Low Genotyping Error Rates and Noninvasive Sampling in Bighorn Sheep

Abstract Noninvasive DNA sampling allows studies of natural populations without disturbing the target animals. Unfortunately, high genotyping error rates often make noninvasive studies difficult. We report low error rates (0.0–7.5%/locus) when genotyping 18 microsatellite loci in only 4 multiplex polymerase chain reaction amplifications using fecal DNA from bighorn sheep (Ovis canadensis). The average locus-specific error rates varied significantly between the 2 populations (0.13% vs. 1.6%; P < 0.001), as did multi-locus genotype error rates (2.3% vs. 14.1%; P < 0.007). This illustrates the importance of quantifying error rates in each study population (and for each season and sample preservation method) before initiating a noninvasive study. Our error rates are among the lowest reported for fecal samples collected noninvasively in the field. This and other recent studies suggest that noninvasive fecal samples can be used in species with pellet-form feces for nearly any study (e.g., of population structure, gene flow, dispersal, parentage, and even genome-wide studies to detect local adaptation) that previously required high-quality blood or tissue samples.     

Using isolation‐by‐distance‐based approaches to assess the barrier effect of linear landscape elements on badger (Meles meles) dispersal

As the European badger (Meles meles) can be of conservation or management concern, it is important to have a good understanding of the species’ dispersal ability. In particular, knowledge of landscape elements that affect dispersal can contribute to devising effective management strategies. However, the standard approach of using Bayesian clustering methods to correlate genetic discontinuities with landscape elements cannot easily be applied to this problem, as badger populations are often characterized by a strong confounding isolation‐by‐distance (IBD) pattern. We therefore developed a two‐step method that compares the location of pairs of related badgers relative to a putative barrier and utilizes the expected spatial genetic structure characterized by IBD as a null model to test for the presence of a barrier. If a linear feature disrupts dispersal, the IBD pattern characterising pairs of individuals located on different sides of a putative barrier should differ significantly from the pattern obtained with pairs of individuals located on the same side. We used our new approach to assess the impact of rivers and roads of different sizes on badger dispersal in western England. We show that a large, wide river represented a barrier to badger dispersal and found evidence that a motorway may also restrict badger movement. Conversely, we did not find any evidence for small rivers and roads interfering with badger movement. One of the advantages of our approach is that potentially it can detect features that disrupt gene flow locally, without necessarily creating distinct identifiable genetic units.     

Assessment of 17 new whiskered auklet (Aethia pygmaea) microsatellite loci in 42 seabirds identifies 5–15 polymorphic markers for each of nine Alcinae species

We isolated 17 microsatellite loci in the whiskered auklet (Aethia pygmaea) and tested them for amplification in 48 species from 13 seabird families (including 42 seabirds). Fifteen of these loci were also tested for polymorphism in 38 of the species, which included nine species of Alcinae (four auklets, Atlantic puffin, dovekie, razorbill and two murre species). On the average, nine loci were polymorphic per Alcinae species.     

Contrasting patterns of population structure in the montane caddisflies Hydropsyche tenuis and Drusus discolor in the Central European highlands

1. In this study, we compared mitochondrial sequence data (cytochrome oxidase I) to infer the population structure of the two montane caddisflies Hydropsyche tenuis and Drusus discolor. The two species are contrasting examples of montane aquatic insects with insular distributions: D. discolor is restricted to altitudes above 600 m, H. tenuis is limited to the same mountain ranges in Central Europe but inhabits lower altitudes. 2. In particular, we ask whether these two species with similar regional distributions show similar patterns of population structure and haplotype diversity, and whether any differences can be attributed to population history and/or autecology. 3. To determine the population structure of both species, we applied conventional population genetics analyses to mitochondrial sequence data. We collected and sampled 121 specimens of H. tenuis from 29 sites in 10 different regions of the Central European highlands and 138 individuals of D. discolor from 40 sites in 11 different regions. 4. Nine unique haplotypes were identified for H. tenuis and 34 for D. discolor. There were eight variable positions in H. tenuis and 41 in D. discolor. The maximum difference between haplotypes was 0.8% (4 bp) for H. tenuis and 4.2% (21 bp) for D. discolor. We observed haplotype overlap between geographic regions for both species. Analysis of molecular variance showed that two‐thirds of the total variance in H. tenuis was found among regions while in D. discolor, a larger portion of variance was found within regions and populations due to a higher number of haplotypes observed within regions. Mantel test showed a significant relationship between genetic and geographic distance in D. discolor, but no significant relationship in H. tenuis. 5. Our analyses show that, despite their very similar overall distribution pattern in Europe, the two species exhibit distinct population structures, which may reflect differences in phylogeographic history, dispersal capabilities, habitat specifity or within‐region geographic occurrence.     

Exploitation of prey by a river bird, the dipper Cinclus cinclus (L.), along acidic and circumneutral streams in upland Wales

SUMMARY. 1. The diet of the Eurasian dipper Cinclus cinclus. a riverine bird from a globally widespread genus, was assessed through all stages of its annual cycle using published data and field studies from streams of contrasting chemistry. Time-activity budgets were also compiled throughout the year and used to estimate annual energy requirements from the stream ecosystem. 2. The annual energy requirements for a territorial pair ranged from 148,000 to 158,000 kJ yr^?1 depending on whether one or two broods were reared. After allowing for assimilation efficiency, these requirements were estimated to represent 10.5–11.0 kg dry mass of fish and invertebrates. Using representative values for territory size (4680–11,250 m²), annual exploitation of secondary production was estimated at 0.93–2.35 g dry mass m^?2. 3. Several features combined to focus the predatory load on certain organisms over different stages of the annual cycle. These included the availability and selection of alternative prey, the need to provision nestlings with large items such as trichopteran larvae, and the use by females of calcium-rich prey such as fish prior to egg formation. 4. Across their range of territory size, annual exploitation (dry mass) by dippers was estimated at 0.06–0.29 g m^?2 for Plecoptera. 0.02–0.22 g m^?2 for Ephemeroptera. 0.59–1.11 g m^?2 for Trichoptera and 0–0.78 g m^?2 for fish. Exploitation of Ephemeroptera. I richoptera and fish were all highest in circumneutral streams, but exploitation of Plecoptera was highest in acidic streams because other prey were scarce. 5. Cottids dominated the fish component of the diet. Influences on their density could be substantial according to available data on production in Welsh streams. Hydropsychids and limnephilids dominated the trichopteran component, with exploitation again representing potentially substantial amounts of production. Contemporaneous data are required on benthic production and exploitation by the birds. 6. The ecological role of birds in rivers particularly, and aquatic ecosystems generally, is currently neglected but worthy of considerable research effort.     

Genetic structure among populations in the endemic Hawaiian Plantago lineage: insights from microsatellite variation

Endemic Hawaiian species in the genus Plantago show considerable morphological and ecological diversity. Despite their variation, a recent phylogenetic analysis based on DNA sequence data showed that the group is monophyletic and that sequence variation among species and morphotypes is low. This lack of sequence polymorphisms resulted in an inability to resolve species and population affinities within the most recently derived clade of this lineage. To assess species boundaries, population genetic structure and interpopulation connectivity among the morphologically and ecologically distinct populations within this clade, genetic variation was examined using eight microsatellite loci. Within‐population genetic diversity was found to be lowest in the Maunaiu, Hawai'i population of the endangered P. hawaiensis, and highest in the large P. pachyphylla population from 'Eke, West Maui. Isolation by distance across the range of populations was detected and indicated restricted dispersal. This result is likely to be attributable to few interisland dispersal events in the evolutionary history of this lineage. Genetic differentiation within islands tended to be higher among populations occurring in contrasting bog and woodland habitats, suggesting ecological barriers to gene flow and the potential role of ecological divergence in population diversification. Overall, these results are consistent with findings from phylogenetic analysis of the entire lineage. Our data bring new insights regarding patterns of dispersal and population genetic structure to this endemic and endangered group of island taxa. As island environments become increasingly fragmented, information of this type has important implications for the successful management of these fragile populations and habitats.     

Morphological functions of gibberellins in leptosporangiate fern gametophytes: insights into the evolution of form and gender expression

In addition to genetic load, the induction of maleness in leptosporangiate gametophytes by the pheromone antheridiogen may facilitate rates of outcrossing similar to those found in angiosperms. The antheridiogens that have been chemically identified are similar to gibberellins and probably evolved from this common plant hormone. The purposes of this study were to determine the functions of endogenous gibberellins in morphological development and gender expression in leptosporangiate fern gametophytes and to elucidate how antheridiogens may have evolved from gibberellin precursors. We grew gametophytes of Osmunda regalis and Athyrium filix‐femina on nutrient agar enriched with APOGEE, which blocks gibberellin synthesis. Osmunda regalis is a member of Osmundaceae, the only family in Osmundales, the sister group of all remaining extant leptosporangiate ferns. This family possesses a male‐first gender in isolation and lacks any known antheridiogen systems. In contrast, A. filix‐femina is a member of a derived family, Woodsiaceae, which possesses antheridiogen systems. Disruption of gibberellin synthesis retarded notch development and expression of both maleness and femaleness (i.e. gender status) in both species. On the basis of these results, we offer a simple model of gametophyte evolution driven by gender‐based fitness gain curves and the influence of exogenous gibberellins. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 599–615.     

Physiology and proteomics of the water-deficit stress response in three contrasting peanut genotypes

Peanut genotypes from the US mini-core collection were analysed for changes in leaf proteins during reproductive stage growth under water-deficit stress. One- and two-dimensional gel electrophoresis (1- and 2-DGE) was performed on soluble protein extracts of selected tolerant and susceptible genotypes. A total of 102 protein bands/spots were analysed by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI–TOF MS) and by quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS) analysis. Forty-nine non-redundant proteins were identified, implicating a variety of stress response mechanisms in peanut. Lipoxygenase and 1 l -myo-inositol-1-phosphate synthase, which aid in inter- and intracellular stress signalling, were more abundant in tolerant genotypes under water-deficit stress. Acetyl-CoA carboxylase, a key enzyme of lipid biosynthesis, increased in relative abundance along with a corresponding increase in epicuticular wax content in the tolerant genotype, suggesting an additional mechanism for water conservation and stress tolerance. Additionally, there was a marked decrease in the abundance of several photosynthetic proteins in the tolerant genotype, along with a concomitant decrease in net photosynthesis in response to water-deficit stress. Differential regulation of leaf proteins involved in a variety of cellular functions (e.g. cell wall strengthening, signal transduction, energy metabolism, cellular detoxification and gene regulation) indicates that these molecules could affect the molecular mechanism of water-deficit stress tolerance in peanut.