Genetic diversity of Asian water buffalo (Bubalus bubalis): mitochondrial DNA D-loop and cytochrome b sequence variation

Swamp and river buffalo mitochondrial DNA (mtDNA) was sequenced for 303 bp of the cytochrome b gene for 54 animals from 14 populations, and for 158 bp of the D-loop region for 80 animals from 11 populations. Only one cytochrome b haplotype was found in river buffalo. Of the four haplotypes identified in swamp buffalo, one found in all populations is apparently ancestral both to the other swamp haplotypes and to the river haplotype. The phylogenetic relationships among the 33 D-loop haplotypes, with a cluster of 11 found in swamp buffalo only, also support the evolution of domesticated swamp and river buffalo from an ancestral swamp-like animal, most likely represented today by the wild Asian buffalo ( Bubalus arnee ). The time of divergence of the swamp and river types, estimated from the D-loop data, is 28 000 to 87 000 years ago. We hypothesise that the species originated in mainland south-east Asia, and that it spread north to China and west to the Indian subcontinent, where the rive type evolved and was domesticated. Following domestication in China, the domesticated swamp buffalo spread through two separate routes, through Taiwan and the Philippines to the eastern islands of Borneo and Sulawesi, and south through mainland southeast Asia and then to the western islands of Indonesia.     

Domestication in the silver fox (Vulpes fulvus Desm): Changes in physiological boundaries of the sensitive period of primary socialization

The physiological boundaries of the sensitive period of primary socialization were studied in the silver fox (Vulpes fulvus Desm). A total of 273 farm-bred foxes from 59 litters were observed from 1976 to 1978; pups were produced by vixens from two populations, one selected for domesticated behaviour and the other unselected. Results indicate that the age when the eyes are fully open, when the response to sound first appears and when exploratory behaviour is first shown in strange surroundings is 3 weeks, on average. The age when the socialization period starts appears to be 20–25 days old. The optimum period of the formation of primary social bonds appears to be 30–35 days, when maximum exploration in a novel situation is shown. The 40–45 days period appears to be the upper boundary of primary socialization in unselected foxes because pups show fear in response to novel stimuli, which prevents exploration. In pups from the population of domesticated foxes, the sensitive period of socialization is prolonged to over 60–65 days old.     

Breeding of the Russian sable: Stages of industrial domestication and genetic variability

Creating farms for sable breeding was associated with the commercial destruction of natural populations and, consequently, the overall decline in the species number. The gene pool of the first farm-bred sable population in Russia, established in the vicinity of Moscow (“Pushkinskiy” fur farm), was formed by crossing of animals removed from nine natural populations. In the first eight years of farm operation, approximately one thousand animals were used for sable breeding; some of these animals were able to adapt to the farm management and, subsequently, to the selection for a number of quantitative traits in the period of industrial domestication. It took about ten years for breeders to work out the breeding and selection technologies, which became successfully employed in the established affiliated sable breeding farms. The main achievement in sable breeding over the 85-year historical period of breeding in Russia is the creation of two unique breeds, black sable (1969) and Saltykovskaya 1 (2007). In general, industrial domestication in fur farming and the subsequent breeding works made the fur of many species (mink, fox, Arctic fox) obtained from natural populations uncompetitive, which undoubtedly reduced the hunting interest in the animals living in the wild. Consequently, hunting for fur-bearing animals of most species decreased and has only local importance. Owing to the specific features of sable biology, the fur of farm-bred animals cannot yet completely replace the furs obtained by hunting; however, the farm-bred sable population is constantly growing. This review presents the results of the analysis of the level of genetic variability in natural and farm populations at nuclear and mitochondrial loci. The comparative analysis makes it possible to estimate the loss of genetic diversity upon the species adaptation to the new conditions of existence.     

Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia

Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c . 400 000 years before present ( bp ): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (≥ 99% Bayesian posterior probability); two that were more recently derived (rho estimate c . 20 000 bp ) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c . 45 000 bp ) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000–130 000 bp ), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000–10 000 bp ). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.     

Sex ratio in silver foxes: effects of domestication and the star gene

The course of changes in secondary sex ratio (proportion of males at birth) in silver foxes bred at the fur farm of this Institute was analyzed. Data collected over several years of breeding of a domesticated (experimental) population selected for amenability to domestication and of a commercial (control) were compared. A tendency to increase in secondary sex ratio was demonstrated in both populations. However, the proportion of males at birth was higher in domestic foxes. This proportion, calculated from the combined data for 1978–1993, was 0.538±0.005 and 0.511±0.007 in the selected and commercial populations, respectively. The minimal departure of the observed sex ratio from 0.5 was demonstrated for litters with five pups, which is close to the average litter size in fox populations. The proportion of males increases with both increasing and decreasing litter size. An analysis of secondary sex ratio with respect to maternal age revealed a minimal departure of sex ratio from the expected in offspring from foxes of optimal reproductive age (2–4 years). An effect of the autosomal semidominant coat color mutation star on male excess at birth was also found: secondary sex ratio was higher (0.583±0.015) in offspring of mothers heterozygous for the star mutation than from standard types of the domesticated population. The increase in secondary sex ratio in the analyzed fox populations is viewed as a correlated response to selection for domestication. The hormonal mechanisms mediating the effects of both this selection and the star mutation on sex ratio at birth are discussed.     

Hematology and serum biochemistry of captive swift foxes (Vulpes velox)

Blood samples were taken from 23 swift foxes (Vulpes velox) which were to be used in a reintroduction program. The foxes originated from two different captive breeding programs: one at the Calgary Zoo (CZ) and one at the Wildlife Reserve of Western Canada (WRWC). Several differences between swift fox and domestic canine hematology were seen, including an increased number of smaller red blood cells and lower absolute leukocyte counts in swift foxes. Serum glutamic pyruvic transaminase was higher than in the domestic canine normal range while serum creatinine values were lower. Hemoglobin, serum potassium, total protein, globulin in the two groups (CZ and WRWC) were statistically different as were male versus female mean corpuscular volume values.     

Inter- and intraspecific competition between the fox species Alopex lagopus and Vulpes vulpes: an evaluation trial under penned conditions

This study compared competition capacity and dominance relations between arctic foxes (Alopex lagopus) and red foxes (Vulpes vulpes). Experiments were carried out in semi-natural earthen floor enclosures using farm-bred colour types of both species (blue fox and silver fox) as subjects. Results of the dominance scoring and open field behaviour after weaning in August-September showed that blue foxes dominated over silver foxes. Thereafter, the situation gradually became reversed and silver foxes were dominant during the breeding and whelping seasons. Housing both species together from weaning produced more curious animals as compared to when these species were placed in common quarters after the autumn equinox. In the case of blue foxes, the male dominated highly over all females. In silver foxes, the difference in dominance between the sexes was, however, less pronounced. The most dominant individuals in the study groups were typically among the heaviest. Breedings and whelpings succeeded better in silver than in blue foxes. However, none of litters born survived more than one week. The present results support the conclusion that when both fox species are housed together, Vulpus vulpus tends to dominate over Alopex lagopus. Received: 22 March 1996/Accepted: 30 June 1996     

草鱼野生与选育群体线粒体DNA控制区D-loop遗传变异分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化, 研究对4个野生群体(邗江、九江、石首和吴江)和2个选育世代(F1和F2)进行了线粒体DNA控制区(D-loop)序列的遗传变异分析。实验结果表明, 4个野生群体在单倍型数目(H)、单倍型多样性(H_d)、核苷酸多样性(π)、平均核苷酸差异数(K)水平上均高于2个选育世代, 在2个选育世代内表现为F1代群体的核苷酸多样性(π)和平均核苷酸差异数(K)大于F2代群体, 但单倍型多样性(H_d)小于F2代群体; 单倍型分析结果表明, 6个群体间无共享单倍型, 4个野生群体间共发现2种共享单倍型(Hap1和Hap3), 石首群体和2个选育世代共享1种单倍型(Hap15); 遗传分化指数(F_st)分析结果表明, 邗江、九江、吴江3个野生群体和2个选育世代间存在较大的遗传分化(F_st范围为0.41475—0.55128), 石首群体与F1代群体之间存在较小的遗传分化, 与F2代群体之间存在中等水平的遗传分化, 同时F1代群体与F2代群体之间存在较小的遗传分化; 基于6个群体276个个体构建的邻接(Neighbor-Joining, NJ)进化树和基于27种单倍型构建的单倍型网络图也得到了相似的结论, 即邗江、九江、吴江3个野生群体和2个选育世代间的亲缘关系较远, 石首群体和2个选育世代两两之间的亲缘关系较近。以上结果表明, 经过2个世代的选择育种, 选育群体的遗传结构已发生了变化, 并且随着选育的进行, 选育世代的遗传多样性下降的较为明显, 这警示着我们在今后的育种工作中应适当改变现有的选育方案, 并实时监测选育群体的遗传多样性, 以便为今后进一步的选育工作打下坚实的基础。     

Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes)

The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.     

Habitat use and home range size of red foxes in Prince Edward Island (Canada) based on snow-tracking and radio-telemetry data

There is a lack of information regarding the ecology and behaviour of red foxes that can be used to elaborate effective management programs for this species on Prince Edward Island (Canada). The main goal of this study was to provide baseline information on habitat selection and home range size of red foxes on Prince Edward Island. Data were collected from snow-tracking and radio-telemetry sessions conducted in two study sites (including one site within Prince Edward Island National Park). Our results indicated that red foxes selected for roads and human-use areas during both the breeding and the kit-rearing seasons in the park. Outside the park, however, the data failed to conclusively show that foxes have a unique preference for human-use habitats or roads. Forests were selected against in both study sites. Although roads are frequently visited by foxes during the kit-rearing season in the park, each individual fox typically stays in this habitat only for short periods of time (< 15 min). This finding suggests that foraging efficiency along the roads is very high possibly reflecting the abundance of anthropogenic food sources. Overall, we present the largest amount of data on habitat selection ever collected for red foxes in Prince Edward Island, Canada. Our results show that food sources in human-use areas and roads are altering the selection and/or use of habitats of red foxes in some areas of Prince Edward Island.     

Foraging ecology and spatial behaviour of the red fox (Vulpes vulpes) in a wet grassland ecosystem

We investigated diet composition, habitat selection and spatial behaviour of the red fox (Vulpes vulpes) in relation to the availability of wader nests in a coastal polder area in southwest Denmark. The predatory role of the red fox in wet grassland ecosystems has profound implications for conservation status of declining populations of grassland breeding waders. However, few studies have focussed on the foraging ecology and behaviour of the red fox in these landscapes. Faecal analyses revealed that fox diet consisted of birds (43 % of prey remains?/?32 % of biomass), rodents (39 %?/?21 %), sheep (mainly as carrion, 14 %?/?41 %) and lagomorphs (4 %?/?7 %). Charadriiformes (including waders) comprised 3–12 % of prey remains throughout the year. Telemetry data and spotlight counts indicated that foxes did not select areas with high densities of breeding waders, suggesting that foxes did not target wader nests while foraging. Foxes maintained stable home ranges throughout their lives, indicating that the area sustained a permanent fox population all year round. The population densities, estimated from spotlight surveys, were 0.74 visible foxes km^?2 (95 % CI; 0.34–1.61) on the preferred breeding habitat for waders and 1.21 km^?2 in other open habitats such as cultivated fields. Our results indicate that red fox predation on wader nests is incidental, consistent with the notion that red foxes are generalist predators that opportunistically subsist on many prey groups.     

The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox

Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.     

The breeding productivity of dark-bellied brent geese and curlew sandpipers in relation to changes in the numbers of arctic foxes and lemmings on the Taimyr Peninsula, Siberia —

There were about three-year cycles in the populations of arctic foxes, and the breeding productivities of brent geese and curlew sandpipers on the Taimyr Peninsula, Russia, The populations of arctic foxes and lemmings changed in synchrony. The breeding productivities of the birds tended to be good when the arctic foxes were increasing in numbers and poor when the arctic foxes were decreasing. There was a negative relationship between arctic fox numbers (or occupied lairs) and the breeding productivity of brent geese in the following year. Although there was evidence of wide-spread synchrony In the lemming cycle across the Taimyr Peninsula, some localities showed differences, However, such sites would still have been influenced by the general pattern of fox abundance in the typical tundra zone of the Taimyr Peninsula, where most of the arctic foxes breed and from which extensive movements of foxes occur after a decline in lemming numbers. The results support a prey-switching hypothesis (also known as the alternative prey hypothesis) whereby arctic foxes, and other predators, feed largely on lemmings when these are abundant or increasing, but switch to birds when the lemming population is small or declining. The relationships between arctic foxes, lemmings and brent geese may be further influenced by snowny owls which create fox-exclusion zones around their nests, thus providing safe nesting areas for the geese.     

Distribution and phylogeography of Blanford’s Fox,Vulpes cana (Carnivora: Canidae), in Africa and the Middle East

The distribution of Vulpes cana in the extreme eastern Sahara is described on the basis of new photographic and sight records, as well as a recently acquired specimen from south-eastern Egypt. The proven range of this elusive fox now extends about 1000 km south into Africa along the Red Sea coastal mountains. The proven and predicted distribution ranges of this fox are discussed. Its phylogeography and evolutionary relationship to other foxes of the region are gleaned from analysis of mitochondrial cytochrome b DNA sequence and are discussed in light of climatic and paleogeographic history of the area. The results show that the species could have initially moved into Africa during the Pliocene-Pleistocene transition period when several land bridges occurred across the Gulf of Suez. More recent land bridges between the mountains of the Sinai Peninsula and the Eastern Desert of Egypt seem to have developed and disappeared several times during the Pleistocene, possibly allowing genetic exchange between V. cana populations in these two areas. The last of this population exchange and genetic flow between the two areas seems to have ended some 14,000 years ago when the present Gulf of Suez inundation took place.     

Exclusion by interference competition? The relationship between red and arctic foxes

The distribution of many predators may be limited by interactions with larger predator species. The arctic fox in mainland Europe is endangered, while the red fox is increasing its range in the north. It has been suggested that the southern distribution limit of the arctic fox is determined by interspecific competition with the red fox. This has been criticised, on the basis that the species co-exist on a regional scale. However, if the larger red fox is superior and interspecific competition important, the arctic fox should avoid close contact, especially during the breeding season. Consequently, the distribution of breeding dens for the two species would be segregated on a much smaller spatial and temporal scale, in areas where they are sympatric. We tested this hypothesis by analysing den use of reproducing arctic and red foxes over 9 years in Sweden. High quality dens were inhabited by reproducing arctic foxes more often when no red foxes bred in the vicinity. Furthermore, in two out of three cases when arctic foxes did reproduce near red foxes, juveniles were killed by red foxes. We also found that breeding arctic foxes occupied dens at higher altitudes than red foxes did. In a large-scale field experiment, red foxes were removed, but the results were not conclusive. However, we conclude that on the scale of individual territories, arctic foxes avoid areas with red foxes. Through interspecific interference competition, the red fox might thus be excluding the arctic fox from breeding in low altitude habitat, which is most important in years when food abundance is limited and competition is most fierce. With high altitude refuges being less suitable, even small-scale behavioural effects could scale up to significant effects at the population level.     

Distribution, habitat utilization and age structure of a suburban fox (Vulpes vulpes) population

The occurrence of wild foxes in suburbia is discussed. It is shown that in London breeding populations of foxes are found 5 km from the city centre, and in the last 3 years foxes have been recorded in the very centre of the city. The fox population in London is shown to be heavily dependent on residential habitats for both daytime harbourage and when selecting sites for natal earths. The fox population is unevenly distributed in London, with a marked clumping of the adult population during most of the year. The age structure of the population is presented, and these data are compared with data for other canid populations. Conclusions are drawn as to the effects of conventional control techniques on the age structure of a fox population.     

Non-native carp of the genus <Emphasis Type="Italic">Cyprinus</Emphasis> in Lake Xingyun,China, as revealed by morphology and mitochondrial DNA analysis

Lake Xingyun is a major body of water in Yunnan Province, China. Previous investigations suggested that the lake contained native populations of carp of the genus Cyprinus, but it is believed that these native populations disappeared due to overfishing. However, one or more Cyprinus species are currently abundant in Lake Xingyun but their identity and origin are unclear. To determine if the existing Cyprinus population is indeed non-native, we compared the morphologies of fish (n = 62) recently captured (2007) to museum preserved Cyprinus collected in the lake in the 1960s. In addition, we conducted mitochondrial DNA analyses of Cyprinus (n = 65) recently taken from the lake and found 28 haplotypes. The genetics of the lake’s sample were compared to Cyprinus from a wide range of other locations within and outside China. Together with previously published Japanese and Eurasian haplotypes, phylogenetic analysis demonstrated 28 haplotypes and these were classified into five different units. One of the five units included 16 closely related haplotypes that formed a monophyletic group apart from the Eurasian clade. Given their monophyly that included 3 native carp haplotypes, haplotypes from this unit were thought to originate from the native strain of Lake Xingyun. Furthermore, combining this with result from morphological analysis, it was concluded that these haplotypes were likely hybrid carp. Conversely, haplotypes from the other 4 units nested into the Eurasian clade. Their phylogenetic affinities to Eurasian lineages indicated that these haplotypes were domesticated strains introduced from other parts of China, Vietnam and Europe. These conclusions were supported by historical records on introduction. This study revealed that almost all carp from current Lake Xingyun may be originated from hybrid strains and domesticated strains introduced from Eurasia.     

Mitochondrial DNA analysis reveals cryptic large-scale invasion of non-native genotypes of common carp (Cyprinus carpio) in Japan

Wild common carp ( Cyprinus carpio ) are probably suffering from biological invasions of conspecific domesticated strains. However, such invasions may be largely camouflaged by morphological similarities between introduced and native strains. We conducted a large survey of mitochondrial DNA sequences (complete D-loop region) from 11 localities in Japan. From a total of 166 individuals, 28 haplotypes were determined to fit into six divergent clades. One of the six clades included 19 closely related haplotypes with moderate nucleotide differences; however, the remaining five clades each included either a single haplotype or two almost identical haplotypes. Phylogenetic analysis together with the previously published Eurasian haplotypes further demonstrated that the 'monotypic' clades were sisters to various Eurasian lineages, whereas the 19 related haplotypes formed a monophyletic group apart from the whole Eurasian clade. Given their monophyly and genetic diversity, the 19 related haplotypes were thought to originate from the Japanese native strain. Conversely, their phylogenetic affinities to Eurasian lineages and unnaturally low genetic diversities caused the haplotypes of the five monotypic clades to be considered as domesticated strains introduced from Eurasia. These hypotheses were supported by further evidences; i.e. the probable non-native haplotypes were frequently found from Japanese domesticated strains, and the probable native population structure was rescued when the probable non-native haplotypes were excluded from the analyses. This study revealed that almost half or more of the haplotypes in all of the locations studied originated from domesticated strains introduced from Eurasia.     

Adiponectin and peptide YY in the fasting blue fox (Alopex lagopus)

Adiponectin (Acrp30) and peptide YY (PYY) are weight-regulatory hormones participating in the control of energy homeostasis. This study investigated the effects of long-term wintertime fasting on plasma Acrp30 and PYY levels in the carnivorous blue fox, a farm-bred variant of the arctic fox (Alopex lagopus). Plasma Acrp30 and PYY concentrations were determined with radioimmunoassays during a 22-day period of fasting, which led to a 20.3% reduction in body mass of the animals (n=32). Sixteen fed blue foxes served as the control group. Acrp30 and PYY were present in blue fox plasma at similar or lower levels as reported previously for other mammals. Fasting had no acute effects on Acrp30 or PYY concentrations of the blue foxes. However, the Acrp30 levels of the fasted blue foxes were 24%-48% higher than in the fed animals between days 8-22 of fasting. Fasted blue foxes also had 6.2-fold higher plasma PYY concentrations after 15 days of fasting. Acrp30 and PYY seem to play roles in the body weight-regulation of the blue fox during long-term fasting, but their specific functions and physiological significance remain to be determined.     

Genetic structure of Eurasian and North American mallard ducks based on mtDNA data

To elucidate the origin and genetic structure of the domesticated duck in Eurasia and North America, we sequenced 114 duck D-loop sequences and retrieved 489 D-loop sequences from GenBank. In total, 603 ducks including 50 duck breeds/populations from eight countries (China, France, Russia, India, Kazakhstan, Mongolia, Thailand and USA) were used in this study. One hundred and thirty-four haplotypes and 81 variable sites were detected. H49 was the predominant haplotype, which was considered to be the same dominant haplotype found in the previous studies, and was found in 309 birds. The smallest values for both genetic differentiation index (F(ST), 0.04156) and the number of the net nucleotide substitutions between two populations (D(A), 0.00018) were observed between Eurasian domestic ducks and Eurasian mallards. No geography, breed or population clusters were observed in the Eurasian domestic ducks and mallards. Five haplotypes were shared by USA mallards and Eurasian domestic duck/Eurasian mallards. Only one haplotype (H49) was shared by Eurasian domestic ducks and China spot-billed ducks. By combining phylogenetic analyses, haplotype network profile, genetic distances and shared haplotypes, we can draw two major conclusions: (i) Eurasian and North American mallards show a clear geographic distribution pattern; (ii) Eurasian domestic ducks are derived from the Eurasian mallards, not from the spot-billed ducks.