Genetic structure of three populations of rhesus macaques (Macaca mulatta): Implications for genetic management

One of the prime concerns at zoos and at primate breeding facilities is to maintain genetic variability. This can be accomplished by avoiding inbreeding. It is relatively easy to assess genetic variability and the level of inbreeding by using pedigree information and genetic markers. In this study we used genetic markers controlled by 6 independent polymorphic loci (GPI, PGD, CA2, MPI, DIA1, Tf) to ascertain genetic variation in two captive and one wild population of rhesus monkeys. Two other loci ADA and NP were also examined and found to be monomorphic in the three populations. F-statistics and contingency chi-square analyses indicated that there was significant genetic differentiation among the populations. We also found that the mean heterozygosities were very similar in the three populations, in spite of the diverse breeding strategies. These data are important because rhesus monkeys are frequently used for biomedical research; and the genetic markers provide useful information for genetic management of captive colonies of nonhuman primates. © 1992 Wiley-Liss, Inc.     

Genetic diversity of north-east Asian cattle based on microsatellite data

In order to assess the genetic variability and population structure of north-east Asian cattle, 13 microsatellite loci were analysed for a total of 200 individuals including Korean, Chinese, Japanese Black and European Holstein cattle. Observed and expected heterozygosity, two estimators (F(ST) and G(ST)) of gene differentiation, and Nei's DA distance were evaluated. Based on expected mean heterozygosity, the lowest genetic diversity was exhibited in Japanese Black cattle (H(E)=0.471), and the highest in Chinese cattle (H(E)=0.744). Korean cattle revealed a relatively high degree of genetic diversity (H(E)=0.728). Average proportion of genetic variation because of interpopulation subdivision among north-east Asian cattle varied between 10.9 and 9.9%, depending on the estimator used. N-J tree based on Nei's DA genetic distance showed that Korean and Chinese cattle are closely related, whereas Japanese Black cattle are clearly distinct from the other two populations, forming a north-east Asian outgroup.     

The Statistical Properties of Genetic Absolute Distance

The statistical properties of one estimator of absolute genetic distance (1/2) ^K∑_i=1 |pxi-yr|, tween two populations X and Y, are presented. It is shown that using this distance in small samples can be misleading particularly when populations are close to each other.     

Genetic studies of human diversity in East Asia

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.     

Genetic variation and population structure in desert bighorn sheep: implications for conservation

Bighorn sheep populations experienced a drastic reduction in both distribution and abundance until the advent of modern wildlife management, where improving viability of extant populations and translocating animals into historical habitat range have been the most important management policies. The fact that subspecies relationships among bighorn are ambiguous,together with the importance of selecting appropriate source stock and the expense of translocation projects, makes an understanding of subspecies relationships and genetic variation, within and between populations, important for the management and conservation of this species. In this study, genetic variation in 279 bighorn sheep from 13 study sites in Arizona, California, New Mexico and Alberta, Canada were examined by analyzing ten microsatellite loci to determine interpopulation differentiation and relationships between closely related taxa. All populations contained a substantial amount of genetic variation. Genetic differences between populations were large and roughly proportional to geographic distance. The significance of this to desert subspecies relationships and management is discussed.     

Genetic control and population survey of transferrin in the Japanese quail

Transferrin types in the Japanese quail Coturnix coturnix japonica are controlled by a single autosomal locus Tf with at least two codominant alleles Tf^B and Tf^c. The frequencies of Tf^B and Tf^c in a commercial population of the domestic quail were 1.00 and 0.00, respectively.
Previous studies demonstrated that in the domestic populations of the Japanese quail three electrophoretic patterns AB, B and BC existed in egg white conalbumin and that the electrophoretic variation of conalbumin occurred in parallel with that of serum transferrin. Furthermore, from the preliminary mating experiments the transferrin-conalbumin variation was proposed to be under the control of at least two codominant alleles 77^s and Tf^c at an autosomal locus (Kimura et al., 1977, 1978).
The present study was designed (1) to report a large amount of family data from three generations in order to support the previously published hypothesis on genetic control of electrophoretic patterns of transferrin, and (2) to survey the gene constitution of transferrin in a commercial population of the domestic quail.
Sera were added with iron, heated for 5 min at 65°C (Stratil, 1967), then were investigated by means of horizontal starch gel electrophoresis. Hydrolysed starch from Connaught Medical Laboratories, Toronto, was used. A discontinuous citrate/Tris/LiOH/borate buffer system (pH 8.0) of Ferguson & Wallace (1961) was employed. The gels were stained with Amido Black 10B.     

Genetic structure of wild and cultivated olives in the central Mediterranean basin

BACKGROUND AND AIMS: Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS: The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS: The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS: On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.     

Development of intervention behavior in Japanese macaques: Testing the targeting hypothesis

Matrilineal dominance systems, which characterize several species of cercopithecines, are determined largely by the patterning of third-party aggressive interventions in conflicts. Although the role of interventions in structuring rank relations has received much attention, very few studies have dealt specifically with the development of intervention behavior. In other words,most studies have focused on the interventions received and their effect on the recipients rather than on the interventions performed and the goals of the interveners. We analyzed the intervention behavior of 10 juvenile females in a colony of 40 Japanese macaques (Macaca fuscata)housed at the University of Montreal Laboratory of Behavioral Primatology. The analysis of 749 interventions performed by the juveniles over their first 4 years and 2425 interventions received over the same period reveals that (1) juvenile females intervened selectively against females ranking below their mother, (2) they began to intervene at about the same time that they began to challenge the latter females in dyadic contests, (3) they sided with females as well as with males against these females, (4) juvenile interveners incurred little risks in terms of aggressive retaliation from their targets, (5) they derived immediate benefits in terms of conflicts won over stronger targets, (6) interventions often did not take place when the possible recipients needed support, and (7) interveners did not conform to a pattern of mutually preferential support. These results support the view that interventions by juveniles are selfish (vs altruistic) and constitute a low-cost and effective means to target and to outrank prospectively subordinate females.     

Polymorphic microsatellite loci for population studies of the Japanese scallop,Patinopecten yessoensis

Fifteen microsatellite loci were developed to examine the population structure of Japanese scallop, Patinopecten yessoensis. These markers were tested in samples from two geographically distant populations: the Sakhalin Island (Russia) and Dalian City (China). The mean numbers of alleles, observed and expected heterozygosities between the two populations were summarized by locus, but none of them show significant divergence between the two populations. Most loci conformed to Hardy–Weinberg expectation with the exception of loci HLJX‐06, HLJX‐12, HLJX‐13 and HLJX‐28, which had heterozygote deficits.     

Genetic structure among and within peripheral and central populations of three endangered floodplain violets

Understanding the partitioning of genetic variance in peripheral and central populations may shed more light on the effects of genetic drift and gene flow on population genetic structure and, thereby, improve attempts to conserve genetic diversity. We analysed genetic structure of peripheral and central populations of three insect-pollinated violets (Viola elatior, Viola pumila, Viola stagnina) to evaluate to what extent these patterns can be explained by gene flow and genetic drift. Amplified fragment length polymorphism was used to analyse 930 individuals of 50 populations. Consistent with theoretical predictions, peripheral populations were smaller and more isolated, differentiation was stronger, and genetic diversity and gene flow lower in peripheral populations of V. pumila and V. stagnina. In V. elatior, probably historic fragmentation effects linked to its specific habitat type were superimposed on the plant geographic (peripheral-central) patterns, resulting in lower relative importance of gene flow in central populations. Genetic variation between regions (3-6%), among (30-37%) and within populations (60-64%) was significant. Peripheral populations lacked markers that were rare and localized in central populations. Loss of widespread markers in peripheral V. stagnina populations indicated genetic erosion. Autocorrelation within populations was statistically significant up to a distance of 10-20 m. Higher average genetic similarity in peripheral populations than in central ones indicated higher local gene flow, probably owing to management practices. Peripheral populations contributed significantly to genetic variation and contained unique markers, which made them valuable for the conservation of genetic diversity.     

Toothcomb origins: Support for the grooming hypothesis

Debate over the original adaptive significance of the lemuriform toothcomb, whether it was principally a grooming organ or a scraper-feeding tool, currently hinges upon the functional morphology of the lower incisors and canines of lemurs and lorises, and the fossil adapids thought to be their ancestors or structural prototypes. We suggest that the morphology of the upper incisors and the oronasal complex of the latter, given the context of a more general theory of incisor evolution within the primates, exhibits preadaptive conditions foreshadowing the emergence of the toothcomb and also evidence of strepsirhine monophyly. We find in all underived lemuriforms and in most fossil adapids where the elements are known, a striking continuity in upper incisor form, including such derived features as an interincisal diastema, strong central incisor prong, low-crowned morphology and reduced premaxillary size. The pattern suggests a basic strepsirhine reduction in the functional significance of the anterior dentition in feeding and harvesting roles. These features may be related to a novel connection of the rhinarium with the vomeronasal organ via a sulcate pair of labial folds, which serves as a component of a specialized behavioral-physiological complex dealing with olfactory communication. Rather than being the anatomical nucleus of this system, the toothcomb may have been added secondarily in the lemuriform descendants of the preadapted adapids, possibly as a device to stimulate glandular secretion of pheromones by direct pressure, and to simultaneously distribute odorants through the fur.     

Genetic structure of the Iberian pig breed using microsatellites

An analysis of 25 microsatellite loci in 210 animals has been used to define the genetic structure of the Iberian pig, traditionally classified into several varieties. In addition, a sample of 20 Duroc pigs was used as an outgroup for topology trees. Inter-variety genetic variation was estimated by unbiased average heterozygosity and the number of alleles observed. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were shown for 19 loci across the whole population. By contrast, equilibrium deviation within varieties was much lower. Genetic variation measures, genetic distance values and a neighbour-joining tree were used to estimate subdivision. In addition, an individual tree was constructed to contrast the assignation of animals into varieties. Despite the low bootstrap values obtained in the varieties neighbour-joining tree, the degree of genetic variation found was sufficient to support the division of the Iberian pig into varieties, although in some cases the traditional classification cannot be accepted. These results have shown the value of this marker panel in the study of intra-breed genetic structures.     

A first-generation microsatellite linkage map of the Japanese quail

A linkage map of the Japanese quail (Coturnix japonica) genome was constructed based upon segregation analysis of 72 microsatellite loci in 433 F(2) progeny of 10 half-sib families obtained from a cross between two quail lines of different genetic origins. One line was selected for long duration of tonic immobility, a behavioural trait related to fearfulness, while the other was selected based on early egg production. Fifty-eight of the markers were resolved into 12 autosomal linkage groups and a Z chromosome-specific linkage group, while the remaining 14 markers were unlinked. The linkage groups range from 8 cM (two markers) to 206 cM (16 markers) and cover a total map distance of 576 cM with an average spacing of 10 cM between loci. Through comparative mapping with chicken (Gallus gallus) using orthologous markers, we were able to assign linkage groups CJA01, CJA02, CJA05, CJA06, CJA14 and CJA27 to chromosomes. This map, which is the first in quail based solely on microsatellites, is a major step towards the development of a quality molecular genetic map for this valuable species. It will provide an important framework for further genetic mapping and the identification of quantitative trait loci controlling egg production and fear-related behavioural traits in quail.     

Genetic population structure of two cryptic Gammarus fossarum types across a contact zone

Previous studies have revealed inconsistent results about the taxonomic status of European Gammarus fossarum forms. The variability in morphology and hybridization ability has not shown clear geographic patterns, whereas on a genetical basis two Central European G. fossarum forms have been proposed. In the present study the genetic structure of G. fossarum populations was investigated across a natural contact zone. For the first time direct comparisons of allotopic versus syntopic populations were feasible. 24 Populations of G. fossarum plus 4 populations of G. pulex (as outgroup) were sampled along 2 transects across the contact zone. The genotypes of about 60 individuals per population were revealed by allozyme electrophoresis at 6 polymorphic loci. Parallel step ‘clines’ in allele frequencies indicate secondary contact of the two G. fossarum forms. The level of genetic variation between the forms was comparable to an interspecific level (G. pulex versus G. fossarum). The pronounced genetic bipartition in syntopic G. fossarum populations and the lack of potential F1-hybrids further corroborated the taxonomic status of the G. fossarum types. The geographic patterns of the genetic differentiation between and within the G. fossarum types, the allelic diversities and the genotypic disequilibria revealed recent introgression at the analysed loci to be insignificant. In addition it is shown that the population structure of the western G. fossarum type is out of equilibrium, which suggest a recent colonization of this type probably by displacement of the other type.     

A River Metapopulation Structure of a Japanese Freshwater Goby, Odontobutis Obscura, Deduced from Allozyme Genetic Indices

Gene products of 18 allozyme loci from 1268 individuals of a Japanese freshwater goby called donko, Odontobutis obscura (Odontobutidae; Gobioidei), from 33 localities in the Koya River, Yamaguchi Prefecture, Japan, were investigated to determine the extent of genetic divergence and gene flow within a river metapopulation. Genetic indices including GST(mean FST 0.182), FIT(mean 0.192) and D(mean 0.015) indicated a considerable divergence of local populations in the river. The genetic distance (D) and channel distance between pairs of populations did not show a good correlation, and geographical neighbors were not always genetic neighbors. Therefore, the genetic divergence of populations is attributable to independent genetic drift with restricted gene flow among populations. The agricultural dams and weirs constructed across the river must be responsible for the restricted gene flow. The metapopulation structure of O. obscura in the Koya River may be barely sustained by one-way gene flow only from the upper to the lower populations. An occasional artificial transplantation of some individuals from the lower to the upper populations may be one alternative to maintain a river metapopulation structure safely.     

Genetic diversity and multilocus structure in sexual Otiorhynchus alpicola populations (Goleoptera: Gurculionidae)

Otiorhynchus alpicola Boh. (Coleoptera: Curculionidae) is distributed on high mountains of central, southern and south-eastern Europe. On the Balkan peninsula, this species is patchily distributed on mountain peaks at heights over 1800 m. To examine the organization of isoenzyme variation of the ten sexual (diploid) populations, starch gel electrophoresis of enzymes was used. The average heterozygosity over 14 gene loci was 0.11. For diploid O. alpicola, F-statistics were used to assess population heterogeneity and substructuring. The data indicate that, compared with other insects, this high-altitude weevil species is genetically very differentiated (the average F _ST= 0.35). In addition, gene-flow among populations was extremely low (the estimates of N_em from Wright's F _ST and Slatkin private-allele methods were 0.47 and 0.83, respectively). Pairwise linkage disequilibrium (LD) parameters were estimated from zygotic frequencies using Burrows' method. The average rate of significant LD in analysed populations of O. alpicola was about 27%. The pattern of LD over the diploid populations indicates that stochastic factors might be a primary cause of the observed multilocus associations.     

Genetic variation and population structure of cod, Gadus morhua L., in some fjords in northern Norway

Biochemical genetic polymorphism in cod from several fjords in Troms, northern Norway was analysed. Gene frequencies at several polymorphic loci ( Hb, Pgi, Ldh, Pgm, Gpd and Idh ) are given. Significant variation was found both within and between fjords, and even between samples from the same locality sampled in different years, indicating a mosaic structure of the cod population in the area studied. The results of the haemoglobin variation are compared to similar results obtained more than 20 years ago in the same and adjacent areas. The biochemical genetic variation is discussed in relation to stability of gene frequencies, isolation mechanisms and migration patterns.     

Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond

There is growing interest in quantifying genetic population structure across the geographical ranges of species to understand why species might exhibit stable range limits and to assess the conservation value of peripheral populations. However, many assertions regarding peripheral populations rest on the long-standing but poorly tested supposition that peripheral populations exhibit low genetic diversity and greater genetic differentiation as a consequence of smaller effective population size and greater geographical isolation relative to geographically central populations. We reviewed 134 studies representing 115 species that tested for declines in within-population genetic diversity and/or increases in among-population differentiation towards range margins using nuclear molecular genetic markers. On average, 64.2% of studies detected the expected decline in diversity, 70.2% of those that tested for it showed increased differentiation and there was a positive association between these trends. In most cases, however, the difference in genetic diversity between central and peripheral population was not large. Although these results were consistent across plants and animals, strong taxonomic and biogeographical biases in the available studies call for a cautious generalization of these results. Despite the large number of studies testing these simple predictions, very few attempted to test possible mechanisms causing reduced peripheral diversity or increased differentiation. Almost no study incorporated a phylogeographical framework to evaluate historical influences on contemporary genetic patterns. Finally, there has been little effort to test whether these geographical trends in putatively neutral variation at marker loci are reflected by quantitative genetic trait variation, which is likely to influence the adaptive potential of populations across the geographical range.     

The origins of agriculture in the Americas

Three independent centers of domestication and agricultural origin have been identified in the Americas: the south-central Andes, Mexico, and most recently, eastern North America. Much of the evidence for early domesticates in these three regions has been excavated from higher elevation dry caves and rock shelters. These sites contain remarkably well preserved plant and animal remains, along with a record of short-term occupation by small groups of hunter-gatherers and early cultivators. As a result it has long been thought that plants and animals were brought under domestication in the Americas by small, seasonally mobile societies living in upland settings. The age of small seeds and other plant materials recovered from such dry caves and believed to represent early domesticates was, of necessity, determined indirectly, through conventional large-sample radiocarbon dating of organic material thought to be contemporaneous. In each of the three regions, the earliest domesticates were believed to date between 7,000 and 10,000 B.P. The origin of agriculture in the Americas was thought to be roughly contemporary with the transition from foraging to farming in the Near East (Fertile Crescent, ca. 10,000 B.P.) and China (Yangtze Corridor, ca. 8,500 B.P.). Since the mid-1980s, however, the age of many of the proposed early domesticates in the Americas, as well as their contexts of domestication, have been re-examined, beginning in eastern North America. The excavation of larger and more sedentary river valley settlements in eastern North America has yielded ample evidence of the cultivation of domesticated seed plants. This evidence is as old as or older than that recovered from seasonally occupied upland caves and rock shelters. In addition, a new and more rigorous standard for evidence of domestication has been adopted in eastern North America. That standard, which requires direct dating of seeds and other plant parts that exhibit clear, unequivocal, and well-documented morphological markers of domestication, is now being applied throughout the Americas, producing conservative timetables of domestication and agricultural origins that contradict alternative, more speculative chronological frameworks. Under the new standard of evidence, domestication of plants in all three independent centers (and in the Andes, domestication of animals) appears to have taken place between about 5,500 and 4,000 years ago, much more recently than previously was thought. Several lines of evidence also suggest that the Native American societies that first brought these species under domestication may not have been exclusively seasonally mobile hunter-gatherers of higher-elevation environments. In each of the three regions, domesticates recovered from upland caves may reflect a transition to a farming way of life accomplished by societies occupying more sedentary settlements in river valleys. In some cases, upland caves containing domesticates may represent one component in the seasonal round of early food production by societies occupying nearby river valleys; in others, they may mark the subsequent expansion of food production economies out of rich river valley resource zones into adjacent upland environments.