Female Fertility and Mating Type Distribution in a South African Population of Fusarium subglutinans f. sp. pini

Fusarium subglutinans f. sp. pini is the causal agent of pitch canker disease of pines. The initial occurrence of F. subglutinans f. sp. pini in South Africa was limited to a single nursery, and isolates from this population are capable of reproducing sexually. We determined the effective population number, N_e, of this population by using mating type and male/hermaphrodite polymorphisms as indicators. The effective population number for mating type, N_e(mt), is 99% of the count (total population), and that for male/hermaphrodite status, N_e(f), is 42 to 46% of the count (total population). The number of strains that can function as the female parent limits the effective population number of this population. If this population is stable, then, depending upon assumptions about mutation and selection, sexual reproduction need occur only once per 26 to 153 asexual generations to maintain this level of sexual fertility.     

Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis

The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla—with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed.     

Effect of Drosophila melanogaster Female Size on Male Mating Success

In this study, we examined the influence of female size on mating success in Drosophila melanogaster. The results that were obtained from experiments performed in mating chambers allowed us to confirm the results of previous studies, demonstrating higher mating success of larger D. melanogaster males, and to conclude that female size also affects mating success, either when considering a single male or two competing males. We observed that the advantage for larger males depends on their size relative to that of the female, demonstrating a previously unknown role for female size in mating behavior studies. This effect of female size on mating success depends on various factors: males take longer to initiate courtship toward larger females, large females receive more wing vibrations from males prior to mating, and large females tend to keep moving for longer periods during male courtship. The importance of this finding is discussed in the context of recent reports on sexual conflict in D. melanogaster, in which males were observed to depress fitness in females as a result of intercourse.     

Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (N_b), and (2) mixed-age samples reflect the effective size per generation (N_e). We calculated true N_e and N_b, using the model species’ vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by N_b and N_e and confirm this with simulated results: N^b was a linear (r² = 0.98) function of the harmonic mean of N_e and N_b. We provide a quantitative bias correction for raw N^b based on the ratio N_b/N_e, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true N_b for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both N_e (which influences long-term evolutionary processes) and N_b (which is more important for understanding eco-evolutionary dynamics and mating systems).     

Alu Evolution in Human Populations: Using the Coalescent to Estimate Effective Population Size

There are estimated to be ~1000 members of the Ya5 Alu subfamily of retroposons in humans. This subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLa-derived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of ~18,000 during the last one to two million years.     

Independent Mating Preferences for Male Body Size and Coloration in Female Trinidadian Guppies

Although females in numerous species generally prefer males with larger, brighter and more elaborate sexual traits, there is nonetheless considerable intra‐ and interpopulation variation in mating preferences amongst females that requires explanation. Such variation exists in the Trinidadian guppy, Poecilia reticulata, an important model organism for the study of sexual selection and mate choice. While female guppies tend to prefer more ornamented males as mates, particularly those with greater amounts of orange coloration, there remains variation both in male traits and female mating preferences within and between populations. Male body size is another trait that is sexually selected through female mate choice in some species, but has not been examined as extensively as body coloration in the guppy despite known intra‐ and interpopulation variation in this trait among adult males and its importance for survivorship in this species. In this study, we used a dichotomous‐choice test to quantify the mating preferences of female guppies, originating from a low‐predation population in Trinidad, for two male traits, body length and area of the body covered with orange and black pigmentation, independently of each other. We expected strong female mating preferences for both male body length and coloration in this population, given relaxation from predation and presumably relatively low cost of choice. Females indeed exhibited a strong preference for larger males as expected, but surprisingly a weaker (but nonetheless significant) preference for orange and black coloration. Interestingly, larger females demonstrated stronger preferences for larger males than did smaller females, which could potentially lead to size‐assortative mating in nature.     

Size Effects on Mating and Egg Production in the Miami Blue Butterfly

Body size is often related to reproductive success in insects, but the direction and strength of this relationship differs greatly among systems. We studied the effects of adult size on probability of mating and egg production in the Miami blue butterfly. We found that likelihood of mating was invariant with respect to size. Larger females lived longer, and both size and lifespan positively influenced egg production. However, neither the number of copulations nor the size of male mates had any effect on female fecundity. We discuss these results in the context of butterfly mating systems, larval growth strategies and the possible effects of captive conditions on reproductive behavior.     

Exact Inbreeding Coefficient and Effective Size of Finite Populations under Partial Sib Mating

An exact recurrence equation for inbreeding coefficient is derived for a partially sib-mated population of N individuals mated in N/2 pairs. From the equation, a formula for effective size (N(e)) taking second order terms of 1/Ninto consideration is derived. When the family sizes are Poisson or equally distributed, the formula reduces to N(e) = [(4 - 3β)N/(4 - 2β)] + 1 or N(e) = [(4 - 3β)N/(2 - 2β)] - 8/(4 - 3β), approximately. For the special case of sib-mating exclusion and Poisson distribution of family size, the formula simplifies to N(e) = N + 1, which differs from the previous results derived by many authors by a value of one. Stochastic simulations are run to check our results where disagreements with others are involved.     

Filamentous Fungi and Bacteria in Macaroni and Spaghetti Products

Filamentous fungi, especially Aspergillus flavus-oryzae, and bacteria were present in all samples of macaroni and spaghetti products tested. No aflatoxin was detected in the three samples, all relatively high in A. flavus-oryzae, that were tested for it. Five of the nine isolates of A. flavus-oryzae from macaroni and sphaghetti grown in corn, incorporated into an otherwise balanced ration, and given to ducklings resulted in death of one to five ducklings within six days.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

The Effect of Nonindependent Mate Pairing on the Effective Population Size

The effective population size (N_e) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for N_e typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, including humans. To explore the effects on N_e of nonindependent mate pairing across breeding events, we simulated the genetic drift of mitochondrial DNA, autosomal DNA, and sex chromosome DNA under three mating systems. Nonindependent mate pairing across breeding seasons has no effect when all adults mate pair for life, a small or moderate effect when females reuse stored sperm, and a large effect when there is intense male–male competition for reproduction in a harem social system. If adult females reproduce at a constant rate irrespective of the type of mate pairing, the general effect of nonindependent mate pairing is to decrease N_e for paternally inherited components of the genome. These findings have significant implications for the relative N_e values of different genomic regions, and hence for the expected levels of DNA sequence diversity in these regions.THE effective population size (N_e) is a fundamental parameter of population genetics, which quantifies the effect of genetic drift, the stochastic change in allele frequencies over time in a population of finite size (Wright 1931). The magnitude of N_e affects both the level of genetic variability within a population and the efficiency with which populations retain mildly beneficial mutations and purge mildly deleterious ones. This influences a myriad of genetic phenomena, such as the level of DNA sequence polymorphism, the rate of substitution of nonsynonymous and functional noncoding nucleotide positions, the abundance of transposable elements, levels of variation, and the rate of evolution of gene expression, the persistence of duplicate genes, and genome size and organization (Lynch 2007; Charlesworth 2009). There are a variety of definitions of N_e; here we use the definition in terms of the mean coalescence time of a pair of neutral alleles, which is given by 2N_e (Charlesworth 2009). This definition has the useful feature that the expected pairwise nucleotide site diversity under the widely used infinite sites model is equal to 4N_eμ, where μ is the neutral mutation rate (Kimura 1971).As a result of differences in their ploidy level and mode of inheritance, autosomal DNA (aDNA), the X chromosome (xDNA), the Y chromosome (yDNA), and maternally transmitted organelle DNA such as mitochondrial DNA (mtDNA) generally have a different N_e values. Under certain conditions, such as constant population size, discrete generations, a Poisson distribution of reproductive success, and a sex ratio equal to one, the relative N_e values of these genomic regions (N_e-a, N_e-x, N_e-mt, and N_e-y) are expected to be 4:3:1:1 (Charlesworth 2009). This is because aDNA is biparentally inherited and diploid; xDNA is biparentally inherited, diploid in females, and haploid in males (with female heterogamety, the reverse applies to the Z chromosome), and yDNA (the W chromosome, with female heterogamety) and mtDNA are both effectively uniparentally inherited and haploid in most species.However, several characteristics of natural populations, such as unequal numbers of males and females and nonrandom variation in reproductive success, can affect the value of N_e, even for populations with discrete generations (reviewed in Caballero 1994; Hedrick 2007; Charlesworth 2009). In addition, natural selection at sites linked to neutral markers also has the potential to increase N_e (under balancing selection) (Charlesworth 2006) or to decrease N_e (with background selection or selective sweeps) (Hudson and Kaplan 1988; Charlesworth et al. 1993). Because the nature of natural selection varies in different genomic regions, especially in relation to the rate of recombination, N_e may also vary among unlinked regions with the same ploidy and mode of inheritance, for example, different portions of an autosomal chromosome (Gossmann et al. 2011). In natural populations, these factors can skew the relative N_e values away from the 4:3:1:1 expectation. Even when the effects of natural selection and “nonideal” demography are ignored, the 4:3:1:1 relation still has a large variance when applied to individual loci (Hudson and Turelli 2003).When generations overlap, an additional source of possible deviations from these idealized relations arises from variation among individuals in survival and reproductive success among breeding seasons (Felsenstein 1971; Hill 1972, 1979; Johnson 1977) and from sex differences in demographic parameters and stochastic changes in population size (Engen et al. 2007). In contrast, the effect of a high variance in reproductive success caused by male–male competition is lessened when generations overlap for many breeding seasons (Nunney 1993; Charlesworth 2001). Conversely, overlapping generations with nonindependent mate pairing across breeding seasons could increase the variance in reproductive success. For example, in humans, paternity is correlated with paternal confidence in paternity (Anderson 2006), and married individuals tend to repeatedly produce offspring with each other more frequently than expected by chance. Nonindependent mate pairing among breeding seasons occurs in many other species as well—for example, long-term pair bonding in prairie voles (DeVries et al. 1995), harems in gorillas (Gatti et al. 2004), and sperm storage in fruit flies (Neubaum and Wolfner 1999).Current theoretical models that allow calculation of the effective population size with overlapping generations and age structure make several simplifying assumptions, notably constant sizes of each age class, sufficiently large numbers of individuals in each age class that second-order terms in their reciprocals can be neglected, and independent sampling of offspring genotypes from the same individual reproducing at different times (Hill 1972; Nunney 1991, 1993; Caballero 1994; Charlesworth 1994, 2001). The latter assumption in particular makes it difficult to provide accurate expressions for species such as humans and Drosophila, which reproduce nonindependently because of long-term pair bonds and sperm storage, respectively (Charlesworth 2001).The goal of this study is therefore to explore the consequences of nonindependence of reproductive events across time in different social systems and with different age structures, using simulations of genetic drift in two types of age-structured populations, under different scenarios of independent and nonindependent mate pairing among breeding events. We have explored how these scenarios affect the relative values of N_e-a, N_e-x, N_e-mt, and N_e-y using the infinite alleles model of mutation (Kimura and Crow 1964), with particular emphasis on comparisons of similar mating systems that differ in the extent of nonindependence among breeding events.     

Autophagy During Conidiation and Conidial Germination in Filamentous Fungi

Filamentous fungi form aerial hyphae on solid medium, and some of these differentiate into conidiophores for asexual sporulation (conidiation). In the filamentous deuteromycete, Aspergillus oryzae, aerial hyphae are formed from the foot cells and some differentiate into conidiophores, which are composed of vesicles, phialides and conidia. Recently, we isolated the yeast ATG8 gene homologue Aoatg8 from A. oryzae, and visualized autophagy by the expression of an EGFP (enhanced green fluorescent protein)–AoAtg8 fusion protein and DsRed2 protein in this fungus. Furthermore, by constructing the Aoatg8 deletion and conditional mutants, we demonstrated that autophagy functions during the process of differentiation of aerial hyphae, conidiation and conidial germination in A. oryzae. Here, we discuss the contribution of autophagy towards the differentiation and germination processes in filamentous fungi.

Addendum to:

Functional Analysis of the ATG8 Homologue Aoatg8 and Role of Autophagy in Differentiation and Germination in Aspergillus oryzae

T. Kikuma, M. Ohneda, M. Arioka and K. Kitamoto

Eukaryot Cell 2006; 5:1328-36     

Effects of Male age and Size on Mating Success in the Bumblebee Bombus terrestris

In social insects, the reproductive strategies adopted by colonies emerge as a complex property of individual behaviours, but as yet we are often unable to fully explain them in evolutionary terms. In bumblebees, colonies adopt either a short-lived strategy specializing in male production, or a longer-lived strategy in which mainly new queens are produced, but this results in males emerging long before mates are available; this strategy can only easily be explained if older males are at a significant reproductive advantage. Here we examine how age and morphological characters influence mating success of male bumblebees. In two separate experiments in which single virgin males and females were confined together, we found that young males and heavy males mated more swiftly and copulated for less time compared to old males or lighter males, respectively. However, in competitive situations age proved to be unimportant and the only factors to influence mating success were the lengths of the fore and hind tibiae, with strong directional selection for long leg length. Fore and hind legs are both used in courtship, so both traits are associated with plausible mechanisms under selection. It has previously been argued that, in times of food stress, bumblebee colonies should produce males as male size is less likely to be strongly correlated with fitness than female size. Our results suggest that this may not be so, since aspects of male size directly impact on their mating success. Our results leave unexplained the emergence of males many days before new queens.     

Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans

Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200–2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.     

交配和温度对小地老虎雌蛾性信息素产生的影响

研究了交配和温度对小地老虎雌蛾性信息素产生的影响,结果表明,交配对性信息素各组分的滴度无显著影响,因此不影响小地老虎在下一暗期的再次求偶和交配.但环境温度对小地老虎性信息素的含量则有显著的影响,20～25℃最有利于小地老虎性信息素的生物合成,而低温和高温则均不利于小地老虎性信息素的正常产生与释放.     

Condition-Dependent Effects of Mating on Longevity and Fecundity of Female Medflies: The Interplay between Nutrition and Age of Mating

Background

In various species mating exerts direct and indirect effects on female demographic traits ranging from life span shortening to behavioural shifts. A wealth of data regarding effects of nutrition on longevity and reproduction output also exists. Nonetheless, little is known regarding the interaction between the age of mating and nutrition on female fitness.

Methodology

We studied, the effects of protein deprivation and age of mating on female fitness traits, using a wild population of the Mediterranean fruit fly (medfly). We tested the hypotheses that (a) protein availability increases female lifespan and fecundity, (b) female longevity and egg production are independent of mating and the age of mating, and (c) female mating behaviour is independent of their age and nutritional status. Thus, we recorded the mating success and the copulation characteristics, as well as the egg production and survival of females mated at young or at old age and fed a full or a protein-deprived diet.

Results

Mating boosts egg production and reduces longevity of protein-fed females. On the contrary, mating increases the longevity of protein-deprived females. Mortality responses (negative or positive) to mating are expressed after a long lag phase. Old females are more receptive and less selective than young females regardless of the food regime.

Conclusions

Our findings suggest that condition (nutritional status and age) defines the positive or negative output of mating in female medflies. These results contribute towards understanding the effects of mating, aging, resource allocation and their interactions on survival and female reproduction.     

Diploids in the Cryptococcus neoformans Serotype A Population Homozygous for the α Mating Type Originate via Unisexual Mating

The ubiquitous environmental human pathogen Cryptococcus neoformans is traditionally considered a haploid fungus with a bipolar mating system. In nature, the α mating type is overwhelmingly predominant over a. How genetic diversity is generated and maintained by this heterothallic fungus in a largely unisexual α population is unclear. Recently it was discovered that C. neoformans can undergo same-sex mating under laboratory conditions generating both diploid intermediates and haploid recombinant progeny. Same-sex mating (α-α) also occurs in nature as evidenced by the existence of natural diploid αADα hybrids that arose by fusion between two α cells of different serotypes (A and D). How significantly this novel sexual style contributes to genetic diversity of the Cryptococcus population was unknown. In this study, ∼500 natural C. neoformans isolates were tested for ploidy and close to 8% were found to be diploid by fluorescence flow cytometry analysis. The majority of these diploids were serotype A isolates with two copies of the α MAT locus allele. Among those, several are intra-varietal allodiploid hybrids produced by fusion of two genetically distinct α cells through same-sex mating. The majority, however, are autodiploids that harbor two seemingly identical copies of the genome and arose via either endoreplication or clonal mating. The diploids identified were isolated from different geographic locations and varied genotypically and phenotypically, indicating independent non-clonal origins. The present study demonstrates that unisexual mating produces diploid isolates of C. neoformans in nature, giving rise to populations of hybrids and mixed ploidy. Our findings underscore the importance of same-sex mating in shaping the current population structure of this important human pathogenic fungus, with implications for mechanisms of selfing and inbreeding in other microbial pathogens.     

土壤肥力对绞股蓝种群行为的影响

利用半控制实验生态学方法探讨土壤肥力对绞股蓝种群行为的影响。结果表明：土壤肥力的提高可显著提高繁殖器官生物量分配比,显著降低非繁殖器官生物量分配比,叶片、支持结构生物量分配随土壤肥力的提高略有降低;提高土壤肥力对绞股蓝种群形态特征和平均相对生长速率的影响不明显;多数繁殖特征对土壤肥力的提高有显著响应。总之,绞股蓝种群的不同行为对土壤肥力变化的敏感性各异。