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PubMed2004

Microsatellite null alleles in parentage analysis.

Highly polymorphic microsatellite markers are widely employed in population genetic analyses (eg, of biological parentage and mating systems), but one potential drawback is the presence of null alleles that fail to amplify to detected levels in the PCR assays. Here we examine 233 published articles in which authors reported the suspected presence of one or more microsatellite null alleles, and we review how these purported nulls were detected and handled in the data analyses. We also employ computer simulations and analytical treatments to determine how microsatellite null alleles might impact molecular parentage analyses. The results indicate that whereas null alleles in frequencies typically reported in the literature introduce rather inconsequential biases on average exclusion probabilities, they can introduce substantial errors into empirical assessments of specific mating events by leading to high frequencies of false parentage exclusions.

Alleles↗

PubMed2003

Delayed selfing as an optimal mating strategy in preferentially outcrossing species: theoretical analysis of the optimal age at first reproduction in relation to mate availability.

The evolution of mating systems and that of life history have usually been modeled separately. However, they may be to some extent coupled in natural situations because they rely on the same phenotypic traits. Here, we focus on one of these traits, the age at first reproduction, in a species able to self- and cross-fertilize. When inbreeding depression is strong, self-fertile species preferentially cross-fertilize. However, outcrossing is not always possible when the availability of sexual partners is limited. The optimal reproductive strategy in this case would be to wait for a sexual partner for a certain period of time (the waiting time) and then switch to selfing if no mates have been encountered (reproductive assurance strategy). We predict the evolution of an optimal waiting time depending on the efficiency of resource reallocation to late fecundity, on the inbreeding depression, and on the instantaneous probability of encountering a partner versus dying. As a consequence of reduced mate availability, intermediate selfing rates can be generated in preferentially outcrossing populations, but they are lowered by the existence of a waiting time. Our model may thus explain low selfing rates observed in natural populations of many self-fertile, preferentially outcrossing plants or animal species.

Age Factors↗

PubMed2001

Sexual dimorphism in primate evolution.

Sexual dimorphism is a pervasive phenomenon among anthropoid primates. Comparative analyses over the past 30 years have greatly expanded our understanding of both variation in the expression of dimorphism among primates, and the underlying causes of sexual dimorphism. Dimorphism in body mass and canine tooth size is familiar, as is pelage and "sex skin" dimorphism. More recent analyses are documenting subtle differences in the pattern of skeletal dimorphism among primates. Comparative analyses have corroborated the sexual selection hypotheses, and have provided a more detailed understanding of the relationship between sexual selection, natural selection, and mating systems in primates. A clearer picture is emerging of the relative contribution of various selective and nonselective mechanisms in the evolution and expression of dimorphism. Most importantly, recent studies have shown that dimorphism is the product of changes in both male and female traits. Developmental studies demonstrate the variety of ontogenetic pathways that can lead to dimorphism, and provide additional insight into the selective mechanisms that influence dimorphism throughout the lifetime of an animal. Evidence from the fossil record suggests that dimorphism probably evolved in parallel twice, and the dimorphism in some extinct hominoids probably exceeded that of any living primate. Our advances in understanding the behavioral/ecological correlates of dimorphism in living primates have not improved our ability to reconstruct social systems in extinct species on the basis of dimorphism alone, beyond the inference of polygyny or intense male-male competition. However, our understanding of the behavioral/ecological correlates of growth and development, and of the expression of dimorphism as a function of separate changes in male and female traits, offers great potential for inferring evolutionary changes in behavior over time.

Animals↗

PubMedDate not supplied

Multiplexed systems of microsatellite markers for genetic analysis of mahogany, Swietenia macrophylla King (Meliaceae), a threatened neotropical timber species.

Mahogany (Swietenia macrophylla King [Meliaceae]) is the most valuable hardwood species in the neotropics. Its conservation status has been the subject of increasing concern due to overexploitation and habitat destruction. In this work we report the development and characterization of 10 highly variable microsatellite loci for S. macrophylla. Twenty-nine percent of the 126 sequenced mahogany clones yielded useful microsatellite loci. Three high-throughput genotyping systems were developed based on polymerase chain reaction (PCR) multiplexing of these mahogany loci. We identified a total of 158 alleles in 121 adult individuals of S. macrophylla, with an average of 15.8 alleles (range 11-25) per locus. All loci showed Mendelian inheritance in open-pollinated half-sib families. The mean expected heterozygosity was 0.84 and the mean observed heterozygosity was 0.73. The combined probability of identity-the probability that two individuals selected at random from a population would have identical genotypes--was 7.0 x 10(-15), and combined probability of paternity exclusion was 0.999998 overall loci. These microsatellite loci permit precise estimates of parameters such as gene flow, mating system, and paternity, thus providing important insights into the population genetics and conservation of S. macrophylla.

DNA↗

PubMed1997

Molecular analysis of paternity shows promiscuous mating in female humpback whales (Megaptera novaeangliae, Borowski).

It is widely assumed that the mating system of the humpback whale. Magaptera novaeangliae, is similar to that of most mammals in that it represents some form of polygyny or promiscuity, but this cannot be tested without observations of copulation or data on paternity of offspring. Microsatellite DNA markers were used to examine the paternity of calves born to individually identified mature female humpback whales from the Gulf of Maine. Skin biopsies were obtained from three females, and several (range: three to five) of their known offspring. Multiple paternity of offspring, indicated by the presence of at least three different paternal alleles, was evident in all three females at either three or four of the six microsatellite loci surveyed. Such promiscuous mating is expected given current knowledge of the social ecology of this species. It is also consistent with resightings of individually identified female humpbacks with different male associates during two or more breeding seasons.

Animals↗

PubMed2002

A generalized heterozygote deficiency assessed with microsatellites in French common ash populations.

Common ash is a temperate forest tree with a colonizing behaviour, a discontinuous spatial distribution and a peculiar and poorly known mating system. Microsatellite markers were used to study the genetic structure in natural populations of common ash. Twelve populations located in northeastern France were analysed at five loci. Levels of genetic variability within and among stands were estimated for the seedling and adult stages. As expected for a forest tree, our results reveal high levels of intrapopulation diversity and a low genetic differentiation between stands. However, a general and significant heterozygote deficiency was found, with a mean F(IS) of 0.163 for the seedlings and of 0.292 for the adult trees. The different explanations for such an excess homozygosity are discussed: a nonMendelian inheritance of alleles, the presence of null alleles, a Wahlund effect and assortative mating.

France↗

PubMed1969

Functions of F pili in mating-pair formation and male bacteriophage infection studies by blending spectra and reappearance kinetics.

The extent of removal at various blending speeds (blending spectrum) and the kinetics of reappearance after blending of the ability of male Escherichia coli bacteria to form mating pairs, to adsorb and be infected by ribonucleic acid male phage, and to adsorb and be infected by deoxyribonucleic male phage were identical to the blending spectrum and reappearance kinetics of microscopically visible F pili. The same results were obtained with an Hfr (high-frequency recombinant), F', or resistance transfer factor (RTF) fi(+) mating system. Blending did not affect the viability, growth rate, ability to adsorb T4 phage, or ability to produce new F pili at any of the speeds used. It can be concluded that microscopically visible F pili are an absolute requirement for all three functions. Three classes of F pili have been found in bacterial cultures: attached, adsorbed, and free. Bacteria with adsorbed F pili in addition to attached ones were proportionately more susceptible to male phage infection, suggesting that adsorbed F pili may be at least partially functional. Free F pili did not compete with bacteria for phage. Some implications of the virus-like nature of F-pilus outgrowth for the mechanisms of mating and male phage infection are discussed.

Adsorption↗

PubMed1989

Brahman bull fertility in a north Australian rangeland herd.

Low and variable bull fertility was identified as a constraint on reproductive rates in beef cattle grazed in an extensive, multiple sire mating regimen on Mount Bundey station in the Darwin pastoral district of northwestern Australia. Erratic conception patterns were attributed to a high proportion of bulls with low breeding soundness evaluation scores (BSE), a high proportion of aged bulls (40%>8 yr), and to running bulls of mixed age groups. Liveweight, scrotal circumference (SC) and age were positively correlated. An experiment was subsequently designed to investigate the ability of a number of bull measurements to predict fertility in an extensively-managed, multiple-sire mating system. Blood typing was used to match calves to sires. It proved to be an accurate and useful technique which successfully identified the parentage of 94% of calves examined. Single measurements of serum testosterone after administration of gonadotrophin-releasing hormone (GnRH) were not correlated with fertility. However six of the seven most fertile bulls exhibited high peak serum testosterone levels in summer, and lower levels in the winter. In contrast, the less fertile bulls did not exhibit seasonal variation in GnRH-induced serum testosterone levels. Social dominance ratio was weakly related to fertility (r=0.51: P<0.05). BSE (r=0.51: P<0.05) and SC (r=0.49: P<0.05) prior to, but not subsequent to, mating were correlated with bull fertility. Under the conditions of this experiment, a bull to cow ratio of 1:20 was excessive for bulls with a satisfactory BSE score.

Journal Article↗

PubMed1998

Dispensable and indispensable genes in an ameiotic fish, the Amazon molly Poecilia formosa.

All-female vertebrates are excellent model systems for studying many evolutionary problems. One of these is the Amazon molly. In this review, three aspects of its biology are discussed: (1) An important question is how dispensable genes, such as all male coding genes, evolve in this species. A number of studies found that most of these genes remain remarkably stable and functional. (2) The gynogenetic Amazon mollies have to live in sympatry with males of a gonochoristic species, because sperm are needed to trigger embryogenesis. Yet, Amazon mollies cannot replace their sexual competitors, because this would lead to their own extinction. Studies on the behavior of Amazon mollies and their sperm-donor species indicate that a number of behavior patterns stabilize the mating system by providing Amazon mollies with the copulations they need to reproduce. (3) The age of Amazon mollies has been estimated to be approximately 100,000 years. This is older than predicted by some theoretical models. In Amazon mollies two ways to occasionally incorporate fresh genetic material have evolved. One way is to add one complete set of paternal chromosomes, which, in nature, leads to stable triploid lineages. The second way is the incorporation of minute, centromere-containing microchromosomes. The evolutionary impact of these phenomena, however, is not resolved so far and needs further study.

Animals↗

PubMed1997

Determinants of primate social organization: comparative evidence and new insights from Malagasy lemurs.

The aim of this review is to summarize newly available information on lemur social systems, to contrast it with the social organization of other primates and to relate it to existing models of primate social evolution. Because of their evolutionary history, the primates of Madagascar constitute a natural experiment in social evolution. During millions of years of isolation, they converged with other primates only in the most fundamental way in the evolution of solitary, pair-living and group-living species, but deviate in several respects within these basic categories of social organization. Solitary lemurs remain poorly studied, but their social organization appears to be broadly similar to that of other solitary primates, even though the unexpected lack of sexual dimorphism may indicate that similar types of social organization can give rise to different mating systems. The determinants of a solitary lifestyle remain elusive. Pair-living lemurs show striking convergences with other monogamous primates in several behavioural traits, but also deviate in that the majority of species are at least partly nocturnal and do not exhibit direct paternal care of dependent young. Group-living lemurs have not evolved single-male groups, male-bonded and multi-level societies, and polyandrous groups may also be lacking. Female philopatry is common, but female bonds are generally weakly developed and eviction of females from natal groups is not unusual. Group-living lemurs also differ from anthropoids in that their groups have even adult sex ratios, smaller average size and may split up on a seasonal basis. Feeding competition, predation risk and reproductive competition can not fully explain these unusual aspects of lemur social organization. It has therefore been suggested that the social consequences of the risk of infanticide and of recent changes in activity may be ultimately responsible for these idiosyncracies of group-living lemurs, an explanation largely supported by the available evidence. Thus, social factors and fundamental life-history traits, in addition to ecological factors, contribute importantly to variation in social systems among lemurs, and possibly other primates. However, neither the diversity of lemur social systems, nor the evolutionary forces and mechanisms operating in these and other primates are yet fully understood.

Animals↗

PubMed2004

Sexual selection, redundancy and survival of the most beautiful.

A model is described of a highly redundant complex organism that has overlapping banks of genes such that each vital function is specified by several different genetic systems. This generates a synergistic profile linking probability of survival to the number of deleterious mutations in the genome. Computer models show that there is a dynamic interaction between the mean number of new deleterious mutations per generation (X), the mean number of deleterious mutations in the genome of the population (Y) and percentage zygote survival (Zs). Increased X leads to increased Y and a fall in Zs but it takes several generations before a new equilibrium is reached. If sexual attraction is influenced by the number of deleterious mutations in the genome of individuals then Y is reduced and Zs increased for any given value of X. This fall in Y and rise in Zs is more marked in polygamous than monogamous mating systems. The model is specified such that deleterious mutations can occur without any observable or measurable effect on function. Thus sexual selection, in this organism, for low levels of deleterious mutations cannot be based on assessment of performance. Instead it is based on a simple symmetrical surface pattern that is flawlessly reproduced by organisms with no deleterious mutations, but is less than perfect, and therefore less attractive, if genetic systems have been deleted. A complex vital task requires a system with a high level of redundancy that acts so that the loss of one component has no observable effect and therefore cannot be used for sexual selection. The reproduction of a beautiful surface pattern also requires a low error, high redundancy genetic system; however, in this case there is advantage if a single deleterious mutation produces a recognisable change. This leads to the conclusion that sexual selection and sexual attraction should be based on beauty rather than utility, and explains the common observation in nature that it is the most beautiful that survive.

Animals↗

PubMed2006

Genetic mating patterns studied in pools with manipulated nest site availability in two populations of Pomatoschistus minutus.

Pomatoschistus minutus show paternal care in a resource defence mating system. We investigated the effect of nest-site availability on parasitic spawning. Each experimental pool contained four potentially nest-building males, four females and nests-sites in shortage (2) or excess (6). Both treatments were conducted in two populations; one with natural nest-sites in excess, one with a nest-site shortage. Microsatellite-DNA revealed that all nest-holders had fertilized most of the eggs they tended. Yet, 35% of the nests contained eggs fertilized by another male and 14.4% of the males had performed parasitic spawning. There was no site or treatment effect. Several females spawned in two nests, which coincided with parasitic spawnings, suggesting a cost to the nest-holder in terms of lost mating success. Nest-holders with and without eggs and non-nesting males all spawned parasitically, generating a significantly lower opportunity for sexual selection compared to if there had been no parasitic spawning.

Animals↗

PubMed2001

A bayesian framework for parentage analysis: the value of genetic and other biological data.

We develop fractional allocation models and confidence statistics for parentage analysis in mating systems. The models can be used, for example, to estimate the paternities of candidate males when the genetic mother is known or to calculate the parentage of candidate parent pairs when neither is known. The models do not require two implicit assumptions made by previous models, assumptions that are potentially erroneous. First, we provide formulas to calculate the expected parentage, as opposed to using a maximum likelihood algorithm to calculate the most likely parentage. The expected parentage is superior as it does not assume a symmetrical probability distribution of parentage and therefore, unlike the most likely parentage, will be unbiased. Second, we provide a mathematical framework for incorporating additional biological data to estimate the prior probability distribution of parentage. This additional biological data might include behavioral observations during mating or morphological measurements known to correlate with parentage. The value of multiple sources of information is increased accuracy of the estimates. We show that when the prior probability of parentage is known, and the expected parentage is calculated, fractional allocation provides unbiased estimates of the variance in reproductive success, thereby correcting a problem that has previously plagued parentage analyses. We also develop formulas to calculate the confidence interval in the parentage estimates, thus enabling the assessment of precision. These confidence statistics have not previously been available for fractional models. We demonstrate our models with several biological examples based on data from two fish species that we study, coho salmon (Oncorhychus kisutch) and bluegill sunfish (Lepomis macrochirus). In coho, multiple males compete to fertilize a single female's eggs. We show how behavioral observations taken during spawning can be combined with genetic data to provide an accurate calculation of each male's paternity. In bluegill, multiple males and multiple females may mate in a single nest. For a nest, we calculate the fertilization success and the 95% confidence interval of each candidate parent pair.

Animals↗

PubMed2000

Relative fitness components measured with competitive PCR.

In mating systems with sperm competition, paternity is frequently established with modern DNA techniques. These methods are often expensive and cumbersome, and can be especially difficult for highly fecund species. An additional objective of many paternity studies is to discover the relationship between sperm number and paternity. We present here a competitive polymerase chain reaction (PCR) protocol, coupled with the use of an automated sequencer, that has two functions: (i) to measure directly relative sperm output of males in sperm competition; and (ii) to estimate paternity distributions of large numbers of offspring simultaneously. Our technique was calibrated using a microsatellite locus of the bluehead wrasse, Thalassoma bifasciatum, with the result that product ratio after competitive PCR accurately reflected the initial template proportions of known mixtures of DNA. When we applied our technique to multiple larvae of separate mating events we found that paternity distributions estimated with the competitive PCR technique closely matched the estimates derived from the traditional method of pooling paternity data from individual larvae. Finally, we compared paternity of these spawns with relative sperm contribution estimates. This comparison suggests that ejaculate size alone does not predict a male's proportion of paternity within the group.

Animals↗

PubMed2004

On the evolutionary costs of self-incompatibility: incomplete reproductive compensation due to pollen limitation.

Pollen limitation affects plants with diverse reproductive systems and ecologies. In self-incompatible (SI) species, pollen limitation may preclude full reproductive compensation for prezygotic rejection of pollen. We present a model designed to explore the effects of incomplete reproductive compensation on evolutionary changes at a modifier locus that regulates the level of SI expression. Our results indicate that incomplete reproductive compensation greatly increases the evolutionary costs of SI, particularly in populations with low S-allele diversity. The evolutionary fate of modifiers of SI expression depends on the rate at which they are transmitted to future generations as well as the effects of SI on offspring number and quality. Partial SI expression can represent a stable condition rather than an evolutionarily transient state between full expression and full suppression. This unanticipated result provides the first theoretical support for the evolutionary stability of such mixed mating systems, the existence of which has recently been documented.

Evolution, Molecular↗

PubMed2002

Female-biased sexual size dimorphism in the yellow-pine chipmunk (Tamias amoenus): sex-specific patterns of annual reproductive success and survival.

Sexual size dimorphism is ultimately the result of independent, sex-specific selection on body size. In mammals, male-biased sexual size dimorphism is the predominant pattern, and it is usually attributed to the polygynous mating system prevalent in most mammals. This sole explanation is unsatisfying because selection acts on both sexes simultaneously, therefore any explanation of sexual size dimorphism should explain why one sex is relatively large and the other is small. Using mark-recapture techniques and DNA microsatellite loci to assign parentage, we examined sex-specific patterns of annual reproductive success and survival in the yellow-pine chipmunk (Tamias amoenus), a small mammal with female-biased sexual size dimorphism, to test the hypothesis that the dimorphism was related to sex differences in the relationship between body size and fitness. Chipmunks were monitored and body size components measured over three years in the Kananaskis Valley, Alberta, Canada. Male reproductive success was independent of body size perhaps due to trade-offs in body size associated with behavioral components of male mating success: dominance and running speed. Male survival was consistent with stabilizing selection for overall body size and body size components. The relationship between reproductive success and female body size fluctuated. In two of three years the relationship was positive, whereas in one year the relationship was negative. This may have been the result of differences in environmental conditions among years. Large females require more energy to maintain their soma than small females and may be unable to maintain lactation in the face of challenging environmental conditions. Female survival was positively related to body size, with little evidence for stabilizing selection. Sex differences in the relationship between body size and fitness (reproductive success and survival) were the result of different processes, but were ultimately consistent with female-biased sexual size dimorphism evident in this species.

Animals↗

PubMed1975

Performance of Holstein and crossbred dairy cattle in Louisiana. III. Health and viability.

Viability and health disorders were compared for straightbred Holsteins and crosses between Holsteins, Brown Swiss, Jerseys, and Red Sindhis. In addition, effects of mating systems and effects of various parts of Red Sindhi heredity on these traits were evaluated. Losses before first calving per 100 females born alive were: Holsteins 22; Holstein-sired crosses 20: Brown Swiss-sired crosses 26; daughters of crossbred sires group I (sires had from 1/4 to 1/16 Red Sindhi heredity) 24; and group II (sires were all European breeds) 31. Losses in first-gestation from abortions and stillbirths were: Holsteins 20% and crossbreds 9%. In first lactation, incidence of foot rot and anaplasmosis was higher among Holsteins (13% and 16%) than in crossbreds (5% and 8%) whereas the incidence was less among crosses with Red Sindhi heredity (3% and 2%) than in all European breed crosses (9% and 17%). When progeny produced by criss-crossing to purebred sires were compared with progeny from random mating to crossbred sires, the former had a greater incidence of mastitis (30% versus 19%) and anaplasmosis (11% versus 2%). There was no differences between Holsteins and crossbreds in overall viability. However, there was considerable variation between breeds at the various ages.

Abortion, Veterinary↗

PubMed2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

MAT genes↗