Explicit formulae are given for the effects of a barrier to gene flow on random fluctuations in allele frequency; these formulae can also be seen as generating functions for the distribution of coalescence times. The formulae are derived using a continuous diffusion approximation, which is accurate over all but very small spatial scales. The continuous approximation is confirmed by comparison with the exact solution to the stepping stone model. In both one and two spatial dimensions, the variance of fluctuations in allele frequencies increases near the barrier; when the barrier is very strong, the variance doubles. However, the effect on fluctuations close to the barrier is much greater when the population is spread over two spatial dimensions than when it occupies a linear, one-dimensional habitat: barriers of strength comparable with the dispersal range (B≈σ) can have an appreciable effect in two dimensions, whereas only barriers with strength comparable with the characteristic scale () are significant in one dimension (μ is the rate of mutation or long-range dispersal). Thus, in a two-dimensional population, barriers to gene flow can be detected through their effect on the spatial pattern of genetic marker alleles.

The most prominent feature of Y chromosomes is that they do not recombine and are usually genetically degenerate, containing only a few genes. White campion Silene latifolia has evolved sex chromosomes relatively recently, probably within the last 10–15 million years. Perhaps due to its recent origin, the Y chromosome in this species has not completely degenerated and most isolated X-linked genes have intact Y-linked homologues. A gene encoding a protein with strong homology to spermidine synthases, Slss, is the exception to this rule, as the Y-linked copy of this gene has apparently lost its function. Here I report evidence for a recent selective sweep in the X-linked copy of this gene (SlssX) that could reflect compensatory evolution in an X-linked gene that has lost a functional Y-linked homologue. The spread and fixation of an advantageous mutation in SlssX has resulted in a dramatic loss of genetic diversity and an excess of high-frequency derived polymorphisms in this gene. As the sweep has not affected the closely linked DD44X gene, the selective advantage of the mutation that has driven the sweep in the SlssX gene might have been less than 1%.

Non-random mating in plant populations can be influenced by numerous reproductive and demographic factors, including floral morphology and inter-plant distance. Here, we investigate patterns of outcrossed mating through male function in Narcissus triandrus, a tristylous, bee-pollinated wild daffodil from the Iberian Peninsula, to test pollen transfer models which predict that floral morphology promotes asymmetrical mating and biased morph ratios. Unlike other tristylous species, N. triandrus has an incompatibility system that permits intra-morph mating and long-level rather than mid-level stamens in the L-morph. Incomplete sex-organ reciprocity should result in significant intra-morph mating in the L-morph. We measured mating patterns in two L-biased populations – dimorphic (two style morphs) and trimorphic (three style morphs) – using multilocus genotyping and maximum-likelihood-based paternity analysis. We also examined the spatial distribution of style morphs and neutral markers to investigate the potential consequence of spatially restricted mating on morph ratios. As predicted, we detected significant amounts of intra-morph mating in the L-morph in both populations. Pollen transfer coefficients generally supported predictions based on the Darwinian hypothesis that anthers and stigmas of equivalent level promote pollinator-mediated cross-pollination in heterostylous populations. There was evidence of significant spatial aggregation of both style morphs and neutral markers in populations of N. triandrus, probably as a result of restricted pollen and seed dispersal. Our results provide empirical support for theoretical models of pollen transfer, which indicate that the commonly observed L-biased morph ratios in Narcissus species result from significant intra-morph mating in the L-morph because of its atypical floral morphology.

The genetic consequences of inbreeding is a subject that has received thorough theoretical attention and has been of interest to empirical biologists since the time of Darwin. Particularly for species with genetically controlled mechanisms to promote outcrossing (self-incompatibility or SI systems), it is expected that high levels of genetic load should accumulate through sheltering of deleterious recessive mutations. Nevertheless, transitions to selfing are common across angiosperms, which suggests that the potentially negative consequences of reduced heterozygosity and genetic diversity are balanced by other factors, such as reproductive assurance. This mini-review focuses on empirical research in the Brassicaceae to emphasize some of the genetic consequences of shifts to inbreeding in terms of mechanisms for loss of SI, changes in genetic diversity following loss of SI, and inbreeding depression in relation to outcrossing history. Despite the long history of theoretical attention, there are still some surprisingly large gaps in our understanding in each of these areas. Rather than providing a complete overview, examples are drawn predominantly from published and emerging data from Arabidopsis thaliana and its relatives to highlight recent progress and remaining questions. We are currently on the brink of major breakthroughs in understanding due both to advances in sequencing technology and a shift in focus from crop plants to natural populations, where critical factors such as population structure, phylogeography, demographic history, partial compatibility and individual variation can be taken into account when investigating the nature of the selective forces regulating mating system evolution.

One of the long-standing mysteries in genomic evolution is the observation that much of the genome is composed of repetitive DNA, resulting in inter- and intraspecific variation in nuclear DNA content. Our discovery of a negative correlation between nuclear DNA content and flower size in Silene latifolia has been supported by our subsequent investigation of changes in DNA content as a correlated response to selection on flower size. Moreover, we have observed a similar trend across a range of related dioecious species in Silene sect. Elisanthe. Given the presence of sex chromosomes in dioecious Silene species, and the tendency of sex chromosomes to accumulate repetitive DNA, it seems plausible that dioecious species undergo genomic evolution in ways that differ from what one might expect in hermaphroditic species. Specifically, we query whether the observed relationship between nuclear DNA content and flower size observed in dioecious Silene is a peculiarity of sex chromosome evolution. In the present study we investigated nuclear DNA content and flower size variation in hermaphroditic species of Silene sect. Siphonomorpha, as close relatives of the dioecious species studied previously. Although the nuclear DNA contents of these species were lower than those for species in sect. Elisanthe, there was still significant intra- as well as interspecific variation in nuclear DNA content. Flower size variation was found among species of sect. Siphonomorpha for petal claw and petal limb lengths, but not for calyx diameter. This last trait varies extensively in sect. Elisanthe, in part due to sex-specific selection. A negative correlation with nuclear DNA content was found across populations for petal limb length, but not for other floral dimensions. We conclude that impacts of nuclear DNA content on phenotypic evolution do manifest themselves in hermaphroditic species, so that the effects observed in sect. Elisanthe, and particularly in S. latifolia, while perhaps amplified by the genomic impacts of sex chromosomes, are not limited to dioecious taxa.

Inbreeding species of hermaphroditic animals practising copulation have been characterized by few copulations, no waiting time (the time that an isolated individual waits for a partner before initiating reproduction compared with paired individuals) and limited inbreeding (self-fertilization) depression. This syndrome, which has never been fully studied before in any species, is analysed here in the highly selfing freshwater snail Biomphalaria pfeifferi. We conducted an experiment under laboratory conditions over two generations (G1 and G2) using snails sampled from two populations (100 individuals per population). G1 individuals were either isolated or paired once a week (potentially allowing for crosses), and monitored during 29 weeks for growth, fecundity and survival. Very few copulations were observed in paired snails, and there was a positive correlation in copulatory activity (e.g. number of copulations) between the male and female sexual roles. The waiting time was either null or negative, meaning that isolated individuals initiated reproduction before paired ones. G2 offspring did not differ in hatching rate and survival (to 28 days) between treatments, but offspring from paired individuals grew faster than those from isolated individuals. On the whole, the self-fertilization depression was extremely low in both populations. Another important result is that paired G1 individuals began laying (selfed) eggs several weeks prior to initiating copulation: this is the first characterization of prior selfing (selfing initiated prior to any outcrossing) in a hermaphroditic animal. A significant population effect was observed on most traits studied. Our results are discussed with regard to the maintenance of low outcrossing rates in highly inbreeding species.

Hitch-hiking to a site under balancing selection is expected to produce a local increase in nucleotide polymorphism and a decrease in population differentiation compared with the background genomic level, but empirical evidence supporting these predictions is scarce. We surveyed molecular diversity at four genes flanking the region controlling self-incompatibility (the S-locus) in samples from six populations of the herbaceous plant Arabidopsis halleri, and compared their polymorphism with sequences from five control genes unlinked to the S-locus. As a preliminary verification, the S-locus flanking genes were shown to co-segregate with SRK, the gene involved in the self-incompatibility reaction at the pistil level. In agreement with theory, our results demonstrated a significant peak of nucleotide diversity around the S-locus as well as a significant decrease in population genetic structure in the S-locus region compared with both control genes and a set of seven unlinked microsatellite markers. This is consistent with the theoretical expectation that balancing selection is increasing the effective migration rate in subdivided populations. Although only four S-locus flanking genes were investigated, our results suggest that these two signatures of the hitch-hiking effect are localized in a very narrow genomic region.

Androdioecy, where males co-occur with hermaphrodites, is a rare sexual system in plants and animals. It has a scattered phylogenetic distribution, but it is common and has persisted for long periods of evolutionary time in branchiopod crustaceans. An earlier model of the maintenance of males with hermaphrodites in this group, by Otto et al. (1993), considered the importance of male–hermaphrodite encounter rates, sperm limitation, male versus hermaphrodite viability and inbreeding depression suffered by selfed progeny. Here I advance this model in two ways: (1) by exploring the conditions that would allow the invasion of hermaphrodites into a dioecious population and that of females into an androdioecious population; and (2) by incorporating a term that accounts for the potential effects of genetic load linked to a dominant hermaphrodite-determining allele in androdioecious populations. The new model makes plausible sense of observations made in populations of the species Eulimnadia texana, one of a number of related species whose common ancestor evolved hermaphroditism (and androdioecy) from dioecy. In particular, it offers an explanation for the long evolutionary persistence of androdioecy in branchiopods and suggests reasons for why dioecy has not re-evolved in the clade. Finally, it provides a rather unusual illustration of the implications of the degeneration of loci linked to a sex-determining locus.

Cytoplasmic genomes typically lack recombination, implying that genetic hitch-hiking could be a predominant force structuring nucleotide polymorphism in the chloroplast and mitochondria. We test this hypothesis by analysing nucleotide polymorphism data at 28 loci across the chloroplast and mitochondria of the outcrossing plant Arabidopsis lyrata, and compare patterns with multiple nuclear loci, and the highly selfing Arabidopsis thaliana. The maximum likelihood estimate of the ratio of effective population size at cytoplasmic relative to nuclear genes in A. lyrata does not depart from the neutral expectation of 0·5. Similarly, the ratio of effective size in A. thaliana is close to unity, the neutral expectation for a highly selfing species. The results are thus consistent with neutral organelle polymorphism in these species or with comparable effects of hitch-hiking in both cytoplasmic and nuclear genes, in contrast to the results of recent studies on gynodioecious taxa. The four-gamete test and composite likelihood estimation provide evidence for very low levels of recombination in the organelles of A. lyrata, although permutation tests do not suggest that adjacent polymorphic sites are more closely linked than more distant sites across the two genomes, suggesting that mutation hotspots or very low rates of gene conversion could explain the data.

Mating systems and recombination are thought to have a deep impact on the organization and evolution of genomes. Because of the decline in effective population size and the interference between linked loci, the efficacy of selection is expected to be reduced in regions with low recombination rates and in the whole genome of self-fertilizing species. At the molecular level, relaxed selection is expected to result in changes in the rate of protein evolution and the pattern of codon bias. It is increasingly recognized that recombination also affects non-selective processes such as the biased gene conversion towards GC alleles (bGC). Like selection, this kind of meiotic drive in favour of GC over AT alleles is expected to be reduced in weakly recombining regions and genomes. Here, we investigated the effect of mating system and recombination on molecular evolution in four Triticeae species: two outcrossers (Secale cereale and Aegilops speltoides) and two selfers (Triticum urartu and Triticum monococcum). We found that GC content, possibly driven by bGC, is affected by mating system and recombination as theoretically predicted. Selection efficacy, however, is only weakly affected by mating system and recombination. We investigated the possible reasons for this discrepancy. A surprising one is that, in outcrossing lineages, selection efficacy could be reduced because of high substitution rates in favour of GC alleles. Outcrossers, but not selfers, would thus suffer from a ‘GC-induced’ genetic load. This result sheds new light on the evolution of mating systems.

In gametophytic self-incompatibility systems, many specificities (different ‘lock-and-key’ combinations) are maintained by frequency-dependent selection for very long evolutionary times. In Solanaceae, trans-specific evolution (the observation that an allele from one species may be more closely related to an allele from another species than to others from the same species) has been taken as an argument for the very old age of specificities. In this work, by determining, for the first time, the age of extant Prunus species, we show that this reasoning cannot be applied to Prunoideae. Furthermore, since our sample size is large (all S-RNase encoding the female component and SFB encoding the male component GenBank sequences), we were able to estimate the age of the oldest Prunus specificities. By doing so, we show that the lower variability levels at the Prunus S-locus, in comparison with Solanaceae, is due to the younger age of Prunus alleles, and not to a difference in silent mutation rates. We show that the ancestor to extant Prunus species harboured at least 102 specificities, in contrast to the maximum of 33 observed in extant Prunus species. Since the number of specificities that can be maintained in a population depends on the effective population size, this observation suggests a bottleneck in Prunus evolutionary history. Loss of specificities may have occurred during this event. Using only information on amino acid sites that determine specificity differences, and a simulation approach, we show that a model that assumes closely related specificities are not preferentially lost during evolution, fails to predict the observed degree of specificity relatedness.

The occurrence of gynodioecy among angiosperms appears to be associated with self-compatibility. We use individual-based simulations to investigate the conditions for breakdown of a gametophytic self-incompatibility system in gynodioecious populations and make a comparison with hermaphroditic populations where the conditions are well known. We study three types of mutations causing self-compatibility. We track the fate of these mutations in both gynodioecious and hermaphroditic populations, where we vary the number of S-alleles, inbreeding depression and selfing rate. We find that the conditions for breakdown are less stringent if the population is gynodioecious and that the breakdown of self-incompatibility tends to promote stability of gynodioecious populations since it results in a higher frequency of females. We also find that fecundity selection has a large effect on the probability of breakdown of self-incompatibility, in particular if caused by a mutation destroying the female function of the S-locus.

The problem of jointly estimating the intensity of past selection affecting an allele and the allele's age is formulated in a Bayesian framework. The prior distribution of allele age given its frequency is obtained from existing population genetics theory. The prior distribution of selection intensity is assumed to reflect the fact that positive selection on a new mutant is more likely to be weak than strong. The general approach is illustrated by the development of an importance sampling method applicable to low-frequency alleles. This method can be used either when the haplotypes of closely linked marker loci are known or when the lengths of linked ancestral chromosomal segments can be inferred. The method is illustrated with an application to the A− allele of G6PD in Africa. Because changes in allele frequency and recombination are both intrinsically stochastic, there are limits to the accuracy achievable with any method.

This paper analyses the effect of caponisation at 8 weeks on growth and on carcass and meat characteristics of Castellana Negra chickens slaughtered at 29 weeks. Caponisation did not result in weight improvements as compared with uncastrated birds. No changes were observed in the growth rate or in the parameters determining the point of inflection in the growth curve (sexual maturity). Regarding carcass characteristics, castration resulted in a wider breast angle and heavier pectoral muscles in caponised birds than in uncastrated birds, but with no differences in thigh and drumstick weight and length. Capon meat showed a higher fat content than that of cocks, making it juicier and less fibrous. No differences were found in fatty acid content (C 14:0, C 18:0, C 18:1 and C 18:2). Nor were there any differences in colour measurements, pH or water loss from the meat. While cocks’ thighs + drumsticks were found to be tougher than their breasts, there were no such differences in capons because after castration, thigh + drumstick meat became more tender.

The objective of the current study was to compare tick loads, growth and carcass characteristics of dipped and non-dipped Nguni, Bonsmara and Angus steers raised on natural pasture. One hundred 7-month-old castrated weaners were kept at the University of Fort Hare Farm for 12 months. There were 30 weaners each of Angus and Bonsmara, and 40 weaners of the Nguni breed. Half the Bonsmara, Angus and 14 Nguni weaners were dipped every fortnight. The rest were not dipped. Monthly weights and tick counts under the tail, on scrotum, belly, sternum and ears of the steers were recorded. The dipped Nguni steers had lowest (P < 0.05) tick counts, and the non-dipped Angus steers had the highest (P < 0.05) tick counts. There were more ticks (P < 0.05) during the warm wet season than during the cool dry season. Ears had the highest (P < 0.05) tick infestation. Average daily gain (ADG) was similar (P > 0.05) among the three breeds. The non-dipped Bonsmara steers had the heaviest (P < 0.05) carcasses (142 ± 5.4) while the non-dipped Nguni steers had the lightest (P < 0.05) carcasses (111 ± 4.5 kg). The non-dipped Bonsmara had the highest (P < 0.05) eye muscle area (3996 ± 120.8 mm2) while the non-dipped Angus had the smallest (P < 0.05) eye muscle area (3291 ± 210.6 mm2). The non-dipped Bonsmara also had the highest (P < 0.05) dressing percentage (53.8 ± 1.01) while the non-dipped Nguni had the lowest (P < 0.05) dressing percentage (50.3 ± 0.84). The current study has shown that while the non-dipped steers had higher (P < 0.05) tick loads than the dipped steers, their growth and carcass characteristics were similar (P > 0.05). The study has also shown that, despite being a small-framed breed, the Nguni steers had similar (P > 0.05) ADG to the large-framed Bonsmara and Angus steers. Therefore, the Nguni cattle have the potential to produce organic beef. However, a reasonable assessment of organic beef production potential of the Nguni requires an evaluation of its meat quality traits under natural pasture.

The aim of this study was to investigate chromosomal regions affecting gestation length in sows. An experimental F2 cross between Iberian and Meishan pig breeds was used for this purpose and we genotyped 119 markers covering the 18 porcine autosomal chromosomes. Within this context, we have developed a new empirical Bayes factor (BF) approach to compare between nested models, with and without the quantitative trait loci (QTL) effect, and after including the location of the QTL as an unknown parameter in the model. This empirical BF can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null QTL effects. Linkage analyses were performed in each chromosome using an animal model to account for infinitesimal genetic effects. Initially, three QTL were detected at chromosomes 6, 8 and 11 although, after correcting for multiple testing, only the additive QTL located in cM 110 of chromosome 8 remained. For this QTL, the allelic effect of substitution of the Iberian allele increased gestation length in 0.521 days, with a highest posterior density region at 95% ranged between 0.121 and 0.972 days. Although future studies are necessary to confirm if detected QTL is relevant and segregating in commercial pig populations, a hot-spot on the genetic regulation of gestation length in pigs seems to be located in chromosome 8.

Sixty twin-bearing ewes were allocated to one of four dietary treatments investigating the effects of supplementary iodine or cobalt during late pregnancy on lamb serum immunoglobulin G (IgG), triiodothyronine (T3), thyroxine (T4) and vitamin E concentrations, and lamb IgG absorption efficiency. Ewes were offered grass silage ad libitum supplemented with 800 g per ewe per day of a 190 g/kg crude protein (CP) concentrate from day 126 of gestation until parturition plus one of the following supplements (n = 15 per treatment); no supplement (C); 26.6 mg iodine per day for final 3 weeks pre partum (I-3); 26.6 mg iodine/day for final week pre partum (I-1); 20 mg cobalt/day for final 3 weeks pre partum (Co-3). Lambs were blood sampled at 24 and 72 h post partum for serum IgG and vitamin E concentrations. Ten lambs from C and I-3 were blood sampled at 1 h post partum for serum IgG, vitamin E, T3 and T4 concentrations. There were no differences in serum IgG, vitamin E or T4 values (P > 0.05) at 1 h post partum between lambs born to the C and I-3 ewes. T3 levels were lower in I-3 compared with C progeny (P < 0.05). Supplemental iodine reduced colostral IgG absorption efficiency (P < 0.001) and lamb serum IgG concentrations at 24 and 72 h post partum (P < 0.001). Serum vitamin E concentration in I-3 and I-1 lambs was lower than in Co-3 lambs at 24 h post partum, while at 72 h post partum I-3, I-1 and Co-3 lambs had significantly lower concentrations than C lambs (P < 0.001). Supplementing the ewe’s diet with 26.6 mg/day of iodine for the final week of pregnancy reduced lamb serum IgG concentration at 24 and 72 h post partum. The lower total and free T3 values in the progeny of I-3-treated ewes suggest interference in the synthesis and metabolism of thyroid hormones when ewes receive excessive dietary iodine for 3 weeks immediately pre partum. Based on these findings, the indications are that the toxicity level for iodine in the diet of the pregnant ewe should be lowered to 20 mg per ewe per day, equivalent to 40% of its current level. The finding that high-level cobalt supplementation during the final 3 weeks of pregnancy will have a negative effect on serum vitamin E concentration at 72 h post partum is a new and significant finding and previously has not been reported in the literature.

Social learning can be of critical importance to cattle grazing rangeland environments with high variability of food resources across space and time. Experienced individuals can greatly facilitate foraging decisions (what to eat and where to eat) of naïve peers in such settings. We conducted an experiment with cattle to investigate strength and persistence of socially induced food and feeding site avoidance behaviours. Sixteen naïve yearling steers were paired with 16 social models that had either not been trained (control) or been trained with an emetic (LiCl), electrical shock or both to avoid: (a) an unsafe high-quality food (LiCl); (b) an unsafe high-quality feeding site (shock); or (c) both the unsafe high-quality food and the unsafe high-quality feeding site (LiCl + shock). Ten-minute trials were conducted in an experimental arena containing three artificial feeding sites each consisting of groups of bowls with either high- (HQ) or moderate-quality (MQ) foods (HQ = barley and oat grain; MQ = Bermuda grass hay). Unsafe high-quality (UHQ, surrounded by traffic cones) and safe moderate-quality (SMQ) feeding sites consisted of nine rubber bowls containing either HQ or MQ foods. The safe high-quality (SHQ) feeding site consisted of two groups of eight bowls containing HQ food, which surrounded the UHQ and SMQ feeding sites. Social models did not induce diet and feeding site avoidance behaviours in naïve steers; they exerted small and transient changes in the feeding behaviour of their naïve counterparts. Consequences to the individual outweighed social influences; when naïve animals experienced the same punishment contingencies as their social models, their behavioural patterns closely resembled those of their social model. Conditioned food and location aversions via LiCl were apparently influenced by prior exposure to target foods and the experimental arena. Conversely, conditioned feeding site avoidance via shock was apparently not influenced by prior exposure to target foods or the experimental arena.