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.     

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.     

The geographic distribution of metazoan microfauna on East Antarctic nunataks

The abundance and distribution of nematodes, rotifers and tardigrades in samples from nunataks in continental Antarctica were investigated during four Antarctic expeditions in the austral summers of 1991/92, 1993/94, 1996/97 and 2001/02. Altogether 368 samples were collected from 14 nunataks and one oasis in East Antarctica. Nematodes were found in 35%, rotifers in 67% and tardigrades in 40% of all samples. Fifty-four microfaunal taxa were identified. Of these, 27 were nematodes, 8 tardigrades and 19 rotifers. The size and geographic location of the nunatak and oasis influenced the abundance and taxonomic composition of the microfauna. The highest abundance and diversity of nematodes were found on large nunataks close to the coast. Nematodes were not found on small inland nunataks. Very high population densities of tardigrades and rotifers were found on two small and isolated nunataks. No microfauna was found on the two southernmost nunataks (Okkenhaugrusta and Vardeklettane), or on the smallest one (Utsikta). The Sørensens Quotient of Similarity was generally low, especially between faunas on nunataks in different mountain ridges. The results indicate rather limited rates of dispersal and colonization between nunataks.     

ACEH/ACE2 is a novel mammalian metallocarboxypeptidase and a homologue of angiotensin-converting enzyme insensitive to ACE inhibitors

A human zinc metalloprotease (termed ACEH or ACE2) with considerable homology to angiotensin-converting enzyme (ACE) (EC 3.4.15.1) has been identified and subsequently cloned and functionally expressed. The translated protein contains an N-terminal signal sequence, a single catalytic domain with zinc-binding motif (HEMGH), a transmembrane region, and a small C-terminal cytosolic domain. Unlike somatic ACE, ACEH functions as a carboxypeptidase when acting on angiotensin I and angiotensin II or other peptide substrates. ACEH may function in conjunction with ACE and neprilysin in novel pathways of angiotensin metabolism of physiological significance. In contrast with ACE, ACEH does not hydrolyse bradykinin and is not inhibited by typical ACE inhibitors. ACEH is unique among mammalian carboxypeptidases in containing an HEXXH zinc motif but, in this respect, resembles a bacterial enzyme, Thermus aquaticus (Taq) carboxypeptidase (EC 3.4.17.19). Collectrin, a developmentally regulated renal protein, is homologous with the C-terminal region of ACEH but has no similarity with ACE and no catalytic domain. Thus, the ACEH protein may have evolved as a chimera of a single ACE-like domain and a collectrin domain. The collectrin domain may regulate tissue response to injury whereas the catalytic domain is involved in peptide processing events.     

Scandinavian CDG-Ia patients: genotype/phenotype correlation and geographic origin of founder mutations

Congenital disorders of glycosylation type Ia, (previous name carbohydrate-deficient glycoprotein syndrome type Ia; CDG-Ia) is an inherited disorder of the glycosylation of certain glycoproteins. The defect is caused by mutations in the phosphomannomutase 2 (PMM2) gene located in chromosome region 16p13. The purpose of this study was twofold: (1) to investigate the possible correlation between certain genotypes and the phenotype of the patients and their PMM activity, and (2) to study further the founder origin of the Scandinavian mutations. Sixty-four CDG-Ia patients were studied. Regardless of mutation combination, the patients showed the basic neurological symptoms associated with CDG-Ia. However, patients carrying the mutation 548T-->C had less severe disease, e.g., no pericardial effusions, malnutrition, or clinical coagulation disturbances. Liver dysfunction and peripheral neuropathy were milder. In contrast, patients carrying mutation 691G-->A showed a high incidence of severe malnutrition and hepatopathy, and they had the highest mortality including affected siblings. Heterozygotes for the two most common mutations (422G-->A and 357C-->A) displayed a phenotype of variable severity sometimes leading to early death. PMM activity showed no correlation with either genotype or phenotype but was reduced in most patients. There was a pronounced geographic clustering for some of the Scandinavian mutations. For example, 548T-->C was almost exclusively found in patients stemming from southeastern parts of Sweden, whereas 26G-->A was found to cluster in a region in the most southern parts of Sweden, suggesting that these mutations originated in these two regions separately as founder mutations. The most frequent mutation (422G-->A) did not show a specific geographic focus. The widespread 422G-->A mutation is probably an older mutation, although haplotype data from intragenic polymorphisms indicate that this mutation also arose only once. The detailed information of the origin of mutations and their respective associated phenotypic pattern should enable improvements to be made regarding tools for genetic counseling and for prenatal diagnoses in CDG-Ia families.     

A survey of the geographic distribution of Ophiocordyceps sinensis

Ophiocordyceps sinensis is one of the best known fungi in Traditional Chinese Medicine. Many efforts have been devoted to locating the production areas of this species resulting in various reports; however, its geographic distribution remains incompletely understood. Distribution of O. sinensis at the county level is clarified in this work based on both a literature search and fieldwork. More than 3600 publications related to O. sinensis were investigated, including scientific papers, books, and online information. Herbarium specimens of O. sinensis and field collections made by this research group during the years 2000-2010 were examined to verify the distribution sites. A total of 203 localities for O. sinensis have been found, of which 106 are considered as confirmed distribution sites, 65 as possible distribution sites, 29 as excluded distribution sites and three as suspicious distribution sites. The results show that O. sinensis is confined to the Tibetan Plateau and its surrounding regions, including Tibet, Gansu, Qinghai, Sichuan, and Yunnan provinces in China and in certain areas of the southern flank of the Himalayas, in the countries of Bhutan, India and Nepal, with 3,000 m as the lowest altitude for the distribution. The fungus is distributed from the southernmost site in Yulong Naxi Autonomous County in northwestern Yunnan Province to the northernmost site in the Qilian Mountains in Qilian County, Qinghai Province, and from the east edge of the Tibetan Plateau in Wudu County, Gansu Province to the westernmost site in Uttarakhand, India. The clarification of the geographic distribution of O. sinensis will lay the foundation for conservation and sustainable use of the species.