvae into the wild. In the present study, the genetic diversity of wild and hatchery populations of R. caspicus was investigated using ten microsatellite loci. Also, microsatellite analysis was performed to compare the population structure of Caspian roach over a time frame of about 11 years. Although the allelic and gene diversity of hatchery populations tended to be lower than those of the wild populations, no significant differences in genetic diversity parameters were observed among the wild and hatchery populations. Similar variation levels were noticed among temporal samples of the same population, suggesting temporal stability in the genetic diversity of the wild populations. In most cases, significant departure from the Hardy-Weinberg equilibrium was observed after sequential Bonferroni correction. Results from analysis showed that a captive hatchery population was the most differentiated group. Also, the UPGMA dendrogram showed that the captive population was the most distant group. The stability of genetic composition between the two periods was noticed by the low and non-significant and estimates. The results from this study are anticipated to provide important information for setting up more efficient strategies for the conservation and restocking of R. caspicus.

Heterologous microsatellite-based genetic diversity in blue mussel (Mytilus chilensis) and differentiation among localities in southern Chile

Mussels (Mytilus spp.) are one of the most cultivated and commercialized bivalves in southern Chile; culture is currently supplied almost entirely from wild-caught seed obtained from relatively few collection centers. The genetic diversity and differentiation of the blue mussel in southern Chile was investigated by sampling six locations: one natural bank and five seed collection centers. Nine polymorphic microsatellite (SSR) loci were genotyped (Mgu1, Mgu3, MT203, MT282, Mg15, Mg56, Med737, MIT02 and MGE005). We found 75 different alleles, six of which were private alleles. Of the analyzed loci, 45 of 54 tests performed deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction (P < 0.05), revealing significant heterozygote deficiencies. The polymorphic information content (PIC) ranged from 0.322 (MGE005) to 0.893 (Mgu1). Despite the long distance between some sampling sites (up to 1360 km), genetic differentiation among the sites was low (FST = 0.043, P < 0.0001). The Bayesian cluster analysis (STRUCTURE) indicated two probable clusters, while the non-parametric cluster analysis (AWclust) identified two to four clusters. Both analyses showed a high level of admixture within clusters. Our results indicate that blue mussels in southern Chile show lower genetic diversity than in other countries, low inbreeding levels, and limited genetic differentiation among locations.