Efficient experimental designs for the estimation of genetic parameters in plant populations.

Procedures for estimating the genetic parameters of plant populations frequently employ progeny testing to ascertain the genotype of maternal plants. However, when experimental resources are limited (e.g., electrophoretic markers), the large progeny sizes required for accurate typing severely restricts the numbers of families which can be tested. In this paper, four experimental designs with partial progeny testing are compared with the standard procedure of complete testing for their statistical efficiency in estimating the gene frequency, fixation index, and outcrossing rate at a single diallelic locus. It is shown that substantial increases in efficiency can be obtained (especially in inbred populations) if one or two individuals per family are assayed, and then further progeny testing is confined to those families which give rise to a heterozygote in this initial screening. Sample size for various purposes are computed and factors affecting the applicability of such "censored" designs are discussed.     

Genetic Variation in a Heterogeneous Environment. II. Temporal Heterogeneity and Directional Selection

The maintenance of genetic variation is investigated in a finite population where selection at an autosomal locus with two alleles varies temporally between two environments and the heterozygote has an intermediate fitness value. When there is additive gene action and equal selection in both environments, the autocorrelation between subsequent environments must be negative for more maintenance of genetic variation than for neutrality. The maximum maintenance occurs when there is equal selection in the two environments and the autocorrelation approaches ^-1.0 (for a stochastic model), or when there is short repeating cycle such as one related to seasons. Also comparison of the effects of stochastic variation in selection in finite and infinite populations is made by using Monte Carlo simulation. One situation was found where temporal environmental variation maintains genetic variation very effectively even in a small population and that is when there is evolution of dominance, i.e., the heterozygote is closer in fitness to the favored homozygote than the other homozygote. An important conclusion is that in a finite population genetic tracing of environmental change, particularly when there is a positive autocorrelation between environments or a long environmental cycle, leads to an increased loss of genetic variation making such a response undesirable in the long term, a result different from that in infinite populations.     

Single-locus polymorphism in a heterogeneous two-deme model

Environmental heterogeneity has long been considered a likely explanation for the high levels of genetic variation found in most natural populations: selection in a spatially heterogeneous environment can maintain more variation. While this theoretical result has been extensively studied in models with limited parameters (e.g., two alleles, fixed gene flow, and particular selection schemes), the effect of spatial heterogeneity is poorly understood for models with a wider range of parameters (e.g., multiple alleles, different levels of gene flow, and more general selection schemes). We have compared the volume of fitness space that maintains variation in a single-deme model to the volume in a two-deme model for multiple alleles, random selection schemes, and various levels of migration. Furthermore, equilibrium allele-frequency vectors were examined to see if particular patterns of variation are more prevalent than first expected. The two-deme model maintains variation for substantially larger volumes of fitness space with lower heterozygote fitness than the single-deme model. This result implies that selection schemes in the two-deme model can have a wider range of fitness patterns while still maintaining variation. The equilibrium allele-frequency patterns emerging from the two-deme model are more variable and strongly influenced by gene flow.     

种子与花粉的随机迁移对植物群体遗传结构分化的影响

将Ｗｒｉｇｈｔ的经典岛屿模型拓广到植物群体上,同时考虑了含有花粉和种子随机迁移的影响。并给出了３种不同遗传方式的基因（双亲遗传,父本和母本遗传）频率的期望均值和方差。理论结果证明花粉或种子的随机迁移可增加基因频率方差,其幅度取决于迁移率和迁移基因频率的方差。同绝对迁移率一样,花粉和种子的迁移率方差及迁移基因频率的方差对群体遗传结构的分化有着同样的重要。一个重要结论就是花粉或种子的随机迁移率和随机迁     

Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals

In recent years, the new phenomenon of intracolonial genetic variability within a single coral colony has been described. This connotes that coral colonies do not necessarily consist of only a single genotype, but may contain several distinct genotypes. Harboring more than one genotype could improve survival under stressful environmental conditions, e.g., climate change. However, so far it remained unclear whether the intracolonial genetic variability of the adult coral is also present in the gametes. We investigated the occurrence of intracolonial genetic variability in 14 mature colonies of the coral Acropora hyacinthus using eight microsatellite loci. A grid was placed over each colony before spawning, and the emerging egg/sperm bundles were collected separately in each grid. The underlying tissues as well as the egg/sperm bundles were genotyped to determine whether different genotypes were present. Within the 14 mature colonies, we detected 10 colonies with more than one genotype (intracolonial genetic variability). Four out of these 10 mature colonies showed a transfer of different genotypes via the eggs to the next generation. In two out of these four cases, we found additional alleles, and in the two other cases, we found only a subset of alleles in the unfertilized eggs. Our results suggest that during reproduction of A. hyacinthus, more than one genotype per colony is able to reproduce. We discuss the occurrence of different genotypes within a single coral colony and the ability for those to release eggs which are genetically distinct.     

Disequilibrium in Two-Locus Mutation-Selection Balance Models

Equilibrium behavior of two-locus mutation-selection balance models is analyzed using perturbation techniques. The classical result of Haldane for one locus is shown to carry over to two loci, if fitnesses are replaced by marginal fitnesses. If the fitness of the double heterozygote is smaller than would be produced by a multiplicative model, as in additive or quantitative fitness models, the disequilibrium is negative--an excess of gametes with one rare allele. In this case the disequilibrium can be as large as one-half its maximum value possible, if the recombination rate is small, not greater than the strength of selection. If the fitness of the double heterozygote is larger than would be produced by a multiplicative model, the disequilibrium is positive, and is very small relative to its maximum value possible, even if the recombination rate is zero.     

THE INFLUENCE OF SELF-FERTILIZATION AND POPULATION DYNAMICS ON THE GENETIC STRUCTURE OF SUBDIVIDED POPULATIONS: A CASE STUDY USING MICROSATELLITE MARKERS IN THE FRESHWATER SNAIL BULINUS TRUNCATUS

The distribution of neutral genetic variability within and among sets of populations results from the combined actions of genetic drift, migration, extinction and recolonization processes, mutation, and the mating system. We here analyzed these factors in 38 populations of the hermaphroditic snail Bulinus truncatus. The sampling area covered a large part of the species range. The variability was analyzed using four polymorphic microsatellite loci. A very large number of alleles (up to 55) was found at the level of the whole study. Observed heterozygote deficiencies within populations are consistent with very high selfing rates, generally above 0.80, in all populations. These should depress the variability within populations, because of low effective size, genetic hitchhiking, and background selection, whatever the model of mutation assumed. However, that some populations exhibit much more variability than others suggests that historical demographic processes (e.g., population size variation, bottlenecks, or founding events) may play a significant role. A hierarchical analysis of the distribution of the variability across populations indicates a strong pattern of isolation by distance, whatever the geographical scale considered. Our analysis also illustrates how the mutation rate may affect population differentiation, as different mutation rates result in different levels of homoplasy at microsatellite loci. The effects of both genetic drift and gene flow vary with the temporal and spatial scales considered in B. truncatus populations.     

Breeding latitude predicts timing but not rate of spring migration in a widespread migratory bird in South America

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The expected number of heterozygous sites in a subdivided population.

A simple, exact formula is derived for the expected number of heterozygous sites per individual at equilibrium in a subdivided population. The model of infinitely many neutral sites is posited; the linkage map is arbitrary. The monoecious, diploid population is subdivided into a finite number of panmictic colonies that exchange gametes. The backward migration matrix is arbitrary, but time independent and ergodic (i.e., irreducible and aperiodic). With suitable weighting, the expected number of heterozygous sites is 4Neu, where Ne denotes the migration effective population number and u designates the total mutation rate per gene (or DNA sequence). For diploid migration, this formula is a good approximation if Ne >> 1.     

Apparent Differential Selection at an Isozyme Locus between Queens and Workers of the Ant APHAENOGASTER RUDIS

The frequencies of two alleles at a cathodal malate dehydrogenase locus in populations of A. rudis were studied in 47 colonies from three localities in Georgia and one in New Jersey. The male gene frequencies of the New Jersey and one Georgia locality differ significantly. All the queens at one Georgia locality were heterozygotes. This genotypic distribution differs strongly from that of the workers, in which approximately equal numbers of heterozygotes and homozygotes were found. The heterozygote excess among queens but not their worker progeny suggests differential selection between these castes. This study also shows that rudis colonies consist of a single, once-mated queen and her worker progeny.     

The exact values of the probability of fixation of underdominant chromosomal rearrangements.

A numerical analysis of the probability of fixation of a chromosomal mutation with partial sterility of the heterozygote in a single population is performed. Three different genetic models are considered: the first model entails constant selection against the heterozygote and is the model almost universally used in previous works; in the other two models selection against the heterozygote depends on its frequency. The exact values of the fixation probability are found by iterating transition matrices with genotype specification. Differences in results among models are small. The exact values found in the first model are compared to estimates obtained from approximations. Solutions based on diffusion models give good approximations when selection against the heterozygote is low, especially if the population is very small. For the higher values of the selection coefficient against the heterozygote, the estimates are rather imprecise, especially when the populations are not very small.     

Ongoing changes in migration phenology and winter residency at Bracken Bat Cave

Bats play an important role in agroecology and are effective bioindicators of environmental conditions, but little is known about their fundamental migration ecology, much less how these systems are responding to global change. Some of the world's largest bat populations occur during the summer in the south‐central United States, when millions of pregnant females migrate from lower latitudes to give birth in communal maternity colonies. Despite a relatively large volume of research into these colonies, many fundamental questions regarding their abundance—including their intra‐ and interseasonal variability—remain unanswered, and even estimating the size of individual populations has been a long‐running challenge. Overall, monitoring these bat populations at high temporal resolution (e.g., nightly) and across long time spans (e.g., decades) has been impossible. Here, we show 22 continuous years of nightly population counts at Bracken Cave, a large bat colony in south‐central Texas, enabling the first climate‐scale phenological analysis. Using quantitative radar monitoring, we found that spring migration and the summer reproductive cycle have advanced by approximately 2 weeks over the study period. Furthermore, we quantify the ongoing growth of a newly—established overwintering population that indicates a system‐wide response to changing environmental conditions. Our observations reveal behavioral plasticity in bats’ ability to adapt to changing resource availability, and provide the first long‐term quantification of their response to a changing climate. As aerial insectivores, these changes in bat phenology and propensity for overwintering indicate probable shifts in prey availability, with clear implications for pest management across wider regional agrisystems.     

Genetic variation and population structuring in two brooding coral species (<Emphasis Type="Italic">Siderastrea stellata</Emphasis> and <Emphasis Type="Italic">Siderastrea radians</Emphasis>) from Brazil

Siderastrea stellata and S. radians are scleractinian coral species that present a remarkable overlap of diagnostic characteristics and sympatric distribution. Moreover, both are viviparous with similar reproductive strategies and with a gregarious larval behavior. Samples of both species from the Brazilian coast were analyzed using 18 isozymic loci to quantify their genetic variability and populational structure. Results confirmed species identity, high intrapopulational variability and revealed moderate genetic structuring among all samples (S. stellata: F (ST) = 0.070; S. radians: F (ST) = 0.092). Based on genotypic diversity analysis, there was evidence that local recruitment may have a minor role in the populations (mean, G ( o ):G ( e )= 1.00 +/- 0.0003 SD for S. stellata and 0.99 +/- 0.0023 SD for S. radians). Deviations towards heterozygote deficiencies found in both Siderastrea species could be explained by the Wahlund effect, since there was evidence that populations might be composed of colonies of different ages. In S. radians it is also likely that there is some inbreeding occurring in the studied populations. Despite the brooding pattern and the gregarious larval behavior, our data suggest the occurrence of gene flow along the Brazilian coast. This is the first study on population genetics of Brazilian reef corals.     

Effect of population structure on the amount of polymorphism and the fixation probability under overdominant selection

Under overdominant selection, mutants substantially contribute to increase the amount of polymorphism. It is also known that under neutrality as the migration rates among demes decrease in a subdivided population, the amount of polymorphism increases along with the increase of the effective population size, N(e). In this study, under overdominant selection the effect of population subdivision on the amount of polymorphism was investigated using the diffusion approximation and the low migration approximation. It was shown that if selection is medium or strong (e.g., N(T)s > 1, where N(T) is the population size and s is the selective advantage of heterozygotes), the nucleotide diversity, pi, decreases along with the decrease of Nm against the increase of N(e), where N is the size of demes and m is the migration rate per deme. In addition, the ratio of the nucleotide diversity to the evolutionary rate also decreases along with the decrease of Nm. In some cases the ratio becomes smaller than that expected under neutrality as Nm decreases.     

THE EFFECT OF COLLECTIVE DISPERSAL ON THE GENETIC STRUCTURE OF A SUBDIVIDED POPULATION

Correlated dispersal paths between two or more individuals are widespread across many taxa. The population genetic implications of this collective dispersal have received relatively little attention. Here we develop two‐sample coalescent theory that incorporates collective dispersal in a finite island model to predict expected coalescence times, genetic diversities, and F‐statistics. We show that collective dispersal reduces mixing in the system, which decreases expected coalescence times and increases F_ST. The effects are strongest in systems with high migration rates. Collective dispersal breaks the invariance of within‐deme coalescence times to migration rate, whatever the deme size. It can also cause F_ST to increase with migration rate because the ratio of within‐ to between‐deme coalescence times can decrease as migration rate approaches unity. This effect is most biologically relevant when deme size is small. We find qualitatively similar results for diploid and gametic dispersal. We also demonstrate with simulations and analytical theory the strong similarity between the effects of collective dispersal and anisotropic dispersal. These findings have implications for our understanding of the balance between drift–migration–mutation in models of neutral evolution. This has applied consequences for the interpretation of genetic structure (e.g., chaotic genetic patchiness) and estimation of migration rates from genetic data.     

Polymorphism in multiallelic migration–selection models with dominance

The evolution of the gene frequencies at a single multiallelic locus under the joint action of migration and viability selection with dominance is investigated. The monoecious, diploid population is subdivided into finitely many panmictic colonies that exchange adult migrants independently of genotype. Underdominance and overdominance are excluded. If the degree of dominance is deme independent for every pair of alleles, then under the Levene model, the qualitative evolution of the gene frequencies (i.e., the existence and stability of the equilibria) is the same as without dominance. In particular: (i) the number of demes is a generic upper bound on the number of alleles present at equilibrium; (ii) there exists exactly one stable equilibrium, and it is globally attracting; and (iii) if there exists an internal equilibrium, it is globally asymptotically stable. Analytic examples demonstrate that if either the Levene model does not apply or the degree of dominance is deme dependent, then the above results can fail. A complete global analysis of weak migration and weak selection on a recessive allele in two demes is presented.     

Sylvatic plague reduces genetic variability in black-tailed prairie dogs

Small, isolated populations are vulnerable to loss of genetic diversity through in-breeding and genetic drift. Sylvatic plague due to infection by the bacterium Yersinia pestis caused an epizootic in the early 1990s resullting in declines and extirpations of many black-tailed prairie dog (Cynomys ludovicianus) colonies in north-central Montana, USA. Plague-induced population bottlenecks may contribute to significant reductions in genetic variability. In contrast, gene flow maintains genetic variability within colonies. We investigated the impacts of the plague epizootic and distance to nearest colony on levels of genetic variability in six prairie dog colonies sampled between June 1999 and July 2001 using 24 variable randomly amplified polymorphic DNA (RAPD) markers. Number of effective alleles per locus (n(e)) and gene diversity (h) were significantly decreased in the three colonies affected by plague that were recovering from the resulting bottlenecks compared with the three colonies that did not experience plague. Genetic variability was not significantly affected by geographic distance between colonies. The majority of variance in gene fieqnencies was found within prairie clog colonies. Conservation of genetic variability in black-tailed prairie dogs will require the preservation of both large and small colony complexes and the gene flow amonog them.     

Heterogeneous activity causes a nonlinear increase in the group energy use of ant workers isolated from queen and brood

Increasing evidence has shown that the energy use of ant colonies increases sublinearly with colony size so that large colonies consume less per capita energy than small colonies. It has been postulated that social environment (e.g., in the presence of queen and brood) is critical for the sublinear group energetics, and a few studies of ant workers isolated from queens and brood observed linear relationships between group energetics and size. In this paper, we hypothesize that the sublinear energetics arise from the heterogeneity of activity in ant groups, that is, large groups have relatively more inactive members than small groups. We further hypothesize that the energy use of ant worker groups that are allowed to move freely increases more slowly than the group size even if they are isolated from queen and brood. Previous studies only provided indirect evidence for these hypotheses due to technical difficulties. In this study, we applied the automated behavioral monitoring and respirometry simultaneously on isolated worker groups for long time periods, and analyzed the image with the state‐of‐the‐art algorithms. Our results show that when activity was not confined, large groups had lower per capita energy use, a lower percentage of active members, and lower average walking speed than small groups; while locomotion was confined, however, the per capita energy use was a constant regardless of the group size. The quantitative analysis shows a direct link between variation in group energy use and the activity level of ant workers when isolated from queen and brood.     

Migration between nests in the Australian arid-zone ant Rhytidoponera sp. 12 revealed by DGGE analyses of mitochondrial DNA

Denaturing gradient gel electrophoresis (DGGE) of a PCR-amplified region of the mitochondrial DNA (mtDNA) including a large part of the cytochrome b gene revealed four haplotypes among worker ants from 75 colonies of the queenless ant Rhytidoponera sp. 12. The DGGE results were checked by sequencing examples of the haplotypes; all changes were transitions and two haplotypes differed by only a single substitution. Previous work (e.g. Crozier et al. 1984) showed that intranest relatedness is low for nuclear genes yet neighbouring nests are related; gene flow via winged males appeared the best explanation for this phenomenon. Two mtDNA haplotypes were found in 34.7% of the colonies studied, showing that female movement also occurs between nests. Migration of mated individuals on such a large scale when the number of reproductives is relatively small is unexpected (Crozier & Pamilo 1996). An observed tendency to clumping of the haplotypes is in accordance with the wingless nature of the female dispersers.     

Wingless and intermorphic males in the ant <Emphasis Type="Italic">Cardiocondyla venustula</Emphasis>

The ant genus Cardiocondyla is characterized by a pronounced male diphenism with wingless fighter males and winged disperser males. Winged males have been lost convergently in at least two species-rich clades. Here, we describe the morphological variability of males of Cardiocondyla venustula from uThukela valley, South Africa. Winged males appear to be absent from this species. However, in addition to wingless (“ergatoid”) males with widely fused thoracic sutures and without ocelli, “intermorphic” males exist that combine the typical morphology of wingless males with characteristics of winged males, e.g., more pronounced thoracic sutures, rudimentary ocelli, and vestigial wings. Similar “intermorphic” males have previously been described from one of several genetically distinct lineages of the Southeast Asian “Cardiocondyla kagutsuchi” complex (Insect. Soc. 52: 274-281, 2005). To determine whether male morphology is associated with distinct clades also in C. venustula, we sequenced a 631 bp fragment of mitochondrial DNA of workers from 13 colonies. We found six haplotypes with a sequence variation of up to 5.7 %. Intermorphic and wingless males did not appear to be associated with a particular of these lineages and within colonies showed the same sequence. Interestingly, two colonies contained workers with different haplotypes, suggesting the occasional migration of queens and/or workers between colonies.