中国红原鸡和泰国红原鸡遗传多样性分析

利用29个微卫星DNA标记对来自中国的红原鸡Gallus gallus spadiceus亚种和来自泰国的红原鸡Gallus gallus gallus亚种进行遗传多样性分析, 评估亚种内的遗传变异和亚种间的遗传分化, 结果表明: 共检测到168个等位基因, 每个位点的等位基因数从2到13不等, 所有位点平均的期望杂合度和PIC值分别为0.5780和0.53。中国和泰国红原鸡29个微卫星位点平均有效等位基因数分别为3.79和4.79, 平均基因杂合度为0.5379和0.6385, 两个红原鸡亚种均表现出较高的群体杂合度和丰富的遗传多样性。群体分化系数为19.4%(P<0.01), 两个红原鸡亚种间的Reynolds’遗传距离和Nm值分别为0.157和1.040。由此可见, Gallus gallus spadiceus亚种和Gallus gallus gallus亚种群体具有不同的群体遗传结构, 群体之间存在明显的遗传分化, 并不能将其认定为是同一亚种, 这也为中国家鸡具有独立的起源提供了一定的佐证。     

Cryopreservation of Indian red jungle fowl (Gallus gallus murghi) semen with polyvinylpyrrolidone

The Indian red jungle fowl is a sub-species of the genus Gallus native to South Asia; facing high risk of extinction in its native habitat. During cryopreservation, permeable cryoprotectants like glycerol are usually employed and we previously showed encouraging results with 20% glycerol. Because bird spermatozoa contain very little intracellular water, the possibility of replacing an internal cryoprotectant by an external one is opened. In the present study, we tested the replacement of internal cryoprotectant glycerol by the external cryoprotectant Polyvinylpyrrolidone (PVP). PVP is a non-permeable cryoprotectant and keeps the sperm in glassy state both in cooling and warming stages without making ice crystallization within the sperm cell. We evaluated the effect of various levels of polyvinylpyrrolidone (PVP) on Indian red jungle fowl semen quality and fertility outcomes. The qualifying semen ejaculates collected from eight mature cocks were pooled, divided into five aliquots, diluted (37 °C) with red fowl semen extender having PVP [0% (control) 4% (w/v), 6% (w/v), 8% (w/v) and 10% (w/v)]. Diluted semen was cryopreserved and stored in liquid nitrogen. The whole experiment was repeated/replicated for five times independently. Sperm motility, plasma membrane integrity, viability and acrosome integrity were recorded highest (P < 0.05) with 6% PVP at post-dilution, cooling, equilibration and freeze-thawing. Higher (P < 0.05) no. of fertile eggs, fertility, no. of hatched chicks, percent hatch and hatchability was recorded with 6% PVP compared to control. It is concluded that 6% PVP maintained better post-taw quality and fertility of Indian red jungle fowl spermatozoa than glycerol and can be used in routine practice avoiding the contraceptive effects of glycerol.     

Repeatability of mate choice in female red jungle fowl

We staged female mate choice trials between pairs of males andrepeated the process for each female to determine the repeatabilityof female preference for males in red jungle fowl (Gallus gallus)in the first and second half of the breeding season. We measuredmale morphological traits (the size and color of the comb andthe brightness of the hackle feathers) that females are knownto use in choosing a mate. In the first half of the breedingseason, females showed repeatability in their choices of matewith respect to the male's comb characters. Females did notshow a repeatable preference with respect to male hackle feathers,and we found no repeatability of mate choice in the second halfof the season. Females seem to primarily look at the male'scomb when choosing a mate, and other ornaments seem only ofsecondary importance.[Behav Ecol 7: 243-246 (1996)]     

Temporal structure of red jungle fowl crow sequences: single-case analysis

Vocalisations can be indicators of the physical state or condition of an animal, for instance the crow of a rooster. There are no published data on the temporal structure of crow sequences. In this paper 536 crows in 22 sequences of one red jungle fowl rooster (rooster 1) were recorded and analysed. Calls were very characteristic and there was little variation between the calls. Rooster 1 crowed with a mean latency of 287 s after onset of a light in the early morning. The average crow sequence consisted of 29 calls which lasted for 1416 ms on average. A gradual increase in pre-call interval was characteristic of each sequence. The variation in note durations is systematic and especially the last note correlated highly with the total call duration. Both the pre-call interval and the duration of the 4th note (doooo) may be parameters of fatigue and thus of physical condition. The number of crows in a sequence was positively related to air pressure outdoors. An experiment is done in which the physical condition of a rooster (rooster 2) is manipulated by food deprivation. The results are analysed with single case randomisation tests. The number of crows in a sequence is significantly reduced after food deprivation, while the pre-call intervals are significantly increased. Prediction of the number of crows in the sequence can be done on base of the pre-call interval of the second call: both rooster 1 and 2 showed long pre-call intervals in short call sequences. Food deprivation and the possible loss of condition have a significant effect on the temporal structure of crow sequences and cause a decrease in the number of crows in a call sequence.     

Lemdana latifi n. sp. (Filarioidea: Onchocercidae) from the red jungle fowl (Gallus gallus spadiceus)

Lemdana latifi n. sp. was found in connective tissues around the trachea and crop and in the body-cavity of seven of 14 Malayan red jungle fowl Gallus gallus spadiceus. The new species is described and illustrated. Morphologically it is most closely related to Lemdana pavonica and Lemdana francolini. Lemdana latifi is distinguished from the eight valid species of Lemdana by the mean spicular ratio of 1.7:1; the right spicule with a right margin 18–29% (15–31 m; mean 24 m) longer than the left margin; the distal half of the left spicule twisted and S-shaped; and the absence of unpaired papillae at tip of male tail. The new species has smaller adults, a shorter left spicule and a shorter glandular oesophagus than those of L. pavonica and a wider male, shorter spicules and a longer muscular oesophagus than those of L. francolini. The male of L. latifi is 7–9 (8.1)mm long, the left spicule 164–215 (184)m long and the right spicule 98–117 (108)m long. The female is 17–23 (21)mm in length. Sheathed microfilariae from blood smears are 78–100 m long and those from the uterus are 89–103 m long. This is the sixth valid species of Lemdana in the Phasianidae.     

Single locus typing of MHC class I and class II B loci in a population of red jungle fowl

In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the ‘minimal essential’ MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.     

Structural and dynamic analysis of G558R mutation in chicken TSHR gene shows altered signal transduction and corroborates its role as a domestication gene

The thyroid-stimulating hormone receptor (TSHR) has been indicated as a putative domestication gene in chicken. Comparison of WGS identified a variant in residue 558 of the transmembrane domain (TM) of TSHR, where the domestic chicken (GGD) presents an arginine, whereas the red jungle fowl (RJF) shares a conserved glycine with other vertebrates. This variant has been demonstrated to be associated with phenotypes that are important for domestication and related to thyroid regulation, such as less fearful behavior, reduced aggressive behavior and reduced dependence on seasonal reproduction in GGD as compared with RJF. By means of molecular dynamics simulations, we highlighted the structural and dynamic differences of variant Gly558Arg in the TSHR TM domain. Alterations in TM helix flexibility, structure and protein overall motion are described. The so-called ‘arginine snorkeling’ of residue 568 in GGD is observed and we hypothesize it as the originating force that produces the observed whole-protein perturbation in the helix bundle dynamics, capable of altering the TSHR signal transduction. The results are discussed in the context of their implications for a better understanding of biological mechanisms in chicken under control of the thyroid, such as body metabolism, as well as for their usefulness in biomedical research.     

The direction of mothers' and daughters' preferences and the heritability of male ornaments in red jungle fowl (Gallus gallus)

We used a breeding design involving 18 sires and 108 dams tostudy the heritabilities of male ornaments in red jungle fowl(Gallus gallus). Ornaments used by females to choose mates showedlow heritabilities, with the exception of comb and wattle measures.The general absence of heritability suggests that a geneticcovariance did not exist at the time of this study between mostmale ornaments and female preferences for those ornaments. Thisresult is contrary to a key prediction of the arbitrary or Fisherianhypothesis of sexual selection. Comb size and color are condition-dependenttraits that reflect short-term changes in health, and comb sizeof males was positively correlated with offspring weight. Ourresults are consistent with the expectation of good-genes hypothesesthat male ornaments reflect the ability of males to withstandenvironmental stresses.     

Genetic diversity of carrion and jungle crows from RAPD-PCR analysis data

RAPD-PCR analysis of the genetic diversity of the carrion crow (Corvus corone) and jungle crow (C. macrorhynchos) living in the continental parts of their species ranges and on some Russian and Japanese Far Eastern islands has been performed. Taxon-specific molecular markers have been found for each species. The genetic diversity of the carrion crow is considerably less than that of the jungle crow at the same genetic distance (P95 = 68.2%, DN = 0.27 and P95 = 88.4%, DN = 0.24, respectively). In both species, the genetic polymorphism of island samples is almost two times greater than that of continental samples (62 and 31.8%, respectively, for C. corone and 81.5 and 47.2%, respectively, for C. macrorhynchos). In addition, differences in genetic diversity between males and females (P95 = 55.1 and P95 = 72.1, respectively) has been found in the carrion crow but not in the jungle crow. The gene diversity of C. macrorhynchos is greater than that of C. corone: the mean numbers of alleles per locus are 2 and 1.81, effective numbers of alleles are 1.62 and 1.43, and the mean expected heterozygosities are 0.39 and 0.30, respectively. The phenograms and phylograms significantly segregate the clusters of the carrion and jungle crows. The clustering patterns of carrion crows corresponds to the intraspecies taxonomic and geographic differentiation: subspecies C. c. corone and C.c. orientalis living in the western and eastern parts of the species range, respectively, form different subclusters. The cluster of the jungle crow does not exhibit differentiation into subspecies C. m. mandshuricus and C. m. japonensis; molecular genetic differences between them are small.     

Behavioural differences between two captive populations of red jungle fowl (Gallus gallus) with different genetic background,raised under identical conditions

Ex situ conservation of threatened species may lead to behavioural adaptation, which can affect success of reintroduction attempts. In previous studies, we investigated the effects of captivity on the behaviour of red jungle fowl (Gallus gallus) and found that captive populations differed behaviourally as well as genetically. The aim of the present study was to compare the behaviour of two of the previously studied populations, raised under identical conditions. Eggs were collected from birds at Copenhagen zoo (Cop) and Götala research station (Got) and were incubated and hatched together. Twenty-eight birds (16 Got and 12 Cop) were reared together and tested in eight different behavioural tests, measuring different aspects of fear-related behaviours as well as exploratory and social behaviours. The study revealed several differences in fear-related behaviours between the populations but none in exploratory or social behaviours. In general, one of the populations (Cop) showed more intense fear behaviours than the other (Got), which instead were less fearful in their behaviours. This indicates that breeding animals in captivity may lead to behavioural modifications, which can affect the outcome of reintroductions. The results further suggest that fear-related behaviours are dependent on the genetic background of the animals while social behaviours may be more influenced by the social environment. Since fear-related behaviours, such as predator avoidance and fear of humans, are essential for a life in the wild, these aspects are crucial for the breeding of animals in captivity for conservation purposes.     

Genetic diversity of donkey populations from the putative centers of domestication

Donkey domestication drastically changed ancient transport systems in Africa and Asia, enabling overland circulation of people and goods and influencing the organization of early cities and pastoral societies. Genetic studies based on mtDNA have pointed to the African wild ass as the most probable ancestor of the domestic donkey, but questions regarding its center of origin remain unanswered. Endeavoring to pinpoint the geographical origin of domestic donkey, we assessed levels and patterns of genetic diversity at 15 microsatellite loci from eight populations, representing its three hypothesized centers of origin: northeast Africa, the Near East and the Arabian Peninsula. Additionally, we compared the donkey genotypes with those from their wild relative, the African wild ass (Equus africanus somaliensis) to visualize patterns of differentiation among wild and domestic individuals. Obtained results revealed limited variation in levels of unbiased expected heterozygosity across populations in studied geographic regions (ranging from 0.637 in northeast Africa to 0.679 in the Near East). Both allelic richness (Ar) and private allelic richness presented considerably higher values in northeast Africa and in the Arabian Peninsula. By looking at variation at the country level, for each region, we were able to identify Sudan and Yemen as the countries possessing higher allelic richness and, cumulatively, Yemen also presented higher values for private allelic richness. Our results support previously proposed northeast Africa as a putative center of origin, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center of origin for this species.     

Genetic evidence for a recent origin by hybridization of red wolves

Genetic data suggest that red wolves ( Canis rufus ) resulted from a hybridization between coyotes ( C. latrans ) and grey wolves ( C. lupus ). The date of the hybridization, however, is uncertain. According to one hypothesis, the two species came into contact as coyotes increased their geographical range in conjunction with the advance of European settlers and as grey wolves were extirpated from the American south. Alternatively, the red wolves could have originated tens of thousands of years ago as a result of climate and habitat changes that disturbed the ecology of the two parent species. To obtain an upper limit on the date of hybridization that would help to distinguish the two scenarios, we compared microsatellite allele length distributions from red wolves, coyotes and grey wolves. Subject to the assumptions of our analysis, we conclude that the red wolves originated as a result of hybridizations that occurred during the past 12 800 years, and probably during the past 2500 years.     

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.