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PubMed2000

Marker-assisted selection to increase effective population size by reducing Mendelian segregation variance.

Using both the genetic drift and inbreeding approaches, we derive more general equations for effective size (N(e)) of a diploid species under random mating. These equations show explicitly that inbreeding or genetic drift comes from two sources, the variation in the number of offspring from each parent and the variation in contribution between these parents' own paternally and maternally derived genes to their offspring. The first source can be easily and effectively controlled by choosing an equal number of offspring from each family, while the second can be manipulated by using information on genetic markers to reduce the variance due to Mendelian segregation. Marker-assisted selection (MAS) methods to increase N(e) for the whole genome with single or multiple marker loci per chromosome, different numbers of males, and females are developed and implemented in stochastic simulations. The analytical and simulation results show that, although in principle N(e) can be increased indefinitely, the efficiency of MAS is restricted in practice by the amount of marker information, the genome size, and the number of marker-genotyped offspring per family. The assumptions made in developing the theory and methods and the applications of MAS in conservation are discussed.

Chromosome Mapping↗
PubMed2002

Genetic analysis of traits distinguishing outcrossing and self-pollinating forms of currant tomato, Lycopersicon pimpinellifolium (Jusl.) Mill.

The evolution of inbreeding is common throughout the angiosperms, although little is known about the developmental and genetic processes involved. Lycopersicon pimpinellifolium (currant tomato) is a self-compatible species with variation in outcrossing rate correlated with floral morphology. Mature flowers from inbreeding and outcrossing populations differ greatly in characters affecting mating behavior (petal, anther, and style lengths); other flower parts (sepals, ovaries) show minimal differences. Analysis of genetic behavior, including quantitative trait locus (QTL) mapping, was performed on representative selfing and outcrossing plants derived from two contrasting natural populations. Six morphological traits were analyzed: flowers per inflorescence; petal, anther, and style lengths; and lengths of the fertile and sterile portions of anthers. All traits were smaller in the selfing parent and had continuous patterns of segregation in the F(2). Phenotypic correlations among traits were all positive, but varied in strength. Quantitative trait locus mapping was done using 48 RFLP markers. Five QTL total were found involving four of the six traits: total anther length, anther sterile length, style length, and flowers per inflorescence. Each of these four traits had a QTL of major (>25%) effect on phenotypic variance.

Chromosome Mapping↗
PubMed1980

The theory of speciation via the founder principle.

The founder principle has been used to explain many instances of rapid speciation. Advances from theoretical population genetics are incorporated into MAYR's original founder-effect genetic-revolution model to yield a newer model called the genetic transilience. The basic theoretical edifice lies upon the fact that founder event can sometimes lead to an accumulation of inbreeding and an induction of gametic disequilibrium. This, in turn, causes alleles to be selected more for their homozygous fitness effects and for their effects on a more stable genetic background. Selection occurring in multi-locus systems controlling integrated developmental, physiological, behavioral, etc, traits is particularly sensitive to these founder effects. If sufficient genetic variability exists in the founder population, such multilocus genetic systems can respond to drift and the altered selective forces by undergoing a rapid shift to a new adaptive peak known as the genetic transilience. A genetic transilience is, therefore, most likely to occur when the founder event causes a rapid accumulation of inbreeding without a severe reduction in genetic variability. The implications of this model are then examined for three aspects of the founder-effect genetic-transilience model: the attributes of the ancestral population, the nature of the sampling process used to generate the founders and the attributes of the founder population. The model is used to explain several features of the evolution of the Hawaiian Drosophila, and experimental designs are outlined to test the major predictions of the theory. Hence, this theory of speciation can be tested in the laboratory, using systems and techniques that already exist--a rare attribute of most models of speciation.

Animals↗
PubMed2006

Extended tracts of homozygosity in outbred human populations.

Long tracts of consecutive homozygous single nucleotide polymorphisms (SNPs) can arise in the genome through a number of mechanisms. These include inbreeding in which an individual inherits chromosomal segments that are identical by descent from each parent. However, recombination and other processes break up chromosomal segments over generations. The longest tracts are therefore to be expected in populations with an appreciable degree of inbreeding. We examined the length, number and distribution of long tracts of homozygosity in the apparently outbred HapMap populations. We observed 1393 tracts exceeding 1 Mb in length among the 209 unrelated HapMap individuals. The longest was an uninterrupted run of 3922 homozygous SNPs spanning 17.9 Mb in a Japanese individual. We find that homozygous tracts are significantly more common in regions with high linkage disequilibrium and low recombination, and the location of tracts is similar across all populations. The Yoruba sample has the fewest long tracts per individual, consistent with a larger number of generations (and hence amount of recombination) since the founding of that population. Our results suggest that multiple-megabase-scale ancestral haplotypes persist in outbred human populations in broad genomic regions which have lower than average recombination rates. We observed three outlying individuals who have exceptionally long and numerous homozygous tracts that are not associated with recombination suppressed areas of the genome. We consider that this reflects a high level of relatedness in their ancestry which is too recent to have been influenced by the local recombination intensity. Possible alternative mechanisms and the implications of long homozygous tracts in the genome are discussed.

Asian People↗
PubMed2006

Mouse phenome research: implications of genetic background.

Now that sequencing of the mouse genome has been completed, the function of each gene remains to be elucidated through phenotypic analysis. The "genetic background" (in which each gene functions) is defined as the genotype of all other related genes that may interact with the gene of interest, and therefore potentially influences the specific phenotype. To understand the nature and importance of genetic background on phenotypic expression of specific genes, it is necessary to know the origin and evolutionary history of the laboratory mouse genome. Molecular analysis has indicated that the fancy mice of Japan and Europe contributed significantly to the origin of today's laboratory mice. The genetic background of present-day laboratory mice varies by mouse strain, but is mainly derived from the European domesticus subspecies group and to a lesser degree from Asian mice, probably Japanese fancy mice, which belong to the musculus subspecies group. Inbred laboratory mouse strains are genetically uniform due to extensive inbreeding, and they have greatly contributed to the genetic analysis of many Mendelian traits. Meanwhile, for a variety of practical reasons, many transgenic and targeted mutant mice have been created in mice of mixed genetic backgrounds to elucidate the function of the genes, although efforts have been made to create inbred transgenic mice and targeted mutant mice with coisogenic embryonic stem cell lines. Inbred mouse strains have provided uniform genetic background for accurate evaluation of specific genes phenotypes, thus eliminating the phenotypic variations caused by mixed genetic backgrounds. However, the process of inbreeding and selection of various inbred strain characteristics has resulted in inadvertent selection of other undesirable genetic characteristics and mutations that may influence the genotype and preclude effective phenotypic analysis. Because many of the common inbred mouse stains have been established from relatively small gene pools, common inbred strains have limitations in their genetic polymorphisms and phenotypic variations. Wild-derived mouse strains can complement deficiencies of common inbred mouse strains, providing novel allelic variants and phenotypes. Although wild-derived strains are not as tame as the common laboratory strains, their genetic characteristics are attractive for the future study of gene function.

Animals↗
PubMedDate not supplied

Microsatellite analysis of genetic diversity of the Vietnamese sika deer (Cervus nippon pseudaxis).

The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies of economic and traditional value in Vietnam. Most living individuals are held in traditional farms in central Vietnam, others being found in zoos around the world. Here we study the neutral genetic diversity and population structure of this subspecies using nine microsatellite loci in order to evaluate the consequences of the limited number of individuals from which this population was initiated and of the breeding practices (i.e., possible inbreeding). Two hundred individuals were sampled from several villages. Our data show both evidence for limited local inbreeding and isolation by distance with a mean F(ST) value of 0.02 between villages. This suggests that exchange of animals occurs at a local scale, at a rate such that highly inbred mating is avoided. However, the genetic diversity, with an expected heterozygosity (H(e)) of 0.60 and mean number of alleles (k) of 5.7, was not significantly larger than that estimated from zoo populations of much smaller census size (17 animals sampled; H(e) = 0.65, k = 4.11). Our results also suggest that the Vietnamese population might have experienced a slight bottleneck. However, this population is sufficiently variable to constitute a source of individuals for reintroduction in the wild in Vietnam.

Animals↗
PubMed2006

Mating patterns of black oak Quercus velutina (Fagaceae) in a Missouri oak-hickory forest.

Wind-pollinated forest trees usually have high outcrossing rates, but allogamy does not necessarily translate into high pollen movement. The goal of this study was to determine the outcrossing rates, pollen pool genetic structure, and the size of the effective pollination neighborhood in a population of black oak, Quercus velutina, in a Missouri oak-hickory forest. Based on 6 allozyme loci, 12 maternal trees, and 439 progenies sampled along a transect of 1300 m, we found complete outcrossing (t(m) = 1.000, P < 0.001) and small amounts of biparental inbreeding. Using a TwoGener analysis of the pollen gene pool, we found significant structure across maternal plants (Phi(FT) = 0.078, P < 0.001), which when corrected for adult inbreeding translates into Phi(FT) = 0.066 that corresponds to an effective number of pollen donors of 7.5 individuals. Assuming a bivariate normal distribution and an adult density of 16.25 trees ha(-1), we estimated that the effective pollination neighborhood area had a radius of 41.9 m. Even assuming that our estimates may be conservative, these findings join a growing body of evidence that suggest that the local neighborhood of wind-pollinated forest tree populations may be relatively small creating opportunities for local selection and genetic drift.

Crosses, Genetic↗
PubMedDate not supplied

Mammalian cytogenetics and conservation of species.

The proposition is examined that cytogenetic studies are needed in the conservation of wild captive animals. Several cases of polymorphic species have hybridized to produce infertile offspring. In several gazelle species, this accidental hybridization among look-alike animals has led to the extinction of zoo populations. The suggestion that this is always the result of inbreeding is thus erroneous. Cytogenetic study is also needed in animals that are destined for reintroduction, as accidental release of chromosomally different species is counterproductive to the reestablishment of wild stock. Several examples of mammalian species that have flourished from an extremely small founder stock are here examined to draw attention to the possibility that "inbreeding" is not invariably disadvantageous. The karyotypes of two hybridizing Kobus species with divergent chromosomal numbers are described.

Animals↗
PubMed2001

A method for distinguishing consanguinity and population substructure using multilocus genotype data.

We use the patterns of homozygosity at multiple loci to distinguish between excess homozygosity caused by consanguineous mating and that due to undetected population subdivision (the Wahlund effect). Clarification of the underlying causes of excess homozygosity is of practical importance in explaining the occurrence of recessive genetic disorders and in forensic match probability calculations. We calculated a likelihood surface for two parameters: C, the proportion of the population practicing consanguinity, and theta, the genetic correlation due population subdivision. To illustrate the method, we applied it to multilocus genotypic data of two U.K. Asian populations, one practicing a high frequency of cousin marriage, and another in which caste endogamy was suspected. The method was able to successfully distinguish the different patterns of relatedness. The method also returned accurate estimates of C and theta using simulated data sets. We show how our method can be extended to allow for degrees of inbreeding closer than cousin unions, including selfing. With closer inbreeding, the relatedness of recent ancestors beyond the parents becomes an issue.

Algorithms↗
PubMed2003

Histocompatible miniature swine: an inbred large-animal model.

Three herds of miniature swine, each homozygous for a different set of alleles at the major histocompatibility complex (MHC), and five intra-MHC recombinant strains, have been reported by the authors' laboratory. One herd (SLAdd) was selected for further inbreeding to achieve a histocompatible line. It has undergone seven additional generations of sequential brother-sister or father-daughter matings (termed G7). To determine the level of histocompatibility of these animals, the authors performed skin and heart transplantation without immunosuppression. In contrast to MHC-matched, minor antigen-mismatched animals that rejected skin in 11 days (median survival time [MST], n=6) and hearts in 35 days (MST, n=4), G7 animals accepted skin for greater than 340 days (>340, >448, and >677 days) and hearts for greater than 265 days (>265 and >269 days). Nevertheless, rejection of second grafts could be induced by sensitization, indicating that weak minor antigens remain, requiring further inbreeding to achieve full histocompatibility. We conclude that G7 animals are sufficiently inbred to accept first set skin and heart grafts indefinitely.

Animals↗
PubMed1979

The evolutionary genetics of sexual systems in flowering plants.

Population genetic studies of the evolution of breeding systems in flowering plants are reviewed. The selective advantage of a gene's increasing the selfing rate is stressed. In the evolution of outbreeding mechanisms, some strong disadvantage to selfing must therefore be acting; it is suggested that this disadvantage is inbreeding depression. Populations with no absolute barrier to selfing, and with intermediate levels of self-fertilization, appear to be the most likely starting state for the evolution of outbreeding mechanisms. There is some evidence for inbreeding depression in such populations. The evolution of distyly and dioecy are considered in some detail. An explanation for the existence of supergenes controlling these systems is proposed. The breakdown of distyly and tristyly are also considered. The evolution of recombination rates in selfing and outcrossing species is examined briefly.

Biological Evolution↗
PubMed1998

Birth weight and neonatal survival of harbour seal pups are positively correlated with genetic variation measured by microsatellites.

We examined the relations between fitness-related traits of wild harbour seal (Phoca vitulina) pups with microsatellite heterozygosity, and with a measure of genomic diversity based on the mean squared distance between microsatellite alleles within an individual, mean d2. Birth weight was positively influenced by maternal age, pup sex, and either mean d2 or individual heterozygosity in separate multiple regression models. The association of birth weight with mean d2 was stronger than that with heterozygosity, however. The factors maternal age, pup sex, and mean d2 combined to account for 36.8% of the variation in birth weight, with mean d2 accounting for the greatest explanatory power (52.3% of the variance explained). Pups which survived until weaning had significantly higher mean d2 than pups which died, independent of birth weight. These effects are consistent with heterosis resulting from recent population mixing, and/or inbreeding depression in this population. Mean d2 thus provides (i) a better measure of individual genetic variability than heterozygosity for microsatellite data; and (ii) a convenient tool for assessing the effects of inbreeding and outbreeding in natural populations.

Animals↗
PubMed2001

Reproductive suppression in female Damaraland mole-rats Cryptomys damarensis: dominant control or self-restraint?

Colonies of Damaraland mole-rats Cryptomys damarensis exhibit a high reproductive skew. Typically one female breeds and the others are anovulatory. Two models, the dominant control model (DCM) and the self-restraint model (SRM), have been proposed to account for this reproductive suppression. The DCM proposes that suppression is under the control of the dominant breeder and is imposed by mechanisms such as aggression, pheromones and interference with copulation, whereas the SRM does not involve aggression directed towards non-breeders and may function in order to minimize inbreeding. We investigated potential proximate mechanisms involved in the suppression of females in a series of experiments. Socially induced stress through aggression did not appear to be responsible for anovulation. Nor did breeders actively interfere with subordinate copulation. Females were physiologically suppressed when housed in intact colonies. However, as predicted by the DCM, they did not become reproductively active when removed from the presence of breeders. We found no evidence that pheromonal cues block ovulation. We suggest that the SRM is the basic model found in the Damaraland mole-rat and that self-restraint functions in order to minimize inbreeding by restricting reproduction until an unrelated male is present. This would explain the rapid onset of reproductive activation in females when paired with an unrelated male, as demonstrated in this study.

Analysis of Variance↗
PubMed2001

Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers.

Population bottlenecks are often invoked to explain low levels of genetic variation in natural populations, yet few studies have documented the direct genetic consequences of known bottlenecks in the wild. Empirical studies of natural population bottlenecks are therefore needed, because key assumptions of theoretical and laboratory studies of bottlenecks may not hold in the wild. Here we present microsatellite data from a severe bottleneck (95% mortality) in an insular population of song sparrows (Melospiza melodia). The major findings of our study are as follows: (i) The bottleneck reduced heterozygosity and allelic diversity nearly to neutral expectations, despite non-random survival of birds with respect to inbreeding and wing length. (ii) All measures of genetic diversity regained pre-bottleneck levels within two to three years of the crash. This rapid recovery was due to low levels of immigration. (iii) The rapid recovery occurred despite a coincident, strong increase in average inbreeding. These results show that immigration at levels that are hard to measure in most field studies can lead to qualitatively very different genetic outcomes from those expected from mutations only. We suggest that future theoretical and empirical work on bottlenecks and metapopulations should address the impact of immigration.

Animals↗
PubMed2004

The effects of nectar addition on pollen removal and geitonogamy in the non-rewarding orchid Anacamptis morio.

It has been suggested that the absence of floral rewards in many orchid species causes pollinators to probe fewer flowers on a plant, and thus reduces geitonogamy, i.e. self-pollination between flowers, which may result in inbreeding depression and reduced pollen export. We examined the effects of nectar addition on pollinator visitation and pollen transfer by tracking the fate of colour-labelled pollen in Anacamptis morio, a non-rewarding orchid species pollinated primarily by queen bumble-bees. Addition of nectar to spurs of A. morio significantly increased the number of flowers probed by bumble-bees, the time spent on an inflorescence, pollinarium removal and the proportion of removed pollen involved in self-pollination through geitonogamy, but did not affect pollen carryover (the fraction of a pollinarium carried over from one flower to the next). Only visits that exceeded 18 s resulted in geitonogamy, as this is the time taken for removed pollinaria to bend into a position to strike the stigma. A mutation for nectar production in A. morio would result in an initial 3.8-fold increase in pollinarium removal per visit, but also increase geitonogamous self-pollination from less than 10% of pollen depositions to ca. 40%. Greater efficiency of pollen export will favour deceptive plants when pollinators are relatively common and most pollinaria are removed from flowers or when inbreeding depression is severe. These findings provide empirical support both for Darwin's contention that pollinarium bending is an anti-selfing mechanism in orchids and for the idea that floral deception serves to maximize the efficiency of pollen export.

Animals↗
PubMed1988

The rare-male effect: what is its evolutionary significance?

Negatively frequency-dependent male mating success, the rare-male effect (RME), has been reported from many laboratory experiments, particularly with Drosophila spp. Problems with observer bias, lack of repeatability, with experimental design and with the analysis of data may indicate that the RME is considerably less well documented than has been supposed, even in the laboratory. Male competition is unlikely to be a common cause of the RME, except where there are behavioural differences between competing strains that result in lower competition between them than within them. A mixture of fixed female preferences seems the most likely cause, and further behavioural studies are required to investigate this mechanism. There is no convincing evidence that the RME is a consequence of frequency-dependent female preferences. An RME in the absence of negative assortment is not in general expected to lead to the avoidance of inbreeding because matings between relatives will not be reduced. Nor is it likely to contribute to the high levels of genetic polymorphism found in nature, because females would be required to base their mating preferences on genotypes at all or most loci, to show individual variation in respect of their preferences and to sum the information into an index of genomic rarity. Given the levels of polymorphism involved, all males are likely to be rare by some criterion. A varying direction of female preference, required for a two-sided RME and for the maintenance of genetic polymorphism, has yet to be reported from wild populations. The RME is therefore probably of limited evolutionary significance. Disassortative mating with respect to self-incompatibility alleles in plants, and possibly major histocompatibility complex (MHC) alleles in vertebrates, results in an RME, inbreeding avoidance and high levels of genetic polymorphism at these loci.

Alleles↗
PubMed1996

The genetical history of an isolated population of the endangered grey wolf Canis lupus: a study of nuclear and mitochondrial polymorphisms.

The grey wolf was thought to have been exterminated in the Scandinavian peninsula when the sudden appearance of a few animals in southern Sweden was reported in 1980. These wolves founded a new Swedish population which currently numbers at least 25 individuals, one of the world's smallest populations of the species. The sudden occurrence of the founder animals caused speculation that these had not appeared by 'natural' means but rather were Swedish zoo animals deliberately released by man. To analyse if this was the case and to elucidate the genetic status of this small and isolated population, we assessed nuclear and mitochondrial (mt) genetic variability in wild and captive grey wolves, using microsatellite typing and sequence analysis of the mtDNA D-loop. The new population was found to be monomorphic for a mtDNA haplotype which also was present in the Swedish zoo population. A total of four different mtDNA haplotypes were found among all captive and wild wolves (including two animals from an occasional establishment of a few wolves in northern Sweden in the late 1970s), with a maximum sequence divergence of 3.1%. Despite the mtDNA congruence, animals from the zoo population could most likely be excluded as founders for the wild population since the latter group of animals displayed several unique microsatellite alleles (i.e. alleles not found in the zoo population). Moreover, a phylogenetic analysis of individual wolves, using microsatellite allele sharing as distance measure, placed all wild animals on a branch separated from that of the captive animals. The average degree of nuclear variability as well as allelic diversity was similar in the wild and the captive populations, respectively, but was lower than that reported for North-American populations of grey wolves. Polymorphism has declined in wild wolves born in recent years suggesting that this small population is currently suffering from a loss of genetic variability due to inbreeding. Inbreeding depression is documented in captive wolves and the long-term survival of the wild Swedish population may therefore depend on immigration of animals from Russia. This study illustrates the usefulness of microsatellites for dissecting close genetic relationships and for addressing the genetic status of individuals.

Animals↗
PubMed2000

Extraordinary multilocus genetic organization in mole crickets, Gryllotalpidae.

Allozymic diversity at 21 loci was analyzed in 470 individuals of three species of mole cricket superspecies, Gryllotalpa gryllotalpa (two new chromosomal species, G. tali and G. marismortui) and G. africana in Israel, which are distributed along a southward transect of increasing aridity. Two outstanding findings emerged in G. tali and G. marismortui: (1) genetic polymorphism was high but heterozygosity very low, indicating significant deviations from Hardy-Weinberg expectations; and (2) significant linkage disequilibria at an unprecedented level for outbreeders and remarkable intersite differences. The results may characterize subterranean gryllotalpids worldwide because a single sample of Neocurtilla hexadactyla from Tefé, Amazonia, shows the same features. Significant variation of heterozygote paucity among loci, combined with the biology of the species, rejects the simple explanation of inbreeding or any other single explanatory model. Likewise, direct selection against heterozygotes or specific multilocus associations can explain, but is not necessary nor likely to explain, the observed results in mole crickets. To explain these results, we developed a multiple-factor mathematical model combining niche viability selection, niche choice, and positive assortative mating. This model involves a special case of Wahlund effect and inbreeding. Simulations based on this model showed that a combination of these three mechanisms may produce the observed distribution of alleles, via selection on a few loci, to affect the entire genome organization.

Animals↗