How do misassigned paternities affect the estimation of heritability in the wild?

Studies of birds have recently played an important role in the increasing success of quantitative genetics applied to natural populations. However, these studies mostly base their pedigree relationships on social information, despite the known widespread genetic polygamy in avian species. Here, we study the influence of misassigned paternities, combined with the effect of pedigree size and depth, on the estimation of heritability. First, we compute simulations of a polygenic trait for two levels of heritability (0.1 and 0.4), several extra-pair paternity rates (ranging from 5% to 40%), and varying sample sizes (20, 50 and 100 broods) or pedigree depth (2 or 4 generations). We compare heritability estimates from the social and the genetic pedigree, running a restricted maximum-likelihood 'animal model'. Social pedigree underestimates heritability by an average of 0-17% for 5-20% extra-pair paternities and by up to 18% for 40% extra-pair paternities and a heritability of 0.4. Second, we identifyied extra-pair offspring using microsatellite loci in two populations of blue tits (Parus caeruleus) showing high levels of extra-pair paternities (15% and 25% of extra-pair offspring). We compare heritabilities of tarsus length and body mass estimated with pedigrees of increasing accuracy. These analyses suggest that the bias induced by misassigned paternities on heritability estimation depends on the level of heritability and the rate of paternity error. Typical rates of extra-pair paternities in birds (around 20% of offspring) should result in an underestimation of heritability of less than 15% when estimated over a minimum of 100 broods.     

Male competition and paternity in wild chimpanzees of the Taï forest

In social animals, competition among males for mates affects individual reproductive success. The priority‐of‐access model attempts to account for the influence of demographic conditions within groups upon male reproductive success, but empirical data for testing this model are scarce. Our long‐term study of chimpanzees in the Taï National Park, Côte d'Ivoire, encompasses a period of steady decrease in community size and fluctuating numbers of competing males and sexually receptive females. These demographic changes, in combination with genetic assessment of paternity for 48 offspring from three communities, allowed us to quantify the effects of varying levels of competition upon male reproductive success. On average, the highest‐ranking male sired 50% of all analyzed offspring during a 14‐year period from 1987–2000. Competition among males strongly decreased the relative reproductive success of the alpha male, such that the alpha male's rate of success decreased from 67% with few competitors to only 38% with four or more competitors. The increasing number of synchronously receptive females in large groups also reduced the proportion of paternities by the alpha male. Thus, patterns of paternity in Taï chimpanzees fit well the predictions of the priority‐of‐access model. We also found that despite the inability of dominants to monopolize reproduction, they achieved a higher reproductive rate in large multimale groups, because these have more females and a higher infant survival rate. Varied levels of male competition within communities seem to explain differences in the reproductive success of alpha males observed in different chimpanzee populations, and in other primate species. Am J Phys Anthropol, 2006. © 2005 Wiley‐Liss, Inc.     

Assessment of the importance of α-amylase inhibitor-2 in bruchid resistance of wild common bean

Both α-amylase inhibitor-2 (αAI-2) and arcelin have been implicated in resistance of wild common bean (Phaseolus vulgaris L.) to the Mexican bean weevil (Zabrotes subfasciatus Boheman). Near isogenic lines (NILs) for arcelin 1–5 were generated by backcrossing wild common bean accessions with a cultivated variety. Whereas seeds of a wild accession (G12953) containing both αAI-2 and arcelin 4 were completely resistant to Z. subfasciatus, those of the corresponding NIL were susceptible to infestation, suggesting that the principal determinant of resistance was lost during backcrossing. Three independent lines of transgenic azuki bean [Vigna angularis (Willd.) Ohwi and Ohashi] expressing αAI-2 accumulated high levels of this protein in seeds. The expression of αAI-2 in these lines conferred protection against the azuki bean weevil (Callosobruchus chinensis L.), likely through inhibition of larval digestive α-amylase. However, although the seed content of αAI-2 in these transgenic lines was similar to that in a wild accession of common bean (G12953), it did not confer a level of resistance to Z. subfasciatus similar to that of the wild accession. These results suggest that αAI-2 alone does not provide a high level of resistance to Z. subfasciatus. However, αAI-2 is an effective insecticidal protein with a spectrum of activity distinct from that of αAI-1, and it may prove beneficial in genetic engineering of insect resistance in legumes.     

Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in eucalyptus

Marker-based methods for estimating heritability and genetic correlation in the wild have attracted interest because traditional methods may be impractical or introduce bias via G x E effects, mating system variation, and sampling effects. However, they have not been widely used, especially in plants. A regression-based approach, which uses a continuous measure of genetic relatedness, promises to be particularly appropriate for use in plants with mixed-mating systems and overlapping generations. Using this method, we found significant narrow-sense heritability of foliar defense chemicals in a natural population of Eucalyptus melliodora. We also demonstrated a genetic basis for the phenotypic correlation underlying an ecological example of conditioned flavor aversion involving different biosynthetic pathways. Our results revealed that heritability estimates depend on the spatial scale of the analysis in a way that offers insight into the distribution of genetic and environmental variance. This study is the first to successfully use a marker-based method to measure quantitative genetic parameters in a tree. We suggest that this method will prove to be a useful tool in other studies and offer some recommendations for future applications of the method.     

Mapping the genomic architecture of ecological speciation in the wild: does linkage disequilibrium hold the key?

The hunt for the genes underlying ecological speciation has now closed in on a number of candidates, but making the link from genotype to phenotype continues to pose a significant challenge. This is partly because genetic studies in many systems remain impeded by long generation times or an inability to perform controlled crosses. Now, in this issue of Molecular Ecology, Malek et al. (2012) demonstrate the utility of a novel admixture mapping approach that can be used to identify genomic regions contributing to adaptive trait divergence between natural populations. Remarkably, they validate their approach by mapping traits associated with mate choice in a wild limnetic and benthic threespine stickleback (Gasterosteus aculeatus) species pair, finding several loci associated with male nuptial coloration and shape. While this study benefited from tried‐and‐true microsatellites in a well‐characterized species with a detailed genetic map (and genome sequence), the field is quickly moving towards the use of next‐generation sequencing, especially for nonmodel systems. The ability to characterize molecular polymorphisms for any system suggests that molecular ecologists working on virtually any species may benefit from applying Malek et al.'s approach, if naturally admixed populations are available.     

Changes in the activity of superoxide dismutase isoforms in the course of low-temperature adaptation in potato plants of wild type and transformed with Δ12-acyl-lipid desaturase gene

We investigated the changes in the total activity of superoxide dismutase (SOD) and the role of its isoforms in hardening potato (Solanum tuberosum L., cv. Desnitsa) plants of wild type and transformed with desA gene of Δ12-acyl-lipid desaturase from Synechocystis sp. PCC 6803. Hydroponically grown 8-week-old plants were exposed for six days to hardening temperature of 5°C. Before chilling, the total SOD activity in the transformed plants was somewhat greater than in the control plants. By the first day of hardening, SOD activity in both potato genotypes rose almost 1.5 times; however, the absolute value of SOD activity was considerably greater in the transformed plants. Subsequently, the total SOD activity in both genotypes decreased and by the end of the 6th day, it almost returned to the initial level. Electrophoretic and inhibitor analyses of potato plants revealed three types of SOD with one isoform of Mn-SOD, four isoforms of Fe-SOD, and two isoforms of Cu/Zn-SOD. In both genotypes, Fe-SOD3 manifested the greatest activity before chilling and in the course of hardening. Such changes in SOD activity corresponded to the rate of generation of superoxide anion radical and elevation of the content of products of peroxide oxidation of lipids (POL). Our data suggest that in the course of hardening of cold-resistant potato plants, the total SOD activity changed mostly due to Fe-SOD3 and to some extent as a result of elevated Cu/Zn-SOD2 activity, which was particularly evident at the beginning of hardening and more pronounced in the transformed plants. We assume that such temporal pattern is related to a greater rate of superoxide anion generation in the transformed plants as compared with control plants.     

Pollination crisis in the butterfly-pollinated wild carnation Dianthus carthusianorum?

Knowledge of pollination services provided by flower visitors is a prerequisite for understanding (co)evolutionary processes between plants and their pollinators, for evaluating the degree of specialization in the pollination system, and for assessing threats from a potential pollination crisis. This study examined pollination efficiency and visitation frequency of pollinators--key traits of pollinator-mediated fecundity--in a natural population of the wild carnation Dianthus carthusianorum. The five lepidopteran pollinator species observed differed in pollination efficiency and visitation frequency. Pollinator importance, the product of pollination efficiency and visitation frequency, was determined by the pollinator's visitation frequency. Pollination of D. carthusianorum depended essentially on only two of the five recorded pollinator species. Seed set was pollen-limited and followed a saturating dose-response function with a threshold of c. 50 deposited pollen grains for fruit development. Our results confirm that D. carthusianorum is specialized to lepidopteran pollinators, but is not particularly adapted to the two main pollinator species identified. The local persistence of D. carthusianorum is likely to be at risk as its reproduction depends essentially on only two of the locally abundant, but generally vulnerable, butterfly species.     

Epichloë endophyte affects the root colonization pattern of belowground symbionts in a wild grass

Plants host multiple symbionts that interact with each other affecting plant performance and regulating their establishment. Here, we analyzed how the association with Epichloë endophytes affects belowground colonization by Dark Septate Endophytes (DSE) and arbuscular mycorrhizal fungi (AMF) in the grass Bromus auleticus. Epichloë-symbiotic (E+) and Epichloë-non symbiotic (E−) plants were sampled from a long-term experimental plot and colonization structures were analyzed in the roots. We also examined the influence of Epichloë exudates on the in vitro growth of DSE Microdochium bolleyi isolated from roots. Epichloë symbiosis increased AMF colonization, although differences were not significant. Despite the lack of differences in total DSE colonization, in concordance with in vitro findings, a higher significant abundance of microsclerotia was observed in E+ plants. A negative correlation between total mycorrhizal and DSE was found. Our findings show a more uniform root colonization pattern in E+ plants, suggesting a root symbiosis modulating role.     

Distribution, abundance, and utilization of wild berries by the gwich’in people in the Mackenzie River Delta region

This paper examines the abundance and Aboriginal use of botanical non-timber forest products in the Gwich’in Settlement Area in the Northwest Territories, Canada. Informants indicated that wild berries are important to Gwich’in diets and an important factor in culture and traditional land use. People collected mostly cloudberries (Rubus chamaemorus), blueberries (Vaccinium uliginosum), and lingonberries (Vaccinium vitisidaea). The total quantities collected were estimated to be greater than other published accounts of berry gathering by northern Aboriginal peoples in North America. The total collected by the 450 households in the year 2000 was about 16,000 L. Inventories of wild berries on the landscape suggest that substantial quantities could be collected for commercial production, although the between-year supply can show considerable variation.     

Silver spoons in the rough: can environmental enrichment improve survival of hatchery Atlantic salmon Salmo salar in the wild?

This study tested the ‘silver spoon’ hypothesis which posits that individuals that develop under favourable conditions should enjoy a fitness advantage later in life because they are more likely to recognize and settle in high‐quality habitats. Atlantic salmon Salmo salar of two age classes (0+ and 1+ years) were reared in environmentally enriched or standard hatchery tanks for a short period (c. 10 weeks), were then released into a natural river and sampled on repeated occasions to test for silver‐spoon effects. Compared with controls, enriched fish had a 6·4% higher recapture rate and settled in higher velocity habitats when they were stocked as 0+ year fry, but not when they were stocked as 1+ year parr. The opportunity for selection was generally higher for environmentally enriched fish than for controls, and also higher for 0+ than for 1+ year fish. Selection favoured individuals with high condition factor, extensive fat reserves and longer than average pectoral fins in both age classes but favoured a small body size in 1+ year and a large body size in 0+ year releases. Stomach analysis showed that enriched fish ate more, and adapted quicker to natural prey than controls. These results provide support for silver‐spoon effects in fish and indicate that enrichment can improve post‐release performance in conservation programmes, but seemingly only if fish are not kept in captivity for too long.     

Estimation of in situ mating systems in wild sorghum (Sorghum bicolor (L.) Moench) in Ethiopia using SSR-based progeny array data: implications for the spread of crop genes into the wild

Because transgenic sorghum (Sorghum bicolor L.) is being developed for Africa, we investigated the potential for transgenes to spread to conspecific wild/weedy sorghum populations in Ethiopia, which is considered the centre of origin of cultivated sorghum. In the current study, the extent of outcrossing, and uniparental and biparental inbreeding were investigated in seven wild/weedy sorghum populations collected at elevations ranging from 631 to 1709 m. Based on allele frequency data of 1120 progenies and 140 maternal plants from five polymorphic microsatellite markers, outcrossing rates were estimated using standard procedures. The average multilocus outcrossing rate was 0.51, with a range of 0.31–0.65 among populations, and the family outcrossing rate was in the extreme range of 0 to 100%. The highest outcrossing (t _m?=?0.65) was recorded in a weedy population that was intermixed with an improved crop variety in Abuare (Wello region). It was also observed that the inbreeding coefficient of the progenies (F _p) tend to be more than the inbreeding coefficient of both their maternal parents (F _m) and the level of inbreeding expected at equilibrium (F _eq), which is a characteristic of predominantly outbreeding species. Biparental inbreeding was evident in all populations and averaged 0.24 (range = 0.10–0.33). The high outcrossing rates of wild/weedy sorghum populations in Ethiopia indicate a high potential for crop genes (including transgenes) to spread within the wild pool. Therefore, effective risk management strategies may be needed if the introgression of transgenes or other crop genes from improved cultivars into wild or weedy populations is deemed to be undesirable.     

Is hissing behaviour of incubating great tits related to reproductive investment in the wild?

Anti-predator behaviour of breeding animals is a complex trait that depends on current reproductive investment as well as individual differences in risk-taking propensities. In response to nest predation, many bird species produce specific sounds, such as the hissing calls in incubating great tits (Parus major), that may provoke an acoustic startle response in the predator. However, it is still unclear whether the propensity of incubating females to produce hissing calls towards nest predators depends on the reproductive investment. With our 3-year study, we show that response type (females that do not hiss versus females giving hissing calls) to a potential nest predator, the woodpecker, is a repeatable trait. We found no differences in the studied reproductive traits between hissing and non-hissing birds. Interestingly, among hissing birds, fast-responding females started egg-laying earlier than slow-responding ones. Among non-hissing birds, heavier birds initiated clutches earlier. We also revealed that hissing birds breed in areas with decreased nest-box occupancy, suggesting either that they potentially select different areas to breed or that territory size is larger as a result of hissing birds being more aggressive. These findings demonstrate that response type is not related to the early reproductive value of the brood across distinct behavioural groups. However, our results do suggest that non-hissing and hissing females differ in terms of individual quality or dominance or personality related aspects.     

Polymorphisms in the α-amy1 gene of wild and cultivated barley revealed by the polymerase chain reaction

-Amylases are the key enzymes involved in the hydrolysis of starch in plants. The polymerase chain reaction (PCR) was used to detect polymorphisms in the length of amplified sequences between the annealing sites of two primers derived from published -amy1 gene sequences in barley. These two primers (Bsw1 and Bsw7), flanking the promoter region and the first exon, amplified two PCR fragments in barley. One of the amplified products, with the expected length of 820 bp, appeared together with another shorter PCR band of around 750 bp. This 750-bp fragment seems to be derived from an -amylase gene not reported previously. Both of the PCR products could be amplified from the two-rowed barley varieties tested, including cv Himalaya from which the sequence information was obtained. Five of the six-rowed barley varieties also have the two PCR fragments whereas another two have only the long fragment. These two fragments seem to be unique to barley, neither of them could be amplified from other cereals; for example, wheat, rye or sorghum. These two -amylase fragments were mapped to the long arm of 6H, the location of the -amy1 genes, using wheat-barley addition lines. Amplification of genomic DNA from wild barley accessions with primers Bsw1 and Bsw7 indicated that both of the fragments could be present, or the long and short fragments could be present alone. The results also demonstrated that the genes specifying these two fragments could be independent from each other in barley. The conserved banding pattern of these two fragments in the two-rowed barley varieties implies that artificial selection from these genes may have played an important role in the evolution of cultivated barley from wild barley.     

Are the early holocene cattle in the eastern sahara domestic or wild?

Questions relating to the antiquity of domestic cattle in the Sahara are among the most controversial in North African prehistory. It is generally believed that cattle were first domesticated in southwest Asia, particularly Anatolia, or in southeast Europe, where their remains have been found in several sites dated between 9,000 and 8,000 years ago.1 The discovery, in several small sites in the Western Desert of Egypt, of large bovid bones identified as domestic cattle and having radiocarbon dates ranging between 9,500 and 8,000 B.P. has raised the possibility that there was a separate, independent center for cattle domestication in northeast Africa (Fig. 1).^2–4 However, it has not been universally accepted that these bones are from cattle or, if so, that the cattle were domestic.     

Does habitat use and ecological niche shift over the lifespan of wild species? Patterns of the bearded vulture population in the Western Alps

We analysed bearded vulture (Gypaetus barbatus) occurrences collected through long-term monitoring (from 1993 to 2010) in the Western Alps (1) to test whether ecological niches shift due to individual development and (2) to verify whether these patterns could reflect their spatial distribution. Thus, we compared the distribution patterns of three age classes (‘young’, ‘sub-adults’ and ‘adults’) through the K-select analysis. We then computed ten species distribution models (SDMs) and their average prediction to test for differences in age class distribution. The K-select analysis showed highly significant differences in the ecological niche among all the age classes and we also found highly significant differences in all the SDMs among the three age classes considered. Our results quantitatively showed that target species exhibits age specific shifts in the ecological niche and changes in the spatial distribution of individuals. Our methods are potentially widely applicable for testing differences among age classes of other species and thus, defining the best conservation actions (such as re-introduction) by taking into account different requirements in different stages of the individuals’ life.     

Farming of agarophytes in India—a long-time sustainability for the industry and preserving wild stocks

In India, food-grade agar is produced from Gracilaria edulis while bacteriological-grade agar is extracted from Gelidiella acerosa. Agarose is directly obtained from Gracilaria dura. Seaweeds for agar production mainly come from wild stocks located in reefs of the Gulf of Mannar, southeast coast. Landings of Gr. edulis were peak (982 dry t) during 1990 while landings of Ge. acerosa reached maximum (665 dry t) during 2002–2003. Overexploitation is leading to a decrease in biomass of these two algae at an alarming rate for the last decade. Commercial cultivation of agarophytes is yet to increase in India in spite of growing pressure on wild stocks triggered by increase in demand of raw material by the industry. Taking this into consideration, a number of efforts have been initiated to develop feasible cultivation methods for agarophytes. The present paper summarizes various methods developed for commercial cultivation of Gr. edulis, Gr. dura, Gracilaria verrucosa and Ge. acerosa in the open sea. We also discuss the challenges in the development of commercial farming of agarophytes in India.