Genetic population structure of the Greater Bilby Macrotis lagotis, a marsupial in decline

The Greater Bilby has shown a rapid decline in range during this century and now occupies only a small isolated area in south-western Queensland (QLD) and a larger, but mostly low-density area in the north-western deserts of the Northern Territory (NT) and Western Australia (WA). We have examined variation in the control region of mitochondrial DNA (mtDNA) and at nine microsatellite loci in order to investigate the extent of current and historical subdivision across the species range, and to provide a preliminary assessment of genetic structuring and mating system on a finer scale within the QLD population. Both mtDNA and microsatellite loci had substantial variation within and among populations, with mtDNA divergence being greater between QLD and NT than between NT and WA. The QLD population had two unique and divergent mtDNA lineages, but there was no evidence for strong phylogeographical structure across the range. The available evidence suggests that the bilby should be considered as a single Evolutionarily Significant Unit consisting of multiple Management Units. Augmentation of the remnant QLD population from the NT does not appear necessary at this stage, at least not on genetic grounds. Finer-scale analysis of microsatellite variation for two QLD colonies revealed a deficiency of heterozygotes and significantly greater relatedness within than between colonies. However, structuring was observed only for males; relatedness values for females did not depart from those expected under panmixia. Parentage exclusion analysis for one colony allowed the construction of a partial pedigree which indicated strong polygyny, with one male fathering all but one of the eight offspring assigned. The extent to which fine-scale genetic structuring and differences between sexes is due to sex-biased dispersal vs. effects of mating system remain to be determined.     

Estimating seed dispersal distance: A comparison of methods using animal movement and plant genetic data on two primate‐dispersed Neotropical plant species

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Fitness,risk taking,and spatial behavior covary with boldness in experimental vole populations

Individuals of a population may vary along a pace‐of‐life syndrome from highly fecund, short‐lived, bold, dispersive “fast” types at one end of the spectrum to less fecund, long‐lived, shy, plastic “slow” types at the other end. Risk‐taking behavior might mediate the underlying life history trade‐off, but empirical evidence supporting this hypothesis is still ambiguous. Using experimentally created populations of common voles (Microtus arvalis)—a species with distinct seasonal life history trajectories—we aimed to test whether individual differences in boldness behavior covary with risk taking, space use, and fitness. We quantified risk taking, space use (via automated tracking), survival, and reproductive success (via genetic parentage analysis) in 8 to 14 experimental, mixed‐sex populations of 113 common voles of known boldness type in large grassland enclosures over a significant part of their adult life span and two reproductive events. Populations were assorted to contain extreme boldness types (bold or shy) of both sexes. Bolder individuals took more risks than shyer ones, which did not affect survival. Bolder males but not females produced more offspring than shy conspecifics. Daily home range and core area sizes, based on 95% and 50% Kernel density estimates (20 ± 10 per individual, n = 54 individuals), were highly repeatable over time. Individual space use unfolded differently for sex‐boldness type combinations over the course of the experiment. While day ranges decreased for shy females, they increased for bold females and all males. Space use trajectories may, hence, indicate differences in coping styles when confronted with a novel social and physical environment. Thus, interindividual differences in boldness predict risk taking under near‐natural conditions and have consequences for fitness in males, which have a higher reproductive potential than females. Given extreme inter‐ and intra‐annual fluctuations in population density in the study species and its short life span, density‐dependent fluctuating selection operating differently on the sexes might maintain (co)variation in boldness, risk taking, and pace‐of‐life.     

Long distance pollen-mediated gene flow at a landscape level: the weed beet as a case study

Gene flow is a crucial parameter that can affect the organization of genetic diversity in plant species. It has important implications in terms of conservation of genetic resources and of gene exchanges between crop to wild relatives and within crop species complex. In the Beta vulgaris complex, hybridization between crop and wild beets in seed production areas is well documented and the role of the ensuing hybrids, weed beets, as bridges towards wild forms in sugar beet production areas have been shown. Indeed, in contrast to cultivated beets that are bi-annual, weed beets can bolt, flower and reproduce in the same crop season. Nonetheless, the extent of pollen gene dispersal through weedy lineages remains unknown. In this study, the focus is directed towards weed-to-weed gene flow, and we report the results of a pollen-dispersal analysis within an agricultural landscape composed of five sugar beet fields with different levels of infestation by weed beets. Our results, based on paternity analysis of 3240 progenies from 135 maternal plants using 10 microsatellite loci, clearly demonstrate that even if weedy plants are mostly pollinated by individuals from the same field, some mating events occur between weed beets situated several kilometres apart (up to 9.6 km), with rates of interfield-detected paternities ranging from 11.3% to 17.5%. Moreover, we show that pollen flow appears to be more restricted when individuals are aggregated as most mating events occurred only for short-distance classes. The best-fit dispersal curves were fat-tailed geometric functions for populations exhibiting low densities of weed beets and thin-tailed Weibull function for fields with weed beet high densities. Thus, weed beet populations characterized by low density with geographically isolated individuals may be difficult to detect but are likely to act as pollen traps for pollen emitted by close and remote fields. Hence, it appears evident that interfield pollen-mediated gene flow between weed beets is almost unavoidable and could contribute to the diffusion of (trans)genes in the agricultural landscape.     

Development and characterization of nine polymorphic microsatellite markers in the sand goby Pomatoschistus minutus (Gobiidae)

A microsatellite‐enriched genomic library was constructed for the sand goby, Pomatoschistus minutus (Pallas 1770), and nine polymorphic DNA microsatellite markers of high quality were successfully optimized. Characterization of 96 individuals from the Vaccarès lagoon (France) showed moderate to high levels of polymorphism (two to 54 alleles). All the markers conformed to Hardy–Weinberg equilibrium and showed no evidence of null alleles, large allele dropout, stuttering and linkage disequilibrium between pairs of loci. These markers successfully amplify in three closely related species and can be employed to investigate population genetic structure and to clarify paternity in Pomatoschistus species.     

大麦主栽品种亲缘系数和对叶斑病的抗性分析

为明确我国大麦主栽品种的遗传多样性及其对叶斑病的抗性来源,采用亲缘系数(COP,coefficient of parentage)分析方法对155个主栽大麦品种的遗传系谱进行聚类分析,同时对其中79个供试大麦品种在苗期和成株期分别接种2个强毒性菌株进行抗性鉴定。结果显示,155个品种聚为6个类群,有亲缘关系的品种占全部品种14.77%。在品种间组成的11935个组合中,1763个组合间存在亲缘关系,其COP值变化范围在0~0.7500之间,亲缘系数总和为157.5867,平均值为0.0132。根据系谱分析发现了不同育种单位所育品种的核心亲本,并追溯其主要的祖先亲本。此外,通过对叶斑病的抗性鉴定,发现大多数供试的大麦品种感叶斑病,高抗品种主要集中在垦啤麦系列品种和蒙啤麦3号,部分华大麦和驻大麦系列的品种在苗期或成株期中抗叶斑病。系谱分析及抗性鉴定结果揭示了我国大麦叶斑病抗性基因存在不同来源,分析结果有利于提高抗叶斑病基因筛选效率和缩小筛选范围,也将促进抗叶斑病新基因资源的发掘和利用。     

Methods of parentage analysis in natural populations

The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.     

Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid

We present a novel approach to investigating sibling relationships and reconstructing parental genotypes from a progeny array. The Bayesian method we have employed is flexible and may be applicable to a variety of situations in addition to the one presented here. While mutation rates and breeding population allele frequencies can be taken into account, the model requires relatively few loci and makes few assumptions. Paternity of 270 veined squid (Loligo forbesi) hatchlings from three egg strings collected from one location was assigned using five microsatellite loci. Paternal and maternal genotypes reconstructed for each of the three strings were identical, strongly indicating that a single female produced the strings that were fertilized by the same four males. The proportion of eggs fertilized was not equal between males in all three strings, with male 1 siring most offspring (up to 68% in string 1), through to male 4 siring the least (as low as 2.4% in string 1). Although temperature had a profound effect on incubation time, paternity did not affect this trait at 12 degrees C or 8 degrees C.     

Complex patterns of mating revealed in a Eucalyptus regnans seed orchard using allozyme markers and the neighbourhood model

The neighbourhood model apportions offspring of individual mother plants to self-fertilization, outcrossing to males within a circumscribed area around the mother plant (the neighbourhood), and outcrossing to males outside the neighbourhood. Formerly the model was applied only to haploid pollen gametes in the offspring of conifers, but is extended so that it can be used with genotypic data from diploid offspring of both angiosperms and gymnosperms. In addition, it is shown that the mating parameters can be estimated without independent estimates of allele frequencies in the pollen pools outside the neighbourhood; thus the model might be applied effectively to natural populations exposed to unknown external pollen sources. Parameters of the neighbourhood mating model were estimated for a 10-year-old seed orchard population of the insect-pollinated tree, Eucalyptus regnans, in southeast Australia, which contained a mixture of two geographical provenances (Victoria and Tasmania). The mating patterns revealed were complex. Crosses between trees of the same provenance occurred three times more often than crosses between trees of different provenances. Levels of self-fertilization and patterns of mating within neighbourhoods were influenced by provenance origin, crop fecundity and orchard position (central vs. edge) of mother trees. Gene dispersal, however, was extensive, with approximately 50% of effective pollen gametes coming from males more than 40 m away from mother trees (average distance between neighbouring trees was 7.4 m). Thus, insect pollinators are efficient promoters of cross-fertilization in this orchard, with the result that the effective number of males mating with each female is large.