The evolution of novel herbicide tolerance in a noxious weed: the geographic mosaic of selection

Understanding how genetic variation is organized over geography has long been of interest to evolutionary biologists given that traits can vary within and among populations, across regions, and at continental or global scales. The pattern of regional variation can have an important impact on trait evolution at the local or population level. Using a common garden, we asked whether a geographically variable mosaic of tolerance to the widely applied herbicide RoundUp^® existed in two closely related co-occurring species of morning glory, Ipomoea purpurea and I. hederacea. We assayed RoundUp tolerance in over 1,700 plants representing 290 families from 29 populations in the southeastern United States. Our findings suggest that the two species of morning glory partition their respective levels of genetic variation for tolerance to glyphosate differently. Variation for tolerance in I. purpurea appears to exist among maternal lines and regions, whereas in I. hederacea, variation in tolerance existed only among populations. In addition, we find a significant hotspot of tolerance or positive spatial aggregation of this trait on a local scale in I. purpurea populations from the Coastal Plain. This suggests that either similar regimes of selection or gene flow between populations can produce a geographic mosaic of tolerance. These results highlight the fact that the genetic variation underlying an adaptive trait can exist at many different scales, whether it be within- or among-populations, among geographical ‘hotspots,’ or among distinct ecological regions. Given these results, the partitioning of genetic variation should be considered before making predictions about an adaptive trait’s evolutionary trajectory.     

Diversity and geographic distribution of benthic foraminifera: a molecular perspective

The diversity and distribution of modern benthic foraminifera has been extensively studied in order to aid the paleoecological interpretation of their fossil record. Traditionally, foraminiferal species are identified based on morphological characters of their organic, agglutinated or calcareous tests. Recently, however, new molecular techniques based on analysis of DNA sequences have been introduced to study the genetic variation in foraminifera. Although the number of species for which DNA sequence data exist is still very limited, it appears that morphology-based studies largely underestimated foraminiferal diversity. Here, we present two examples of the use of DNA sequences to examine the diversity of benthic foraminifera. The first case deals with molecular and morphological variations in the well-known and common calcareous genus Ammonia. The second case presents molecular diversity in the poorly documented group of monothalamous (single-chambered) foraminifera. Both examples perfectly illustrate high cryptic diversity revealed in almost all molecular studies. Molecular results also confirm that the majority of foraminiferal species have a restricted geographic distribution and that globally distributed species are rare. This is in opposition to the theory that biogeography has no impact on the diversity of small-sized eukaryotes. At least in the case of foraminifera, size does not seem to have a main impact on dispersal capacities. However, the factors responsible for the dispersal of foraminiferal species and the extension of their geographic ranges remain largely unknown. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype

High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation. Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms.     

Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise

The diversity associated with a microbial mat sample collected from a deep-sea hydrothermal vent on the Southern East Pacific Rise was determined using a molecular phylogenetic approach based on the comparison of sequences from the small subunit ribosomal RNA gene (16S rDNA). The DNA was extracted from the sample and the 16S rDNA was amplified by PCR. Sixteen different phylotypes were identified by restriction fragment length polymorphism analysis; four phylotypes were later identified as putative chimeras. Analysis of the 16S rDNA sequences placed all the phylotypes within the Proteobacteria. The majority of the sequences (98%) were most closely related to a new clade of epsilon-Proteobacteria that were initially identified from an in situ growth chamber deployed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge in 1995. The similarity between phylotypes identified from Atlantic and Pacific deep-sea hydrothermal vent sites indicates that this new clade of Proteobacteria may be endemic to and widely distributed among deep-sea hydrothermal vents.     

The demographics and distribution of type B Niemann-Pick disease: novel mutations lead to new genotype/phenotype correlations

We have collected demographic and/or mutation information on a worldwide sample of 394 patients with type B Niemann-Pick disease (NPD). The disorder is panethnic, with the highest incidence occurring in individuals of Turkish, Arabic, and North African descent. Only five of the 394 patients were Ashkenazi Jewish, revealing that, unlike the type A form of NPD, type B NPD does not occur frequently within this population. Mutation analysis of the acid sphingomyelinase (ASM) gene (designated "SMPD1") was performed on 228 patients (324 unique alleles), and several novel, "common" mutations were found. Among these were the L137P, fsP189, and L549P mutations, which accounted for approximately 75% of the alleles in Turkish patients, the H421Y and K576N mutations, which accounted for approximately 85% of the alleles in Saudi Arabian patients, the S379P, R441X, R474W, and F480L mutations, which accounted for approximately 55% of the alleles in Portuguese/Brazilian patients, and the A196P mutation, which accounted for approximately 42% of the alleles in Scottish/English patients. The previously reported DeltaR608 mutation occurred on approximately 12% of the alleles studied. Overall, a total of 45 novel mutations were found, and several new genotype/phenotype correlations were identified. In particular, the L137P, A196P, and R474W mutations were consistent with a less severe form of type B NPD, whereas the H421Y and K576N mutations led to an early-onset, more severe form that was specific to Saudi Arabia. These data provide the first extensive demographic assessment of this disorder and describe several new mutations that can be used to predict phenotypic outcome and to gain new insights into the structure and function of ASM.     

GEL: a novel genotype calling algorithm using empirical likelihood

MOTIVATION: Preliminary results on the data produced using the Affymetrix large-scale genotyping platforms show that it is necessary to construct improved genotype calling algorithms. There is evidence that some of the existing algorithms lead to an increased error rate in heterozygous genotypes, and a disproportionately large rate of heterozygotes with missing genotypes. Non-random errors and missing data can lead to an increase in the number of false discoveries in genetic association studies. Therefore, the factors that need to be evaluated in assessing the performance of an algorithm are the missing data (call) and error rates, but also the heterozygous proportions in missing data and errors. RESULTS: We introduce a novel genotype calling algorithm (GEL) for the Affymetrix GeneChip arrays. The algorithm uses likelihood calculations that are based on distributions inferred from the observed data. A key ingredient in accurate genotype calling is weighting the information that comes from each probe quartet according to the quality/reliability of the data in the quartet, and prior information on the performance of the quartet. AVAILABILITY: The GEL software is implemented in R and is available by request from the corresponding author at nicolae@galton.uchicago.edu.     

中国三种水韭属植物的地理分布与生境特征

水韭属（Isoetes）是水韭科中的孑遗属,分类上属拟蕨类,对研究蕨类植物的系统演化具有重要价值。由于人类活动对其水生生境的破坏,水韭属植物在我国的分布范围及其种群数量日趋减少,濒临灭绝,其中,高寒水韭(I. hypsophila)、云贵水韭(I. yunguiensis)和中华水韭(I. sinensis)已被列为国家一级重点保护野生植物。对原产中国的3种水韭的地理分布与生境特征进行调查,将为合理保护该属植物提供相关基础数据和科学依据。本文野外实地考察了原产中国的3种水韭属植物的现存种群及历史记载曾经分布但现已绝迹的水韭属植物种群(绝迹种群)所在地。在每一调查点,测定了各样点的海拔高度、水体基底状况以及水体pH值等生境特征;在现存种群所在地,分别记载了所见水生植物种类、水韭种群规模及其生长状况,并采集和鉴定了3种水韭属植物及其伴生种。调查发现3种水韭属植物种与种之间为间断分布,且具有垂直梯度差异;种内各种群之间相互隔离,各种群的个体数均偏少;现存种群所生长的水体及其水体基底的pH特性无明显差异,为酸性或中性;绝迹种群所在的原生境已遭到严重破坏,一些地点的水体pH和基底pH与以往存在水韭的时期相比已明显升高。此外,调查还发现沼泽地带的水韭种群正面临着其他水生植物的激烈竞争而处于随时灭绝的危险之中,而淡水潮间带沿岸的水韭种群因周期性的水位波动而生长良好。调查结果表明3种水韭属植物的地理分布及其生长状况与海拔、水体pH值、基底pH值以及种间竞争和水位波动密切相关。本文还讨论了保护水韭属植物的基本策略和具体措施。     

The geographic distribution of mammal body size in Europe

Aims  To describe the pattern of mean body size of native mammals in Europe, and to investigate its relationships with environmental predictors related to four hypotheses: (1) dispersal; (2) heat conservation; (3) heat dissipation; and (4) resource availability.
Location  Continental western Europe and Great Britain.
Methods  We used range maps to estimate the mean body size (average log mass) of mammals in 386 cells of 12,100 km² each. Environmental conditions in each cell were quantified using nine historical, climatic and primary production variables. We attempted to tease apart the effects of these variables using correlation, multiple regression and spatial autocorrelation analyses.
Results  In the part of the continent covered by ice during the Pleistocene, body mass decreases southwards, and annual average temperature explains 73% of the variance in body size, consistent with the heat-conservation hypothesis. However, in warmer, non-glaciated areas the best predictor is an estimate of seasonality in plant production, but it explains only 18% of the variance. Carnivores, omnivores and herbivores show similar relationships, but the pattern for herbivores is substantially weaker than for the other groups.
Main conclusions  Overall, the relationship between mean body size and temperature is non-linear, being strong in cold environments but virtually disappearing above a temperature threshold.     

The geographic distribution of seed-dispersal mutualisms in North America

It is often difficult to determine the relative importance of different sorts of species interactions in shaping community structure or how communities function because we lack basic information on patterns of occurrence of biotic interactions. Here we determine the geographic distribution of seed-dispersal mutualisms across North America, and then test the hypotheses that those patterns are correlated with mean annual precipitation and latitude. We analyze the floras of 197 sites across North America to identify which species of native seed plants are dispersed by animals in one of three types of plant-animal mutualisms: frugivory, scatter hoarding, and ants. We identified 1655 plant species that are involved in these seed-dispersal mutualisms. 16.5 ± 6.5% of all seed plants across North America are dispersed by animals; 10.0 ± 4.2% by frugivores, 3.7 ± 1.7% by scatter hoarders, and 3.9 ± 2.2% by ants. Secondary dispersal by a different mode and vector (e.g., wind dispersal followed by scatter hoarding, or ballistic dispersal followed by myrmecochory) occurred in 16.8% of all plant mutualist records. Although each mode of dispersal showed a different pattern, the prevalence of seed-dispersal mutualisms increased with mean annual precipitation. The prevalence of seed dispersal by frugivory and scatter-hoarding decreased with increasing latitude. The prevalence of seed-dispersal interactions varies dramatically across North America. The center of greatest diversity for all three types of seed-dispersal mutualisms is the eastern United States, roughly coincident with the eastern deciduous forest. Knowing the distribution of species interactions improves our understanding of how the structure and functioning of communities varies across environmental gradients.     

中国蛱蝶科昆虫地理分布与区系分析

分析了中国蛱蝶科已知324种昆虫的分布与区系组成,主要由古北区、东洋区、古北一东洋区共有种类组成,共计309种,占总数的95．37％;其种类组成与澳洲区、新北区有明显差异;特有种类较少,占总数的12．65％;广布种很少,仅占1．74％。同时统计分析了324种蛱蝶在我国各省的贫富指数。     

Identification of a novel Cryptosporidium genotype in pigs

Over a 3-year period, a total of 646 fecal samples from pigs in 22 indoor and outdoor herds from Western Australia were screened for Cryptosporidium spp. by microscopy. Results revealed that 39 of 646 samples (6.03%) were positive for Cryptosporidium. Cryptosporidium was much more common in outdoor herds (17.2%) than in indoor herds (0.5%) and was more common in animals between the ages of 5 and 8 weeks (69.2%) than in younger animals (P < 0.0001). Molecular characterization of the positive samples at the 18S ribosomal DNA locus identified two distinct genotypes of Cryptosporidium: the previously identified pig genotype I and a novel pig genotype (pig genotype II), both of which warrant species status.     

The importance of defining the geographic distribution of species for conservation: The case of the Bearded Wood-Partridge

Delimitation of the distribution areas of species has fundamental implications for the understanding of biodiversity and for decision-making in conservation. This is illustrated by the case of the Bearded Wood-Partridge (Dendrortyx barbatus), which is endemic to Mexico and was classified as threatened by the IUCN. Recently the discovery of this species in new locations caused an increase in the known distribution area whereupon it was reclassified in a lower risk category. In our study, delimitation and comparison of the Bearded Wood-Partridge distribution area is carried out utilising five different methods: minimum convex polygon; areographic; cartographic; ecological niche modeling; and, “free hand”. A number of locality records are also used to demonstrate the chronological order of appearance. The results show that the size and shape of the distribution area of this species vary depending on the number of records and on their spatial and environmental location, as well as on the particular delimitation method used. However, ecological niche modeling provides the best results in terms of spatial and numerical sensitivity as well as lower values of omission and a moderate extent of predicted areas. We suggest that decisions related to species conservation (categories of risk, areas of endemism, etc.), particularly those species of high geographical restriction, should be contingent on the formalised delimitation of distribution areas based on ecological niche modeling methods.     

The role of immigration in the geographic distribution of the HBs antigen]

The study of HBs antigen frequency among almost 130 000 donors,--according to their place of birth--,shows a significantly higher frequency among foreign residents. The general frequency represents the arithmetic average between that of natives and that of foreign residents. The distribution of ad and ay subtypes is analogous to that observed in the different native countries.