A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations.

PubMed

Agrawal, Anurag A; Johnson, Marc T J; Hastings, Amy P; Maron, John L

2013-05-01

The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, ≈5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was only partially the result of differential seed production; genotypic variation in seed germination also contributed to the observed evolutionary response. Since evening primrose genotypes exhibited heritable variation for resistance to insect herbivores, which was related to flowering time, we predicted that evolutionary changes in genotype frequencies would feed back to influence populations of a seed predator moth that specializes on O. biennis. By the conclusion of the experiment, variation in the genotypic composition among our eight replicate field populations was highly predictive of moth abundance. These results demonstrate how rapid evolution in field populations of a native plant can influence ecological interactions.

Incidence of Hepatocellular Carcinoma According to Hepatitis B Virus Genotype in Alaska Native People

PubMed Central

Ching, Lance K.; Gounder, Prabhu P.; Bulkow, Lisa; Spradling, Philip R.; Bruce, Michael; Negus, Susan; Snowball, Mary; McMahon, Brian J.

2016-01-01

Background & Aims Most regions of the world have <3 co-circulating hepatitis B virus (HBV) genotypes, which limits direct comparisons of hepatocellular carcinoma (HCC) risk among HBV-infected persons by genotype. We evaluated HCC incidence by HBV genotype in a cohort of Alaska Native (AN) persons where 5 HBV genotypes (A, B, C, D, F) have been identified. Methods Our cohort comprised AN persons with chronic HBV infection identified during 1983–2012 who consented to participate in the study. Cohort persons were offered annual hepatitis B e antigen (HBeAg) testing and semiannual HCC screening. We developed a logistic regression model to compare HCC risk by genotype, adjusting for age, sex, region, and HBeAg status. Results Among the 1,235 consenting study participants, 711 (57.6%) were male, 510 (41.3%) were HBeAg positive at cohort entry, and 43 (3.5%) developed HCC. The HBV genotype was known for 1,142 (92.5%) persons (13.5% A, 3.9% B, 6.7% C, 56.9% D, 19.0% F). The HCC incidence/1,000 person-years of follow-up for genotypes A, B, C, D, and F was 1.3, 0, 5.5, 0.4, and 4.2, respectively. Compared with persons with HBV genotype B/D infection, the HCC risk was higher for persons with genotypes A (adjusted odds ratio [aOR]: 3.9, 95% CI: 1.14–13.74), C (aOR: 16.3, 95% CI: 5.20–51.11), and F (aOR: 13.9, 95% CI: 5.30–36.69). Conclusion HBV genotype is independently associated with HCC risk. AN persons with genotypes A, C, and F are at higher risk compared with genotypes B or D. PMID:27009849

Hepatitis B virus infection in Latin America: A genomic medicine approach

PubMed Central

Roman, Sonia; Jose-Abrego, Alexis; Fierro, Nora Alma; Escobedo-Melendez, Griselda; Ojeda-Granados, Claudia; Martinez-Lopez, Erika; Panduro, Arturo

2014-01-01

Hepatitis B virus (HBV) infection is the leading cause of severe chronic liver disease. This article provides a critical view of the importance of genomic medicine for the study of HBV infection and its clinical outcomes in Latin America. Three levels of evolutionary adaptation may correlate with the clinical outcomes of HBV infection. Infections in Latin America are predominantly of genotype H in Mexico and genotype F in Central and South America; these strains have historically circulated among the indigenous population. Both genotypes appear to be linked to a benign course of disease among the native and mestizo Mexicans and native South Americans. In contrast, genotypes F, A and D are common in acute and chronic infections among mestizos with Caucasian ancestry. Hepatocellular carcinoma is rare in Mexicans, but it has been associated with genotype F1b among Argentineans. This observation illustrates the significance of ascertaining the genetic and environmental factors involved in the development of HBV-related liver disease in Latin America, which contrast with those reported in other regions of the world. PMID:24966588

Market perceptions and opportunities for native plant production on the southern Colorado Plateau

Treesearch

Donna L. Peppin; Peter Z. Fule; Janet C. Lynn; Anne L. Mottek-Lucas; Carolyn Hull Sieg

2010-01-01

Increases in revegetation activities have created a large demand for locally adapted native plant materials (NPM) in the southwestern United States. Currently, there is a minimal supply of local genotypes to meet this demand. We investigated the potential for the initiation of a native plant market in the southern Colorado Plateau. Through a literature search,...

News from the protein mutability landscape.

PubMed

Hecht, Maximilian; Bromberg, Yana; Rost, Burkhard

2013-11-01

Some mutations of protein residues matter more than others, and these are often conserved evolutionarily. The explosion of deep sequencing and genotyping increasingly requires the distinction between effect and neutral variants. The simplest approach predicts all mutations of conserved residues to have an effect; however, this works poorly, at best. Many computational tools that are optimized to predict the impact of point mutations provide more detail. Here, we expand the perspective from the view of single variants to the level of sketching the entire mutability landscape. This landscape is defined by the impact of substituting every residue at each position in a protein by each of the 19 non-native amino acids. We review some of the powerful conclusions about protein function, stability and their robustness to mutation that can be drawn from such an analysis. Large-scale experimental and computational mutagenesis experiments are increasingly furthering our understanding of protein function and of the genotype-phenotype associations. We also discuss how these can be used to improve predictions of protein function and pathogenicity of missense variants. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

High prevalence of HBV/A1 subgenotype in native south Americans may be explained by recent economic developments in the Amazon.

PubMed

Godoy, Bibiane A; Gomes-Gouvêa, Michele S; Zagonel-Oliveira, Marcelo; Alvarado-Mora, Mónica V; Salzano, Francisco M; Pinho, João R R; Fagundes, Nelson J R

2016-09-01

Native American populations present the highest prevalence of Hepatitis B Virus (HBV) infection in the Americas, which may be associated to severe disease outcomes. Ten HBV genotypes (A–J) have been described, displaying a remarkable geographic structure, which most likely reflects historic patterns of human migrations. In this study, we characterize the HBV strains circulating in a historical sample of Native South Americans to characterize the historical viral dynamics in this population. The sample consisted of 1070 individuals belonging to 38 populations collected between 1965 and 1997. Presence of HBV DNA was checked by quantitative real-time PCR, and determination of HBV genotypes and subgenotypes was performed through sequencing and phylogenetic analysis of a fragment including part of HBsAg and Pol coding regions (S/Pol). A Bayesian Skyline Plot analysis was performed to compare the viral population dynamics of HBV/A1 strains found in Native Americans and in the general Brazilian population. A total of 109 individuals were positive for HBV DNA (~ 10%), and 70 samples were successfully sequenced and genotyped. Subgenotype A1 (HBV/A1), related to African populations and the African slave trade, was the most prevalent (66–94%). The Skyline Plot analysis showed a marked population expansion of HBV/A1 in Native Americans occurring more recently (1945–1965) than in the general Brazilian population. Our results suggest that historic processes that contributed to formation of HBV/A1 circulating in Native American are related with more recent migratory waves towards the Amazon basin, which generated a different viral dynamics in this region.

Tamarix (Tamaricaceae) hybrids: most dominant invasive genotype in southern Africa

USDA-ARS?s Scientific Manuscript database

Hybridization can potentially enhance invasiveness. Tamarix (Tamaricaceae) hybrids appear to be the dominant genotypes in their invasions. Exotic Tamarix are declared invasive in South Africa and the exotic T. chinensis and T. ramosissima are known to hybridize between themselves, and with the nativ...

Trends and differences in tuberculosis incidences and clustering among natives in Denmark, Sweden and Finland: comparison of native incidences and molecular epidemiology among three low-incidence countries.

PubMed

Pedersen, M K; Lillebaek, T; Andersen, A B; Soini, H; Haanperä, M; Groenheit, R; Jonsson, J; Svensson, E

2018-07-01

To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control. TB incidence trends from 1990 through 2015 were compared among the countries. In addition, for the periods 2012-2013 and 2014-2015, genotyping data were compared. Genotyping was performed using the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) method in Denmark and Sweden. For Finland, spoligotyping in conjunction with the 15-locus MIRU-VNTR method was used for 2012-2013 and translated into the 24-locus MIRU-VNTR when feasible, and for 2014-2015 only MIRU-VNTR was used. Both incidence trends and molecular epidemiology were assessed for native cases. The average annual rate of change in TB incidence for native Danes was -2.4% vs. -6.1% and -6.9% for native Swedes and Finns respectively. In 2012-2013 Denmark had 52 native cases in the largest transmission chain vs. three cases in Sweden and ten in Finland, and during the same period the clustering rate for native Danes was 48.8% vs. 6.5% and 18.2% for native Swedes and Finns respectively. For 2014-2015, a similar pattern was seen. The decline of TB among natives in Denmark is slower than for Sweden and Finland, and it seems Denmark has more active transmission among natives. The focused assessment on basic native TB epidemiology reveals striking differences in TB transmission among otherwise similar low-TB-incidence countries. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

MIRU-VNTR typing of drug-resistant tuberculosis isolates in Greece.

PubMed

Rovina, Nikoletta; Karabela, Simona; Constantoulakis, Pantelis; Michou, Vassiliki; Konstantinou, Konstantinos; Sgountzos, Vassileios; Roussos, Charis; Poulakis, Nikolaos

2011-08-01

The increasing immigration rate in Greece from countries with a high prevalence of Mycobacterium tuberculosis (MTB) and multidrug-resistant tuberculosis (MDR-TB) may have an impact οn the number of MDR-TB cases in Greece. The aim of this study was to genotypically characterize the MTB isolates from patients with pulmonary drug-resistant tuberculosis (DR-TB) in Greece, and to determine whether there is any association between the prevalent genotypes and drug resistance. Fifty-three drug-resistant MTB strains isolated from culture specimens of clinical material from native Greeks and immigrant patients with pulmonary tuberculosis were genotyped using the mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) method. The phylogenetically distinct groups of isolates identified were: the Beijing (34%), the LAM (11%), the Haarlem (24.5%), the Uganda I (9.4%), the Ural (3.8%), the Delhi/CAS (9.4%) and the Cameroon (3.8%) families. Greek patients were more likely to have monoresistant and polyresistant TB with the most prevalent isolates belonging to the Haarlem family. Among foreign-born patients with MDR-TB, the most prevalent genotypes belonged to the Beijing family. MIRU-VNTR rapidly obtained clinically useful genotyping data, by characterizing clonal MTB heterogeneity in the isolated strains. Our results underline the need for more effective antituberculosis control programs in order to control the expansion of DR-TB in Greece.

Genotype distribution and allele frequencies of the genes associated with body composition and locomotion traits in Myanmar native horses.

PubMed

Okuda, Yu; Moe, Hla Hla; Moe, Kyaw Kyaw; Shimizu, Yuki; Nishioka, Kenji; Shimogiri, Takeshi; Mannen, Hideyuki; Kanemaki, Misao; Kunieda, Tetsuo

2017-08-01

Myanmar native horses are small horses used mainly for drafting carts or carriages in rural areas and packing loads in mountainy areas. In the present study, we investigated genotype distributions and allele frequencies of the LCORL/NCAPG, MSTN and DMRT3 genes, which are associated with body composition and locomotion traits of horses, in seven local populations of Myanmar native horses. The genotyping result of LCORL/NCAPG showed that allele frequencies of C allele associated with higher withers height ranged from 0.08 to 0.27, and 0.13 in average. For MSTN, allele frequencies of C allele associated with higher proportion of Type 2B muscular fiber ranged from 0.05 to 0.23, and 0.09 in average. For DMRT3, allele frequencies of A allele associated with ambling gait ranged from 0 to 0.04, and 0.01 in average. The presences of the minor alleles of these genes at low frequencies suggest a possibility that these horse populations have not been under strong selection pressure for particular locomotion traits and body composition. Our findings of the presence of these minor alleles in Southeast Asian native horses are also informative for considering the origins of these minor alleles associated with body composition and locomotion traits in horse populations. © 2016 Japanese Society of Animal Science.

MRSA USA300 at Alaska Native Medical Center, Anchorage, Alaska, USA, 2000–2006

PubMed Central

Rudolph, Karen M.; Hennessy, Thomas W.; Zychowski, Diana L.; Asthi, Karthik; Boyle-Vavra, Susan; Daum, Robert S.

2012-01-01

To determine whether methicillin-resistant Staphylococcus aureus (MRSA) USA300 commonly caused infections among Alaska Natives, we examined clinical MRSA isolates from the Alaska Native Medical Center, Anchorage, during 2000–2006. Among Anchorage-region residents, USA300 was a minor constituent among MRSA isolates in 2000–2003 (11/68, 16%); by 2006, USA300 was the exclusive genotype identified (10/10). PMID:22264651

Geographic distribution of genetic variation among native and introduced populations of Chinese tallow tree, Triadica sebifera (Euphorbiaceae).

PubMed

DeWalt, Saara J; Siemann, Evan; Rogers, William E

2011-07-01

Invasive plants often display genetically determined variation in patterns of growth and resource allocation between native and introduced genotypes, as well as among genotypes within different regions of the introduced range. We examined patterns of genetic variation within and among native and introduced populations of the tetraploid Chinese tallow tree (Triadica sebifera, Euphorbiaceae) to determine whether nonselective evolutionary processes or the introduction history could contribute to previously observed phenotypic differences between native and introduced populations as well as among introduced populations. We used six microsatellite markers to study 12 native populations in China, 51 introduced populations in the southeastern USA, and one introduced population in Australia. Genetic diversity was greater within and among native populations than introduced populations. Within the southeastern USA, populations in Georgia and South Carolina differed substantially in their genetic composition and had greater genetic diversity than the rest of the southeastern USA. Greater genetic similarity between some populations in the native range and introduced range indicate a common provenance for Georgia and South Carolina populations that could have come from any of several western or southern Chinese populations and a different provenance for other southeastern USA populations and the Australian population, which were most similar to more northeastern Chinese populations. Differences among introduced populations in potentially adaptive traits (e.g., herbivore tolerance, herbivore resistance, growth rates) may result in part from the introduction history, in particular from differences present among source populations in the native range.

Propagating native Salicaceae for afforestation and restoration in New York City's five boroughs

Treesearch

Ronald S. Zalesny; Richard A. Hallett; Nancy Falxa-Raymond; Adam H. Wiese; Bruce A. Birr

2014-01-01

Identifying superior Salicaceae genotypes for afforestation and restoration activities in urban areas can greatly increase the provision of ecosystem services for long-term ecological sustainability. To address this opportunity, we collected native Populus L. (Salicaceae) and Salix L. (Salicaceae) scions from 3 sites on Staten...

Polymorphism of the bovine POU1F1 gene: allele frequencies and effects on milk production in three Iranian native breeds and Holstein cattle of Iran.

PubMed

Zakizadeh, S; Reissmann, M; Rahimi, G; Javaremi, A Nejati; Reinecke, P; Mirae-Ashtiani, S R; Shahrbabak, M Moradi

2007-08-01

The aim of this study was to estimate the allele frequencies in polymorphic site of exon six of POU1F1 gene in three Iranian native and Holstein cattle. Genomic DNA was extracted from 3 Iranian native cattle breeds, including 97 Mazandarani, 87 Sarabi, 112 Golpaygani and also 110 Holstein cattle. A 451 bp fragment of intron 5 and exon 6 were amplified and digested with HinfI restriction enzyme. Frequencies of allele A were 0.37, 0.27, 0.34 and 0.21 for Mazandarani, Sarabi, Golpaygani and Holstein cattle, respectively. Significant differences in genotype frequencies were found between Mazandarani or Golpaygani and Holstein cattle. No significant differences in genotype frequencies were found between Sarabi and Holstein cattle. Transition A to G in nucleotide 1256 is responsible for HinfI(-) allele. No significant association was observed between POU1F1 polymorphism and milk production. Differences in allelic frequency between native Bos indicus breeds (Mazandarani, Golpaygani) and Holstein at the present study might be due to differences in origin breeds, low number of samples and/or as the effect of natural selection in native breeds.

Incidence of hepatocellular carcinoma according to hepatitis B virus genotype in Alaska Native people.

PubMed

Ching, Lance K; Gounder, Prabhu P; Bulkow, Lisa; Spradling, Philip R; Bruce, Michael G; Negus, Susan; Snowball, Mary; McMahon, Brian J

2016-10-01

Most regions of the world have ≤3 co-circulating hepatitis B virus (HBV) genotypes, which limits direct comparisons of hepatocellular carcinoma (HCC) risk among HBV-infected persons by genotype. We evaluated HCC incidence by HBV genotype in a cohort of Alaska Native (AN) persons where five HBV genotypes (A, B, C, D, F) have been identified. Our cohort comprised AN persons with chronic HBV infection identified during 1983-2012 who consented to participate in this study. Cohort persons were offered annual hepatitis B e antigen (HBeAg) testing and semi-annual HCC screening. We developed a logistic regression model to compare HCC risk by genotype, adjusting for age, sex, region and HBeAg status. Among the 1235 consenting study participants, 711 (57.6%) were male, 510 (41.3%) were HBeAg positive at cohort entry and 43 (3.5%) developed HCC. The HBV genotype was known for 1142 (92.5%) persons (13.5% A, 3.9% B, 6.7% C, 56.9% D, 19.0% F). The HCC incidence/1000 person-years of follow-up for genotypes A, B, C, D and F was 1.3, 0, 5.5, 0.4 and 4.2 respectively. Compared with persons with HBV genotype B/D infection, the HCC risk was higher for persons with genotypes A [adjusted odds ratio (aOR): 3.9, 95% confidence interval (CI): 1.14-13.74], C (aOR: 16.3, 95% CI: 5.20-51.11) and F (aOR: 13.9, 95% CI: 5.30-36.69). HBV genotype is independently associated with HCC risk. AN persons with genotypes A, C and F are at higher risk compared with genotypes B or D. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Outlining the Ancestry Landscape of Colombian Admixed Populations

PubMed Central

Ossa, Humberto; Aquino, Juliana; Pereira, Rui; Ibarra, Adriana; Ossa, Rafael H; Pérez, Luz Adriana; Granda, Juan David; Lattig, Maria Claudia; Groot, Helena; Fagundes de Carvalho, Elizeu; Gusmão, Leonor

2016-01-01

The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population. Considering the importance of population substructure in both clinical and forensic genetics, we sought to investigate and compare patterns of genetic ancestry in Colombia by studying samples from Native and non-Native populations living in its 5 continental regions: the Andes, Caribe, Amazonia, Orinoquía, and Pacific regions. For this purpose, 46 AIM-Indels were genotyped in 761 non-related individuals from current populations. Previously published genotype data from 214 Colombian Natives from five communities were used for population comparisons. Significant differences were observed between Native and non-Native populations, among non-Native populations from different regions and among Native populations from different ethnic groups. The Pacific was the region with the highest African ancestry, Amazonia harboured the highest Native ancestry and the Andean and Orinoquían regions showed the highest proportion of European ancestry. The Andean region was further sub-divided into 6 sub-regions: North East, Central West, Central East, West, South West and South East. Among these regions, the South West region showed a significantly lower European admixture than the other regions. Hardy-Weinberg equilibrium and variance values of ancestry among individuals within populations showed a potential stratification of the Pacific population. PMID:27736937

Meat quality and fatty acid profile of Brazilian goats subjected to different nutritional treatments.

PubMed

Lopes, L S; Martins, S R; Chizzotti, M L; Busato, K C; Oliveira, I M; Machado Neto, O R; Paulino, P V R; Lanna, D P D; Ladeira, M M

2014-08-01

This study evaluated the effect of feed restriction and goat genotype on meat quality. Three genotypes (Brazilian native breed Canindé; Brazilian native breed Moxotó; and F1 Boer crossbred animals obtained by crossing Boer bucks with local breed does) and three different feeding regimens (ad libitum fed, AL; restricted fed at 75% of the ad libitum, R.75; or restricted fed at 50% of the average ad libitum intake, R.50) were used. There was no difference (P>0.05) in chemical composition, total and soluble collagen, and shear force of the Longissimus lumborum muscle among genotypes. However, AL had greater amounts of soluble collagen and crude protein in the muscle (P<0.05) than R.75. No difference (P>0.05) was observed for the myofibrillar fragmentation index. The goat genotype presented few differences in their fatty acid profiles. However, goats fed ad libitum had a more favorable fatty acid profile for human health with greater concentrations of oleic acid, unsaturated fatty acids, and conjugated linoleic acid. Copyright © 2014 Elsevier Ltd. All rights reserved.

PrP genotype frequencies and risk evaluation for scrapie in dairy sheep breeds from southern Italy.

PubMed

Martemucci, Giovanni; Iamartino, Daniela; Blasi, Michele; D'Alessandro, Angela Gabriella

2015-12-01

Concerns regarding scrapie in sheep breeding have increased in the last few decades. The present study was carried out in dairy sheep breeds from southern Italy. In order to find breeding animals resistant to scrapie, the PrP genes of 1,205 animals from entire flocks of dairy native Apulian Leccese and Altamurana breeds, and Sicilian Comisana breed, were analysed for polymorphisms at codons 136, 154, and 171 related to scrapie resistance/susceptibility. The Altamurana breed was considered as two populations (Alt-Cav and Alt-Cra-Zoe), based on presumed cross-breeding. A total of five alleles and ten different genotypes were found. The ARQ allele was predominant for all breeds followed by ARR, the most resistant allele to scrapie, which was highly prevalent in Comisana (50%) and in native Alt-Cav (42.4%). The VRQ allele, associated with the highest susceptibility to scrapie, was detected at not negligeable levels in allocthonous Comisana (3.5%), at a low frequency (0.2%) in native Leccese and Alt-Cra-Zoe, while it was absent in Alt-Cav. The frequencies of PrP genotypes with a very low susceptibility risk to scrapie (R1) was higher in Comisana and Alt-Cav. The most susceptible genotype, ARQ/VRQ, was found only in Comisana. Within the Altamurana breed, there were notable differences between Alt-Cav and Alt-Cra-Zoe sheep. The Alt-Cav was characterised by the absence of VRQ and AHQ alleles and by the higher frequency of the ARR/ARR genotype (18.7%). Breeding programs, mainly in endangered breeds such as Altamurana, should be conducted gradually, combining resistance to scrapie, maintenance of genetic variability, and production. Copyright © 2015 Elsevier B.V. All rights reserved.

Phenotypic and genotypic analysis of a U.S. native fine-leaved Festuca population portends its potential use for low-input urban landscapes

USDA-ARS?s Scientific Manuscript database

Continued reduction in limited natural resources worldwide increasingly necessitates the incorporation of low maintenance and input plant materials into urban landscapes. Although some fine-leaved Festuca grass species have been utilized in formal gardens and native urban landscapes because of thei...

Native valve endocarditis due to a novel strain of Legionella.

PubMed

Pearce, Meghan M; Theodoropoulos, Nicole; Noskin, Gary A; Flaherty, John P; Stemper, Mary E; Aspeslet, Teresa; Cianciotto, Nicholas P; Reed, Kurt D

2011-09-01

Legionellae are Gram-negative bacteria which are capable of causing disease, most commonly in the form of pneumonia. We describe a case of native valve endocarditis caused by a Legionella strain which by genotypic (16S rRNA and mip gene sequencing) and phenotypic analyses is unlike previously described strains of Legionella.

Variation in resistance of hard pines to mouse damage

Treesearch

Frank S., Jr. Santamour; Frank E. Cunningham; Richard J. Peterson

1963-01-01

The most rapid progress in forest-tree improvement will be attained through artificial reforestation with superior genotypes. These trees may be native species, exotics, or hybrid combinations involving several species of diverse origins. Any tree planting creates an artificial situation, which is made even more artificial by the introduction of non-native types. In...

Assessing the cryptic invasion of a domestic conspecific: American mink in their native range

PubMed Central

Beauclerc, Kaela B; Bowman, Jeff; Schulte-Hostedde, Albrecht I

2013-01-01

Control of invasions is facilitated by their early detection, but this may be difficult when invasions are cryptic due to similarity between invaders and native species. Domesticated conspecifics offer an interesting example of cryptic invasions because they have the ability to hybridize with their native counterparts, and can thus facilitate the introgression of maladaptive genes. We assessed the cryptic invasion of escaped domestic American mink (Neovison vison) within their native range. Feral mink are a known alien invader in many parts of the world, but invasion of their native range is not well understood. We genetically profiled 233 captive domestic mink from different farms in Ontario, Canada and 299 free-ranging mink from Ontario, and used assignments tests to ascertain genetic ancestries of free-ranging animals. We found that 18% of free-ranging mink were either escaped domestic animals or hybrids, and a tree regression showed that these domestic genotypes were most likely to occur south of a latitude of 43.13°N, within the distribution of mink farms in Ontario. Thus, domestic mink appear not to have established populations in Ontario in locations without fur farms. We suspect that maladaptation of domestic mink and outbreeding depression of hybrid and introgressed mink have limited their spread. Mink farm density and proximity to mink farms were not important predictors of domestic genotypes but rather, certain mink farms appeared to be important sources of escaped domestic animals. Our results show that not all mink farms are equal with respect to biosecurity, and thus that the spread of domestic genotypes can be mitigated by improved biosecurity. PMID:23919171

Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad

PubMed Central

Sievers, Caya; Willing, Eva-Maria; Hoffmann, Margarete; Dreyer, Christine; Ramnarine, Indar; Magurran, Anne

2012-01-01

The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype. PMID:22693621

Reproductive system, social organization, human disturbance and ecological dominance in native populations of the little fire ant, Wasmannia auropunctata.

PubMed

Foucaud, Julien; Orivel, Jérôme; Fournier, Denis; Delabie, Jacques H C; Loiseau, Anne; Le Breton, Julien; Cerdan, Philippe; Estoup, Arnaud

2009-12-01

The invasive ant species Wasmannia auropunctata displays both ecologically dominant and non-dominant populations within its native range. Three factors could theoretically explain the ecological dominance of some native populations of W. auropunctata: (i) its clonal reproductive system, through demographic and/or adaptive advantages; (ii) its unicolonial social organization, through lower intraspecific and efficient interspecific competition; (iii) the human disturbance of its native range, through the modification of biotic and abiotic environmental conditions. We used microsatellite markers and behavioural tests to uncover the reproductive modes and social organization of dominant and non-dominant native populations in natural and human-modified habitats. Microsatellite and mtDNA data indicated that dominant and non-dominant native populations (supercolonies as determined by aggression tests) of W. auropunctata did not belong to different evolutionary units. We found that the reproductive system and the social organization are neither necessary nor sufficient to explain W. auropunctata ecological dominance. Dominance rather seems to be set off by unknown ecological factors altered by human activities, as all dominant populations were recorded in human-modified habitats. The clonal reproductive system found in some populations of W. auropunctata may however indirectly contribute to its ecological dominance by allowing the species to expand its environmental niche, through the fixation over time of specific combinations of divergent male and female genotypes. Unicoloniality may rather promote the range expansion of already dominant populations than actually trigger ecological dominance. The W. auropunctata model illustrates the strong impact of human disturbance on species' ecological features and the adaptive potential of clonal reproductive systems.

[Correlation between adenylosuccinate lyase (ADSL) gene polymorphism and inosine monophosphate acid (IMP) content in domestic fowl and genetic relationship between red jungle fowl and domestic fowl].

PubMed

Shu, Jing-Ting; Bao, Wen-Bin; Zhang, Hong-Xia; Zhang, Xue-Yu; Ji, Cong-Liang; Chen, Guo-Hong

2007-03-01

This study investigates single nucleotide polymorphism (SNP) of the adenylosuccinate lyase(ADSL) gene in variety chicken breeds, including Recessive White chickens, Silkies chickens, Baier chickens, Tibetan chickens and two red jungle fowls. Primers for exon 2 in ADSL gene were designed based on the chicken genomic sequence and a SNP(C/T at 3484) was detected by PCR-SSCP and DNA sequencing. Three genotypes within all breeds were found and least square analysis showed that TT genotype birds had a significant higher inosine monophosphate acid (IMP) content than TC (P < 0.01) and CC (P < 0.05) genotype birds, TC genotype birds had a little higher IMP content than CC genotype birds, but the difference was not significant. We proposed this SNP site correlated with IMP content in chickens. A neighbour-joining dendrogram was constructed based on the Nei's genentic distance. The genetic relationship between Chinese red jungle fowl and Tibetan chickens was the nearest, whereas Baier chickens were more closer to Silkies chickens. The Chinese red jungle fowls were relatively closer to the domestic fowls, whereas Thailand red jungle fowls were relatively diverging to the Chinese native breeds. These results supported the theory concerning the independent origins of Chinese native fowl breeds.

Native Valve Endocarditis Due to a Novel Strain of Legionella ▿

PubMed Central

Pearce, Meghan M.; Theodoropoulos, Nicole; Noskin, Gary A.; Flaherty, John P.; Stemper, Mary E.; Aspeslet, Teresa; Cianciotto, Nicholas P.; Reed, Kurt D.

2011-01-01

Legionellae are Gram-negative bacteria which are capable of causing disease, most commonly in the form of pneumonia. We describe a case of native valve endocarditis caused by a Legionella strain which by genotypic (16S rRNA and mip gene sequencing) and phenotypic analyses is unlike previously described strains of Legionella. PMID:21795511

Geographical Distribution of Trypanosoma cruzi Genotypes in Venezuela

PubMed Central

Carrasco, Hernán J.; Segovia, Maikell; Llewellyn, Martin S.; Morocoima, Antonio; Urdaneta-Morales, Servio; Martínez, Cinda; Martínez, Clara E.; Garcia, Carlos; Rodríguez, Marlenes; Espinosa, Raul; de Noya, Belkisyolé A.; Díaz-Bello, Zoraida; Herrera, Leidi; Fitzpatrick, Sinead; Yeo, Matthew; Miles, Michael A.; Feliciangeli, M. Dora

2012-01-01

Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI – TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela. PMID:22745843

Geographical distribution of Trypanosoma cruzi genotypes in Venezuela.

PubMed

Carrasco, Hernán J; Segovia, Maikell; Llewellyn, Martin S; Morocoima, Antonio; Urdaneta-Morales, Servio; Martínez, Cinda; Martínez, Clara E; Garcia, Carlos; Rodríguez, Marlenes; Espinosa, Raul; de Noya, Belkisyolé A; Díaz-Bello, Zoraida; Herrera, Leidi; Fitzpatrick, Sinead; Yeo, Matthew; Miles, Michael A; Feliciangeli, M Dora

2012-01-01

Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI - TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela.

A tale of agriculturalists and hunter-gatherers: Exploring the thrifty genotype hypothesis in native South Americans.

PubMed

Reales, Guillermo; Rovaris, Diego L; Jacovas, Vanessa C; Hünemeier, Tábita; Sandoval, José R; Salazar-Granara, Alcibiades; Demarchi, Darío A; Tarazona-Santos, Eduardo; Felkl, Aline B; Serafini, Michele A; Salzano, Francisco M; Bisso-Machado, Rafael; Comas, David; Paixão-Côrtes, Vanessa R; Bortolini, Maria Cátira

2017-07-01

To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations. 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed. We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (F CT ) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals. A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations. © 2017 Wiley Periodicals, Inc.

Ostreid herpesvirus type 1 genomic diversity in wild populations of Pacific oyster Crassostrea gigas from Italian coasts.

PubMed

Burioli, E A V; Prearo, M; Riina, M V; Bona, M C; Fioravanti, M L; Arcangeli, G; Houssin, M

2016-06-01

Ostreid herpesvirus 1 (OsHV-1) is a significant pathogen affecting the young Pacific oyster Crassostrea gigas, worldwide. A new variant, OsHV-1 μVar, has been associated with recurrent mortality events in Europe since 2008. Epidemiological data collection is key for global risk assessment; however little is known about health status and genotypes present in European wild oyster beds. Most studies to date have involved only cultivated individuals during mortality events, and reported low genotype diversity. With this study, conducted along the Italian coasts, we investigated for the first time the presence of OsHV-1 in European natural oyster beds. Analysis of three genomic regions revealed the presence of at least nine different genotypes, including two variants close to the OsHV-1 reference, known since the early 1990s but with no European record reported since 2010, and highlights relevant genotype diversity in natural environment. Phylogenetic analysis distinguished two distinct clusters and geographical distribution of genotypes, with the exception of a variant very closely related to the μVar, which appeared the single genotype present in all the Adriatic sites. Interestingly, these wild symptom free populations could represent, in Europe, an accessible alternative to the import of OsHV-1-resistant oyster strains from the East Pacific, the native area of C. gigas, avoiding the high-risk of non-native marine species and new pathogen introductions. Copyright © 2016 Elsevier Inc. All rights reserved.

AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

PubMed

Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

2016-04-01

Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

Self-reported Ethnicity, Genetic Structure and the Impact of Population Stratification in a Multiethnic Study

PubMed Central

Wang, Hansong; Haiman, Christopher A.; Kolonel, Laurence N.; Henderson, Brian E.; Wilkens, Lynne R.; Le Marchand, Loïc; Stram, Daniel O.

2011-01-01

It is well-known that population substructure may lead to confounding in case-control association studies. Here, we examined genetic structure in a large racially and ethnically diverse sample consisting of 5 ethnic groups of the Multiethnic Cohort study (African Americans, Japanese Americans, Latinos, European Americans and Native Hawaiians) using 2,509 SNPs distributed across the genome. Principal component analysis on 6,213 study participants, 18 Native Americans and 11 HapMap III populations revealed 4 important principal components (PCs): the first two separated Asians, Europeans and Africans, and the third and fourth corresponded to Native American and Native Hawaiian (Polynesian) ancestry, respectively. Individual ethnic composition derived from self-reported parental information matched well to genetic ancestry for Japanese and European Americans. STRUCTURE-estimated individual ancestral proportions for African Americans and Latinos are consistent with previous reports. We quantified the East Asian (mean 27%), European (mean 27%) and Polynesian (mean 46%) ancestral proportions for the first time, to our knowledge, for Native Hawaiians. Simulations based on realistic settings of case-control studies nested in the Multiethnic Cohort found that the effect of population stratification was modest and readily corrected by adjusting for race/ethnicity or by adjusting for top PCs derived from all SNPs or from ancestry informative markers; the power of these approaches was similar when averaged across causal variants simulated based on allele frequencies of the 2,509 genotyped markers. The bias may be large in case-only analysis of gene by gene interactions but it can be corrected by top PCs derived from all SNPs. PMID:20499252

Differential physiological and metabolic response to low temperature in two zoysiagrass genotypes native to high and low latitude

PubMed Central

Zhang, Qiang; Liu, Ningfang; Xu, Qingguo

2018-01-01

Low temperature is one of the important limiting factors for growing season and geographical distribution of plants. Zoysiagrass (Zoysia Willd) is one of the widely used warm-season turfgrass that is distribute in many parts of the world. Zoysaigrass native to high latitude may have evolved higher cold tolerance than the ones native to low latitude. The objective of this study was to investigate the cold stress response in zoysiagrass native to diverse latitude at phenotypic, physiological and metabolic levels. Two zoysiagrass (Z. japonica) genotypes, Latitude-40 (higher latitude) and Latitude-22 (lower latitude) were subjected to four temperature treatments (optimum, 30/25°C, day/night; suboptimum, 18/12°C; chilling, 8/2°C; freezing, 2/-4°C) progressively in growth chambers. Low temperature (chilling and freezing) increased leaf electrolyte leakage (EL) and reduced plant growth, turf quality, chlorophyll (Chl) content, photochemical efficiency (Fv/Fm) and photosynthesis (Pn, net photosynthetic rate; gs, stomatal conductance; intercellular CO2; Tr, transpiration rate) in two genotypes, with more rapid changes in Latitude-22. Leaf carbohydrates content (glucose, fructose, sucrose, trehalose, fructan, starch) increased with the decreasing of temperature, to a great extend in Latitude-40. Leaf abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA) content increased, while indole-3-acetic acid (IAA), gibberellic acid (GA3) and trans-zeatin ribside (t-ZR) content decreased with the reduction of temperature, with higher content in Latitude-40 than in Latitude-22. Chilling and freezing induced the up-regulation of C-repeat binding factor (ZjCBF), late embryogenesis abundant (ZjLEA3) and dehydration-responsive element binding (ZjDREB1) transcription factors in two genotypes, whereas those genes exhibited higher expression levels in Latitude-40, particularly under freezing temperature. These results suggested that zoysiagrass native to higher latitude exhibited higher freezing tolerance may attribute to the higher carbohydrates serving as energy reserves and stress protectants that stabilize cellular membranes. The phytohormones may serve signals in regulating plant growth, development and adaptation to low temperature as well as inducing the up-regulated ZjCBF, ZjLEA3 and ZjDREB1 expressions thus result in a higher cold tolerance. PMID:29889884

Red blood cell antigen genotype analysis for 9087 Asian, Asian American, and Native American blood donors.

PubMed

Delaney, Meghan; Harris, Samantha; Haile, Askale; Johnsen, Jill; Teramura, Gayle; Nelson, Karen

2015-10-01

There has yet to be a comprehensive analysis of blood group antigen prevalence in Asian Americans and Native Americans. There may be ethnic differences in blood group frequencies that would result in clinically important mismatches through transfusion. Blood donors who self-identified as Asian or Native American were tested using a single-nucleotide polymorphism (SNP) DNA array (HEA BeadChip kit, Bioarray Solutions Ltd) that predicts expression of 38 human erythrocyte antigens (HEAs) and by serology for ABO, D, C, M, N, Jk(a) , and Jk(b) . The prevalence of blood group antigens was compared to published European prevalence. Discrepancies between SNP-predicted and serology-detected antigens were tallied. A total of 9087 blood donors were tested from nine Asian and Native American heritages. The predicted prevalence of selected antigens in the RHCE, JK, FY, MNS, LU, CO, and DO blood group systems were variable between Asian populations, but overall not significantly different than Europeans. Compared to European frequencies, Kell blood group allele frequencies were significantly different in the Chinese, Native American, Hawaiian/Pacific Islander, South Asian, and Southeast Asian heritage blood donors; Diego antigens Di(a) and Di(b) were different in donors of Native American and South Asian ancestries (p < 0.05). Of the donors tested, 4.5% showed a SNP-serology discrepancy that segregated within specific ethnic groups. This study provides HEA allele frequency and antigen prevalence data in a cohort of Asian and Native Americans donors. Several ethnic groups exhibited differences in HEA frequencies compared to Europeans. Genotype-serotype discrepancies were detected in all systems studied. © 2015 AABB.

Population frequencies of the Triallelic 5HTTLPR in six Ethnicially diverse samples from North America, Southeast Asia, and Africa.

PubMed

Haberstick, Brett C; Smolen, Andrew; Williams, Redford B; Bishop, George D; Foshee, Vangie A; Thornberry, Terence P; Conger, Rand; Siegler, Ilene C; Zhang, Xiaodong; Boardman, Jason D; Frajzyngier, Zygmunt; Stallings, Michael C; Brent Donnellan, M; Halpern, Carolyn T; Harris, Kathleen Mullan

2015-03-01

Genetic differences between populations are potentially an important contributor to health disparities around the globe. As differences in gene frequencies influence study design, it is important to have a thorough understanding of the natural variation of the genetic variant(s) of interest. Along these lines, we characterized the variation of the 5HTTLPR and rs25531 polymorphisms in six samples from North America, Southeast Asia, and Africa (Cameroon) that differ in their racial and ethnic composition. Allele and genotype frequencies were determined for 24,066 participants. Results indicated higher frequencies of the rs25531 G-allele among Black and African populations as compared with White, Hispanic and Asian populations. Further, we observed a greater number of 'extra-long' ('XL') 5HTTLPR alleles than have previously been reported. Extra-long alleles occurred almost entirely among Asian, Black and Non-White Hispanic populations as compared with White and Native American populations where they were completely absent. Lastly, when considered jointly, we observed between sample differences in the genotype frequencies within racial and ethnic populations. Taken together, these data underscore the importance of characterizing the L-G allele to avoid misclassification of participants by genotype and for further studies of the impact XL alleles may have on the transcriptional efficiency of SLC6A4.

Rapid growth of a Eurasian haplotype of Phragmites australis in a restored brackish marsh in Louisiana, USA

USGS Publications Warehouse

Howard, R.J.; Travis, S.E.; Sikes, B.A.

2008-01-01

While numerous studies have documented patterns of invasion by non-indigenous plant species, few have considered the invasive properties of non-native genotypes of native species. Characteristics associated with specific genotypes, such as tolerance to disturbance, may mistakenly be applied to an entire species in the absence of genetic information, which consequently may affect management decisions. We report here on the incidence and growth of an introduced lineage of Phragmites australis in the Gulf of Mexico coastal zone of Louisiana. P. australis was collected from nine separate locations for inclusion in a series of growth experiments. Chloroplast DNA analysis indicated that specimens collected from four locations in the Mississippi River Delta represented the introduced Eurasian haplotype; the remainder represented the gulf coast haplotype. Three distinct genotypes, or clones, were identified within each haplotype via analysis using amplified fragment length polymorphisms, which also revealed reduced genetic diversity of the gulf coast clones compared to the Eurasian clones. Clones of each haplotype were planted along with three other native macrophytes at similar densities in a restored brackish marsh and monitored for growth. After 14 months, the Eurasian haplotype had spread vegetatively to cover about 82% of the experimental plots, more than four times the coverage (18%) of the gulf coast haplotype. Thus, the use of P. australis plantings for wetland restoration should consider the genetic lineage of plants used since our results indicate the potential of the Eurasian haplotype to grow rapidly at newly restored sites. This rapid growth may limit the establishment of more slowly growing native species. ?? 2007 Springer Science+Business Media B.V.

Changes in Soil Physical and Chemical Properties in Long Term Improved Natural and Traditional Agroforestry Management Systems of Cacao Genotypes in Peruvian Amazon

PubMed Central

Arévalo-Gardini, Enrique; Canto, Manuel; Alegre, Julio; Loli, Oscar; Julca, Alberto; Baligar, Virupax

2015-01-01

Growing cacao (Theobroma cacao L.) in an agroforestry system generates a productive use of the land, preserves the best conditions for physical, chemical and biological properties of tropical soils, and plays an important role in improving cacao production and fertility of degraded tropical soils. The aim of this study was to evaluate the impact of two long term agroforestry systems of cacao management on soil physical and chemical properties in an area originally inhabited by 30 years old native secondary forest (SF). The two agroforestry systems adapted were: improved natural agroforestry system (INAS) where trees without economic value were selectively removed to provide 50% shade and improved traditional agroforestry system (ITAS) where all native trees were cut and burnt in the location. For evaluation of the changes of soil physical and chemical properties with time due to the imposed cacao management systems, plots of 10 cacao genotypes (ICS95, UF613, CCN51, ICT1112, ICT1026, ICT2162, ICT2171, ICT2142, H35, U30) and one plot with a spontaneous hybrid were selected. Soil samples were taken at 0-20, 20-40 and 40-60 cm depths before the installation of the management systems (2004), and then followed at two years intervals. Bulk density, porosity, field capacity and wilting point varied significantly during the years of assessment in the different soil depths and under the systems assessed. Soil pH, CEC, exchangeable Mg and sum of the bases were higher in the INAS than the ITAS. In both systems, SOM, Ext. P, K and Fe, exch. K, Mg and Al+H decreased with years of cultivation; these changes were more evident in the 0-20 cm soil depth. Overall improvement of SOM and soil nutrient status was much higher in the ITAS than INAS. The levels of physical and chemical properties of soil under cacao genotypes showed a marked difference in both systems. PMID:26181053

Changes in soil physical and chemical properties in long term improved natural and traditional agroforestry management systems of cacao genotypes in Peruvian Amazon.

PubMed

Arévalo-Gardini, Enrique; Canto, Manuel; Alegre, Julio; Loli, Oscar; Julca, Alberto; Baligar, Virupax

2015-01-01

Growing cacao (Theobroma cacao L.) in an agroforestry system generates a productive use of the land, preserves the best conditions for physical, chemical and biological properties of tropical soils, and plays an important role in improving cacao production and fertility of degraded tropical soils. The aim of this study was to evaluate the impact of two long term agroforestry systems of cacao management on soil physical and chemical properties in an area originally inhabited by 30 years old native secondary forest (SF). The two agroforestry systems adapted were: improved natural agroforestry system (INAS) where trees without economic value were selectively removed to provide 50% shade and improved traditional agroforestry system (ITAS) where all native trees were cut and burnt in the location. For evaluation of the changes of soil physical and chemical properties with time due to the imposed cacao management systems, plots of 10 cacao genotypes (ICS95, UF613, CCN51, ICT1112, ICT1026, ICT2162, ICT2171, ICT2142, H35, U30) and one plot with a spontaneous hybrid were selected. Soil samples were taken at 0-20, 20-40 and 40-60 cm depths before the installation of the management systems (2004), and then followed at two years intervals. Bulk density, porosity, field capacity and wilting point varied significantly during the years of assessment in the different soil depths and under the systems assessed. Soil pH, CEC, exchangeable Mg and sum of the bases were higher in the INAS than the ITAS. In both systems, SOM, Ext. P, K and Fe, exch. K, Mg and Al+H decreased with years of cultivation; these changes were more evident in the 0-20 cm soil depth. Overall improvement of SOM and soil nutrient status was much higher in the ITAS than INAS. The levels of physical and chemical properties of soil under cacao genotypes showed a marked difference in both systems.

The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial DNA genome.

PubMed

Catelli, María Laura; Alvarez-Iglesias, Vanesa; Gómez-Carballa, Alberto; Mosquera-Miguel, Ana; Romanini, Carola; Borosky, Alicia; Amigo, Jorge; Carracedo, Angel; Vullo, Carlos; Salas, Antonio

2011-08-30

The genetic background of Argentineans is a mosaic of different continental ancestries. From colonial to present times, the genetic contribution of Europeans and sub-Saharan Africans has superposed to or replaced the indigenous genetic 'stratum'. A sample of 384 individuals representing different Argentinean provinces was collected and genotyped for the first and the second mitochondrial DNA (mtDNA) hypervariable regions, and selectively genotyped for mtDNA SNPs. This data was analyzed together with additional 440 profiles from rural and urban populations plus 304 from Native American Argentineans, all available from the literature. A worldwide database was used for phylogeographic inferences, inter-population comparisons, and admixture analysis. Samples identified as belonging to hg (hg) H2a5 were sequenced for the entire mtDNA genome. Phylogenetic and admixture analyses indicate that only half of the Native American component in urban Argentineans might be attributed to the legacy of extinct ancestral Argentineans and that the Spanish genetic contribution is slightly higher than the Italian one. Entire H2a5 genomes linked these Argentinean mtDNAs to the Basque Country and improved the phylogeny of this Basque autochthonous clade. The fingerprint of African slaves in urban Argentinean mtDNAs was low and it can be phylogeographically attributed predominantly to western African. The European component is significantly more prevalent in the Buenos Aires province, the main gate of entrance for Atlantic immigration to Argentina, while the Native American component is larger in North and South Argentina. AMOVA, Principal Component Analysis and hgs/haplotype patterns in Argentina revealed an important level of genetic sub-structure in the country. Studies aimed to compare mtDNA frequency profiles from different Argentinean geographical regions (e.g., forensic and case-control studies) should take into account the important genetic heterogeneity of the country in order to prevent false positive claims of association in disease studies or inadequate evaluation of forensic evidence.

Hybridization and cytonuclear associations among native westslope cutthroat trout, introduced rainbow trout, and their hybrids within the Stehekin River drainage, North Cascades National Park

USGS Publications Warehouse

Ostberg, C.O.; Rodriguez, R.J.

2006-01-01

Historic introductions of nonnative rainbow trout Oncorhynchus mykiss into the native habitats of cutthroat trout O. clarkii have impacted cutthroat trout populations through introgressive hybridization, creating challenges and concerns for cutthroat trout conservation. We examined the effects of rainbow trout introductions on the native westslope cutthroat trout O. c. lewisii within the Stehekin River drainage, North Cascades National Park, Washington, by analyzing 1,763 salmonid DNA samples from 18 locations with nine diagnostic nuclear DNA markers and one diagnostic mitochondrial DNA (mtDNA) marker. Pure westslope cutthroat trout populations only occurred above upstream migration barriers in the Stehekin River and Park Creek. Two categories of rainbow trout admixture were observed: (1) less than 10% within the Stehekin River drainage above the Bridge Creek confluence and the middle and upper Bridge Creek drainage and (2) greater than 30% within the Stehekin River below the Bridge Creek confluence and in lower Bridge Creek. Hybrid indices and multilocus genotypes revealed an absence of rainbow trout and reduced hybrid diversity within the Stehekin River above the Bridge Creek confluence relative to hybrid diversity in the Stehekin River below the confluence and within lower Bridge Creek. Cytonuclear disequilibrium statistics revealed assortative mating between westslope cutthroat and rainbow trout but not among hybrids within the same locations. This suggests that a randomly mating hybrid swarm does not currently exist. However, continual migration of parental genotypes into the study location could also create significant cytonuclear disequilibria. The Stehekin River represents a novel and unique example of a dynamic hybridization zone where the invasion of rainbow trout alleles into the Stehekin River westslope cutthroat trout population above the Bridge Creek confluence appears to be impeded, suggesting that divergent ecological or evolutionary mechanisms promote the population structure within the Stehekin River drainage, depending upon location.

The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial DNA genome

PubMed Central

2011-01-01

Background The genetic background of Argentineans is a mosaic of different continental ancestries. From colonial to present times, the genetic contribution of Europeans and sub-Saharan Africans has superposed to or replaced the indigenous genetic 'stratum'. A sample of 384 individuals representing different Argentinean provinces was collected and genotyped for the first and the second mitochondrial DNA (mtDNA) hypervariable regions, and selectively genotyped for mtDNA SNPs. This data was analyzed together with additional 440 profiles from rural and urban populations plus 304 from Native American Argentineans, all available from the literature. A worldwide database was used for phylogeographic inferences, inter-population comparisons, and admixture analysis. Samples identified as belonging to hg (hg) H2a5 were sequenced for the entire mtDNA genome. Results Phylogenetic and admixture analyses indicate that only half of the Native American component in urban Argentineans might be attributed to the legacy of extinct ancestral Argentineans and that the Spanish genetic contribution is slightly higher than the Italian one. Entire H2a5 genomes linked these Argentinean mtDNAs to the Basque Country and improved the phylogeny of this Basque autochthonous clade. The fingerprint of African slaves in urban Argentinean mtDNAs was low and it can be phylogeographically attributed predominantly to western African. The European component is significantly more prevalent in the Buenos Aires province, the main gate of entrance for Atlantic immigration to Argentina, while the Native American component is larger in North and South Argentina. AMOVA, Principal Component Analysis and hgs/haplotype patterns in Argentina revealed an important level of genetic sub-structure in the country. Conclusions Studies aimed to compare mtDNA frequency profiles from different Argentinean geographical regions (e.g., forensic and case-control studies) should take into account the important genetic heterogeneity of the country in order to prevent false positive claims of association in disease studies or inadequate evaluation of forensic evidence. PMID:21878127

Hybridization dynamics between Colorado's native cutthroat trout and introduced rainbow trout.

PubMed

Metcalf, Jessica L; Siegle, Matthew R; Martin, Andrew P

2008-01-01

Newly formed hybrid populations provide an opportunity to examine the initial consequences of secondary contact between species and identify genetic patterns that may be important early in the evolution of hybrid inviability. Widespread introductions of rainbow trout (Oncorhynchus mykiss) into watersheds with native cutthroat trout (Oncorhynchus clarkii) have resulted in hybridization. These introductions have contributed to the decline of native cutthroat trout populations. Here, we examine the pattern of hybridization between introduced rainbow trout and 2 populations of cutthroat trout native to Colorado. For this study, we utilized 7 diagnostic, codominant nuclear markers and a diagnostic mitochondrial marker to investigate hybridization in a population of greenback cutthroat trout (Oncorhynchus clarkii stomias) and a population of Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). We infer that cutthroat-rainbow trout hybrid swarms have formed in both populations. Although a mixture of hybrid genotypes was present, not all genotype combinations were detected at expected frequencies. We found evidence that mitochondrial DNA introgression in hybrids is asymmetric and more likely from rainbow trout than from cutthroat trout. A difference in spawning time of the 2 species or differences in the fitness between the reciprocal crosses may explain the asymmetry. Additionally, the presence of intraspecific cytonuclear associations found in both populations is concordant with current hypotheses regarding coevolution of mitochondrial and nuclear genomes.

Multilocus genotyping of Giardia duodenalis and Enterocytozoon bieneusi in dairy and native beef (Qinchuan) calves in Shaanxi province, northwestern China.

PubMed

Wang, X T; Wang, R J; Ren, G J; Yu, Z Q; Zhang, L X; Zhang, S Y; Lu, H; Peng, X Q; Zhao, G H

2016-03-01

Giardia duodenalis and Enterocytozoon bieneusi are two common protozoa that parasitize the intestinal epithelium of animals and humans. Calves have been identified as important reservoirs of these two pathogens, but limited data is available for these two pathogens in calves in China. In the present study, the prevalence and assemblages/genotypes of both parasites in calves of dairy and native beef (Qinchuan) cattle in Shaanxi province, northwestern China, were analyzed using multilocus genotyping (MLST). Of 371 fecal samples collected from calves (including 198 dairy calves and 173 Qinchuan calves), the respective overall prevalence of G. duodenalis and E. bieneusi was 18.87 (70 of 371) and 19.68 % (73 of 371). Both the zoonotic G. duodenalis assemblage A and animal adapted assemblage E were found in dairy and Qinchuan calves. Seventeen, eight, five, and two G. duodenalis subtypes were detected at the triose phosphate isomerase (tpi), β-giardin (bg), glutamate dehydrogenase (gdh), and small subunit ribosomal RNA (SSU-rRNA) loci, with five and two novel subtypes detected at the tpi and bg loci, forming 25 multiple genotypes (MLGs) (15 and 11 in dairy and Qinchuan calves, respectively). Of 73 samples that were positive for E. bieneusi at the ribosomal RNA internal transcribed spacer (ITS) locus, five ITS genotypes were found, including three known zoonotic genotypes (I, J, CHN1) and two novel genotypes (CSX1 and CSX2). MLST analysis of three microsatellite loci (MS1, MS3, MS7) and one minisatellite locus (MS4) detected six, two, two, and two genotypes at the MS1, MS3, MS4, and MS7 loci, respectively, forming ten MLGs (seven and four in dairy and Qinchuan calves, respectively). These results indicate complex population structures of G. duodenalis and E. bieneusi in calves in Shaanxi province and the zoonotic potential of these two pathogens in calves in this province.

Association of Lactase Persistence Genotypes with High Intake of Dairy Saturated Fat and High Prevalence of Lactase Non-Persistence among the Mexican Population.

PubMed

Ojeda-Granados, Claudia; Panduro, Arturo; Rebello Pinho, João Renato; Ramos-Lopez, Omar; Gleyzer, Ketti; Malta, Fernanda de Mello; Gonzalez-Aldaco, Karina; Roman, Sonia

2016-01-01

Lactase (LCT) -13910 C>T and -22018 G>A polymorphisms associated with the lactase non-persistence (LNP)/persistence (LP) phenotypes vary globally. LP has been associated with obesity in Europeans. However, it has not been genetically evaluated in Mexico, a country with admixed population, recent introduction of dairy, and a high prevalence of obesity. Thus, we aimed to determine the distribution of the LCT polymorphisms and their association with the nutritional profile of West Mexico's populations. Genotyping of 1,196 individuals (natives and mestizos) was carried out by a Taqman allelic discrimination assay. Descriptive statistics and interpopulation analyzes were performed by SPSS, Arlequin, and Structure software. Demographic, anthropometric, biochemical and dietary data were analyzed in 212 mestizos. LNP genotypes mainly prevailed (CC 68.7% and GG 68.2%); both predominated in native Huicholes and Nahuas (>97.7%). Among the mestizos, the LP genotypes were associated with a higher intake of saturated fat (9.9 ± 3.9% vs. 8.5 ± 4.0%, p = 0.018; OR = 2.55, 95% CI 1.29-5.03, p = 0.006) and a daily/more frequent consumption of dairy (88.8 vs. 78.0%; p = 0.049) than LNP genotypes. The LNP trait was predominant in Mexicans with a major Amerindian ancestry. A daily consumption of dairy was associated with a higher intake of saturated fat in LP individuals. © 2016 S. Karger AG, Basel.

Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City.

PubMed

Harris, Stephen E; Xue, Alexander T; Alvarado-Serrano, Diego; Boehm, Joel T; Joseph, Tyler; Hickerson, Michael J; Munshi-South, Jason

2016-04-01

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice,Peromyscus leucopus,in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC. © 2016 The Author(s).

Plant genotypic diversity reduces the rate of consumer resource utilization

PubMed Central

McArt, Scott H.; Thaler, Jennifer S.

2013-01-01

While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore—the Japanese beetle (Popillia japonica)—increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore. PMID:23658201

Plant genotypic diversity reduces the rate of consumer resource utilization.

PubMed

McArt, Scott H; Thaler, Jennifer S

2013-07-07

While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

No evidence for increased performance of a specialist psyllid on invasive French broom

NASA Astrophysics Data System (ADS)

Herrera, Angelica M.; Carruthers, Raymond I.; Mills, Nicholas J.

2011-03-01

Some invasive plants perform better in their area of introduction than in their native region. This may be a consequence of rapid evolutionary change due to different selection pressures encountered in introduced regions. The Evolution of Increased Competitive Ability hypothesis (EICA) suggests that release from natural enemies results in selection of more vigorous plant genotypes as a result of plants allocating resources away from costly herbivore-resistance traits and toward increased growth. We tested the prediction that introduced plant genotypes of Genista monspessulana (Fabaceae) are less resistant to herbivory by a specialist psyllid, Arytinnis hakani (Hemiptera: Psyllidae) by measuring and comparing A. hakani performance on plants from native (southern France) and introduced (California, U.S.) populations. A. hakani performed equally well on plants from the native and introduced regions; there were no significant differences in psyllid egg and nymphal development, nymphal survival rates, female longevity or fecundity between the test plants. Egg survival rates were significantly higher on native populations, but the difference was minimal. These results provide preliminary evidence that native and introduced G. monspessulana populations are equally resistant to A. hakani and do not support the EICA hypothesis prediction of reduced investment in defense in introduced plant populations. Possible explanations for the lack of effects found in this study include the type of parameters measured and the feeding ecology of the herbivore used to test EICA, and finally, that evolutionary changes in plant defense in introduced G. monspessulana populations may not have occurred.

Full-length genomic sequence of hepatitis B virus genotype C2 isolated from a native Brazilian patient.

PubMed

Alvarado-Mora, Mónica Viviana; Santana, Rúbia Anita Ferraz; Sitnik, Roberta; Ferreira, Paulo Roberto Abrão; Mangueira, Cristovão Luís Pitangueira; Carrilho, Flair José; Pinho, João Renato Rebello

2011-06-01

The hepatitis B virus (HBV) is among the leading causes of chronic hepatitis, cirrhosis and hepatocellular carcinoma. In Brazil, genotype A is the most frequent, followed by genotypes D and F. Genotypes B and C are found in Brazil exclusively among Asian patients and their descendants. The aim of this study was to sequence the entire HBV genome of a Caucasian patient infected with HBV/C2 and to infer the origin of the virus based on sequencing analysis. The sequence of this Brazilian isolate was grouped with four other sequences described in China. The sequence of this patient is the first complete genome of HBV/C2 reported in Brazil.

Lagging adaptation to warming climate in Arabidopsis thaliana.

PubMed

Wilczek, Amity M; Cooper, Martha D; Korves, Tonia M; Schmitt, Johanna

2014-06-03

If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species' native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species' native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation.

Lagging adaptation to warming climate in Arabidopsis thaliana

PubMed Central

Wilczek, Amity M.; Cooper, Martha D.; Korves, Tonia M.; Schmitt, Johanna

2014-01-01

If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species’ native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species’ native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation. PMID:24843140

Positive and Negative Impacts of Non-Native Bee Species around the World.

PubMed

Russo, Laura

2016-11-28

Though they are relatively understudied, non-native bees are ubiquitous and have enormous potential economic and environmental impacts. These impacts may be positive or negative, and are often unquantified. In this manuscript, I review literature on the known distribution and environmental and economic impacts of 80 species of introduced bees. The potential negative impacts of non-native bees include competition with native bees for nesting sites or floral resources, pollination of invasive weeds, co-invasion with pathogens and parasites, genetic introgression, damage to buildings, affecting the pollination of native plant species, and changing the structure of native pollination networks. The potential positive impacts of non-native bees include agricultural pollination, availability for scientific research, rescue of native species, and resilience to human-mediated disturbance and climate change. Most non-native bee species are accidentally introduced and nest in stems, twigs, and cavities in wood. In terms of number of species, the best represented families are Megachilidae and Apidae, and the best represented genus is Megachile . The best studied genera are Apis and Bombus , and most of the species in these genera were deliberately introduced for agricultural pollination. Thus, we know little about the majority of non-native bees, accidentally introduced or spreading beyond their native ranges.

Positive and Negative Impacts of Non-Native Bee Species around the World

PubMed Central

Russo, Laura

2016-01-01

Though they are relatively understudied, non-native bees are ubiquitous and have enormous potential economic and environmental impacts. These impacts may be positive or negative, and are often unquantified. In this manuscript, I review literature on the known distribution and environmental and economic impacts of 80 species of introduced bees. The potential negative impacts of non-native bees include competition with native bees for nesting sites or floral resources, pollination of invasive weeds, co-invasion with pathogens and parasites, genetic introgression, damage to buildings, affecting the pollination of native plant species, and changing the structure of native pollination networks. The potential positive impacts of non-native bees include agricultural pollination, availability for scientific research, rescue of native species, and resilience to human-mediated disturbance and climate change. Most non-native bee species are accidentally introduced and nest in stems, twigs, and cavities in wood. In terms of number of species, the best represented families are Megachilidae and Apidae, and the best represented genus is Megachile. The best studied genera are Apis and Bombus, and most of the species in these genera were deliberately introduced for agricultural pollination. Thus, we know little about the majority of non-native bees, accidentally introduced or spreading beyond their native ranges. PMID:27916802

Fast Technology Analysis (FTA) Enables Identification of Species and Genotypes of Latent Microsporidia Infections in Healthy Native Cameroonians

PubMed Central

Ndzi, Edward S.; Asonganyi, Tazoacha; Nkinin, Mary Bello; Xiao, Lihua; Didier, Elizabeth S.; Bowers, Lisa C.; Nkinin, Stephenson W.; Kaneshiro, Edna S.

2015-01-01

Several enteric microsporidia species have been detected in humans and other vertebrates and their identifications at the genotype level are currently being elucidated. As advanced methods, reagents, and disposal kits for detecting and identifying pathogens become commercially available, it is important to test them in settings other than in laboratories with “state-of-the-art” equipment and well-trained staff members. In the present study, we sought to detect microsporidia DNA preserved and extracted from FTA (fast technology analysis) cards spotted with human fecal suspensions obtained from Cameroonian volunteers living in the capital city of Yaoundé to preclude the need for employing spore-concentrating protocols. Further, we tested whether amplicon nucleotide sequencing approaches could be used on small aliquots taken from the cards to elucidate the diversity of microsporidia species and strains infecting native residents. Of 196 samples analyzed, 12 (6.1%) were positive for microsporidia DNA; Enterocytozoon bieneusi (Type IV and KIN-1), Encephalitozoon cuniculi, and Encephalitozoon intestinalis were identified. These data demonstrate the utility of the FTA cards in identifying genotypes of microsporidia DNA in human fecal samples that may be applied to field testing for prevalence studies. PMID:26303263

Association of a single nucleotide polymorphism in the akirin 2 gene with economically important traits in Korean native cattle.

PubMed

Kim, H; Lee, S K; Hong, M W; Park, S R; Lee, Y S; Kim, J W; Lee, H K; Jeong, D K; Song, Y H; Lee, S J

2013-12-01

The akirin 2 gene, located on chromosome 9 in cattle, was previously reported to be associated with nuclear factor-kappa B (NF-κB), involved in immune reactions and marbling of meat. To determine whether a single nucleotide polymorphism (SNP) in akirin 2 is associated with economically important traits of Korean native cattle, the c.*188G>A SNP DNA marker in the 3'-UTR region of akirin 2 was analyzed for its association with carcass weight, longissimus muscle area and marbling. The c.*188G>A SNP was genotyped by polymerase chain reaction restriction fragment length polymorphism, and the frequency of the AA, AG, and GG genotypes were 6.82%, 71.29% and 21.88% respectively. This SNP was significantly associated with longissimus muscle area (Bonferroni corrected P < 0.05), and marbling score (Bonferroni corrected P < 0.01). These results suggest that the c.*188G>A SNP of akirin 2 might be useful as a DNA marker for longissimus muscle area and marbling scores in Korean native cattle. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

Glycosylation Benchmark Profile for HIV-1 Envelope Glycoprotein Production Based on Eleven Env Trimers

PubMed Central

Go, Eden P.; Ding, Haitao; Zhang, Shijian; Ringe, Rajesh P.; Nicely, Nathan; Hua, David; Steinbock, Robert T.; Golabek, Michael; Alin, James; Alam, S. Munir; Cupo, Albert; Haynes, Barton F.; Kappes, John C.; Moore, John P.; Sodroski, Joseph G.

2017-01-01

ABSTRACT HIV-1 envelope glycoprotein (Env) glycosylation is important because individual glycans are components of multiple broadly neutralizing antibody epitopes, while shielding other sites that might otherwise be immunogenic. The glycosylation on Env is influenced by a variety of factors, including the genotype of the protein, the cell line used for its expression, and the details of the construct design. Here, we used a mass spectrometry (MS)-based approach to map the complete glycosylation profile at every site in multiple HIV-1 Env trimers, accomplishing two goals. (i) We determined which glycosylation sites contain conserved glycan profiles across many trimeric Envs. (ii) We identified the variables that impact Env's glycosylation profile at sites with divergent glycosylation. Over half of the gp120 glycosylation sites on 11 different trimeric Envs have a conserved glycan profile, indicating that a native consensus glycosylation profile does indeed exist among trimers. We showed that some soluble gp120s and gp140s exhibit highly divergent glycosylation profiles compared to trimeric Env. We also assessed the impact of several variables on Env glycosylation: truncating the full-length Env; producing Env, instead of the more virologically relevant T lymphocytes, in CHO cells; and purifying Env with different chromatographic platforms, including nickel-nitrilotriacetic acid (Ni-NTA), 2G12, and PGT151 affinity. This report provides the first consensus glycosylation profile of Env trimers, which should serve as a useful benchmark for HIV-1 vaccine developers. This report also defines the sites where glycosylation may be impacted when Env trimers are truncated or produced in CHO cells. IMPORTANCE A protective HIV-1 vaccine will likely include a recombinant version of the viral envelope glycoprotein (Env). Env is highly glycosylated, and yet vaccine developers have lacked guidance on how to assess whether their immunogens have optimal glycosylation. The following important questions are still unanswered. (i) What is the “target” glycosylation profile, when the goal is to generate a natively glycosylated protein? (ii) What variables exert the greatest influence on Env glycosylation? We identified numerous sites on Env where the glycosylation profile does not deviate in 11 different Env trimers, and we investigated the impact on the divergent glycosylation profiles of changing the genotype of the Env sequence, the construct design, the purification method, and the producer cell type. The data presented here give vaccine developers a “glycosylation target” for their immunogens, and they show how protein production variables can impact Env glycosylation. PMID:28202756

Dispersal and selection mediate hybridization between a native and invasive species

USGS Publications Warehouse

Kovach, Ryan P.; Muhlfeld, Clint C.; Boyer, Matthew C.; Lowe, Winsor H.; Allendorf, Fred W.; Luikart, Gordon

2015-01-01

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age—relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) ¼ 0.60; s.e. ¼ 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. .

Endocarditis of native aortic and mitral valves due to Corynebacterium accolens: report of a case and application of phenotypic and genotypic techniques for identification.

PubMed Central

Claeys, G; Vanhouteghem, H; Riegel, P; Wauters, G; Hamerlynck, R; Dierick, J; de Witte, J; Verschraegen, G; Vaneechoutte, M

1996-01-01

Endocarditis of native aortic and mitral valves due to an organism identified as Corynebacterium accolens developed in a 73-year-old patient without predisposing factors. The organism was identified as C. accolens by biochemical identification, amplified rRNA gene restriction analysis, and DNA-DNA hybridization. This is the first case of C. accolens endocarditis reported, adding to the increasing number of Corynebacterium-related cases of endocarditis. PMID:8727922

Endocarditis of native aortic and mitral valves due to Corynebacterium accolens: report of a case and application of phenotypic and genotypic techniques for identification.

PubMed

Claeys, G; Vanhouteghem, H; Riegel, P; Wauters, G; Hamerlynck, R; Dierick, J; de Witte, J; Verschraegen, G; Vaneechoutte, M

1996-05-01

Endocarditis of native aortic and mitral valves due to an organism identified as Corynebacterium accolens developed in a 73-year-old patient without predisposing factors. The organism was identified as C. accolens by biochemical identification, amplified rRNA gene restriction analysis, and DNA-DNA hybridization. This is the first case of C. accolens endocarditis reported, adding to the increasing number of Corynebacterium-related cases of endocarditis.

The Impact of Focus on Pronoun Resolution in Native and Non-Native Sentence Comprehension

ERIC Educational Resources Information Center

Patterson, Clare; Esaulova, Yulia; Felser, Claudia

2017-01-01

Non-native speakers' sensitivity to discourse-level cues in pronoun interpretation has not been widely researched. We carried out three antecedent-choice questionnaire experiments which investigate the impact of focus on within-sentence pronoun resolution in native and non-native speakers of German and native speakers of Russian. Focus was…

Genetic Diversity of Myanmar and Indonesia Native Chickens Together with Two Jungle Fowl Species by Using 102 Indels Polymorphisms

PubMed Central

Maw, Aye Aye; Shimogiri, Takeshi; Riztyan; Kawabe, Kotaro; Kawamoto, Yasuhiro; Okamoto, Shin

2012-01-01

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island. PMID:25049646

Genetic diversity of myanmar and indonesia native chickens together with two jungle fowl species by using 102 indels polymorphisms.

PubMed

Maw, Aye Aye; Shimogiri, Takeshi; Riztyan; Kawabe, Kotaro; Kawamoto, Yasuhiro; Okamoto, Shin

2012-07-01

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island.

Distribution of hepatitis C virus genotypes in a diverse US integrated health care population.

PubMed

Manos, M Michele; Shvachko, Valentina A; Murphy, Rosemary C; Arduino, Jean Marie; Shire, Norah J

2012-11-01

Hepatitis C virus (HCV) genotypes influence response to therapy, and recently approved direct-acting antivirals are genotype-specific. Genotype distribution information can help to guide antiviral development and elucidate infection patterns. HCV genotype distributions were studied in a diverse cross-section of patients in the Northern California Kaiser Permanente health plan. Associations between genotype and race/ethnicity, age, and sex were assessed with multivariate logistic regression models. The 10,256 patients studied were median age 56 years, 62% male, 55% White non-Hispanic. Overall, 70% were genotype 1, 16% genotype 2, 12% genotype 3, 1% genotype 4, <1% genotype 5, and 1% genotype 6. Blacks (OR 4.5 [3.8-5.5]) and Asians (OR 1.2 [1.0-1.4]) were more likely to have genotype 1 than 2/3 versus non-Hispanic Whites. Women less likely had genotype 1 versus 2/3 than did men (OR 0.86 [0.78-0.94]). Versus non-Hispanic Whites, Asians (OR 0.38 [0.31-0.46]) and Blacks (OR 0.73 [0.63-0.84]) were less likely genotype1a than 1b; Hispanics (OR 1.3 [1.1-1.5]) and Native Americans (OR 1.9 [1.2-2.8]) more likely had genotype 1a than 1b. Patients age ≥65 years less likely had genotype 1a than 1b versus those age 45-64 (OR 0.34 [0.29-0.41]). The predominance of genotype 1 among all groups studied reinforces the need for new therapies targeting this genotype. Racial/ethnic variations in HCV genotype and subtype distribution must be considered in formulating new agents and novel strategies to successfully treat the diversity of hepatitis C patients. Copyright © 2012 Wiley Periodicals, Inc.

The Genetic Legacy of the Pre-Colonial Period in Contemporary Bolivians

PubMed Central

Vidal-Bralo, Laura; Gómez-Carballa, Alberto; Catelli, Laura; Pardo-Seco, Jacobo; Pastoriza, Ana; Carracedo, Ángel; Torres-Balanza, Antonio; Rocabado, Omar; Vullo, Carlos

2013-01-01

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1–2%) of a sub-Saharan component in Bolivians. PMID:23527064

The genetic legacy of the pre-colonial period in contemporary Bolivians.

PubMed

Taboada-Echalar, Patricia; Alvarez-Iglesias, Vanesa; Heinz, Tanja; Vidal-Bralo, Laura; Gómez-Carballa, Alberto; Catelli, Laura; Pardo-Seco, Jacobo; Pastoriza, Ana; Carracedo, Angel; Torres-Balanza, Antonio; Rocabado, Omar; Vullo, Carlos; Salas, Antonio

2013-01-01

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1-2%) of a sub-Saharan component in Bolivians.

Dispersal and selection mediate hybridization between a native and invasive species.

PubMed

Kovach, Ryan P; Muhlfeld, Clint C; Boyer, Matthew C; Lowe, Winsor H; Allendorf, Fred W; Luikart, Gordon

2015-01-22

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age--relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) = 0.60; s.e. = 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Effects of nonindigenous tadpoles on native tadpoles in Florida: Evidence of competition

USGS Publications Warehouse

Smith, Kimberly G.

2005-01-01

The impacts of nonindigenous species on native ecosystems can be severe, sometimes leading to the extinction of native taxa. Interspecific competition is a potential mechanism of negative impact of invasive species, but few studies have conclusively demonstrated competition between native and nonindigenous taxa. In this study I used experimental manipulations to examine the competitive effects of the larvae of two widely introduced anurans, the cane toad, Bufo marinus, and the Cuban treefrog, Osteopilus septentrionalis, on the growth and development of the larvae of two native anurans (the southern toad, Bufo terrestris, and the green treefrog, Hyla cinerea). The presence of O. septentrionalis larvae consistently impacted growth and development of native larvae, resulting in reduced growth rates and delayed metamorphosis of both native species and smaller mass at metamorphosis of B. terrestris. Hyla cinerea larvae transformed at greater body masses when reared with the rapidly transforming nonindigenous species as a result of competitive release. The negative effects of O. septentrionalis on native larvae were generally significant whether native tadpoles were exposed to O. septentrionalis alone or in combination with B. marinus. In contrast, B. marinus tadpoles did not significantly impact the growth or development of either native species. Neither nonindigenous species significantly decreased the survivorship of native larvae, although a trend toward decreased survivorship was evident for H. cinerea. These results suggest that nonindigenous larval anurans may adversely impact native tadpole communities as a result of interspecific competition.

Managing Potato Biodiversity to Cope with Frost Risk in the High Andes: A Modeling Perspective

PubMed Central

Condori, Bruno; Hijmans, Robert J.; Ledent, Jean Francois; Quiroz, Roberto

2014-01-01

Austral summer frosts in the Andean highlands are ubiquitous throughout the crop cycle, causing yield losses. In spite of the existing warming trend, climate change models forecast high variability, including freezing temperatures. As the potato center of origin, the region has a rich biodiversity which includes a set of frost resistant genotypes. Four contrasting potato genotypes –representing genetic variability- were considered in the present study: two species of frost resistant native potatoes (the bitter Solanum juzepczukii, var. Luki, and the non-bitter Solanum ajanhuiri, var. Ajanhuiri) and two commercial frost susceptible genotypes (Solanum tuberosum ssp. tuberosum var. Alpha and Solanum tuberosum ssp. andigenum var. Gendarme). The objective of the study was to conduct a comparative growth analysis of four genotypes and modeling their agronomic response under frost events. It included assessing their performance under Andean contrasting agroecological conditions. Independent subsets of data from four field experiments were used to parameterize, calibrate and validate a potato growth model. The validated model was used to ascertain the importance of biodiversity, represented by the four genotypes tested, as constituents of germplasm mixtures in single plots used by local farmers, a coping strategy in the face of climate variability. Also scenarios with a frost routine incorporated in the model were constructed. Luki and Ajanhuiri were the most frost resistant varieties whereas Alpha was the most susceptible. Luki and Ajanhuiri, as monoculture, outperformed the yield obtained with the mixtures under severe frosts. These results highlight the role played by local frost tolerant varieties, and featured the management importance –e.g. clean seed, strategic watering- to attain the yields reported in our experiments. The mixtures of local and introduced potatoes can thus not only provide the products demanded by the markets but also reduce the impact of frosts and thus the vulnerability of the system to abiotic stressors. PMID:24497912

Managing potato biodiversity to cope with frost risk in the high Andes: a modeling perspective.

PubMed

Condori, Bruno; Hijmans, Robert J; Ledent, Jean Francois; Quiroz, Roberto

2014-01-01

Austral summer frosts in the Andean highlands are ubiquitous throughout the crop cycle, causing yield losses. In spite of the existing warming trend, climate change models forecast high variability, including freezing temperatures. As the potato center of origin, the region has a rich biodiversity which includes a set of frost resistant genotypes. Four contrasting potato genotypes--representing genetic variability--were considered in the present study: two species of frost resistant native potatoes (the bitter Solanum juzepczukii, var. Luki, and the non-bitter Solanum ajanhuiri, var. Ajanhuiri) and two commercial frost susceptible genotypes (Solanum tuberosum ssp. tuberosum var. Alpha and Solanum tuberosum ssp. andigenum var. Gendarme). The objective of the study was to conduct a comparative growth analysis of four genotypes and modeling their agronomic response under frost events. It included assessing their performance under Andean contrasting agroecological conditions. Independent subsets of data from four field experiments were used to parameterize, calibrate and validate a potato growth model. The validated model was used to ascertain the importance of biodiversity, represented by the four genotypes tested, as constituents of germplasm mixtures in single plots used by local farmers, a coping strategy in the face of climate variability. Also scenarios with a frost routine incorporated in the model were constructed. Luki and Ajanhuiri were the most frost resistant varieties whereas Alpha was the most susceptible. Luki and Ajanhuiri, as monoculture, outperformed the yield obtained with the mixtures under severe frosts. These results highlight the role played by local frost tolerant varieties, and featured the management importance--e.g. clean seed, strategic watering--to attain the yields reported in our experiments. The mixtures of local and introduced potatoes can thus not only provide the products demanded by the markets but also reduce the impact of frosts and thus the vulnerability of the system to abiotic stressors.

Dr Jekyll and Mrs Hyde: Risky hybrid sex by amphibian-parasitizing chytrids in the Brazilian Atlantic Forests.

PubMed

Ghosh, Pria; Fisher, Matthew C

2016-07-01

In their article in this issue of Molecular Ecology, Jenkinson et al. () and colleagues address a worrying question-how could arguably the most dangerous pathogen known to science, Batrachochytrium dendrobatidis (Bd), become even more virulent? The answer: start having sex. Jenkinson et al. present a case for how the introduction into Brazil of the globally invasive lineage of Bd, BdGPL, has disrupted the relationship between native amphibians and an endemic Bd lineage, BdBrazil. BdBrazil is hypothesized to be native to the Atlantic Forest and so have a long co-evolutionary history with biodiverse Atlantic Forest amphibian community. The authors suggest that this has resulted in a zone of hybrid Bd genotypes which are potentially more likely to cause fatal chytridiomycosis than either parent lineage. The endemic-nonendemic Bd hybrid genotypes described in this study, and the evidence for pathogen translocation via the global amphibian trade presented, highlights the danger of anthropogenic pathogen dispersal. This research emphasizes that biosecurity regulations may have to refocus on lineages within species if we are to mitigate against the danger of new, possibly hypervirulent genotypes of pathogens emerging as phylogeographic barriers are breached. © 2016 John Wiley & Sons Ltd.

Tuberculosis in Sardinia: An investigation into the relationship between natives and immigrants.

PubMed

Ruggeri, Melania; Molicotti, Paola; Cubeddu, Marina; Cannas, Sara; Bua, Alessandra; Zanetti, Stefania

2016-09-01

Tuberculosis (TB) has had a recrudescence in the last few decades in Italy as a result of many factors, among which migration from countries where TB is endemic is one of them. In Sardinia, a major island of Italy, there was no knowledge of the mechanisms of transmission of TB in the immigrant subpopulation and the impact it may have on the native subpopulation and on the community as a whole. Therefore, a molecular epidemiological study was carried out to get a clearer picture of the number and genetic features of Mycobacterium tuberculosis strains isolated from immigrants and from natives in Sardinia. Two groups of clinical isolates of M. tuberculosis, one collected from immigrants and the other one from Sardinians, were analyzed in this study. The genotyping was executed through the variable number tandem repeat-mycobacterial interspersed repetitive units technique and a first-line antimycobacterial drug-susceptibility test was also carried out. Thirty-six clinical isolates from immigrants and 25 from Sardinians were analyzed. Variable number tandem repeat-mycobacterial interspersed repetitive units technique showed that all of them belonged to different strains and there was a quite high allelic diversity among them. Moreover, data collected allowed the finding of, with a good approximation, the phylogenetic relations among the strains isolated and the best-known phylogenetic groups. The study pointed out that since every strain is different, there was no TB transmission in any of the subpopulations and between immigrants and natives. This showed that the presence of immigrants was not a risk factor for contracting TB in the community. Copyright © 2016 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

Impacts of Carpobrotus edulis (L.) N.E.Br. on the Germination, Establishment and Survival of Native Plants: A Clue for Assessing Its Competitive Strength

PubMed Central

Novoa, Ana; González, Luís

2014-01-01

Does Carpobrotus edulis have an impact on native plants? How do C. edulis’ soil residual effects affect the maintenance of native populations? What is the extent of interspecific competition in its invasion process? In order to answer those questions, we established pure and mixed cultures of native species and C. edulis on soil collected from invaded and native areas of Mediterranean coastal dunes in the Iberian Peninsula. We examined the impact of the invader on the germination, growth and survival of seeds and adult plants of two native plant species (Malcolmia littorea (L.) R.Br, and Scabiosa atropurpurea L.) growing with ramets or seeds of C. edulis. Residual effects of C. edulis on soils affected the germination process and early growth of native plants in different ways, depending on plant species and density. Interspecific competition significantly reduced the germination and early growth of native plants but this result was soil, density, timing and plant species dependent. Also, at any density of adult individuals of C. edulis, established native adult plants were not competitive. Moreover, ramets of C. edulis had a lethal effect on native plants, which died in a short period of time. Even the presence of C. edulis seedlings prevents the recruitment of native species. In conclusion, C. edulis have strong negative impacts on the germination, growth and survival of the native species M. littorea and S. atropurpurea. These impacts were highly depended on the development stages of native and invasive plants. Our findings are crucial for new strategies of biodiversity conservation in coastal habitats. PMID:25210924

Impacts of Carpobrotus edulis (L.) N.E.Br. on the germination, establishment and survival of native plants: a clue for assessing its competitive strength.

PubMed

Novoa, Ana; González, Luís

2014-01-01

Does Carpobrotus edulis have an impact on native plants? How do C. edulis' soil residual effects affect the maintenance of native populations? What is the extent of interspecific competition in its invasion process? In order to answer those questions, we established pure and mixed cultures of native species and C. edulis on soil collected from invaded and native areas of Mediterranean coastal dunes in the Iberian Peninsula. We examined the impact of the invader on the germination, growth and survival of seeds and adult plants of two native plant species (Malcolmia littorea (L.) R.Br, and Scabiosa atropurpurea L.) growing with ramets or seeds of C. edulis. Residual effects of C. edulis on soils affected the germination process and early growth of native plants in different ways, depending on plant species and density. Interspecific competition significantly reduced the germination and early growth of native plants but this result was soil, density, timing and plant species dependent. Also, at any density of adult individuals of C. edulis, established native adult plants were not competitive. Moreover, ramets of C. edulis had a lethal effect on native plants, which died in a short period of time. Even the presence of C. edulis seedlings prevents the recruitment of native species. In conclusion, C. edulis have strong negative impacts on the germination, growth and survival of the native species M. littorea and S. atropurpurea. These impacts were highly depended on the development stages of native and invasive plants. Our findings are crucial for new strategies of biodiversity conservation in coastal habitats.

Multiple HPV genotype infection impact on invasive cervical cancer presentation and survival

PubMed Central

Martins, Toni Ricardo; Mendoza Lopez, Rossana V.; Sadalla, José Carlos; de Carvalho, João Paulo Mancusi; Baracat, Edmund Chada

2017-01-01

Background Invasive cervical cancer (ICC) is the third most common malignant neoplasm affecting Brazilian women. Little is known about the impact of specific HPV genotypes in the prognosis of ICC. We hypothesized that HPV genotype would impact ICC clinical presentation and survival. Methods Women diagnosed with ICC at the Instituto do Câncer do Estado de São Paulo (ICESP) between May 2008 and June 2012 were included in the study and were followed until December 2015. HPV genotype was detected from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples using Onclarity™ system (BD Viper™ LT automated system). Results 292 patients aged 50±14 years were analyzed. HPVDNA was detected in 84% of patients. The HPV genotypes studied were: HPV16 (64%), HPV18 (10%), HPV33-58 (7%), HPV45 (5%), HPV31 (4%) and other high-risk HPV genotypes (11%). HPV genotypes showed different distributions regarding histological type and clinical stage. Patients were followed for 35±21 months. The overall survival at 5 years after diagnosis of cervical cancer was 54%. Age, clinical staging, histological type and multiple HPV genotypes infection detected in the same tumor specimen were associated with poorer overall survival on multivariate Cox proportional hazard analysis (p<0.05). No specific HPV genotype affected survival. Conclusion Multiple HPV genotype infection was associated with poorer ICC survival in our study, compared with single genotype infection. HPV genotyping from FFPE tumor tissue using an automated assay such as the Onclarity BD™ assay provides a simpler alternative for routine clinical use. Impact This is the largest study employing an automated HPV genotyping assay using FFPE of ICC. Multiple HPV genotype infection adversely influenced survival. PMID:28829791

Genotype and local environment dynamically influence growth, disturbance response and survivorship in the threatened coral, Acropora cervicornis.

PubMed

Drury, Crawford; Manzello, Derek; Lirman, Diego

2017-01-01

The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.

PubMed

Bizon, Chris; Spiegel, Michael; Chasse, Scott A; Gizer, Ian R; Li, Yun; Malc, Ewa P; Mieczkowski, Piotr A; Sailsbery, Josh K; Wang, Xiaoshu; Ehlers, Cindy L; Wilhelmsen, Kirk C

2014-01-30

The reduction in the cost of sequencing a human genome has led to the use of genotype sampling strategies in order to impute and infer the presence of sequence variants that can then be tested for associations with traits of interest. Low-coverage Whole Genome Sequencing (WGS) is a sampling strategy that overcomes some of the deficiencies seen in fixed content SNP array studies. Linkage-disequilibrium (LD) aware variant callers, such as the program Thunder, may provide a calling rate and accuracy that makes a low-coverage sequencing strategy viable. We examined the performance of an LD-aware variant calling strategy in a population of 708 low-coverage whole genome sequences from a community sample of Native Americans. We assessed variant calling through a comparison of the sequencing results to genotypes measured in 641 of the same subjects using a fixed content first generation exome array. The comparison was made using the variant calling routines GATK Unified Genotyper program and the LD-aware variant caller Thunder. Thunder was found to improve concordance in a coverage dependent fashion, while correctly calling nearly all of the common variants as well as a high percentage of the rare variants present in the sample. Low-coverage WGS is a strategy that appears to collect genetic information intermediate in scope between fixed content genotyping arrays and deep-coverage WGS. Our data suggests that low-coverage WGS is a viable strategy with a greater chance of discovering novel variants and associations than fixed content arrays for large sample association analyses.

Shoal bass hybridization in the Chattahoochee River Basin near Atlanta, Georgia

USGS Publications Warehouse

Taylor, Andrew T.; Tringali, Michael D.; O'Rourke, Patrick M.; Long, James M.

2018-01-01

The shoal bass (Micropterus cataractae) is a sportfish endemic to the Apalachicola-Chattahoochee-Flint Basin of the southeastern United States. Introgression with several non-native congeners poses a pertinent threat to shoal bass conservation, particularly in the altered habitats of the Chattahoochee River. Our primary objective was to characterize hybridization in shoal bass populations near Atlanta, Georgia, including a population inhabiting Big Creek and another in the main stem Chattahoochee River below Morgan Falls Dam (MFD). A secondary objective was to examine the accuracy of phenotypic identifications below MFD based on a simplified suite of characters examined in the field. Fish were genotyped with 16 microsatellite DNA markers, and results demonstrated that at least four black bass species were involved in introgressive hybridization. Of 62 fish genotyped from Big Creek, 27% were pure shoal bass and 65% represented either F1 hybrids of shoal bass x smallmouth bass (M. dolomieu) or unidirectional backcrosses towards shoal bass. Of 29 fish genotyped below MFD and downstream at Cochran Shoals, 45% were pure shoal bass. Six hybrid shoal bass included both F1 hybrids and backcrosses with non-natives including Alabama bass (M. henshalli), spotted bass (M. punctulatus), and smallmouth bass. Shoal bass alleles comprised only 21% of the overall genomic composition in Big Creek and 31% below MFD (when combined with Cochran Shoals). Phenotypic identification below MFD resulted in an overall correct classification rate of 86% when discerning pure shoal bass from all other non-natives and hybrids. Results suggest that although these two shoal bass populations feature some of the highest introgression rates documented, only a fleeting opportunity may exist to conserve pure shoal bass in both populations. Continued supplemental stocking of pure shoal bass below MFD appears warranted to thwart increased admixture among multiple black bass taxa, and a similar stocking program could benefit the Big Creek population. Further, selective removal of non-natives and hybrids, which appears to be practical with phenotypic identification, may provide increased benefits towards conserving genetic integrity of these shoal bass populations.

Shoal Bass hybridization below Morgan Falls Dam.

USGS Publications Warehouse

Taylor, Andrew T.; Tringali, Michael D.; O'Rourke, Patrick M.; Long, James M.

2018-01-01

The shoal bass (Micropterus cataractae) is a sportfish endemic to the Apalachicola-Chattahoochee-Flint Basin of the southeastern United States. Introgression with several non-native congeners poses a pertinent threat to shoal bass conservation, particularly in the altered habitats of the Chattahoochee River. Our primary objective was to characterize hybridization in shoal bass populations near Atlanta, Georgia, including a population inhabiting Big Creek and another in the main stem Chattahoochee River below Morgan Falls Dam (MFD). A secondary objective was to examine the accuracy of phenotypic identifications below MFD based on a simplified suite of characters examined in the field. Fish were genotyped with 16 microsatellite DNA markers, and results demonstrated that at least four black bass species were involved in introgressive hybridization. Of 62 fish genotyped from Big Creek, 27% were pure shoal bass and 65% represented either F1 hybrids of shoal bass x smallmouth bass (M. dolomieu) or unidirectional backcrosses towards shoal bass. Of 29 fish genotyped below MFD and downstream at Cochran Shoals, 45% were pure shoal bass. Six hybrid shoal bass included both F1 hybrids and backcrosses with non-natives including Alabama bass (M. henshalli), spotted bass (M. punctulatus), and smallmouth bass. Shoal bass alleles comprised only 21% of the overall genomic composition in Big Creek and 31% below MFD (when combined with Cochran Shoals). Phenotypic identification below MFD resulted in an overall correct classification rate of 86% when discerning pure shoal bass from all other non-natives and hybrids. Results suggest that although these two shoal bass populations feature some of the highest introgression rates documented, only a fleeting opportunity may exist to conserve pure shoal bass in both populations. Continued supplemental stocking of pure shoal bass below MFD appears warranted to thwart increased admixture among multiple black bass taxa, and a similar stocking program could benefit the Big Creek population. Further, selective removal of non-natives and hybrids, which appears to be practical with phenotypic identification, may provide increased benefits towards conserving genetic integrity of these shoal bass populations.

Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination

PubMed Central

Clark, L V; Jasieniuk, M

2012-01-01

Facultative asexual reproduction is a trait commonly found in invasive species. With a combination of sexual and asexual reproductive modes, such species may adapt to new environments via sexual recombination during range expansion, while at the same time having the benefits of asexuality such as the maintenance of fitness effects that depend upon heterozygosity. In the Western United States, native species of Rubus (Rosaceae) reproduce sexually whereas exotic naturalized Rubus species reproduce by pseudogamous apomixis. We hypothesized that new asexual lineages of Rubus could arise from hybridization in this range. To detect hybridization between native and exotic Rubus, we genotyped 579 individuals collected across California, Oregon and Washington with eight nuclear microsatellites and two chloroplast markers. Principal Coordinate Analysis and Bayesian clustering revealed a limited amount of hybridization of the native R. ursinus with the exotic R. armeniacus and R. pensilvanicus, as well as cultivated varieties. Genetic distances between these hybrids and their offspring indicated that both R. ursinus × R. armeniacus and R. ursinus × R. pensilvanicus produced a mix of apomictic and sexual seeds, with sexual seeds being more viable. Although neither of these hybrid types is currently considered invasive, they model the early stages of evolution of new invasive lineages, given the potential for fixed heterosis and the generation of novel genotypes. The hybrids also retain the ability to increase their fitness via sexual recombination and natural selection. Mixed reproductive systems such as those described here may be an important step in the evolution of asexual invasive species. PMID:22850699

What determines positive, neutral, and negative impacts of Solidago canadensis invasion on native plant species richness?

PubMed

Dong, Li-Jia; Yu, Hong-Wei; He, Wei-Ming

2015-11-17

Whether plant invasions pose a great threat to native plant diversity is still hotly debated due to conflicting findings. More importantly, we know little about the mechanisms of invasion impacts on native plant richness. We examined how Solidago canadensis invasion influenced native plants using data from 291 pairs of invaded and uninvaded plots covering an entire invaded range, and quantified the relative contributions of climate, recipient communities, and S. canadensis to invasion impacts. There were three types of invasion consequences for native plant species richness (i.e., positive, neutral, and negative impacts). Overall, the relative contributions of recipient communities, S. canadensis and climate to invasion impacts were 71.39%, 21.46% and 7.15%, respectively; furthermore, the roles of recipient communities, S. canadensis and climate were largely ascribed to plant diversity, density and cover, and precipitation. In terms of direct effects, invasion impacts were negatively linked to temperature and native plant communities, and positively to precipitation and soil microbes. Soil microbes were crucial in the network of indirect effects on invasion impacts. These findings suggest that the characteristics of recipient communities are the most important determinants of invasion impacts and that invasion impacts may be a continuum across an entire invaded range.

TESOL Teachers' Engagement with the Native Speaker Model: How Does Teacher Education Impact on Their Beliefs?

ERIC Educational Resources Information Center

Nguyen, Mai Xuan Nhat Chi

2017-01-01

This research investigates non-native English teachers' engagement with the native speaker model, i.e. whether they agree/disagree with measuring English teaching and learning performance against native speaker standards. More importantly, it aims to unearth the impact of teacher education on teachers' attitudes and beliefs about…

Impact of Non-Native Birds on Native Ecosystems: A Global Analysis.

PubMed

Martin-Albarracin, Valeria L; Amico, Guillermo C; Simberloff, Daniel; Nuñez, Martin A

2015-01-01

Introduction and naturalization of non-native species is one of the most important threats to global biodiversity. Birds have been widely introduced worldwide, but their impacts on populations, communities, and ecosystems have not received as much attention as those of other groups. This work is a global synthesis of the impact of nonnative birds on native ecosystems to determine (1) what groups, impacts, and locations have been best studied; (2) which taxonomic groups and which impacts have greatest effects on ecosystems, (3) how important are bird impacts at the community and ecosystem levels, and (4) what are the known benefits of nonnative birds to natural ecosystems. We conducted an extensive literature search that yielded 148 articles covering 39 species belonging to 18 families -18% of all known naturalized species. Studies were classified according to where they were conducted: Africa, Asia, Australasia, Europe, North America, South America, Islands of the Indian, of the Pacific, and of the Atlantic Ocean. Seven types of impact on native ecosystems were evaluated: competition, disease transmission, chemical, physical, or structural impact on ecosystem, grazing/ herbivory/ browsing, hybridization, predation, and interaction with other non-native species. Hybridization and disease transmission were the most important impacts, affecting the population and community levels. Ecosystem-level impacts, such as structural and chemical impacts were detected. Seven species were found to have positive impacts aside from negative ones. We provide suggestions for future studies focused on mechanisms of impact, regions, and understudied taxonomic groups.

Effects of Nonnative Ungulate Removal on Plant Communities and Soil Biogeochemistry in Tropical Forests

NASA Astrophysics Data System (ADS)

Cole, R. J.; Litton, C. M.; Giardina, C. P.; Sparks, J. P.

2014-12-01

Non-native ungulates have substantial impacts on native ecosystems globally, altering both plant communities and soil biogeochemistry. Across tropical and temperate ecosystems, land managers fence and remove non-native ungulates to conserve native biodiversity, a costly management action, yet long-term outcomes are not well quantified. Specifically, knowledge gaps include: (i) the magnitude and time frame of plant community recovery; (ii) the response of non-native invasive plants; and (iii) changes to soil biogeochemistry. In 2010, we established a series of paired ungulate presence vs. removal plots that span a 20 yr. chronosequence in tropical montane wet forests on the Island of Hawaii to quantify the impacts and temporal legacy of feral pig removal on plant communities and soil biogeochemistry. We also compared soil biogeochemistry in targeted areas of low and high feral pig impact. Our work shows that both native and non-native vegetation respond positively to release from top-down control following removal of feral pigs, but species of high conservation concern recover only if initially present at the time of non-native ungulate removal. Feral pig impacts on soil biogeochemistry appear to last for at least 20 years following ungulate removal. We observed that both soil physical and chemical properties changed with feral pig removal. Soil bulk density and volumetric water content decreased while extractable base cations and inorganic N increased in low vs. high feral pig impact areas. We hypothesize that altered soil biogeochemistry facilitates continued invasions by non-native plants, even decades after non-native ungulate removal. Future work will concentrate on comparisons between wet and dry forest ecosystems and test whether manipulation of soil nutrients can be used to favor native vs. non-native plant establishment.

Reconstruction of the Strawberry, Fragaria × ananassa, Using Native Genotypes of F. virginiana and F. chiloensis

USDA-ARS?s Scientific Manuscript database

The germplasm base of strawberries is restricted. The major cultivated strawberry species, Fragaria ananassa, originated about 250 years ago when South American F. chiloensis subsp. chiloensis forma chiloensis and North American F. virginiana subsp. virginiana accidentally hybridized in European ga...

Variability in colonization of arbuscular mycorrhizal fungi and its effect on mycorrhizal dependency of improved and unimproved soybean cultivars.

PubMed

Salloum, M S; Guzzo, M C; Velazquez, M S; Sagadin, M B; Luna, C M

2016-12-01

Breeding selection of germplasm under fertilized conditions may reduce the frequency of genes that promote mycorrhizal associations. This study was developed to compare variability in mycorrhizal colonization and its effect on mycorrhizal dependency (MD) in improved soybean genotypes (I-1 and I-2) with differential tolerance to drought stress, and in unimproved soybean genotypes (UI-3 and UI-4). As inoculum, a mixed native arbuscular mycorrhizal fungi (AMF) was isolated from soybean roots, showing spores mostly of the species Funneliformis mosseae. At 20 days, unimproved genotypes followed by I-2, showed an increase in arbuscule formation, but not in I-1. At 40 days, mycorrhizal plants showed an increase in nodulation, this effect being more evident in unimproved genotypes. Mycorrhizal dependency, evaluated as growth and biochemical parameters from oxidative stress was increased in unimproved and I-2 since 20 days, whereas in I-1, MD increased at 40 days. We cannot distinguish significant differences in AMF colonization and MD between unimproved and I-2. However, variability among improved genotypes was observed. Our results suggest that selection for improved soybean genotypes with good and rapid AMF colonization, particularly high arbuscule/hyphae ratio could be a useful strategy for the development of genotypes that optimize AMF contribution to cropping systems.

Dynamic study of yeast species and Saccharomyces cerevisiae strains during the spontaneous fermentations of Muscat blanc in Jingyang, China.

PubMed

Wang, Chunxiao; Liu, Yanlin

2013-04-01

The evolution of yeast species and Saccharomyces cerevisiae genotypes during spontaneous fermentations of Muscat blanc planted in 1957 in Jingyang region of China was followed in this study. Using a combination of colony morphology on Wallerstein Nutrient (WLN) medium, sequence analysis of the 26S rDNA D1/D2 domain and 5.8S-ITS-RFLP analysis, a total of 686 isolates were identified at the species level. The six species identified were S. cerevisiae, Hanseniaspora uvarum, Hanseniaspora opuntiae, Issatchenkia terricola, Pichia kudriavzevii (Issatchenkia orientalis) and Trichosporon coremiiforme. This is the first report of T. coremiiforme as an inhabitant of grape must. Three new colony morphologies on WLN medium and one new 5.8S-ITS-RFLP profile are described. Species of non-Saccharomyces, predominantly H. opuntiae, were found in early stages of fermentation. Subsequently, S. cerevisiae prevailed followed by large numbers of P. kudriavzevii that dominated at the end of fermentations. Six native genotypes of S. cerevisiae were determined by interdelta sequence analysis. Genotypes III and IV were predominant. As a first step in exploring untapped yeast resources of the region, this study is important for monitoring the yeast ecology in native fermentations and screening indigenous yeasts that will produce wines with regional characteristics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

PubMed

Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

2018-05-01

The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

Lack of adaptation from standing genetic variation despite the presence of putatively adaptive alleles in introduced sweet vernal grass (Anthoxanthum odoratum).

PubMed

Gould, B; Geber, M

2016-01-01

Population genetic theory predicts that the availability of appropriate standing genetic variation should facilitate rapid evolution when species are introduced to new environments. However, few tests of rapid evolution have been paired with empirical surveys for the presence of previously identified adaptive genetic variants in natural populations. In this study, we examined local adaptation to soil Al toxicity in the introduced range of sweet vernal grass (Anthoxanthum odoratum), and we genotyped populations for the presence of Al tolerance alleles previously identified at the long-term ecological Park Grass Experiment (PGE, Harpenden, UK) in the species native range. We found that markers associated with Al tolerance at the PGE were present at appreciable frequency in introduced populations. Despite this, there was no strong evidence of local adaptation to soil Al toxicity among populations. Populations demonstrated significantly different intrinsic root growth rates in the absence of Al. This suggests that selection on correlated root growth traits may constrain the ability of populations to evolve significantly different root growth responses to Al. Our results demonstrate that genotype-phenotype associations may differ substantially between the native and introduced parts of a species range and that adaptive alleles from a native species range may not necessarily promote phenotypic differentiation in the introduced range. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds

PubMed Central

2014-01-01

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet (Psittacula krameri), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker (Dendrocopos major). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources. PMID:24822022

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds.

PubMed

Peck, Hannah L; Pringle, Henrietta E; Marshall, Harry H; Owens, Ian P F; Lord, Alexa M

2014-05-01

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet ( Psittacula krameri ), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker ( Dendrocopos major ). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources.

Incorporation of an invasive plant into a native insect herbivore food web

PubMed Central

Santos Pimenta, Lúcia P.; Lammers, Youri; Steenbergen, Peter J.; Flohil, Marco; Beveridge, Nils G.P.; van Duijn, Pieter T.; Meulblok, Marjolein M.; Sosef, Nils; van de Ven, Robin; Werring, Ralf; Beentjes, Kevin K.; Meijer, Kim; Vos, Rutger A.; Vrieling, Klaas; Gravendeel, Barbara; Choi, Young; Verpoorte, Robert; Smit, Chris; Beukeboom, Leo W.

2016-01-01

The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird cherry), with similar proportions of specialists and generalists. While herbivory on P. padus remained stable over the past century, that on P. serotina gradually doubled. We show that P. serotina may have evolved changes in investment in cyanogenic glycosides compared with its native range. In the leaf beetle Gonioctena quinquepunctata, recently shifted from native Sorbus aucuparia to P. serotina, we find divergent host preferences on Sorbus- versus Prunus-derived populations, and weak host-specific differentiation among 380 individuals genotyped for 119 SNP loci. We conclude that evolutionary processes may generate a specialized herbivore community on an invasive plant, allowing prognoses of reduced invasiveness over time. On the basis of the results presented here, we would like to caution that manual control might have the adverse effect of a slowing down of processes of adaptation, and a delay in the decline of the invasive character of P. serotina. PMID:27190702

Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

USGS Publications Warehouse

Kovach, Ryan P.; Hand, Brian K.; Hohenlohe, Paul A.; Cosart, Ted F.; Boyer, Matthew C.; Neville, Helen H.; Muhlfeld, Clint C.; Amish, Stephen J.; Carim, Kellie; Narum, Shawn R.; Lowe, Winsor H.; Allendorf, Fred W.; Luikart, Gordon

2016-01-01

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization

PubMed Central

Montesinos, Daniel; Eren, Özkan; Lortie, Christopher J.; French, Kristine; Cavieres, Lohengrin A.; Sotes, Gastón J.; Hierro, José L.; Jorge, Andreia; Loureiro, João

2017-01-01

Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C. solstitialis had been reported to be diploid (2n = 2x = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C. solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C. solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level. PMID:28828232

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization.

PubMed

Irimia, Ramona-Elena; Montesinos, Daniel; Eren, Özkan; Lortie, Christopher J; French, Kristine; Cavieres, Lohengrin A; Sotes, Gastón J; Hierro, José L; Jorge, Andreia; Loureiro, João

2017-01-01

Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C . solstitialis had been reported to be diploid (2 n  = 2 x  = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C . solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C . solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.

Defining the impact of non-native species.

PubMed

Jeschke, Jonathan M; Bacher, Sven; Blackburn, Tim M; Dick, Jaimie T A; Essl, Franz; Evans, Thomas; Gaertner, Mirijam; Hulme, Philip E; Kühn, Ingolf; Mrugała, Agata; Pergl, Jan; Pyšek, Petr; Rabitsch, Wolfgang; Ricciardi, Anthony; Richardson, David M; Sendek, Agnieszka; Vilà, Montserrat; Winter, Marten; Kumschick, Sabrina

2014-10-01

Non-native species cause changes in the ecosystems to which they are introduced. These changes, or some of them, are usually termed impacts; they can be manifold and potentially damaging to ecosystems and biodiversity. However, the impacts of most non-native species are poorly understood, and a synthesis of available information is being hindered because authors often do not clearly define impact. We argue that explicitly defining the impact of non-native species will promote progress toward a better understanding of the implications of changes to biodiversity and ecosystems caused by non-native species; help disentangle which aspects of scientific debates about non-native species are due to disparate definitions and which represent true scientific discord; and improve communication between scientists from different research disciplines and between scientists, managers, and policy makers. For these reasons and based on examples from the literature, we devised seven key questions that fall into 4 categories: directionality, classification and measurement, ecological or socio-economic changes, and scale. These questions should help in formulating clear and practical definitions of impact to suit specific scientific, stakeholder, or legislative contexts. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

Genotype and local environment dynamically influence growth, disturbance response and survivorship in the threatened coral, Acropora cervicornis

PubMed Central

Drury, Crawford; Manzello, Derek; Lirman, Diego

2017-01-01

The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms. PMID:28319134

The first report of prion-related protein gene (PRNT) polymorphisms in goat.

PubMed

Kim, Yong-Chan; Jeong, Byung-Hoon

2017-06-01

Prion protein is encoded by the prion protein gene (PRNP). Polymorphisms of several members of the prion gene family have shown association with prion diseases in several species. Recent studies on a novel member of the prion gene family in rams have shown that prion-related protein gene (PRNT) has a linkage with codon 26 of prion-like protein (PRND). In a previous study, codon 26 polymorphism of PRND has shown connection with PRNP haplotype which is strongly associated with scrapie vulnerability. In addition, the genotype of a single nucleotide polymorphism (SNP) at codon 26 of PRND is related to fertilisation capacity. These findings necessitate studies on the SNP of PRNT gene which is connected with PRND. In goat, several polymorphism studies have been performed for PRNP, PRND, and shadow of prion protein gene (SPRN). However, polymorphism on PRNT has not been reported. Hence, the objective of this study was to determine the genotype and allelic distribution of SNPs of PRNT in 238 Korean native goats and compare PRNT DNA sequences between Korean native goats and several ruminant species. A total of five SNPs, including PRNT c.-114G > T, PRNT c.-58A > G in the upstream of PRNT gene, PRNT c.71C > T (p.Ala24Val) and PRNT c.102G > A in the open reading frame (ORF) and c.321C > T in the downstream of PRNT gene, were found in this study. All five SNPs of caprine PRNT gene in Korean native goat are in complete linkage disequilibrium (LD) with a D' value of 1.0. Interestingly, comparative sequence analysis of the PRNT gene revealed five mismatches between DNA sequences of Korean native goats and those of goats deposited in the GenBank. Korean native black goats also showed 5 mismatches in PRNT ORF with cattle. To the best of our knowledge, this is the first genetic research of the PRNT gene in goat.

Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range

PubMed Central

Walker, M. Andrew

2017-01-01

Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the sympatric range of the V. vulpina west and V. cinerea populations. PMID:28125736

Effects of transgene-encoded high-molecular weight glutenin proteins in wheat flour blends and sponge and dough baking

USDA-ARS?s Scientific Manuscript database

HMW glutenin subunits are the most important determinants of wheat (Triticum aestivum L.) bread-making quality, and subunit composition explains a large percentage of the variability observed between genotypes. Experiments were designed to elevate expression of a key native HMW glutenin subunit (1D...

Resistance to the crayfish plague, Aphanomyces astaci (Oomycota) in the endangered freshwater crayfish species, Austropotamobius pallipes.

PubMed

Martín-Torrijos, Laura; Campos Llach, Miquel; Pou-Rovira, Quim; Diéguez-Uribeondo, Javier

2017-01-01

The pathogen Aphanomyces astaci Schikora 1906 is responsible for the decline of the native crayfish species of Europe, and their current endangered status. This pathogenic species is native to North America and only colonizes aquatic decapods. The North American crayfish species have a high resistance to this pathogen, while species from other regions are highly susceptible. However, recent field and laboratory observations indicate that there might exist some populations with resistance against this disease. The objective of this study was to test the susceptibility of 8 selected native European crayfish populations of Austropotamobius pallipes Lereboullet 1858 from the Pyrenees. We challenged them against the genome sequenced strain AP03 of A. astaci isolated from a North American red swamp crayfish, Procambarus clarkii Girard 1852, in the Garrotxa Natural Park, Girona. The results showed that there are significant differences (P<0,001) among populations, although most of them show high mortality rates after the zoospore challenge with A. astaci. However, one population from Girona exhibited a 100% survival during a four-month monitoring period under the experimental conditions tested. Histological analyses revealed a high immune reaction in tissues examined, i.e., encapsulation and melanization of hyphae, similar to that found in North American resistant crayfish species. These results represent the first observation of a native European crayfish population showing high resistance towards the most virulent genotype of this pathogen, i.e., genotype Pc. The identification of this population is of key importance for the management of these endangered species, and represents a crucial step forward towards the elucidation of the factors involved in the immune reaction against this devastating pathogen.

Polymorphisms of HIV RT Gene Among the ART Naïve Native Drug Exposed Rural PLHA.

PubMed

Krishnan, K Mohana; Amsavathani, Sk

2012-04-01

The number of people living with human immunodeficiency virus (HIV) is increasing day by day in India. The disease has now spread from urban areas to rural areas. The proof reading of the reverse transcriptase enzyme is poor, which may lead to genetic diversity within the HIV strains, which in turn leads to problems like failure or resistance in antiretroviral treatment. This study is designed to find out the polymorphisms of the reverse transcriptase gene of HIV, after the native drug pressure among antiretroviral therapy (ART) naïve rural people living with HIV/AIDS (RPLHA). A total of 207 HIV-Reactive patients were allowed to take native drugs from the local area and were advised to attend the center for HIV after six months for a follow-up. At the time of the follow-up visit, a second blood sample was taken from 20 reactive native-drug exposed ART-naïve patients. The plasma was separated and transported at 20°C to the YRG Care Center for genotyping. Among the 20 HIV-reactive samples processed for gene sequencing analysis to detect the genotypic variations, only one sample (5%) showed high-level mutational resistance variations and the predominant polymorphisms detected were V35T (100%), K122E (94.44%), and V60I (88.88%). The presence of drug-resistance mutations, although minimal, was important, as the drug-resistant strains could spread among the RPLHA and to their sexual partners. There was a definite need to generate a drug resistance database and the polymorphic pattern of Indian strains concern to the future clinical management of the disease, and a vaccine design to contain the disease.

Resistance to the crayfish plague, Aphanomyces astaci (Oomycota) in the endangered freshwater crayfish species, Austropotamobius pallipes

PubMed Central

Martín-Torrijos, Laura; Campos Llach, Miquel; Pou-Rovira, Quim

2017-01-01

The pathogen Aphanomyces astaci Schikora 1906 is responsible for the decline of the native crayfish species of Europe, and their current endangered status. This pathogenic species is native to North America and only colonizes aquatic decapods. The North American crayfish species have a high resistance to this pathogen, while species from other regions are highly susceptible. However, recent field and laboratory observations indicate that there might exist some populations with resistance against this disease. The objective of this study was to test the susceptibility of 8 selected native European crayfish populations of Austropotamobius pallipes Lereboullet 1858 from the Pyrenees. We challenged them against the genome sequenced strain AP03 of A. astaci isolated from a North American red swamp crayfish, Procambarus clarkii Girard 1852, in the Garrotxa Natural Park, Girona. The results showed that there are significant differences (P<0,001) among populations, although most of them show high mortality rates after the zoospore challenge with A. astaci. However, one population from Girona exhibited a 100% survival during a four-month monitoring period under the experimental conditions tested. Histological analyses revealed a high immune reaction in tissues examined, i.e., encapsulation and melanization of hyphae, similar to that found in North American resistant crayfish species. These results represent the first observation of a native European crayfish population showing high resistance towards the most virulent genotype of this pathogen, i.e., genotype Pc. The identification of this population is of key importance for the management of these endangered species, and represents a crucial step forward towards the elucidation of the factors involved in the immune reaction against this devastating pathogen. PMID:28750039

Belowground competition drives invasive plant impact on native species regardless of nitrogen availability.

PubMed

Broadbent, Arthur; Stevens, Carly J; Peltzer, Duane A; Ostle, Nicholas J; Orwin, Kate H

2018-02-01

Plant invasions and eutrophication are pervasive drivers of global change that cause biodiversity loss. Yet, how invasive plant impacts on native species, and the mechanisms underpinning these impacts, vary in relation to increasing nitrogen (N) availability remains unclear. Competition is often invoked as a likely mechanism, but the relative importance of the above and belowground components of this is poorly understood, particularly under differing levels of N availability. To help resolve these issues, we quantified the impact of a globally invasive grass species, Agrostis capillaris, on two co-occurring native New Zealand grasses, and vice versa. We explicitly separated above- and belowground interactions amongst these species experimentally and incorporated an N addition treatment. We found that competition with the invader had large negative impacts on native species growth (biomass decreased by half), resource capture (total N content decreased by up to 75%) and even nutrient stoichiometry (native species tissue C:N ratios increased). Surprisingly, these impacts were driven directly and indirectly by belowground competition, regardless of N availability. Higher root biomass likely enhanced the invasive grass's competitive superiority belowground, indicating that root traits may be useful tools for understanding invasive plant impacts. Our study shows that belowground competition can be more important in driving invasive plant impacts than aboveground competition in both low and high fertility ecosystems, including those experiencing N enrichment due to global change. This can help to improve predictions of how two key drivers of global change, plant species invasions and eutrophication, impact native species diversity.

Population differences in associations of serotonin transporter promoter polymorphism (5HTTLPR) di- and triallelic genotypes with blood pressure and hypertension prevalence.

PubMed

Williams, Redford B; Bishop, George D; Haberstick, Brett C; Smolen, Andrew; Brummett, Beverly H; Siegler, Ilene C; Babyak, Michael A; Zhang, Xiaodong; Tai, E Shyong; Lee, Jeannette Jen-Mai; Tan, Maudrene; Teo, Yik Ying; Cai, Shiwei; Chan, Edmund; Halpern, Carolyn Tucker; Whitsel, Eric A; Bauldry, Shawn; Harris, Kathleen Mullan

2017-03-01

Based on prior research finding the 5HTTLPR L allele associated with increased cardiovascular reactivity to laboratory stressors and increased risk of myocardial infarction, we hypothesized that the 5HTTLPR L allele will be associated with increased blood pressure (BP) and increased hypertension prevalence in 2 large nationally representative samples in the United States and Singapore. Logistic regression and linear models tested associations between triallelic (L'S', based on rs25531) 5HTTLPR genotypes and hypertension severity and mean systolic and diastolic blood pressure (SBP and DBP) collected during the Wave IV survey of the National Longitudinal Study of Adolescent to Adult Health (Add Health, N=11,815) in 2008-09 and during 2004-07 in 4196 Singaporeans. In US Whites, L' allele carriers had higher SBP (0.9 mm Hg, 95% CI=0.26-1.56) and greater odds (OR=1.23, 95% CI=1.10-1.38) of more severe hypertension than those with S'S' genotypes. In African Americans, L' carriers had lower mean SBP (-1.27mm Hg, 95% CI=-2.53 to -0.01) and lower odds (OR = 0.78, 95% CI=0.65-0.94) of more severe hypertension than those with the S'S' genotype. In African Americans, those with L'L' genotypes had lower DBP (-1.13mm Hg, 95% CI=-2.09 to -0.16) than S' carriers. In Native Americans, L' carriers had lower SBP (-6.05mm Hg, 95% CI=-9.59 to -2.51) and lower odds of hypertension (OR = 0.34, 95% CI=0.13-0.89) than those with the S'S' genotype. In Asian/Pacific Islanders those carrying the L' allele had lower DBP (-1.77mm Hg, 95% CI=-3.16 to -0.38) and lower odds of hypertension (OR = 0.68, 95% CI=0.48-0.96) than those with S'S'. In the Singapore sample S' carriers had higher SBP (3.02mm Hg, 95% CI=0.54-5.51) and DBP (1.90mm Hg, 95% CI=0.49-3.31) than those with the L'L' genotype. These findings suggest that Whites carrying the L' allele, African Americans and Native Americans with the S'S' genotype, and Asians carrying the S' allele will be found to be at higher risk of developing cardiovascular disease and may benefit from preventive measures. Copyright © 2016 Elsevier Inc. All rights reserved.

Population differences in associations of serotonin transporter promoter polymorphism (5HTTLPR) di- and triallelic genotypes with blood pressure and hypertension prevalence

PubMed Central

Williams, Redford B.; Bishop, George D.; Haberstick, Brett C.; Smolen, Andrew; Brummett, Beverly H.; Siegler, Ilene C.; Babyak, Michael A.; Zhang, Xiaodong; Tai, E. Shyong; Lee, Jeannette Jen-Mai; Tan, Maudrene; Teo, Yik Ying; Cai, Shiwei; Chan, Edmund; Halpern, Carolyn Tucker; Whitsel, Eric A.; Bauldry, Shawn; Harris, Kathleen Mullan

2017-01-01

Background Based on prior research finding the 5HTTLPR L allele associated with increased cardiovascular reactivity to laboratory stressors and increased risk of myocardial infarction, we hypothesized that the 5HTTLPR L allele will be associated with increased blood pressure (BP) and increased hypertension prevalence in 2 large nationally representative samples in the United States and Singapore. Methods Logistic regression and linear models tested associations between triallelic (L’S’, based on rs25531) 5HTTLPR genotypes and hypertension severity and mean systolic and diastolic blood pressure (SBP and DBP) collected during the Wave IV survey of the National Longitudinal Study of Adolescent to Adult Health (Add Health, N = 11,815) in 2008–09 and during 2004–07 in 4196 Singaporeans. Results In US Whites, L’ allele carriers had higher SBP (0.9 mm Hg, 95% CI = 0.26–1.56) and greater odds (OR = 1.23, 95% CI = 1.10–1.38) of more severe hypertension than those with S’S’ genotypes. In African Americans, L’ carriers had lower mean SBP (−1.27 mm Hg, 95% CI = −2.53 to −0.01) and lower odds (OR = 0.78, 95% CI = 0.65–0.94) of more severe hypertension than those with the S’S’ genotype. In African Americans, those with L’L’ genotypes had lower DBP (−1.13 mm Hg, 95% CI = −2.09 to −0.16) than S’ carriers. In Native Americans, L’ carriers had lower SBP (−6.05 mm Hg, 95% CI = −9.59 to −2.51) and lower odds of hypertension (OR = 0.34, 95% CI = 0.13–0.89) than those with the S’S’ genotype. In Asian/Pacific Islanders those carrying the L’ allele had lower DBP (−1.77 mm Hg, 95% CI = −3.16 to −0.38) and lower odds of hypertension (OR = 0.68, 95% CI = 0.48–0.96) than those with S’S’. In the Singapore sample S’ carriers had higher SBP (3.02 mm Hg, 95% CI = 0.54–5.51) and DBP (1.90 mm Hg, 95% CI = 0.49–3.31) than those with the L’L’ genotype. Conclusions These findings suggest that Whites carrying the L’ allele, African Americans and Native Americans with the S’S’ genotype, and Asians carrying the S’ allele will be found to be at higher risk of developing cardiovascular disease and may benefit from preventive measures. PMID:28267464

Population variation revealed high-altitude adaptation of Tibetan mastiffs.

PubMed

Li, Yan; Wu, Dong-Dong; Boyko, Adam R; Wang, Guo-Dong; Wu, Shi-Fang; Irwin, David M; Zhang, Ya-Ping

2014-05-01

With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves (Canis lupus). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia.

Conservation and restoration of forest trees impacted by non-native pathogens: the role of genetics and tree improvement

Treesearch

R.A. Sniezko; L.A. Winn

2017-01-01

North American native tree species in forest ecosystems, as well as managed forests and urban plantings, are being severely impacted by pathogens and insects. The impacts of these pathogens and insects often increase over time, and they are particularly acute for those species affected by non-native pathogens and insects. For restoration of affected tree species or for...

Impact of disability and other physical health issues on academic outcomes among American Indian and Alaskan Native college students: an exploratory analysis.

PubMed

Patterson Silver Wolf Adelv Unegv Waya, David A; Vanzile-Tamsen, Carol; Black, Jessica; Billiot, Shanondora M; Tovar, Molly

2015-01-01

This study investigated whether self-identified disabilities among American Indian and Alaskan Native college students impact academic performance and persistence to graduation and explored the differences in health and academic grades between American Indian and Alaskan Native students and students of other racial and ethnic identities using the National College Health Assessment. Findings indicate that American Indian or Alaskan Native students have significantly lower grades than White and Asian students, and American Indian and Alaskan Native women report the highest incidence of health problems of any demographic group. Exploratory results point to future research to determine the full impact of disabilities and poor health on academic success.

Fortune favours the bold: a higher predator reduces the impact of a native but not an invasive intermediate predator.

PubMed

Barrios-O'Neill, Daniel; Dick, Jaimie T A; Emmerson, Mark C; Ricciardi, Anthony; MacIsaac, Hugh J; Alexander, Mhairi E; Bovy, Helene C

2014-05-01

Emergent multiple predator effects (MPEs) might radically alter predictions of predatory impact that are based solely on the impact of individuals. In the context of biological invasions, determining if and how the individual-level impacts of invasive predators relates to their impacts in multiple-individual situations will inform understanding of how such impacts might propagate through recipient communities. Here, we use functional responses (the relationship between prey consumption rate and prey density) to compare the impacts of the invasive freshwater mysid crustacean Hemimysis anomala with a native counterpart Mysis salemaai when feeding on basal cladoceran prey (i) as individuals, (ii) in conspecific groups and (iii) in conspecific groups in the presence of a higher fish predator, Gasterosteus aculeatus. In the absence of the higher predator, the invader consumed significantly more basal prey than the native, and consumption was additive for both mysid species - that is, group consumption was predictable from individual-level consumption. Invaders and natives were themselves equally susceptible to predation when feeding with the higher fish predator, but an MPE occurred only between the natives and higher predator, where consumption of basal prey was significantly reduced. In contrast, consumption by the invaders and higher predator remained additive. The presence of a higher predator serves to exacerbate the existing difference in individual-level consumption between invasive and native mysids. We attribute the mechanism responsible for the MPE associated with the native to a trait-mediated indirect interaction, and further suggest that the relative indifference to predator threat on the part of the invader contributes to its success and impacts within invaded communities. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Host preference, population growth and injuries assessment of Polyphagotarsonemus latus (banks) (ACARI: Tarsonemidae) on Capsicum annuum L. Genotypes.

PubMed

Breda, M O; de Oliveira, J V; Esteves Filho, A B; Barbosa, D R S; de Santana, M F

2016-10-01

Despite the continued efforts on the search for different genotypes, Capsicum annuum (L.) is quite susceptible to attack by pest arthropods, especially the broad mite Polyphagotarsonemus latus Banks. Thus, the host preference, population growth and the injuries assessment of P. latus was studied on six C. annuum genotypes used in Brazil (Atlantis, California Wonder, Impact, Palloma, Rubia and Tendence). Host preference was accessed in choice tests, pairing the several genotypes, and the population growth was observed through non-choice tests in laboratory. The injuries assessments were evaluated in the greenhouse, comparing the injury level among the six genotypes. The results indicate that California Wonder and Palloma genotypes were more preferred by P. latus, and Impact and Tendence were less preferred. P. latus presented positive population growth rates (ri) on all the genotypes, however, Palloma and California Wonder showed the highest values of population growth rate (ri = 0.344 and ri = 0.340, respectively), while Impact had the lowest value (ri = 0.281). All the evaluated C. annuum genotypes showed low tolerance to P. latus and exhibited several injuries, but there was no statistical difference between them. California Wonder had the highest average number of mites/leaf (57.15), while Impact and Tendence obtained the lowest values (36.67 and 35.12, respectively) at the end of the evaluation period. The total average of injuries notes at the end of the bioassay did not differ between the genotypes. The number of mites/leaf was growing for the injury scale to the note 3.0, but when the injury scale approached the note 4.0, there was observed a decrease in the number of mites/leaf for all the genotypes.

The frequency of SLCO1B1*5 polymorphism genotypes among Russian and Sakha (Yakutia) patients with hypercholesterolemia.

PubMed

Sychev, Dmitrij Alekseevitch; Shuev, Grigorij Nikolaevich; Chertovskih, Jana Valer'evna; Maksimova, Nadezhda Romanovna; Grachev, Andrej Vladimirovich; Syrkova, Ol'ga Aleksandrovna

2016-01-01

Statins are the most commonly prescribed medicines for treatment of hypercholesterolemia. At the same time, up to 25% of patients cannot tolerate or have to discontinue the statin therapy due to statin-induced myopathy. In a majority of cases, statin-induced myopathy is attributed to SLCO1B1 gene polymorphism. The strongest association between statin-induced myopathy and SLCO1B1 gene polymorphism was described for simvastatin. Our research was focused on the frequency of SLCO1B1*5 genetic variant in the Russian population and in the native population of Sakha (Yakutia). A total of 1,071 hyperlipidemic Russian and 76 hyperlipidemic Sakha (Yakutian) patients were included in the study. Genotypes of SLCO1B1*5 (c.521T>C, rs4149056) were determined with polymerase chain reaction amplification. The results of our study were compared with data about hyperlipidemic patients in available publications. In the Russian population 665 (62%) patients had TT genotype of SLCO1B1*5, 346 (32%) patients had TC genotype, and in 60 patients (6%) CC variant was found (Hardy-Weinberg's chi-square test was 3.1 P=0.21). In comparison with Brazil, France, the People's Republic of China, Japan, and the native population of Sakha (Yakutia), C-allele, which causes an increased risk of statin-induced myopathy, was found significantly more often in the Russian population. In the native population of Sakha (Yakutia) SLCO1B1 polymorphism was TT - 62 (82%), TC - 11 (14%), CC - 3 (4%) (Hardy-Weinberg's chi-square test was 5.13 P=0.077). In comparison with data from Brazil, France, the People's Republic of China, and Japan, C-allele frequency in the Sakha (Yakutian) population was not significantly different. Thus, we have studied the incidence of pathologic SLCO1B1 c.521C-allele in Russian and Sakha hyperlipidemic patients. The presence of SLCO1B1 C-allele in patients with hyperlipidemia forces us to be more careful in hypolipidemic drug prescription, especially statins, according to a higher risk of statin-induced myopathy development. The fact that SLCO1B1 C-allele is rarer among Sakha patients, could be interesting from the point of studying adverse drug effects frequency and statins' effectiveness.

Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections

USGS Publications Warehouse

Jarvi, S.I.; Farias, M.E.M.; Atkinson, C.T.

2008-01-01

Background: The relatively recent introduction of a highly efficient mosquito vector and an avian pathogen (Plasmodium relictum) to an isolated island ecosystem with nai??ve, highly susceptible avian hosts provides a unique opportunity to investigate evolution of virulence in a natural system. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct impacts on virulence. Toward further understanding of how host-parasite and parasite-parasite relationships may impact virulence, this study characterizes within-host diversity of malaria parasite populations based on genetic analysis of the trap (thrombospondin-related anonymous protein) gene in isolates originating from Hawaii, Maui and Kauai Islands. Methods: A total of 397 clones were produced by nested PCR amplification and cloning of a 1664 bp fragment of the trap gene from two malarial isolates, K1 (Kauai) and KV115 (Hawaii) that have been used for experimental studies, and from additional isolates from wild birds on Kauai, Maui and Hawaii Islands. Diversity of clones was evaluated initially by RFLP-based screening, followed by complete sequencing of 33 selected clones. Results: RFLP analysis of trap revealed a minimum of 28 distinct RFLP haplotypes among the 397 clones from 18 birds. Multiple trap haplotypes were detected in every bird evaluated, with an average of 5.9 haplotypes per bird. Overall diversity did not differ between the experimental isolates, however, a greater number of unique haplotypes were detected in K1 than in KV115. We detected high levels of clonal diversity with clear delineation between isolates K1 and KV115 in a haplotype network. The patterns of within-host haplotype clustering are consistent with the possibility of a clonal genetic structure and rapid within-host mutation after infection. Conclusion: Avian malaria (P. relictum) and Avipoxvirus are the significant infectious diseases currently affecting the native Hawaiian avifauna. This study shows that clonal diversity of Hawaiian isolates of P. relictum is much higher than previously recognized. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct implications for host demographics, disease management strategies, and evolution of virulence. The results of this study indicate a widespread presence of multiple-genotype malaria infections with high clonal diversity in native birds of Hawaii, which when coupled with concurrent infection with Avipoxvirus, may significantly influence evolution of virulence. ?? 2008 Jarvi et al; licensee BioMed Central Ltd.

Native trees of the Northeast Argentine: natural hosts of the Cryptococcus neoformans-Cryptococcus gattii species complex.

PubMed

Cattana, Maria Emilia; Sosa, María de Los Ángeles; Fernández, Mariana; Rojas, Florencia; Mangiaterra, Magdalena; Giusiano, Gustavo

2014-01-01

In Argentina, information about epidemiology and environmental distribution of Cryptococcus is scarce. The city of Resistencia borders with Brazil and Paraguay where this fungus is endemic. All these supported the need to investigate the ecology of the genus and the epidemiology of cryptococcosis in this area. The aim was to investigate the presence of species of Cryptococcus neoformans-Cryptococcus gattii complex and their genotypes in trees of the city of Resistencia. One hundred and five trees were sampled by swabbing technique. The isolates were identified using conventional and commercial methods and genotyped by PCR-RFLP (Restriction Fragment Length Polymorphism). Cryptococcus was found in 7 out of the total trees. 6 out of 7 Cryptococcus isolates were identified as C. neoformans and one as C. gattii. C. gattii was isolated from Grevillea robusta. C. neoformans strains were isolated from Tabebuia avellanedae and Peltophorum dubium. Genotyping showed that all C. neoformans belonged to the VNI type and C. gattii belonged to the VGI type. This represents the first study on the ecology of Cryptococcus spp. associated to trees from northeastern Argentina, and the first report describing Grevillea robusta as a host of members of this fungal genus. Another finding is the isolation of C. neoformans from Tabebuia avellanedae and Peltophorum dubium, both tree species native to northeastern Argentina. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

77 FR 47052 - El Paso Natural Gas Company; Notice of Intent To Prepare an Environmental Impact Statement for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-07

... planned Project under these general headings: Geology and soils; Water resources, fisheries, and wetlands... restore native grassland; Visual impacts in consideration of Native American sacred sites; The creation of...; environmental and public interest groups; Native American Tribes; other interested parties; and local libraries...

Bud characteristics of unrooted stem cuttings affect establishment success of cottonwood.

Treesearch

M.A. Radwan; J.M. Kraft; D.S. DeBell

1987-01-01

Experimental plantings of different genotypes of cottonwood were examined. The four clones tested were: a Populus hybrid (Dula, D-01), a P. trichocarpa x P. deltoides hybrid (Hybrid 11), and two native P. trichocarpa clones (Nisqually 1 and Orting 5). Establishment success and characteristics of hardwood cuttings or resulting plants that might be related to success...

Changes in soil physical and chemical properties in long term improved natural and traditional agroforestry management systems of cacao genotypes in Peruvian Amazon

USDA-ARS?s Scientific Manuscript database

Traditional slash and burn agriculture practiced in the Peruvian Amazon region is leading to soil degradation and deforestation of native forest flora. The only way to stop such destructive processes is through the adoptation of sustainable alternatives such as growing crops in agroforestry systems....

Competitive advantage and higher fitness in native populations of genetically structured planktonic diatoms.

PubMed

Sildever, Sirje; Sefbom, Josefin; Lips, Inga; Godhe, Anna

2016-12-01

It has been shown that the planktonic diatom Skeletonema from neighbouring areas are genetically differentiated despite absence of physical dispersal barriers. We revisited two sites, Mariager Fjord and Kattegat, NE Atlantic, and isolated new strains. Microsatellite genotyping and F-statistics revealed that the populations were genetically differentiated. An experiment was designed to investigate if populations are locally adapted and have a native competitive advantage. Ten strains from each location were grown individually in native and foreign water to investigate differences in produced biomass. Additionally, we mixed six pairs, one strain from each site, and let them grow together in native and foreign water. Strains from Mariager Fjord and Kattegat produced higher biomass in native water. In the competition experiment, strains from both sites displayed higher relative abundance and demonstrated competitive advantage in their native water. The cause of the differentiated growth is unknown, but could possibly be attributed to differences in silica concentration or viruses in the two water types. Our data show that dispersal potential does not influence the genetic structure of the populations. We conclude that genetic adaptation has not been overruled by gene flow, but instead the responses to different selection conditions are enforcing the observed genetic structure. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Adaptive consequences of human-mediated introgression for indigenous tree species: the case of a relict Pinus pinaster population.

PubMed

Ramírez-Valiente, José Alberto; Robledo-Arnuncio, Juan José

2014-12-01

Human-induced gene movement via afforestation and restoration programs is a widespread phenomenon throughout the world. However, its effects on the genetic composition of native populations have received relatively little attention, particularly in forest trees. Here, we examine to what extent gene flow from allochthonous plantations of Pinus pinaster Aiton impacts offspring performance in a neighboring relict natural population and discuss the potential consequences for the long-term genetic composition of the latter. Specifically, we conducted a greenhouse experiment involving two contrasting watering treatments to test for differences in a set of functional traits and mortality rates between P. pinaster progenies from three different parental origins: (i) local native parents, (ii) exotic parents and (iii) intercrosses between local mothers and exotic fathers (intraspecific hybrids). Our results showed differences among crosses in cumulative mortality over time: seedlings of exotic parents exhibited the lowest mortality rates and seedlings of local origin the highest, while intraspecific hybrids exhibited an intermediate response. Linear regressions showed that seedlings with higher water-use efficiency (WUE, δ(13)C) were more likely to survive under drought stress, consistent with previous findings suggesting that WUE has an important role under dry conditions in this species. However, differences in mortality among crosses were only partially explained by WUE. Other non-measured traits and factors such as inbreeding depression in the relict population are more likely to explain the lower performance of native progenies. Overall, our results indicated that intraspecific hybrids and exotic individuals are more likely to survive under stressful conditions than local native individuals, at least during the first year of development. Since summer drought is the most important demographic and selective filter affecting tree establishment in Mediterranean ecosystems, a potential early selective advantage of exotic and hybrid genotypes would enhance initial steps of introgression of non-native genes into the study relict population of P. pinaster. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Obesity and Native Hawaiians/Pacific Islanders

MedlinePlus

... Population Profiles > Native Hawaiian/Other Pacific Islander > Obesity Obesity and Native Hawaiians/Pacific Islanders Native Hawaiians/Pacific ... youthonline . [Accessed 08/18/2017] HEALTH IMPACT OF OBESITY People who are overweight are more likely to ...

Inoculation effects on root-colonizing arbuscular mycorrhizal fungal communities spread beyond directly inoculated plants

PubMed Central

Krak, Karol; Vosátka, Miroslav; Püschel, David; Štorchová, Helena

2017-01-01

Inoculation with arbuscular mycorrhizal fungi (AMF) may improve plant performance at disturbed sites, but inoculation may also suppress root colonization by native AMF and decrease the diversity of the root-colonizing AMF community. This has been shown for the roots of directly inoculated plants, but little is known about the stability of inoculation effects, and to which degree the inoculant and the inoculation-induced changes in AMF community composition spread into newly emerging seedlings that were not in direct contact with the introduced propagules. We addressed this topic in a greenhouse experiment based on the soil and native AMF community of a post-mining site. Plants were cultivated in compartmented pots with substrate containing the native AMF community, where AMF extraradical mycelium radiating from directly inoculated plants was allowed to inoculate neighboring plants. The abundances of the inoculated isolate and of native AMF taxa were monitored in the roots of the directly inoculated plants and the neighboring plants by quantitative real-time PCR. As expected, inoculation suppressed root colonization of the directly inoculated plants by other AMF taxa of the native AMF community and also by native genotypes of the same species as used for inoculation. In the neighboring plants, high abundance of the inoculant and the suppression of native AMF were maintained. Thus, we demonstrate that inoculation effects on native AMF propagate into plants that were not in direct contact with the introduced inoculum, and are therefore likely to persist at the site of inoculation. PMID:28738069

Inoculation effects on root-colonizing arbuscular mycorrhizal fungal communities spread beyond directly inoculated plants.

PubMed

Janoušková, Martina; Krak, Karol; Vosátka, Miroslav; Püschel, David; Štorchová, Helena

2017-01-01

Inoculation with arbuscular mycorrhizal fungi (AMF) may improve plant performance at disturbed sites, but inoculation may also suppress root colonization by native AMF and decrease the diversity of the root-colonizing AMF community. This has been shown for the roots of directly inoculated plants, but little is known about the stability of inoculation effects, and to which degree the inoculant and the inoculation-induced changes in AMF community composition spread into newly emerging seedlings that were not in direct contact with the introduced propagules. We addressed this topic in a greenhouse experiment based on the soil and native AMF community of a post-mining site. Plants were cultivated in compartmented pots with substrate containing the native AMF community, where AMF extraradical mycelium radiating from directly inoculated plants was allowed to inoculate neighboring plants. The abundances of the inoculated isolate and of native AMF taxa were monitored in the roots of the directly inoculated plants and the neighboring plants by quantitative real-time PCR. As expected, inoculation suppressed root colonization of the directly inoculated plants by other AMF taxa of the native AMF community and also by native genotypes of the same species as used for inoculation. In the neighboring plants, high abundance of the inoculant and the suppression of native AMF were maintained. Thus, we demonstrate that inoculation effects on native AMF propagate into plants that were not in direct contact with the introduced inoculum, and are therefore likely to persist at the site of inoculation.

Comparison of milk protein composition and rennet coagulation properties in native Swedish dairy cow breeds and high-yielding Swedish Red cows.

PubMed

Poulsen, Nina A; Glantz, Maria; Rosengaard, Anette K; Paulsson, Marie; Larsen, Lotte B

2017-11-01

Recent studies have reported a very high frequency of noncoagulating milk in Swedish Red cows. The underlying factors are not fully understood. In this study, we explored rennet-induced coagulation properties and relative protein profiles in milk from native Swedish Mountain and Swedish Red Polled cows and compared them with a subset of noncoagulating (NC) and well-coagulating (WC) milk samples from modern Swedish Red cows. The native breeds displayed a very low prevalence of NC milk and superior milk coagulation properties compared with Swedish Red cows. The predominant variants in both native breeds were α S1 -casein (α S1 -CN) B, β-CN A 2 and β-lactoglobulin (β-LG) B. For κ-CN, the B variant was predominant in the Swedish Mountain cows, whereas the A variant was the most frequent in the Swedish Red Polled. The native breeds displayed similar protein composition, but varied in content of α S1 -CN with 9 phosphorylated serines (9P) form. Within the Swedish Mountain cows, we observed a strong inverse correlation between the relative concentration of κ-CN and micelle size and a positive correlation between ionic calcium and gel firmness. For comparison, we investigated a subset of 29 NC and 28 WC milk samples, representing the extremes with regard to coagulation properties based on an initial screening of 395 Swedish Red cows. In Swedish Red, NC milk properties were found to be related to higher frequencies of β-CN A 2 , κ-CN E and A variants, as well as β-LG B, and the predominant composite genotype of β- and κ-CN in the NC group was A 2 A 2 /AA. Generally, the A 2 A 2 /AA composite genotype was related to lower relative concentrations of κ-CN isoforms and higher relative concentrations of α S1 -, α S2 -, and β-CN. Compared with the group of WC milk samples, NC milk contained a higher fraction of α S2 -CN and α-lactalbumin (α-LA) but a lower fraction of α S1 -CN 9P. In conclusion, milk from native Swedish breeds has good characteristics for cheese milk, which could be exploited in niche dairy products. In milk from Swedish Mountain cows, levels of ionic calcium seemed to be more important for rennet-induced gel firmness than variation in the relative protein profile. In Swedish Red, lower protein content as well as higher fraction of α S2 -CN and lower fraction of α S1 -CN 9P were related to NC milk. Further, a decrease in the frequency of the composite β-κ-CN genotype A 2 A 2 /AA through selective breeding could have a positive effect on milk coagulation properties. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Co-introduction vs ecological fitting as pathways to the establishment of effective mutualisms during biological invasions.

PubMed

Le Roux, Johannes J; Hui, Cang; Keet, Jan-Hendrik; Ellis, Allan G

2017-09-01

Contents 1354 I. 1354 II. 1355 III. 1357 IV. 1357 V. 1359 1359 References 1359 SUMMARY: Interactions between non-native plants and their mutualists are often disrupted upon introduction to new environments. Using legume-rhizobium mutualistic interactions as an example, we discuss two pathways that can influence symbiotic associations in such situations: co-introduction of coevolved rhizobia; and utilization of, and adaptation to, resident rhizobia, hereafter referred to as 'ecological fitting'. Co-introduction and ecological fitting have distinct implications for successful legume invasions and their impacts. Under ecological fitting, initial impacts may be less severe and will accrue over longer periods as novel symbiotic associations and/or adaptations may require fine-tuning over time. Co-introduction will have more profound impacts that will accrue more rapidly as a result of positive feedbacks between densities of non-native rhizobia and their coevolved host plants, in turn enhancing competition between native and non-native rhizobia. Co-introduction can further impact invasion outcomes by the exchange of genetic material between native and non-native rhizobia, potentially resulting in decreased fitness of native legumes. A better understanding of the roles of these two pathways in the invasion dynamics of non-native legumes is much needed, and we highlight some of the exciting research avenues it presents. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Cryptosporidium species in Australian wildlife and domestic animals.

PubMed

Ryan, Una; Power, Michelle

2012-11-01

Cryptosporidium is an important enteric parasite that is transmitted via the fecal-oral route, water and food. Humans, wildlife and domestic livestock all potentially contribute Cryptosporidium to surface waters. Most species of Cryptosporidium are morphologically indistinguishable and can only be identified using molecular tools. Over 24 species have been identified and of these, 7 Cryptosporidium species/genotypes are responsible for most human cryptosporidiosis cases. In Australia, relatively few genotyping studies have been conducted. Six Cryptosporidium species (C. hominis, C. parvum, C. meleagridis, C. fayeri, C. andersoni and C. bovis) have been identified in humans in Australia. However, little is known about the contribution of animal hosts to human pathogenic strains of Cryptosporidium in drinking water catchments. In this review, we focus on the available genotyping data for native, feral and domestic animals inhabiting drinking water catchments in Australia to provide an improved understanding of the public health implications and to identify key research gaps.

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

PubMed Central

Cseke, Leland J.; Talley, Sharon M.

2012-01-01

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in 73 different countries throughout Africa, Asia, Europe, New Zealand, Oceania and the Americas1-2. Cogongrass forms rapidly-spreading, monodominant stands that displace a large variety of native plant species and in turn threaten the native animals that depend on the displaced native plant species for forage and shelter. To add to the problem, an ornamental variety [I. cylindrica var. koenigii (Retzius)] is widely marketed under the names of Imperata cylindrica 'Rubra', Red Baron, and Japanese blood grass (JBG). This variety is putatively sterile and noninvasive and is considered a desirable ornamental for its red-colored leaves. However, under the correct conditions, JBG can produce viable seed (Carol Holko, 2009 personal communication) and can revert to a green invasive form that is often indistinguishable from cogongrass as it takes on the distinguishing characteristics of the wild-type invasive variety4 (Figure 1). This makes identification using morphology a difficult task even for well-trained plant taxonomists. Reversion of JBG to an aggressive green phenotype is also not a rare occurrence. Using sequence comparisons of coding and variable regions in both nuclear and chloroplast DNA, we have confirmed that JBG has reverted to the green invasive within the states of Maryland, South Carolina, and Missouri. JBG has been sold and planted in just about every state in the continental U.S. where there is not an active cogongrass infestation. The extent of the revert problem in not well understood because reverted plants are undocumented and often destroyed. Application of this molecular protocol provides a method to identify JBG reverts and can help keep these varieties from co-occurring and possibly hybridizing. Cogongrass is an obligate outcrosser and, when crossed with a different genotype, can produce viable wind-dispersed seeds that spread cogongrass over wide distances5-7. JBG has a slightly different genotype than cogongrass and may be able to form viable hybrids with cogongrass. To add to the problem, JBG is more cold and shade tolerant than cogongrass8-10, and gene flow between these two varieties is likely to generate hybrids that are more aggressive, shade tolerant, and cold hardy than wild-type cogongrass. While wild-type cogongrass currently infests over 490 million hectares worldwide, in the Southeast U.S. it infests over 500,000 hectares and is capable of occupying most of the U.S. as it rapidly spreads northward due to its broad niche and geographic potential3,7,11. The potential of a genetic crossing is a serious concern for the USDA-APHIS Federal Noxious Week Program. Currently, the USDA-APHIS prohibits JBG in states where there are major cogongrass infestations (e.g., Florida, Alabama, Mississippi). However, preventing the two varieties from combining can prove more difficult as cogongrass and JBG expand their distributions. Furthermore, the distribution of the JBG revert is currently unknown and without the ability to identify these varieties through morphology, some cogongrass infestations may be the result of JBG reverts. Unfortunately, current molecular methods of identification typically rely on AFLP (Amplified Fragment Length Polymorphisms) and DNA sequencing, both of which are time consuming and costly. Here, we present the first cost-effective and reliable PCR-based molecular genotyping method to accurately distinguish between cogongrass and JBG revert. PMID:22370715

A PCR-based genotyping method to distinguish between wild-type and ornamental varieties of Imperata cylindrica.

PubMed

Cseke, Leland J; Talley, Sharon M

2012-02-20

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in 73 different countries throughout Africa, Asia, Europe, New Zealand, Oceania and the Americas(1-2). Cogongrass forms rapidly-spreading, monodominant stands that displace a large variety of native plant species and in turn threaten the native animals that depend on the displaced native plant species for forage and shelter. To add to the problem, an ornamental variety [I. cylindrica var. koenigii (Retzius)] is widely marketed under the names of Imperata cylindrica 'Rubra', Red Baron, and Japanese blood grass (JBG). This variety is putatively sterile and noninvasive and is considered a desirable ornamental for its red-colored leaves. However, under the correct conditions, JBG can produce viable seed (Carol Holko, 2009 personal communication) and can revert to a green invasive form that is often indistinguishable from cogongrass as it takes on the distinguishing characteristics of the wild-type invasive variety(4) (Figure 1). This makes identification using morphology a difficult task even for well-trained plant taxonomists. Reversion of JBG to an aggressive green phenotype is also not a rare occurrence. Using sequence comparisons of coding and variable regions in both nuclear and chloroplast DNA, we have confirmed that JBG has reverted to the green invasive within the states of Maryland, South Carolina, and Missouri. JBG has been sold and planted in just about every state in the continental U.S. where there is not an active cogongrass infestation. The extent of the revert problem in not well understood because reverted plants are undocumented and often destroyed. Application of this molecular protocol provides a method to identify JBG reverts and can help keep these varieties from co-occurring and possibly hybridizing. Cogongrass is an obligate outcrosser and, when crossed with a different genotype, can produce viable wind-dispersed seeds that spread cogongrass over wide distances(5-7). JBG has a slightly different genotype than cogongrass and may be able to form viable hybrids with cogongrass. To add to the problem, JBG is more cold and shade tolerant than cogongrass(8-10), and gene flow between these two varieties is likely to generate hybrids that are more aggressive, shade tolerant, and cold hardy than wild-type cogongrass. While wild-type cogongrass currently infests over 490 million hectares worldwide, in the Southeast U.S. it infests over 500,000 hectares and is capable of occupying most of the U.S. as it rapidly spreads northward due to its broad niche and geographic potential(3,7,11). The potential of a genetic crossing is a serious concern for the USDA-APHIS Federal Noxious Week Program. Currently, the USDA-APHIS prohibits JBG in states where there are major cogongrass infestations (e.g., Florida, Alabama, Mississippi). However, preventing the two varieties from combining can prove more difficult as cogongrass and JBG expand their distributions. Furthermore, the distribution of the JBG revert is currently unknown and without the ability to identify these varieties through morphology, some cogongrass infestations may be the result of JBG reverts. Unfortunately, current molecular methods of identification typically rely on AFLP (Amplified Fragment Length Polymorphisms) and DNA sequencing, both of which are time consuming and costly. Here, we present the first cost-effective and reliable PCR-based molecular genotyping method to accurately distinguish between cogongrass and JBG revert.

Impact of 6-month frozen storage of cervical specimens in alkaline buffer conditions on human papillomavirus genotyping.

PubMed

LaMere, Brandon J; Howell, Renee; Fetterman, Barbara; Shieh, Jen; Castle, Philip E

2008-08-01

The impact of 6-month storage of cervical specimens under alkaline conditions that occurs as the result of Hybrid Capture 2 testing on human papillomavirus (HPV) genotyping is not well documented. To examine this issue, 143 frozen hc2-positive specimens in specimen transport medium were selected at random from each of the following groups: specimens stored for 6 months, 4 months, and 2.5 months under alkaline pH (pH 12-13) and specimens stored 1 month at neutral pH (pH 6-7) as controls. Specimens were tested in a masked fashion for 20 HPV genotypes (HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, and 82) using a prototype, research-use-only GP5+/6+ L1 consensus PCR method and multiplex hybridization using Luminex xMAP for detection of specific HPV genotypes One control specimen had missing test results. There were no statistical differences in the number of HPV genotypes detected, number of carcinogenic HPV genotypes detected, or in the signal strength among HPV-positive results across groups. Six-month frozen storage of cervical specimens at alkaline pH had little impact on testing for HPV genotypes among hc2-positive women using this HPV genotyping method.

Economic Impacts of Non-Native Forest Insects in the Continental United States

Treesearch

Juliann E. Aukema; Brian Leung; Kent Kovacs; Corey Chivers; Jeffrey Englin; Susan J. Frankel; Robert G. Haight; Thomas P. Holmes; Andrew M. Liebhold; Deborah G. McCullough; Betsy Von Holle

2011-01-01

Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United...

Elm genetic diversity and hybridization in the presence of Dutch elm disease

USDA-ARS?s Scientific Manuscript database

Dutch elm disease (DED) has devastated native North American elm species for more than 75 years. The impact of DED on the genetic diversity of one native elm species, U. rubra or slippery elm, is summarized and its potential impact on the genetic diversity of the other four North American native elm...

The Impact of Career and Technical Education on Native American Males

ERIC Educational Resources Information Center

Neilson, Brent Alan

2016-01-01

The results of this qualitative descriptive study provide insight into the impact Career and Technical Education has on Native American male students in Northern Arizona. This study was created in response to the lack of research, especially qualitative research in this area. Moreover, it provided Native youth an opportunity to share their stories…

Foraging behavior of European starlings: implications for mitigating their impact on native species

Treesearch

Kathryn L. Purcell

2015-01-01

European starlings (Sturnus vulgaris) are a remarkably successful invasive species known to compete with native bird species for nest sites. The objective of this study was to understand why starlings avoid ungrazed pastures and provide recommendations to help mitigate the impacts of starlings on native bird species. I used aviary trials to examine...

Genomic epidemiology of the emerging pathogen Batrachochytrium dendrobatidis from native and invasive amphibian species in Chile.

PubMed

Valenzuela-Sánchez, A; O'Hanlon, S J; Alvarado-Rybak, M; Uribe-Rivera, D E; Cunningham, A A; Fisher, M C; Soto-Azat, C

2018-04-01

Emerging fungal diseases represent a threat to food security, animal and human health worldwide. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has been associated with catastrophic and well-documented amphibian population declines and extinctions. For the first time, Bd was cultured from native and non-native wild amphibians in Chile. Phylogenomic analyses revealed that Chilean isolates AVS2, AVS4 and AVS7 group within the global panzootic lineage of Bd (BdGPL) in a single highly supported clade that includes a genotype previously isolated from the United Kingdom. Our results extend the known distribution of BdGPL in South America and suggest a single and relatively recent introduction of BdGPL into the country, providing additional support to the role of anthropogenic activity in the global spread of this panzootic lineage. © 2017 Blackwell Verlag GmbH.

Novel microsatellite DNA markers indicate strict parthenogenesis and few genotypes in the invasive willow sawfly Nematus oligospilus.

PubMed

Caron, V; Norgate, M; Ede, F J; Nyman, T; Sunnucks, P

2013-02-01

Invasive organisms can have major impacts on the environment. Some invasive organisms are parthenogenetic in their invasive range and, therefore, exist as a number of asexual lineages (=clones). Determining the reproductive mode of invasive species has important implications for understanding the evolutionary genetics of such species, more especially, for management-relevant traits. The willow sawfly Nematus oligospilus Förster (Hymenoptera: Tenthredinidae) has been introduced unintentionally into several countries in the Southern Hemisphere where it has subsequently become invasive. To assess the population expansion, reproductive mode and host-plant relationships of this insect, microsatellite markers were developed and applied to natural populations sampled from the native and expanded range, along with sequencing of the cytochrome-oxidase I mitochondrial DNA (mtDNA) region. Other tenthredinids across a spectrum of taxonomic similarity to N. oligospilus and having a range of life strategies were also tested. Strict parthenogenesis was apparent within invasive N. oligospilus populations throughout the Southern Hemisphere, which comprised only a small number of genotypes. Sequences of mtDNA were identical for all individuals tested in the invasive range. The microsatellite markers were used successfully in several sawfly species, especially Nematus spp. and other genera of the Nematini tribe, with the degree of success inversely related to genetic divergence as estimated from COI sequences. The confirmation of parthenogenetic reproduction in N. oligospilus and the fact that it has a very limited pool of genotypes have important implications for understanding and managing this species and its biology, including in terms of phenotypic diversity, host relationships, implications for spread and future adaptive change. It would appear to be an excellent model study system for understanding evolution of invasive parthenogens that diverge without sexual reproduction and genetic recombination.

Impact of Anthropogenic Disturbance on Native and Invasive Trypanosomes of Rodents in Forested Uganda.

PubMed

Salzer, Johanna S; Pinto, C Miguel; Grippi, Dylan C; Williams-Newkirk, Amanda Jo; Peterhans, Julian Kerbis; Rwego, Innocent B; Carroll, Darin S; Gillespie, Thomas R

2016-12-01

Habitat disturbance and anthropogenic change are globally associated with extinctions and invasive species introductions. Less understood is the impact of environmental change on the parasites harbored by endangered, extinct, and introduced species. To improve our understanding of the impacts of anthropogenic disturbance on such host-parasite interactions, we investigated an invasive trypanosome (Trypanosoma lewisi). We screened 348 individual small mammals, representing 26 species, from both forested and non-forested habitats in rural Uganda. Using microscopy and PCR, we identified 18% of individuals (order Rodentia) as positive for trypanosomes. Further phylogenetic analyses revealed two trypanosomes circulating-T. lewisi and T. varani. T. lewisi was found in seven species both native and invasive, while T. varani was identified in only three native forest species. The lack of T. varani in non-forested habitats suggests that it is a natural parasite of forest-dwelling rodents. Our findings suggest that anthropogenic disturbance may lead to spillover of an invasive parasite (T. lewisi) from non-native to native species, and lead to local co-extinction of a native parasite (T. varani) and native forest-dwelling hosts.

Advocacy for Native American Indian and Alaska Native Clients and Counselees.

ERIC Educational Resources Information Center

Herring, Roger

Helping professionals need to be more informed and more active advocates for proactive counseling strategies with Native American Indian and Alaska Native peoples. The paper discusses the major advocacy needs of these populations. The negative impact of historical and contemporary discriminatory policies and practices on Native peoples has…

Knowing your genes: does this impact behaviour change?

PubMed

O'Donovan, Clare B; Walsh, Marianne C; Gibney, Michael J; Brennan, Lorraine; Gibney, Eileen R

2017-08-01

It is postulated that knowledge of genotype may be more powerful than other types of personalised information in terms of motivating behaviour change. However, there is also a danger that disclosure of genetic risk may promote a fatalistic attitude and demotivate individuals. The original concept of personalised nutrition (PN) focused on genotype-based tailored dietary advice; however, PN can also be delivered based on assessment of dietary intake and phenotypic measures. Whilst dietitians currently provide PN advice based on diet and phenotype, genotype-based PN advice is not so readily available. The aim of this review is to examine the evidence for genotype-based personalised information on motivating behaviour change, and factors which may affect the impact of genotype-based personalised advice. Recent findings in PN will also be discussed, with respect to a large European study, Food4Me, which investigated the impact of varying levels of PN advice on motivating behaviour change. The researchers reported that PN advice resulted in greater dietary changes compared with general healthy eating advice, but no additional benefit was observed for PN advice based on phenotype and genotype information. Within Food4Me, work from our group revealed that knowledge of MTHFR genotype did not significantly improve intakes of dietary folate. In general, evidence is weak with regard to genotype-based PN advice. For future work, studies should test the impact of PN advice developed on a strong nutrigenetic evidence base, ensure an appropriate study design for the research question asked, and incorporate behaviour change techniques into the intervention.

Minimum number of measurements for evaluating Bertholletia excelsa.

PubMed

Baldoni, A B; Tonini, H; Tardin, F D; Botelho, S C C; Teodoro, P E

2017-09-27

Repeatability studies on fruit species are of great importance to identify the minimum number of measurements necessary to accurately select superior genotypes. This study aimed to identify the most efficient method to estimate the repeatability coefficient (r) and predict the minimum number of measurements needed for a more accurate evaluation of Brazil nut tree (Bertholletia excelsa) genotypes based on fruit yield. For this, we assessed the number of fruits and dry mass of seeds of 75 Brazil nut genotypes, from native forest, located in the municipality of Itaúba, MT, for 5 years. To better estimate r, four procedures were used: analysis of variance (ANOVA), principal component analysis based on the correlation matrix (CPCOR), principal component analysis based on the phenotypic variance and covariance matrix (CPCOV), and structural analysis based on the correlation matrix (mean r - AECOR). There was a significant effect of genotypes and measurements, which reveals the need to study the minimum number of measurements for selecting superior Brazil nut genotypes for a production increase. Estimates of r by ANOVA were lower than those observed with the principal component methodology and close to AECOR. The CPCOV methodology provided the highest estimate of r, which resulted in a lower number of measurements needed to identify superior Brazil nut genotypes for the number of fruits and dry mass of seeds. Based on this methodology, three measurements are necessary to predict the true value of the Brazil nut genotypes with a minimum accuracy of 85%.

The Impact of Native Language Use on Second Language Vocabulary Learning by Saudi EFL Students

ERIC Educational Resources Information Center

Khan, Muhammad Saleem

2016-01-01

This paper strives to explore the impact of Native Language use on Foreign Language vocabulary learning on the basis of empirical and available data. The study is carried out with special reference to the English Language Programme students in Buraydah Community College, Qassim University, Saudi Arabia. The Native Language of these students is…

Rehabilitating downy brome (Bromus tectorum)-invaded scrublands using imazapic and seeding with native shrubs

Treesearch

Suzanne M. Owen; Carolyn Hull Sieg; Catherine A. Gehring

2011-01-01

Rehabilitation of downy brome-infested shrublands is challenging once this invasive grass dominates native communities. The effectiveness of imazapic herbicide in reducing downy brome cover has been variable, and there is uncertainty about the impacts of imazapic on native species. We used a before-after-control-impact (BACI) field experiment and greenhouse studies to...

Evidence of indirect impacts of introduced trout on native amphibians via facilitation of a shared predator

Treesearch

Karen L. Pope; Justin M. Garwood; Hartwell H. Welsh Jr.; Sharon P. Lawler

2008-01-01

Hyperpredation occurs when non-native prey facilitate invasive predators, which then suppress native prey. Direct impacts of introduced fish on amphibians are well studied, but the role of fish in supporting shared predators has not been considered. We present evidence for indirect effects of trout on amphibians through snake predation. Analyses of the diet,...

Hybridization of Tamarix ramosissima and T. chinensis (saltcedars) with T. aphylla (athel) (tamaricaceae) in the southwestern USA dertermined from DNA sequence data

USGS Publications Warehouse

Gaskin, John F.; Shafroth, Patrick B.

2005-01-01

Morphological intermediates between Tamarix ramosissima or T. chinensis (saltcedars) and T. aphylla (athel) were found recently in three locations in the southwestern USA, and were assumed to be hybrids or a previously unreported species. We sequenced chloroplast and nuclear DNA from putative parental and hybrid morphotypes and hybrid status of morphological intermediates was supported. Chloroplast data suggest that the seed source for these hybrids is T. aphylla. Invasive T. aphylla genotypes found in Australia match those found in the USA. Seed was collected from one of the hybrids, and a low percentage of it was viable. This hybrid combination has not been previously reported in the USA or the native ranges of the species. Although populations of this novel Tamarix hybrid appear to be uncommon at present, both parental species are considered invasive (saltcedars in North America; athel in Australia), and it is possible that more aggressive hybrid genotypes could be produced. Therefore, natural resource managers concerned with the potential spread of non-native species should be aware of the existence of these plants and monitor their future spread.

Genetic characterization of hybridization between native and invasive bittersweet vines (Celastrus spp.)

USGS Publications Warehouse

Zaya, David N.; Leicht-Young, Stacey A.; Pavlovic, Noel B.; Feldheim, Kevin A.; Ashley, Mary V.

2015-01-01

Hybridization associated with species introductions can accelerate the decline of native species. The main objective of this study was to determine if the decline of a North American liana (American bittersweet, Celastrus scandens) in the eastern portion of its range is related to hybridization with an introduced congener (oriental bittersweet, C. orbiculatus). We used newly characterized microsatellite loci, a maternally-inherited chloroplast DNA marker, and field observation to survey individuals across the USA to determine the prevalence of hybrids, their importance in the invasion of C. orbiculatus, and the predominant direction of hybridization. We found that only 8.4 % of non-native genotypes were hybrids (20 of 239), and these hybrids were geographically widespread. Hybrids showed reduced seed set (decline of >98 %) and small, likely inviable pollen. Genetic analysis of a maternally inherited chloroplast marker showed that all 20 identified hybrids came from C. scandens seed parents. The strong asymmetry in pollen flow that favors fecundity in introduced males has the potential to greatly accelerate the decline of native species by wasting limited female reproductive effort.

Mycobacterium tuberculosis strains of the Beijing genotype are rarely observed in tuberculosis patients in South America.

PubMed

Ritacco, Viviana; López, Beatriz; Cafrune, Patricia I; Ferrazoli, Lucilaine; Suffys, Philip N; Candia, Norma; Vásquez, Lucy; Realpe, Teresa; Fernández, Jorge; Lima, Karla V; Zurita, Jeannete; Robledo, Jaime; Rossetti, Maria L; Kritski, Afranio L; Telles, Maria A; Palomino, Juan C; Heersma, Herre; van Soolingen, Dick; Kremer, Kristin; Barrera, Lucía

2008-08-01

The frequency of the Beijing genotype of Mycobacterium tuberculosis as a cause of tuberculosis (TB) in South America was determined by analyzing genotypes of strains isolated from patients that had been diagnosed with the disease between 1997 and 2003 in seven countries of the subcontinent. In total, 19 of the 1,202 (1.6%) TB cases carried Beijing isolates, including 11 of the 185 patients from Peru (5.9%), five of the 512 patients from Argentina (1.0%), two of the 252 Brazilian cases (0.8%), one of the 166 patients from Paraguay (0.6%) and none of the samples obtained from Chile (35), Colombia (36) and Ecuador (16). Except for two patients that were East Asian immigrants, all cases with Beijing strains were native South Americans. No association was found between carrying a strain with the Beijing genotype and having drug or multi-drug resistant disease. Our data show that presently transmission of M. tuberculosis strains of the Beijing genotype is not frequent in Latin America. In addition, the lack of association of drug resistant TB and infection with M. tuberculosis of the Beijing genotype observed presently demands efforts to define better the contribution of the virulence and lack of response to treatment to the growing spread of Beijing strains observed in other parts of the world.

Evaluation of Wild Lentil Species as Genetic Resources to Improve Drought Tolerance in Cultivated Lentil.

PubMed

Gorim, Linda Y; Vandenberg, Albert

2017-01-01

Increasingly unpredictable annual rainfall amounts and distribution patterns have far reaching implications for pulse crop biology. Seedling and whole plant survival will be affected given that water is a key factor in plant photosynthesis and also influences the evolving disease spectrum that affects crops. The wild relatives of cultivated lentil are native to drought prone areas, making them good candidates for the evaluation of drought tolerance traits. We evaluated root and shoot traits of genotypes of cultivated lentil and five wild species grown under two water deficit regimes as well as fully watered conditions over a 13 week period indoors. Plants were grown in sectioned polyvinyl chloride (PVC) tubes containing field soil from the A, B, and C horizons. We found that root distribution into different soil horizons varied among wild lentil genotypes. Secondly, wild lentil genotypes employed diverse strategies such as delayed flowering, reduced transpiration rates, reduced plant height, and deep root systems to either escape, evade or tolerate drought conditions. In some cases, more than one drought strategy was observed within the same genotype. Sequence based classification of wild and cultivated genotypes did not explain patterns of drought response. The environmental conditions at their centers of origin may explain the patterns of drought strategies observed in wild lentils. The production of numerous small seeds by wild lentil genotypes may have implications for yield improvement in lentil breeding programs.

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

PubMed Central

Gusmão, Leonor; Gomes, Veronica; González, Miguel; Corach, Daniel; Sala, Andrea; Alechine, Evguenia; Palha, Teresinha; Santos, Ney; Ribeiro-dos-Santos, Andrea; Geppert, Maria; Willuweit, Sascha; Nagy, Marion; Zweynert, Sarah; Baeta, Miriam; Núñez, Carolina; Martínez-Jarreta, Begoña; González-Andrade, Fabricio; Fagundes de Carvalho, Elizeu; da Silva, Dayse Aparecida; Builes, Juan José; Turbón, Daniel; Lopez Parra, Ana Maria; Arroyo-Pardo, Eduardo; Toscanini, Ulises; Borjas, Lisbeth; Barletta, Claudia; Ewart, Elizabeth; Santos, Sidney; Krawczak, Michael

2013-01-01

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. PMID:23593040

The Impact of Non-Native English Teachers' Linguistic Insecurity on Learners' Productive Skills

ERIC Educational Resources Information Center

Daftari, Giti Ehtesham; Tavil, Zekiye Müge

2017-01-01

The discrimination between native and non-native English speaking teachers is reported in favor of native speakers in literature. The present study examines the linguistic insecurity of non-native English speaking teachers (NNESTs) and investigates its influence on learners' productive skills by using SPSS software. The eighteen teachers…

Explaining Behavior Change after Genetic Testing: The Problem of Collinearity between Test Results and Risk Estimates

PubMed Central

Fanshawe, Thomas R.; Prevost, A. Toby; Roberts, J. Scott; Green, Robert C.; Armstrong, David; Marteau, Theresa M.

2010-01-01

This paper explores whether and how the behavioral impact of genotype disclosure can be disentangled from the impact of numerical risk estimates generated by genetic tests. Secondary data analyses are presented from a randomized controlled trial of 162 first-degree relatives of Alzheimer’s disease (AD) patients. Each participant received a lifetime risk estimate of AD. Control group estimates were based on age, gender, family history, and assumed ε4-negative apolipoprotein E (APOE) genotype; intervention group estimates were based upon the first three variables plus true APOE genotype, which was also disclosed. AD-specific self-reported behavior change (diet, exercise, and medication use) was assessed at 12 months. Behavior change was significantly more likely with increasing risk estimates, and also more likely, but not significantly so, in ε4-positive intervention group participants (53% changed behavior) than in control group participants (31%). Intervention group participants receiving ε4-negative genotype feedback (24% changed behavior) and control group participants had similar rates of behavior change and risk estimates, the latter allowing assessment of the independent effects of genotype disclosure. However, collinearity between risk estimates and ε4-positive genotypes, which engender high-risk estimates, prevented assessment of the independent effect of the disclosure of an ε4 genotype. Novel study designs are proposed to determine whether genotype disclosure has an impact upon behavior beyond that of numerical risk estimates. PMID:18666860

Explaining behavior change after genetic testing: the problem of collinearity between test results and risk estimates.

PubMed

Fanshawe, Thomas R; Prevost, A Toby; Roberts, J Scott; Green, Robert C; Armstrong, David; Marteau, Theresa M

2008-09-01

This paper explores whether and how the behavioral impact of genotype disclosure can be disentangled from the impact of numerical risk estimates generated by genetic tests. Secondary data analyses are presented from a randomized controlled trial of 162 first-degree relatives of Alzheimer's disease (AD) patients. Each participant received a lifetime risk estimate of AD. Control group estimates were based on age, gender, family history, and assumed epsilon4-negative apolipoprotein E (APOE) genotype; intervention group estimates were based upon the first three variables plus true APOE genotype, which was also disclosed. AD-specific self-reported behavior change (diet, exercise, and medication use) was assessed at 12 months. Behavior change was significantly more likely with increasing risk estimates, and also more likely, but not significantly so, in epsilon4-positive intervention group participants (53% changed behavior) than in control group participants (31%). Intervention group participants receiving epsilon4-negative genotype feedback (24% changed behavior) and control group participants had similar rates of behavior change and risk estimates, the latter allowing assessment of the independent effects of genotype disclosure. However, collinearity between risk estimates and epsilon4-positive genotypes, which engender high-risk estimates, prevented assessment of the independent effect of the disclosure of an epsilon4 genotype. Novel study designs are proposed to determine whether genotype disclosure has an impact upon behavior beyond that of numerical risk estimates.

Ecological Value of Native Plant Cultivars Versus Wild-Type Native Plants for Promoting Hemipteran Diversity in Suburban Areas.

PubMed

Poythress, J C; Affolter, James M

2018-04-14

Because of concerns over recent declines in overall biodiversity in suburban areas, homeowners are attempting to improve the ecological functioning of their landscapes by incorporating native plants. Native plants are important for supporting native herbivorous insects, but it is unknown whether the native plants that are commercially available, typically cultivated varieties (cultivars) of a single genotype, are equally effective as food sources as the local, wild-type plants. We compared the hemipteran communities feeding on cultivars and wild-propagated plants for four species of native perennials commonly used as ornamentals. Of 65 hemipteran species collected, 35 exhibited a preference for some plant species over others, indicating a high degree of host-plant specialization. Moreover, the insect community associated with cultivars was distinct from the insect community associated with wild-type plants for each plant species, with three to four insect species accounting for most of the observed difference. Total insect abundance and insect biomass differed between cultivars and wild-propagated plants, but the direction of the difference changed over time and was not consistent among plant species. Species richness and a diversity index (the Q statistic) did not differ between cultivars and wild-type plants. These data suggest that abundance and diversity of hemipteran insects does not depend on the source of the plant material per se, but rather on the particular characteristics of cultivars that distinguish them from the wild type.

Native freshwater species get out of the way: Prussian carp (Carassius gibelio) impacts both fish and benthic invertebrate communities in North America.

PubMed

Ruppert, Jonathan L W; Docherty, Cassandra; Neufeld, Kenton; Hamilton, Kyle; MacPherson, Laura; Poesch, Mark S

2017-10-01

Prussian carp ( Carassius gibelio ) are one of the most noxious non-native species in Eurasia. Recently, Prussian carp, a non-native freshwater fish species, were genetically confirmed in Alberta, Canada and have been rapidly expanding their range in North America since establishment. Given their rapid range expansion, there is an increasing need to determine how Prussian carp may impact native species. We assessed the severity of the Prussian carp invasion by (i) determining their impact on fish communities, (ii) assessing their impact on benthic invertebrate communities, (iii) evaluating if Prussian carp alter abiotic conditions, and (iv) identifying where we find higher abundances of Prussian carp. When Prussian carp were established, we found significant changes to the fish community. Correspondingly, the degree of impact to benthic invertebrate communities was related to the stage of invasion (none, early or recent), where changes in fish communities were significantly concordant with changes in benthic invertebrate communities. Finally, we found that higher abundances of Prussian carp were significantly associated with lower abundances of a majority of native fish species. Altogether, using three lines of evidence, we determine that Prussian carp can have wide-ranging impacts on freshwater ecosystems in North America, pressing the need for management intervention.

Native freshwater species get out of the way: Prussian carp (Carassius gibelio) impacts both fish and benthic invertebrate communities in North America

PubMed Central

Ruppert, Jonathan L. W.; Docherty, Cassandra; Neufeld, Kenton; Hamilton, Kyle; MacPherson, Laura

2017-01-01

Prussian carp (Carassius gibelio) are one of the most noxious non-native species in Eurasia. Recently, Prussian carp, a non-native freshwater fish species, were genetically confirmed in Alberta, Canada and have been rapidly expanding their range in North America since establishment. Given their rapid range expansion, there is an increasing need to determine how Prussian carp may impact native species. We assessed the severity of the Prussian carp invasion by (i) determining their impact on fish communities, (ii) assessing their impact on benthic invertebrate communities, (iii) evaluating if Prussian carp alter abiotic conditions, and (iv) identifying where we find higher abundances of Prussian carp. When Prussian carp were established, we found significant changes to the fish community. Correspondingly, the degree of impact to benthic invertebrate communities was related to the stage of invasion (none, early or recent), where changes in fish communities were significantly concordant with changes in benthic invertebrate communities. Finally, we found that higher abundances of Prussian carp were significantly associated with lower abundances of a majority of native fish species. Altogether, using three lines of evidence, we determine that Prussian carp can have wide-ranging impacts on freshwater ecosystems in North America, pressing the need for management intervention. PMID:29134062

Virulence of oomycete pathogens from Phragmites australis-invaded and noninvaded soils to seedlings of wetland plant species

PubMed Central

Crocker, Ellen V; Karp, Mary Ann; Nelson, Eric B

2015-01-01

Soil pathogens affect plant community structure and function through negative plant–soil feedbacks that may contribute to the invasiveness of non-native plant species. Our understanding of these pathogen-induced soil feedbacks has relied largely on observations of the collective impact of the soil biota on plant populations, with few observations of accompanying changes in populations of specific soil pathogens and their impacts on invasive and noninvasive species. As a result, the roles of specific soil pathogens in plant invasions remain unknown. In this study, we examine the diversity and virulence of soil oomycete pathogens in freshwater wetland soils invaded by non-native Phragmites australis (European common reed) to better understand the potential for soil pathogen communities to impact a range of native and non-native species and influence invasiveness. We isolated oomycetes from four sites over a 2-year period, collecting nearly 500 isolates belonging to 36 different species. These sites were dominated by species of Pythium, many of which decreased seedling survival of a range of native and invasive plants. Despite any clear host specialization, many of the Pythium species were differentially virulent to the native and non-native plant species tested. Isolates from invaded and noninvaded soils were equally virulent to given individual plant species, and no apparent differences in susceptibility were observed between the collective groups of native and non-native plant species. PMID:26078850

Impacts of land use and invasive species on native avifauna of Mo’orea, French Polynesia

PubMed Central

Furnas, Brett J.

2017-01-01

Oceanic islands are among the most endemically biodiverse ecosystems in the world. They have been adversely impacted by human expansion, which affects regional biodiversity by altering the natural habitats of vulnerable, indigenous species. Birds represent a valuable indicator species of environmental change due to their ability to adapt quickly. Investigating the relationship between environmental change, abundance, and behaviors of birds can help us better anticipate potential impacts to island ecosystems. In addition, we can understand the population trends and restricted ranges of native avifauna, identify the regions needing protection, and assess habitat vulnerability linked to anthropogenic activities. In Mo’orea, French Polynesia, we studied nine passerine bird species using automated acoustic recording devices placed in agricultural, forested, and mixed habitats. Based on call counts per unit time and occupancy modeling, we found evidence that three non-native species preferred agricultural areas and low-canopy cover over dense forested areas. Furthermore, native bird detectability and possibly abundance was significantly lower than non-native birds. Using hierarchical cluster analysis to support inferences regarding behavioral differences, we found that native bird calling activity was negatively associated with non-native bird calling activity. Altogether, these results suggest native bird populations are at risk in all of the habitats studied, but forests serve as a potential refuge. PMID:28929014

Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.

PubMed

Galanter, Joshua Mark; Fernandez-Lopez, Juan Carlos; Gignoux, Christopher R; Barnholtz-Sloan, Jill; Fernandez-Rozadilla, Ceres; Via, Marc; Hidalgo-Miranda, Alfredo; Contreras, Alejandra V; Figueroa, Laura Uribe; Raska, Paola; Jimenez-Sanchez, Gerardo; Zolezzi, Irma Silva; Torres, Maria; Ponte, Clara Ruiz; Ruiz, Yarimar; Salas, Antonio; Nguyen, Elizabeth; Eng, Celeste; Borjas, Lisbeth; Zabala, William; Barreto, Guillermo; González, Fernando Rondón; Ibarra, Adriana; Taboada, Patricia; Porras, Liliana; Moreno, Fabián; Bigham, Abigail; Gutierrez, Gerardo; Brutsaert, Tom; León-Velarde, Fabiola; Moore, Lorna G; Vargas, Enrique; Cruz, Miguel; Escobedo, Jorge; Rodriguez-Santana, José; Rodriguez-Cintrón, William; Chapela, Rocio; Ford, Jean G; Bustamante, Carlos; Seminara, Daniela; Shriver, Mark; Ziv, Elad; Burchard, Esteban Gonzalez; Haile, Robert; Parra, Esteban; Carracedo, Angel

2012-01-01

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R² > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.

MC1R, KIT, IGF2, and NR6A1 as markers for genetic differentiation in Thai native, wild boars, and Duroc and Chinese Meishan pigs.

PubMed

Klomtong, P; Chaweewan, K; Phasuk, Y; Duangjinda, M

2015-10-19

Mutations in melanocortin 1 receptor (MC1R) gene and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) gene have been shown to affect coat color patterns in pigs. Additional functional marker genes, such as insulin like growth factor-2 (IGF2) and orphan nuclear receptor, germ cell nuclear factor (NR6A1), have been described for variations in factors such as fat deposition, litter size, and vertebra number in pigs. In this study, we investigated 129 pigs representing 4 breeds: Thai indigenous, classified into black (similar to Raad or Ka done pig) and black and white (similar to the Hailum and Kwai pig) coat color types; wild boar; Duroc; and Chinese Meishan. Mutations of MC1R, KIT, IGF2, and NR6A1 were detected using polymerase chain reaction-restriction fragment length polymorphism. The genotypes variation in MC1R and KIT genes could be used to differentiate four groups of coat color: solid black, black and white, red, and wild type. For IGF2, the GG genotype was present in wild boar only; for NR6A1 the TT genotype was found only in Duroc pigs. We identified novel 14-bp deletions in KIT that were associated with black and white coat color in Thai indigenous pigs. Insights into variations in genes presented in this study will be useful in future developmental breeding programs for the Thai native pig.

Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin.

PubMed

Lamer, James T; Ruebush, Blake C; Arbieva, Zarema H; McClelland, Michael A; Epifanio, John M; Sass, Greg G

2015-08-01

Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed-species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species-diagnostic SNPs (57 nuclear and one mitochondrial). Forty-four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental-like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later-generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F1 hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species. © 2015 John Wiley & Sons Ltd.

Genetic variation in plant volatile emission does not result in differential attraction of natural enemies in the field.

PubMed

Wason, Elizabeth L; Hunter, Mark D

2014-02-01

Volatile organic chemical (VOC) emission by plants may serve as an adaptive plant defense by attracting the natural enemies of herbivores. For plant VOC emission to evolve as an adaptive defense, plants must show genetic variability for the trait. To date, such variability has been investigated primarily in agricultural systems, yet relatively little is known about genetic variation in VOCs emitted by natural populations of native plants. Here, we investigate intraspecific variation in constitutive and herbivore-induced plant VOC emission using the native common milkweed plant (Asclepias syriaca) and its monarch caterpillar herbivore (Danaus plexippus) in complementary field and common garden greenhouse experiments. In addition, we used a common garden field experiment to gauge natural enemy attraction to milkweed VOCs induced by monarch damage. We found evidence of genetic variation in the total constitutive and induced concentrations of VOCs and the composition of VOC blends emitted by milkweed plants. However, all milkweed genotypes responded similarly to induction by monarchs in terms of their relative change in VOC concentration and blend. Natural enemies attacked decoy caterpillars more frequently on damaged than on undamaged milkweed, and natural enemy visitation was associated with higher total VOC concentrations and with VOC blend. Thus, we present evidence that induced VOCs emitted by milkweed may function as a defense against herbivores. However, plant genotypes were equally attractive to natural enemies. Although milkweed genotypes diverge phenotypically in their VOC concentrations and blends, they converge into similar phenotypes with regard to magnitude of induction and enemy attraction.

Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas

PubMed Central

Galanter, Joshua Mark; Fernandez-Lopez, Juan Carlos; Gignoux, Christopher R.; Barnholtz-Sloan, Jill; Fernandez-Rozadilla, Ceres; Via, Marc; Hidalgo-Miranda, Alfredo; Contreras, Alejandra V.; Figueroa, Laura Uribe; Raska, Paola; Jimenez-Sanchez, Gerardo; Silva Zolezzi, Irma; Torres, Maria; Ponte, Clara Ruiz; Ruiz, Yarimar; Salas, Antonio; Nguyen, Elizabeth; Eng, Celeste; Borjas, Lisbeth; Zabala, William; Barreto, Guillermo; Rondón González, Fernando; Ibarra, Adriana; Taboada, Patricia; Porras, Liliana; Moreno, Fabián; Bigham, Abigail; Gutierrez, Gerardo; Brutsaert, Tom; León-Velarde, Fabiola; Moore, Lorna G.; Vargas, Enrique; Cruz, Miguel; Escobedo, Jorge; Rodriguez-Santana, José; Rodriguez-Cintrón, William; Chapela, Rocio; Ford, Jean G.; Bustamante, Carlos; Seminara, Daniela; Shriver, Mark; Ziv, Elad; Gonzalez Burchard, Esteban; Haile, Robert

2012-01-01

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2>0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region. PMID:22412386

Effects of an invasive plant on a desert sand dune landscape

USGS Publications Warehouse

Barrows, C.W.; Allen, E.B.; Brooks, M.L.; Allen, M.F.

2009-01-01

Given the abundance of non-native species invading wildland habitats, managers need to employ informed triage to focus control efforts on weeds with the greatest potential for negative impacts. Our objective here was to determine the level of threat Sahara mustard, Brassica tournefortii, represents to meeting regional goals for protecting biodiversity. Sahara mustard has spread throughout much of the Mojave and lower Sonoran Deserts. It has occurred in southern California's Coachella Valley for nearly 80 years, punctuated by years of extremely high abundance following high rainfall. In those years the mustard has clear negative impacts on the native flora. Using mustard removal experiments we identified reductions in native plant reproduction, shifting composition increasingly toward Sahara mustard while decreasing the fraction of native species. High between-year variance in precipitation may be a key to maintaining biodiversity as the mustard is less abundant in drier years. Sahara mustard impacts to the native fauna were much less evident. Of the animal species evaluated, only the Coachella Valley fringe-toed lizard, Uma inornata, demonstrated a negative response to mustard abundance; however the impacts were short-lived, lasting no more than a year after the mustard's dominance waned. Without control measures the long-term impacts to desert biodiversity may rest on the changing climate. Wetter conditions or increased periodicity of high rainfall years will favor Sahara mustard and result in reduced biodiversity, especially of native annual plants. Drier conditions will keep the mustard from becoming dominant but may have other negative consequences on the native flora and fauna. ?? 2008 Springer Science+Business Media B.V.

The C677T polymorphism of the methylenetetrahydrofolate reductase gene in Mexican mestizo neural-tube defect parents, control mestizo and native populations.

PubMed

Dávalos, I P; Olivares, N; Castillo, M T; Cantú, J M; Ibarra, B; Sandoval, L; Morán, M C; Gallegos, M P; Chakraborty, R; Rivas, F

2000-01-01

The C677T mutation of the methylenetetrahydrofolate reductase (MTHFR) gene, associated with the thermolabile form of the enzyme, has reportedly been found to be increased in neural-tube defects (NTD), though this association is still unclear. A group of 107 mestizo parents of NTD children and five control populations: 101 mestizo (M), 50 Huichol (H), 38 Tarahumara (T), 21 Purepecha (P) and 20 Caucasian (C) individuals were typed for the MTHFR C677T variant by the PCR/RFLP (HinfI) method. Genotype frequencies were in agreement with the Hardy-Weinberg expectations in all six populations. Allele frequency (%) of the C677T variant was 45 in NTD, 44 in M, 56 in H, 36 in T, 57 in P, 35 in C. Pairwise inter-population comparisons of allele frequency disclosed a very similar distribution between NTD and M groups (exact test, P=0.92). Among controls, differences between M and individual native groups were NS (0.06

Symbiont interactions with non-native hosts limit the formation of new symbioses.

PubMed

Niepoth, Natalie; Ellers, Jacintha; Henry, Lee M

2018-03-12

Facultative symbionts are common in eukaryotes and can provide their hosts with significant fitness benefits. Despite the advantage of carrying these microbes, they are typically only found in a fraction of the individuals within a population and are often non-randomly distributed among host populations. It is currently unclear why facultative symbionts are only found in certain host individuals and populations. Here we provide evidence for a mechanism to help explain this phenomenon: that when symbionts interact with non-native host genotypes it can limit the horizontal transfer of symbionts to particular host lineages and populations of related hosts. Using reciprocal transfections of the facultative symbiont Hamiltonella defensa into different pea aphid clones, we demonstrate that particular symbiont strains can cause high host mortality and inhibit offspring production when injected into aphid clones other than their native host lineage. However, once established, the symbiont's ability to protect against parasitoids was not influenced by its origin. We then demonstrate that H. defensa is also more likely to establish a symbiotic relationship with aphid clones from a plant-adapted population (biotype) that typically carry H. defensa in nature, compared to clones from a biotype that does not normally carry this symbiont. These results provide evidence that certain aphid lineages and populations of related hosts are predisposed to establishing a symbiotic relationship with H. defensa. Our results demonstrate that host-symbiont genotype interactions represent a potential barrier to horizontal transmission that can limit the spread of symbionts, and adaptive traits they carry, to certain host lineages.

Global Salmonidae introductions reveal stronger ecological effects of changing intraspecific compared to interspecific diversity.

PubMed

Buoro, Mathieu; Olden, Julian D; Cucherousset, Julien

2016-11-01

The introduction of organisms within the native range of wild conspecifics is a widespread phenomenon and locally modifies patterns in intraspecific diversity. However, our knowledge of the resulting ecological effects, as opposed to those caused by invasion-induced changes in interspecific diversity, is still limited. Here, we investigated the ecological effects of native and non-native invaders across levels of biological organisations and recipient organisms using the global and long history introductions of salmonids. Our meta-analysis demonstrated that the global effects of native species introductions exceeded those induced by non-native invaders. The impacts of native invaders were primarily manifested at the individual level on wild conspecifics, but remained largely unexplored on other native organisms and at the community and ecosystem levels. Overlooked and poorly appreciated, quantifying the impacts of native invaders has important implications because human-assisted introductions of domesticated organisms are ubiquitous and likely to proliferate in the future. © 2016 John Wiley & Sons Ltd/CNRS.

Invasive sweetclover (Melilotus alba) impacts native seeding recruitment along floodplains of interior Alaska

Treesearch

Blaine T. Spellman; Tricia L. Wurtz

2011-01-01

Sweetclover (Melilotus alba) is a nonnative legume that has formed dense and extensive patches along several rivers in Alaska. Our research objective was to determine if sweetclover impacts recruitment of native seedlings in floodplain habitats. To determine if sweetclover impacted recruitment, we conducted a removal experiment along two rivers in...

Doublethink and scale mismatch polarize policies for an invasive tree

PubMed Central

Roberts, Caleb P.; Uden, Daniel R.; Allen, Craig R.; Twidwell, Dirac

2018-01-01

Mismatches between invasive species management policies and ecological knowledge can lead to profound societal consequences. For this reason, natural resource agencies have adopted the scientifically-based density-impact invasive species curve to guide invasive species management. We use the density-impact model to evaluate how well management policies for a native invader (Juniperus virginiana) match scientific guidelines. Juniperus virginiana invasion is causing a sub-continental regime shift from grasslands to woodlands in central North America, and its impacts span collapses in endemic diversity, heightened wildfire risk, and crashes in grazing land profitability. We (1) use land cover data to identify the stage of Juniperus virginiana invasion for three ecoregions within Nebraska, USA, (2) determine the range of invasion stages at individual land parcel extents within each ecoregion based on the density-impact model, and (3) determine policy alignment and mismatches relative to the density-impact model in order to assess their potential to meet sustainability targets and avoid societal impacts as Juniperus virginiana abundance increases. We found that nearly all policies evidenced doublethink and policy-ecology mismatches, for instance, promoting spread of Juniperus virginiana regardless of invasion stage while simultaneously managing it as a native invader in the same ecoregion. Like other invasive species, theory and literature for this native invader indicate that the consequences of invasion are unlikely to be prevented if policies fail to prioritize management at incipient invasion stages. Theory suggests a more realistic approach would be to align policy with the stage of invasion at local and ecoregion management scales. There is a need for scientists, policy makers, and ecosystem managers to move past ideologies governing native versus non-native invader classification and toward a framework that accounts for the uniqueness of native species invasions, their anthropogenic drivers, and their impacts on ecosystem services. PMID:29513675

Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping

Treesearch

Jun-Jun Liu; Anna W. Schoettle; Richard A. Sniezko; Rona N. Sturrock; Arezoo Zamany; Holly Williams; Amanda Ha; Danelle Chan; Bob Danchok; Douglas P. Savin; Angelia Kegley

2016-01-01

Linkage of DNA markers with phenotypic traits provides essential information to dissect clustered genes with potential phenotypic contributions in a target genome region. Pinus flexilis E. James (limber pine) is a keystone five-needle pine species in mountain-top ecosystems of North America. White pine blister rust (WPBR), caused by a non-native fungal...

Non-target effects of broadleaf herbicide on a native perennial forb: a demographic framework for assessing and minimizing impacts

Treesearch

Elizabeth E. Crone; Marilyn Marler; Dean E. Pearson

2009-01-01

Invasive species are one of the leading threats to biodiversity worldwide. Therefore, chemical herbicides are increasingly used to control invasive plants in natural and semi-natural areas. Little is known about the non-target impacts of these chemicals on native species. We conducted an experiment to test the demographic effects of the herbicide picloram on a native...

Distribution and Biocontrol Potential of phlD(+) Pseudomonads in Corn and Soybean Fields.

PubMed

McSpadden Gardener, Brian B; Gutierrez, Laura J; Joshi, Raghavendra; Edema, Richard; Lutton, Elizabeth

2005-06-01

ABSTRACT The abundance and diversity of phlD(+) Pseudomonas spp. colonizing the rhizospheres of young, field-grown corn and soybean plants were assayed over a 3-year period. Populations of these bacteria were detected on the large majority of plants sampled in the state of Ohio, but colonization was greater on corn. Although significant variation in the incidence of rhizosphere colonization was observed from site to site and year to year on both crops, the magnitude of the variation was greatest for soybean. The D genotype was detected on plants collected from all 15 counties examined, and it represented the most abundant subpopulation on both crops. Additionally, six other genotypes (A, C, F, I, R, and S) were found to predominate in the rhizosphere of some plants. The most frequently observed of these were the A genotype and a newly discovered S genotype, both of which were found on corn and soybean roots obtained from multiple locations. Multiple isolates of the most abundant genotypes were recovered and characterized. The S genotype was found to be phylogenetically and phenotypically similar to the D genotype. In addition, the novel R genotype was found to be most similar to the A genotype. All of the isolates displayed significant capacities to inhibit the growth of an oomycete pathogen in vitro, but such phenotypes were highly dependent on media used. When tested against multiple oomycete pathogens isolated from soybean, the A genotype was significantly more inhibitory than the D genotype when incubated on 1/10x tryptic soy agar and 1/5x corn meal agar. Seed inoculation with different isolates of the A, D, and S genotypes indicated that significant root colonization, generally in excess of log 5 cells per gram of root, could be attained on both crops. Field trials of the A genotype isolate Wayne1R indicated the capacity of inoculant populations to supplement the activities of native populations so as to increase soybean stands and yields. The relevance of these findings to natural and augmentative biocontrol of root pathogens by these bacteria is discussed.

Evaluating barriers to native seedling establishment in an invaded Hawaiian lowland wet forest

Treesearch

S. Cordell; R. Ostertag; B. Rowe; L. Sweinhart; L. Vasquez-Radonic; J. Michaud; T.C. Cole; J.R. Schulten

2009-01-01

Many tropical island forest ecosystems are dominated by non-native plant species and lack native species regeneration in the understorey. Comparison of replicated control and removal plots offers an opportunity to examine not only invasive species impacts but also the restoration potential of native species. In lowland Hawaiian wet forests little is known about native...

Stable Isotopes of C and N Reveal Habitat Dependent Dietary Overlap between Native and Introduced Turtles Pseudemys rubriventris and Trachemys scripta

PubMed Central

Pearson, Steven H.; Avery, Harold W.; Kilham, Susan S.; Velinsky, David J.; Spotila, James R.

2013-01-01

Habitat degradation and species introductions are two of the leading causes of species declines on a global scale. Invasive species negatively impact native species through predation and competition for limited resources. The impacts of invasive species may be increased in habitats where habitat degradation is higher due to reductions of prey abundance and distribution. Using stable isotope analyses and extensive measurements of resource availability we determined how resource availability impacts the long term carbon and nitrogen assimilation of the invasive red-eared slider turtle (Trachemys scripta elegans) and a native, threatened species, the red-bellied turtle (Pseudemys rubriventris) at two different freshwater wetland complexes in Pennsylvania, USA. At a larger wetland complex with greater vegetative species richness and diversity, our stable isotope analyses showed dietary niche partitioning between species, whereas analyses from a smaller wetland complex with lower vegetative species richness and diversity showed significant dietary niche overlap. Determining the potential for competition between these two turtle species is important to understanding the ecological impacts of red-eared slider turtles in wetland habitats. In smaller wetlands with increased potential for competition between native turtles and invasive red-eared slider turtles we expect that when shared resources become limited, red-eared slider turtles will negatively impact native turtle species leading to long term population declines. Protection of intact wetland complexes and the reduction of introduced species populations are paramount to preserving populations of native species. PMID:23675437

Stable isotopes of C and N reveal habitat dependent dietary overlap between native and introduced turtles Pseudemys rubriventris and Trachemys scripta.

PubMed

Pearson, Steven H; Avery, Harold W; Kilham, Susan S; Velinsky, David J; Spotila, James R

2013-01-01

Habitat degradation and species introductions are two of the leading causes of species declines on a global scale. Invasive species negatively impact native species through predation and competition for limited resources. The impacts of invasive species may be increased in habitats where habitat degradation is higher due to reductions of prey abundance and distribution. Using stable isotope analyses and extensive measurements of resource availability we determined how resource availability impacts the long term carbon and nitrogen assimilation of the invasive red-eared slider turtle (Trachemys scripta elegans) and a native, threatened species, the red-bellied turtle (Pseudemys rubriventris) at two different freshwater wetland complexes in Pennsylvania, USA. At a larger wetland complex with greater vegetative species richness and diversity, our stable isotope analyses showed dietary niche partitioning between species, whereas analyses from a smaller wetland complex with lower vegetative species richness and diversity showed significant dietary niche overlap. Determining the potential for competition between these two turtle species is important to understanding the ecological impacts of red-eared slider turtles in wetland habitats. In smaller wetlands with increased potential for competition between native turtles and invasive red-eared slider turtles we expect that when shared resources become limited, red-eared slider turtles will negatively impact native turtle species leading to long term population declines. Protection of intact wetland complexes and the reduction of introduced species populations are paramount to preserving populations of native species.

Increasing Native Forb Seed Supplies for the Great Basin

Treesearch

Nancy L. Shaw; Scott M. Lambert; Ann M. DeBolt; Mike Pellant

2005-01-01

Over the last 150 years, excessive grazing, annual weed invasions, increased wildfire frequency, and other human disturbances have negatively impacted native plant communities of the Great Basin. Native plant materials and appropriate planting strategies are needed to recreate diverse communities in areas requiring active restoration. Although native forbs are critical...

DISTRIBUTION AND EXTENT OF NON-NATIVE FISH IN WESTERN STREAMS AND RIVERS

EPA Science Inventory

Introduced species can produce a variety of impacts on native assemblages and ecosystems. Reliable knowledge about the extent of non-native species should be a useful tool for effective management of fisheries and aquatic ecosystems. It is well known that many non-native fish s...

Native American Students' Experiences of Cultural Differences in College: Influence and Impact

ERIC Educational Resources Information Center

Clark, Leslie E.

2012-01-01

The culture of most colleges and universities is very different for Native American students with close ties to their traditional communities. "Traditional," in a Native American sense, means multiple interconnections of emotional, physical, intellectual, and spiritual identity that combine to define expectations for the Native American…

Phenolic composition and antioxidant capacity of Ugni molinae Turcz. leaves of different genotypes.

PubMed

Peña-Cerda, Marcelo; Arancibia-Radich, Jorge; Valenzuela-Bustamante, Paula; Pérez-Arancibia, Rodrigo; Barriga, Andrés; Seguel, Ivette; García, Lorena; Delporte, Carla

2017-01-15

Ugni molinae Turcz. is a native shrub of Chile, known for its edible berries and its leaves, which have been the focus of recent attention, as a good source of phenolic compounds to be used in cosmetics and food products. The aim of this study was to assess the differences in the phenolic composition and antioxidant capacity of the ethanolic extracts from the leaves of 10 genotypes of U. molinae, that were cultivated under the same soil, climate and agronomical management. Antioxidant activity was assessed by complementary methods (ORAC-Fl, FRAP and DPPH assay), phenolic composition of each extract was analyzed by LC-MS. Phenolic and flavonoid total contents were determined by Folin-Ciocalteu and AlCl3 methods. Significative differences were found by these methods, and ellagitannins, gallic acid derivatives and flavonols were identified as responsible for these differences, showing the influence of the genotype on the phenolic composition of U. molinae leaves. Copyright © 2016 Elsevier Ltd. All rights reserved.

Invasive lionfish reduce native fish abundance on a regional scale

NASA Astrophysics Data System (ADS)

Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

2016-08-01

Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future.

Invasive lionfish reduce native fish abundance on a regional scale.

PubMed

Ballew, Nicholas G; Bacheler, Nathan M; Kellison, G Todd; Schueller, Amy M

2016-08-31

Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future.

Invasive lionfish reduce native fish abundance on a regional scale

PubMed Central

Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

2016-01-01

Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990–2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future. PMID:27578096

Quantitative analysis of essential oils of Thymus daenensis using laser-induced fluorescence and Raman spectroscopy.

PubMed

Khoshroo, H; Khadem, H; Bahreini, M; Tavassoli, S H; Hadian, J

2015-11-10

Laser-induced fluorescence and Raman spectroscopy are used for the investigation of different genotypes of Thymus daenensis native to the Ilam province of Iran. Different genotypes of T. daenensis essential oils, labeled T1 through T7, possess slight differences with regard to the composition of the thymol. The gas chromatography-mass spectrometry (GC-MS) method is performed to determine the concentration of each constituent as a reference method. The Raman spectra of different concentrations of pure thymol dissolved in hexane as standard samples are obtained via a laboratory prototype Raman spectroscopy setup for the calculation of the calibration curve. The regression coefficient and limit of detection are calculated. The possibility of the differentiation of different genotypes of T. daenensis is also examined by laser-induced fluorescence spectroscopy, although we do not know the exact amounts of their components. All the fluorescence spectral information is used jointly by cluster analysis to differentiate between 7 genotypes. Our results demonstrate the acceptable precision of Raman spectroscopy with GC-MS and corroborate the capacity of Raman spectroscopy in applications in the quantitative analysis field. Furthermore, the cluster analysis results show that laser-induced fluorescence spectroscopy is an acceptable technique for the rapid classification of different genotypes of T. daenensis without having any previous information of their exact amount of constituents. So, the ability to rapidly and nondestructively differentiate between genotypes makes it possible to efficiently select high-quality herbs from many samples.

Ecological impacts of non-native species

USGS Publications Warehouse

Wilkinson, John W.

2012-01-01

Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and management of non-native species has only just begun but some promising results have already emerged (see below), giving hope to a very difficult conservation issue. This chapter provides an overview of the role of non-native species in amphibian declines and summarizes the current state of knowledge of non-native species that are known, or considered to be, a threat to amphibian species and populations. The biological and socio-economic issues of non-native species control are examined and brief case studies of successful eradication programmes are provided.

Ecological impacts of non-native species: Chapter 2

USGS Publications Warehouse

Pilliod, David S.; Griffiths, R.A.; Kuzmin, S.L.; Heatwole, Harold; Wilkinson, John W.

2012-01-01

Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and management of non-native species has only just begun but some promising results have already emerged (see below), giving hope to a very difficult conservation issue. This chapter provides an overview of the role of non-native species in amphibian declines and summarizes the current state of knowledge of non-native species that are known, or considered to be, a threat to amphibian species and populations. The biological and socio-economic issues of non-native species control are examined and brief case studies of successful eradication programmes are provided.

Environment and genotype effects on the content of dietary fiber and its components in wheat in the HEALTHGRAIN diversity screen.

PubMed

Gebruers, Kurt; Dornez, Emmie; Bedõ, Zoltan; Rakszegi, Mariann; Frás, Anna; Boros, Danuta; Courtin, Christophe M; Delcour, Jan A

2010-09-08

Within the HEALTHGRAIN diversity screen, the variability of the contents of dietary fiber (DF) and components thereof was studied in wheat. Furthermore, the contribution of genotype and environment to this variability was estimated. The levels of total DF (TDF), total nonstarch polysaccharide (TOTNSP), water-extractable nonstarch polysaccharide (WENSP), total arabinoxylan (TOTAX), lignin, and beta-glucan in whole meal, flour, and/or bran varied approximately 1.8-fold. The highest variability was observed for the water-extractable arabinoxylan (WEAX) level in flour and bran (approximately 3.7-fold). Genotype and environment contributed to a similar extent to the variability in TDF, TOTNSP, and TOTAX content in wheat. The observed relatively high impact of genotype-environment interaction suggests that the levels of these constituents are weak breeding parameters. The WENSP level is a more stable parameter as the effect of the interaction term was much less than the impact of genotype. For TOTAX and WEAX in flour, WEAX in bran, beta-glucan in whole meal, and extract viscosity, wheat genotype determined approximately 50% or higher of the variation observed, whereas the impact of the genotype-environment interaction was relatively low. These findings suggest that the health-related and technological functionality of wheat can be directed to a certain extent by selection of appropriate wheat varieties.

Preliminary tests for Salix sp. tolerance to heavy metals (Cd, Ni, Pb)

NASA Astrophysics Data System (ADS)

Corneanu, Mihaela; Hernea, Cornelia; Butnariu, Monica; Corneanu, Gabriel; Sărac, Ioan; Hollerbach, Wilhelm; Neţoiu, Constantin; Petcov, Andreea Adriana

2014-05-01

The species of Salix genus constitute potential sources of germplasm in the prevention of the environment degradation, and offer remedy for about two third from the all degradation types. The majority of the willow species, present a good adaptation to hypoxic conditions, feature which suggest that they manifest a preference for mineral nutrition in comparison with organic one. Thus, many of willow species can be developed on soils with a big amount of minerals and/or radionuclides, being both phytoremediatory species, as well as pioneer ones, contributing to the restoration of soil. Thus, the willow species, posses the capacity for development in degraded areas, natural or anthropic, as swamps, abandoning crops areas, sandy dune, riparian sandy areas, gravels, a.o. In this paper are present some laboratory comparative tests of heavy metals tolerance on four Salix sp. genotypes: clone 202 (Salix alba), hybrid 892 (Salix alba), Inger (Salix viminalis) and Gudrun (Salix viminalis). The genotypes of Salix alba are native from Romania, produced in the Forest Research and Management Institute Bucharest, while the genotypes of Salix viminalis are native from Sweden, but the plant material was produced under license in Romania by REBINA Agrar SRL. As plant material were used one-year-old cuttings (5-10 cm long), with 2-6 buds each. Per genotype, per heavy metal and each of three concentration five replication were used. There were ten experimental variants for each genotype: three concentrations for each of the heavy metals; concentrations selected, in the accordance SR ISO 11269-2/March 1999 and Control (tap water). The cuttings were maintained in metalic solutions for 15 days. In the days 7th and 15th, were performed biometrical observations on: the roots number and length, the shoots number and length, the leaves number/shoot, viability of the shoots. At the end of the experiment the content in heavy metals was determined in roots and shoots (by atomic absorption spectrometry). The analysis of variance proved the significant role of the genotype in all analyzed features. The percent of shooting was significant higher in Salix alba (81.90 - 96.26%) in comparison with Salix viminalis (50.43 - 62.67%). The best results for all treatment variants were registered in hybrid 892. Clone 202, hybrid 892 and Inger are sensitive to highest concentration of lead (450.0 ppm) and tolerant to all other treatment variants, while Gudrun is sensitive to Ni, but all the concentrations of Cd and Pb presented a stimulative effect on shoots development. The content of heavy metals in plant was also dependent by the organ (root or shoot) and by the genotype.

Hybridization between a native and introduced predator of Adelgidae: An unintended result of classical biological control

Treesearch

N.P. Havill; Gina Davis; David Mausel; Joanne Klein; Richard McDonald; Cera Jones; Melissa Fischer; Scott Salom; Adelgisa Caccone

2012-01-01

Hybridization between introduced biological control agents and native species has the potential to impact native biodiversity and pest control efforts. This study reports progress towards predicting the outcome of hybridization between two beetle species, the introduced Laricobius nigrinus Fender and the native L. rubidus LeConte...

Response of native versus exotic plant guilds to cattle and elk herbivory in forested rangeland

Treesearch

Burak K. Pekin; Michael J. Wisdom; Catherine G. Parks; Bryan A. Endress; Bridgett J. Naylor; Ralf Ohlemuller

2015-01-01

Questions: Are exotic plant species favoured by non-native ungulate herbivores and disadvantaged by native herbivores in forested rangelands? Do the impacts of ungulates on exotic vs native plants depend on forest management activities such as prescribed fire and stand thinning?Location: Northeastern Oregon, USA....

Rapid movement and instability of an invasive hybrid swarm

USGS Publications Warehouse

Glotzbecker, Gregory J.; Walters, David; Blum, Michael J.

2016-01-01

Unstable hybrid swarms that arise following the introduction of non-native species can overwhelm native congeners, yet the stability of invasive hybrid swarms has not been well documented over time. Here we examine genetic variation and clinal stability across a recently formed hybrid swarm involving native blacktail shiner (Cyprinella venusta) and non-native red shiner (C. lutrensis) in the Upper Coosa River basin, which is widely considered to be a global hotspot of aquatic biodiversity. Examination of phenotypic, multilocus genotypic, and mitochondrial haplotype variability between 2005 and 2011 revealed that the proportion of hybrids has increased over time, with more than a third of all sampled individuals exhibiting admixture in the final year of sampling. Comparisons of clines over time indicated that the hybrid swarm has been rapidly progressing upstream, but at a declining and slower pace than rates estimated from historical collection records. Clinal comparisons also showed that the hybrid swarm has been expanding and contracting over time. Additionally, we documented the presence of red shiner and hybrids farther downstream than prior studies have detected, which suggests that congeners in the Coosa River basin, including all remaining populations of the threatened blue shiner (Cyprinella caerulea), are at greater risk than previously thought.

Genetic Variation and Population Structure in Native Americans

PubMed Central

Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

2007-01-01

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

The role of hybridization in facilitating tree invasion

PubMed Central

2017-01-01

Abstract Hybridization events can generate additional genetic diversity upon which natural selection can act and at times enhance invasiveness of the species. Invasive tree species are a growing ecological concern worldwide, and some of these invasions involve hybridization events pre- or post-introduction. There are 20 hybrid invasive tree taxa in 15 genera (11 plant families) discussed here. When reported, abundance of hybrids comprised 10–100 % of an invasion, the remainder being parental taxa. In seven hybrid taxa, researchers identified phenotypes that may make hybrids better invaders. Twelve hybrid tree taxa involved introgression and more hybrids involved all non-native taxa than native × non-native taxa. Three hybrid tree taxa were the result of intentional crosses, and all hybrid taxa involved intentional introduction of either one or more parental taxon or the hybrid itself. The knowledge gaps present in some hybrid tree taxa can weaken our effectiveness in predicting and controlling invasions, as hybrids can add a level of complexity to an invasion by being morphologically cryptic, causing genetic pollution of a native parental taxon, presenting novel genotypes for which there may not be coevolved biological control agents, or evolving adaptive traits through increased genetic variation. PMID:28028055

Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil

Treesearch

Rodrigo N. Graca; Amy L. Ross-Davis; Ned B. Klopfenstein; Mee-Sook Kim; Tobin L. Peever; Phil G. Cannon; Cristina P. Aun; Eduardo G. Mizubuti; Acelino C. Alfenas

2013-01-01

The rust fungus, Puccinia psidii, is a devastating pathogen of introduced eucalypts (Eucalyptus spp.) in Brazil where it was first observed in 1912. This pathogen is hypothesized to be endemic to South and Central America and to have first infected eucalypts via a host jump from native guava (Psidium guajava). Ten microsatellite markers were used to genotype 148 P....

An efficient method for evaluating black walnut for resistance to walnut anthracnose in filed plots and the identification of resistant genotypes

Treesearch

K.E. Woeste; W.F. Beineke

2001-01-01

Black walnut is native to the eastern USA and prized for its high-quality timber. Walnut anthracnose, the most important foliar disease of black walnut, is caused by Gnomonia leptostyla. There is no germplasm available that is resistant to the disease. Ramets of 42 black walnut clones, comprising about one-third of the Midwestern USA black walnut...

The impact of kin availability, parental religiosity, and nativity on fertility differentials in the late 19th-century United States

PubMed Central

Hacker, J. David; Roberts, Evan

2017-01-01

METHODS Most quantitative research on fertility decline in the United States ignores the potential impact of cultural and familial factors. We rely on new complete-count data from the 1880 U.S. census to construct couple-level measures of nativity/ethnicity, religiosity, and kin availability. We include these measures with a comprehensive set of demographic, economic, and contextual variables in Poisson regression models of net marital fertility to assess their relative importance. We construct models with and without area fixed effects to control for unobserved heterogeneity. CONTRIBUTION All else being equal, we find a strong impact of nativity on recent net marital fertility. Fertility differentials among second generation couples relative to the native-born white population of native parentage were in most cases less than half of the differential observed among first generation immigrants, suggesting greater assimilation to native-born American childbearing norms. Our measures of parental religiosity and familial propinquity indicated a more modest impact on marital fertility. Couples who chose biblical names for their children had approximately 3% more children than couples relying on secular names while the presence of a potential mother-in-law in a nearby households was associated with 2% more children. Overall, our results demonstrate the need for more inclusive models of fertility behavior that include cultural and familial covariates. PMID:29720893

The impact of kin availability, parental religiosity, and nativity on fertility differentials in the late 19th-century United States.

PubMed

Hacker, J David; Roberts, Evan

2017-12-01

Most quantitative research on fertility decline in the United States ignores the potential impact of cultural and familial factors. We rely on new complete-count data from the 1880 U.S. census to construct couple-level measures of nativity/ethnicity, religiosity, and kin availability. We include these measures with a comprehensive set of demographic, economic, and contextual variables in Poisson regression models of net marital fertility to assess their relative importance. We construct models with and without area fixed effects to control for unobserved heterogeneity. All else being equal, we find a strong impact of nativity on recent net marital fertility. Fertility differentials among second generation couples relative to the native-born white population of native parentage were in most cases less than half of the differential observed among first generation immigrants, suggesting greater assimilation to native-born American childbearing norms. Our measures of parental religiosity and familial propinquity indicated a more modest impact on marital fertility. Couples who chose biblical names for their children had approximately 3% more children than couples relying on secular names while the presence of a potential mother-in-law in a nearby households was associated with 2% more children. Overall, our results demonstrate the need for more inclusive models of fertility behavior that include cultural and familial covariates.

Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections

PubMed Central

Jarvi, Susan I; Farias, Margaret EM; Atkinson, Carter T

2008-01-01

Background The relatively recent introduction of a highly efficient mosquito vector and an avian pathogen (Plasmodium relictum) to an isolated island ecosystem with naïve, highly susceptible avian hosts provides a unique opportunity to investigate evolution of virulence in a natural system. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct impacts on virulence. Toward further understanding of how host-parasite and parasite-parasite relationships may impact virulence, this study characterizes within-host diversity of malaria parasite populations based on genetic analysis of the trap (thrombospondin-related anonymous protein) gene in isolates originating from Hawaii, Maui and Kauai Islands. Methods A total of 397 clones were produced by nested PCR amplification and cloning of a 1664 bp fragment of the trap gene from two malarial isolates, K1 (Kauai) and KV115 (Hawaii) that have been used for experimental studies, and from additional isolates from wild birds on Kauai, Maui and Hawaii Islands. Diversity of clones was evaluated initially by RFLP-based screening, followed by complete sequencing of 33 selected clones. Results RFLP analysis of trap revealed a minimum of 28 distinct RFLP haplotypes among the 397 clones from 18 birds. Multiple trap haplotypes were detected in every bird evaluated, with an average of 5.9 haplotypes per bird. Overall diversity did not differ between the experimental isolates, however, a greater number of unique haplotypes were detected in K1 than in KV115. We detected high levels of clonal diversity with clear delineation between isolates K1 and KV115 in a haplotype network. The patterns of within-host haplotype clustering are consistent with the possibility of a clonal genetic structure and rapid within-host mutation after infection. Conclusion Avian malaria (P. relictum) and Avipoxvirus are the significant infectious diseases currently affecting the native Hawaiian avifauna. This study shows that clonal diversity of Hawaiian isolates of P. relictum is much higher than previously recognized. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct implications for host demographics, disease management strategies, and evolution of virulence. The results of this study indicate a widespread presence of multiple-genotype malaria infections with high clonal diversity in native birds of Hawaii, which when coupled with concurrent infection with Avipoxvirus, may significantly influence evolution of virulence. Reviewers This article was reviewed by Joseph Schall (nominated by Laura Landweber), Daniel Jeffares (nominated by Anthony Poole) and Susan Perkins (nominated by Eugene Koonin). PMID:18578879

Invasion of a dominant floral resource: effects on the floral community and pollination of native plants.

PubMed

Goodell, Karen; Parker, Ingrid M

2017-01-01

Through competition for pollinators, invasive plants may suppress native flora. Community-level studies provide an integrative assessment of invasion impacts and insights into factors that influence the vulnerability of different native species. We investigated effects of the nonnative herb Lythrum salicaria on pollination of native species in 14 fens of the eastern United States. We compared visitors per flower for 122 native plant species in invaded and uninvaded fens and incorporated a landscape-scale experiment, removing L. salicaria flowers from three of the invaded fens. Total flower densities were more than three times higher in invaded than uninvaded or removal sites when L. salicaria was blooming. Despite an increase in number of visitors with number of flowers per area, visitors per native flower declined with increasing numbers of flowers. Therefore, L. salicaria invasion depressed visitation to native flowers. In removal sites, visitation to native flowers was similar to uninvaded sites, confirming the observational results and also suggesting that invasion had not generated a persistent build-up of visitor populations. To study species-level impacts, we examined effects of invasion on visitors per flower for the 36 plant species flowering in both invaded and uninvaded fens. On average, the effect of invasion represented about a 20% reduction in visits per flower. We measured the influence of plant traits on vulnerability to L. salicaria invasion using meta-analysis. Bilaterally symmetrical flowers experienced stronger impacts on visitation, and similarity in flower color to L. salicaria weakly intensified competition with the invader for visitors. Finally, we assessed the reproductive consequences of competition with the invader in a dominant flowering shrub, Dasiphora fruticosa. Despite the negative effect of invasion on pollinator visitation in this species, pollen limitation of seed production was not stronger in invaded than in uninvaded sites, suggesting little impact of competition for pollinators on its population demography. Negative effects on pollination of native plants by this copiously flowering invader appeared to be mediated by increases in total flower density that were not matched by increases in pollinator density. The strength of impact was modulated across native species by their floral traits and reproductive ecology. © 2016 The Authors. Ecology, published by Wiley Periodicals, Inc., on behalf of the Ecological Society of America.

Effectiveness of native and exotic arbuscular mycorrhizal fungi on nutrient uptake and ion homeostasis in salt-stressed Cajanus cajan L. (Millsp.) genotypes.

PubMed

Garg, Neera; Pandey, Rekha

2015-04-01

Soil salinity is an increasing problem worldwide, restricting plant growth and production. Research findings show that arbuscular mycorrhizal (AM) fungi have the potential to reduce negative effects of salinity. However, plant growth responses to AM fungi vary as a result of genetic variation in mycorrhizal colonization and plant growth responsiveness. Thus, profitable use of AM requires selection of a suitable combination of host plant and fungal partner. A greenhouse experiment was conducted to compare effectiveness of a native AM fungal inoculum sourced from saline soil and two single exotic isolates, Funneliformis mossseae and Rhizophagus irregularis (single or dual mix), on Cajanus cajan (L.) Millsp. genotypes (Paras and Pusa 2002) under salt stress (0-100 mM NaCl). While salinity reduced plant biomass and disturbed ionic status in both genotypes, Pusa 2002 was more salt tolerant and ensured higher AM fungal colonization, plant biomass and nutrient content with favourable ion status under salinity. Although all AM fungi reduced negative effects of salt stress, R. irregularis (alone or in combination with F. mosseae) displayed highest efficiency under salinity, resulting in highest biomass, yield, nutrient uptake and improved membrane stability with favourable K(+)/Na(+) and Ca(2+)/Na(+) ratios in the host plant. Higher effectiveness of R. irregularis correlated with higher root colonization, indicating that the symbiosis formed by R. irregularis had more stable viability and efficiency under salt stress. These findings enhance understanding of the functional diversity of AM fungi in ameliorating plant salt stress tolerance and suggest the potential use of R. irregularis for increasing Cajanus cajan productivity in saline soils.

Polymorphism and haplotype analyses of swine leukocyte antigen DQA exons 2, 3, 4, and their associations with piglet diarrhea in Chinese native pig.

PubMed

Huang, X Y; Yang, Q L; Yuan, J H; Gun, S B

2015-09-08

In this study, 290 Chinese native Yantai black pig piglets were investigated to identify gene polymorphisms, for haplotype reconstruction, and to determine the association between piglet diarrhea and swine leukocyte antigen (SLA) class II DQA exons 2, 3, and 4 by polymerase chain reaction-single stranded conformational polymorphism and cloning sequencing. The results showed that the 5, 8, and 7 genotypes were identified from SLA-DQA exon 2, 3, and 4, respectively, based on the single-stranded conformational polymorphism banding patterns and found a novel allele D in exon 2 and 2 novel mutational sites of allele C (c.4828T>C) and allele F (c.4617T>C) in exon 3. Polymorphism information content testing showed that exon 2 was moderately polymorphic and that exons-3 and -4 loci were highly polymorphic. The piglet diarrhea scores for genotypes AB (1.40 ± 0.14) and AC (1.54 ± 0.17) in exon 2, AA (1.22 ± 0.32), BC (1.72 ± 0.13), DD (1.67 ± 0.35), and CF (1.22 ± 0.45) in exon 3, and AD (2.35 ± 0.25) in exon 4 were significantly higher than those for the other genotypes (P ≤ 0.05) in DQA exons. There were 14 reconstructed haplotypes in the 3 exons from 290 individuals and Hap12 may be the diarrhea-resistant gene. Haplotype distribution was extremely uneven, and the SLA-DQA gene showed genetic linkage. In this study, we identified molecular genetic markers and provided a theoretical foundation for future pig anti-disease resistance breeding.

Soluble and cell wall-bound phenolic acids and ferulic acid dehydrodimers in rye flour and five bread model systems: insight into mechanisms of improved availability.

PubMed

Dynkowska, Wioletta M; Cyran, Malgorzata R; Ceglińska, Alicja

2015-03-30

The bread-making process influences bread components, including phenolics that significantly contribute to its antioxidant properties. Five bread model systems made from different rye cultivars were investigated to compare their impact on concentration of ethanol-soluble (free and ester-bound) and insoluble phenolics. Breads produced by a straight dough method without acid addition (A) and three-stage sourdough method with 12 h native starter preparation (C) exhibited the highest, genotype-dependent concentrations of free phenolic acids. Dough acidification by direct acid addition (method B) or by gradual production during prolonged starter fermentation (24 and 48 h, for methods D and E) considerably decreased their level. However, breads B were enriched in soluble ester-bound fraction. Both direct methods, despite substantial differences in dough pH, caused a similar increase in the amount of insoluble ester-bound fraction. The contents of phenolic fractions in rye bread were positively related to activity level of feruloyl esterase and negatively to those of arabinoxylan-hydrolysing enzymes in wholemeal flour. The solubility of rye bread phenolics may be enhanced by application of a suitable bread-making procedure with respect to rye cultivar, as the mechanisms of this process are also governed by a response of an individual genotype with specific biochemical profile. © 2014 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Native American ancestry, lung function, and COPD in Costa Ricans.

PubMed

Chen, Wei; Brehm, John M; Boutaoui, Nadia; Soto-Quiros, Manuel; Avila, Lydiana; Celli, Bartolome R; Bruse, Shannon; Tesfaigzi, Yohannes; Celedón, Juan C

2014-04-01

Whether Native American ancestry (NAA) is associated with COPD or lung function in a racially admixed Hispanic population is unknown. We recruited 578 Costa Ricans with and without COPD into a hybrid case-control/family-based cohort, including 316 members of families of index case subjects. All participants completed questionnaires and spirometry and gave a blood sample for DNA extraction. Genome-wide genotyping was conducted with the Illumina Human610-Quad and HumanOmniExpress BeadChip kits (Illumina Inc), and individual ancestral proportions were estimated from these genotypic data and reference panels. For unrelated individuals, linear or logistic regression was used for the analysis of NAA and COPD (GOLD [Global Initiative for Chronic Obstructive Lung Disease] stage II or greater) or lung function. For extended families, linear mixed models and generalized estimating equations were used for the analysis. All models were adjusted for age, sex, educational level, and smoking behavior; models for FEV1 were also adjusted for height. The average proportion of European, Native American, and African ancestry among participants was 62%, 35%, and 3%, respectively. After adjustment for current smoking and other covariates, NAA was inversely associated with COPD (OR per 10% increment, 0.55; 95% CI, 0.41-0.75) but positively associated with FEV1, FVC, and FEV1/FVC. After additional adjustment for pack-years of smoking, the association between NAA and COPD or lung function measures was slightly attenuated. We found that about 31% of the estimated effect of NAA on COPD is mediated by pack-years of smoking. NAA is inversely associated with COPD but positively associated with FEV1 or FVC in Costa Ricans. Ancestral effects on smoking behavior partly explain the findings for COPD but not for FEV1 or FVC.

Native American Ancestry, Lung Function, and COPD in Costa Ricans

PubMed Central

Chen, Wei; Brehm, John M.; Boutaoui, Nadia; Soto-Quiros, Manuel; Avila, Lydiana; Celli, Bartolome R.; Bruse, Shannon; Tesfaigzi, Yohannes

2014-01-01

Background: Whether Native American ancestry (NAA) is associated with COPD or lung function in a racially admixed Hispanic population is unknown. Methods: We recruited 578 Costa Ricans with and without COPD into a hybrid case-control/family-based cohort, including 316 members of families of index case subjects. All participants completed questionnaires and spirometry and gave a blood sample for DNA extraction. Genome-wide genotyping was conducted with the Illumina Human610-Quad and HumanOmniExpress BeadChip kits (Illumina Inc), and individual ancestral proportions were estimated from these genotypic data and reference panels. For unrelated individuals, linear or logistic regression was used for the analysis of NAA and COPD (GOLD [Global Initiative for Chronic Obstructive Lung Disease] stage II or greater) or lung function. For extended families, linear mixed models and generalized estimating equations were used for the analysis. All models were adjusted for age, sex, educational level, and smoking behavior; models for FEV1 were also adjusted for height. Results: The average proportion of European, Native American, and African ancestry among participants was 62%, 35%, and 3%, respectively. After adjustment for current smoking and other covariates, NAA was inversely associated with COPD (OR per 10% increment, 0.55; 95% CI, 0.41-0.75) but positively associated with FEV1, FVC, and FEV1/FVC. After additional adjustment for pack-years of smoking, the association between NAA and COPD or lung function measures was slightly attenuated. We found that about 31% of the estimated effect of NAA on COPD is mediated by pack-years of smoking. Conclusions: NAA is inversely associated with COPD but positively associated with FEV1 or FVC in Costa Ricans. Ancestral effects on smoking behavior partly explain the findings for COPD but not for FEV1 or FVC. PMID:24306962

Overlap in genomic variation associated with milk fat composition in Holstein Friesian and Dutch native dual-purpose breeds.

PubMed

Maurice-Van Eijndhoven, M H T; Bovenhuis, H; Veerkamp, R F; Calus, M P L

2015-09-01

The aim of this study was to identify if genomic variations associated with fatty acid (FA) composition are similar between the Holstein-Friesian (HF) and native dual-purpose breeds used in the Dutch dairy industry. Phenotypic and genotypic information were available for the breeds Meuse-Rhine-Yssel (MRY), Dutch Friesian (DF), Groningen White Headed (GWH), and HF. First, the reliability of genomic breeding values of the native Dutch dual-purpose cattle breeds MRY, DF, and GWH was evaluated using single nucleotide polymorphism (SNP) effects estimated in HF, including all SNP or subsets with stronger associations in HF. Second, the genomic variation of the regions associated with FA composition in HF (regions on Bos taurus autosome 5, 14, and 26), were studied in the different breeds. Finally, similarities in genotype and allele frequencies between MRY, DF, GWH, and HF breeds were assessed for specific regions associated with FA composition. On average across the traits, the highest reliabilities of genomic prediction were estimated for GWH (0.158) and DF (0.116) when the 8 to 22 SNP with the strongest association in HF were included. With the same set of SNP, GEBV for MRY were the least reliable (0.022). This indicates that on average only 2 (MRY) to 16% (GWH) of the genomic variation in HF is shared with the native Dutch dual-purpose breeds. The comparison of predicted variances of different regions associated with milk and milk fat composition showed that breeds clearly differed in genomic variation within these regions. Finally, the correlations of allele frequencies between breeds across the 8 to 22 SNP with the strongest association in HF were around 0.8 between the Dutch native dual-purpose breeds, whereas the correlations between the native breeds and HF were clearly lower and around 0.5. There was no consistent relationship between the reliabilities of genomic prediction for a specific breed and the correlation between the allele frequencies of this breed and HF. In conclusion, most of the genomic variation associated with FA composition in the Dutch dual-purpose breeds appears to be breed-specific. Furthermore, the minor allele frequencies of genes having an effect on the milk FA composition in HF were shown to be much smaller in the breeds MRY, DF, and GWH, especially for the MRY breed. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Arthropod assemblages on native and nonnative plant species of a coastal reserve in California.

PubMed

Fork, Susanne K

2010-06-01

Biological invasions by nonnative plant species are a widespread phenomenon. Many studies have shown strong ecological impacts of plant invasions on native plant communities and ecosystem processes. Far fewer studies have examined effects on associated animal communities. From the perspective of a reserve's land management, I addressed the question of whether arthropod assemblages on two nonnative plant species of concern were impoverished compared with those assemblages associated with two predominant native plant species of that reserve. If the nonnative plant species, Conium maculatum L., and Phalaris aquatica L., supported highly depauperate arthropod assemblages compared with the native plant species, Baccharis pilularis De Candolle and Leymus triticoides (Buckley) Pilger, this finding would provide additional support for prioritizing removal of nonnatives and restoration of natives. I assessed invertebrate assemblages at the taxonomic levels of arthropod orders, Coleoptera families, and Formicidae species, using univariate analyses to examine community attributes (richness and abundance) and multivariate techniques to assess arthropod assemblage community composition differences among plant species. Arthropod richness estimates by taxonomic level between native and nonnative vegetation showed varying results. Overall, arthropod richness of the selected nonnative plants, examined at higher taxonomic resolution, was not necessarily less diverse than two of common native plants found on the reserve, although differences were found among plant species. Impacts of certain nonnative plant species on arthropod assemblages may be more difficult to elucidate than those impacts shown on native plants and ecosystem processes.

Impact of donor and recipient IL28B rs12979860 genotypes on hepatitis C virus liver graft reinfection.

PubMed

Lange, Christian M; Moradpour, Darius; Doehring, Alexandra; Lehr, Hans-Anton; Müllhaupt, Beat; Bibert, Stephanie; Bochud, Pierre-Yves; Antonino, Anca T; Pascual, Manuel; Farnik, Harald; Shi, Ying; Bechstein, Wolf Otto; Moench, Christian; Hansmann, Martin-Leo; Sarrazin, Christoph; Lötsch, Jörn; Zeuzem, Stefan; Hofmann, Wolf-Peter

2011-08-01

Recent studies have described a major impact of genetic variations near the IL28B gene on the natural course and outcome of antiviral therapy in chronic hepatitis C. We therefore, aimed to explore the impact of donor and recipient genotypes of these polymorphisms on hepatitis C virus (HCV) liver graft reinfection. Donor and recipient genotypes of IL28B rs12979860C>T single nucleotide polymorphism were determined in 91 patients with HCV liver graft reinfection, 47 of whom were treated with pegylated interferon-α (PEG-IFN-α) and ribavirin. IL28B genetic polymorphisms were correlated with the natural course and treatment outcome of recurrent hepatitis C. Patients requiring liver transplantation due to end-stage chronic hepatitis C appeared to be selected toward the adverse genotypes rs12979860 CT/TT compared to non-transplanted HCV-infected patients (p=0.046). Patients with the donor genotype rs12979860 CC had higher peak ALT and HCV RNA serum concentrations than those with CT/TT (p=0.04 and 0.06, respectively). No association was observed between ALT/HCV RNA serum concentrations and recipient genotypes (p>0.3). More important, donor IL28B rs12979860 CC vs. CT/TT genotypes were associated with rapid, complete early, and sustained virologic response (RVR, cEVR, SVR) to treatment with PEG-IFN-α and ribavirin (p=0.003, 0.0012, 0.008, respectively), but weaker associations of recipient genotypes with RVR, cEVR, and SVR were observed as well (p=0.0046, 0.115, 0.118, respectively). We provide evidence for a dominant, but not exclusive impact of the donor rather than the recipient IL28B genetic background on the natural course and treatment outcome of HCV liver graft reinfection. Copyright © 2010 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems

DOE PAGES

Morris, Geoffrey P.; Hu, Zhenbin; Grabowski, Paul P.; ...

2015-10-03

The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008–2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars – under low or high species diversity, with or without nitrogen inputs – and quantified establishment, biomass yield,more » and biomass composition. In one experiment (‘agronomic trial’), we compared three switchgrass cultivars in monoculture to a switchgrass cultivar mixture and three different species mixtures, with or without N fertilization. In another experiment (‘diversity gradient’), we varied diversity levels in switchgrass and big bluestem (1, 2, 4, or 6 cultivars per plot), with one or two species per plot. In both experiments, cultivar mixtures produced yields equivalent to or greater than the best cultivars. In the agronomic trial, the three switchgrass mixture showed the highest production overall, though not significantly different than best cultivar monoculture. In the diversity gradient, genotypic mixtures had one-third higher biomass production than the average monoculture, and none of the monocultures were significantly higher yielding than the average mixture. Year-to-year variation in yields was lowest in the three-cultivar switchgrass mixtures and Cave-In-Rock (the southern Illinois cultivar) and also reduced in the mixture of switchgrass and big bluestem relative to the species monocultures. The effects of genotypic diversity on biomass composition were modest relative to the differences among species and genotypes. Our findings suggest that local genotypes can be included in biomass cropping systems without compromising yields and that genotypic mixtures could help provide high, stable yields of high-quality biomass feedstocks.« less

Angiotensin converting enzyme genotype and chronic allograft nephropathy in protocol biopsies.

PubMed

Hueso, Miguel; Alía, Pedro; Moreso, Francesc; Beltrán-Sastre, Violeta; Riera, Luis; González, Carlota; Navarro, Miguel Angel; Grinyó, Josep Maria; Navarro, Estanis; Serón, Daniel

2004-08-01

Genotype DD of the angiotensin-converting enzyme (ACE) is not associated with an increased incidence of native renal diseases, although it could modulate progression to renal failure in patients who already display chronic lesions. Because its role in renal allograft degeneration is not well characterized, whether ACE genotype was associated with the prevalence of chronic allograft nephropathy (CAN) was studied, in a group of protocol biopsies from 180 patients, or with the incidence of CAN in 152 patients with at least two sequential biopsies. As a control group, ACE genotype was also studied in 41 donors and 72 healthy subjects. For analyzing the influence of ACE genotype in graft survival, patients were grouped into six categories (II-normal biopsy, ID-normal, DD-normal, II-CAN, ID-CAN and DD-CAN). Finally, relative renal ACE mRNA levels were measured in 67 cases by real-time PCR using the delta threshold cycle method. ACE-DD genotype was more frequent in patients who received a transplant than in control subjects (43.3% versus 30.1%, P = 0.026), but prevalence (DD = 42.7% versus non-DD = 42.2%) or incidence (DD = 24.6% versus non-DD = 29.9%) of CAN was not different regarding recipient ACE genotype. Furthermore, patients with the ACE-DD genotype and CAN had the poorest graft survival (II-normal = 100%, ID-normal = 91%, DD-normal = 84%, II-CAN = 100%, ID-CAN = 66%, and DD-CAN = 36%; P = 0.034) and higher ACE mRNA levels than non-DD and CAN (DD = -3.36 +/- 2.35 versus non-DD = -5.65 +/- 1.72-fold in ACE copies; P = 0.012). It is concluded that ACE-DD genotype is not associated with an increased prevalence or incidence of CAN but is actually associated with higher ACE mRNA levels and poorer graft survival in patients who already display CAN.

Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, Geoffrey P.; Hu, Zhenbin; Grabowski, Paul P.

The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008–2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars – under low or high species diversity, with or without nitrogen inputs – and quantified establishment, biomass yield,more » and biomass composition. In one experiment (‘agronomic trial’), we compared three switchgrass cultivars in monoculture to a switchgrass cultivar mixture and three different species mixtures, with or without N fertilization. In another experiment (‘diversity gradient’), we varied diversity levels in switchgrass and big bluestem (1, 2, 4, or 6 cultivars per plot), with one or two species per plot. In both experiments, cultivar mixtures produced yields equivalent to or greater than the best cultivars. In the agronomic trial, the three switchgrass mixture showed the highest production overall, though not significantly different than best cultivar monoculture. In the diversity gradient, genotypic mixtures had one-third higher biomass production than the average monoculture, and none of the monocultures were significantly higher yielding than the average mixture. Year-to-year variation in yields was lowest in the three-cultivar switchgrass mixtures and Cave-In-Rock (the southern Illinois cultivar) and also reduced in the mixture of switchgrass and big bluestem relative to the species monocultures. The effects of genotypic diversity on biomass composition were modest relative to the differences among species and genotypes. Our findings suggest that local genotypes can be included in biomass cropping systems without compromising yields and that genotypic mixtures could help provide high, stable yields of high-quality biomass feedstocks.« less

Envirotyping for deciphering environmental impacts on crop plants.

PubMed

Xu, Yunbi

2016-04-01

Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.

Reclaiming the Gift: Indigenous Youth Counter-Narratives on Native Language Loss and Revitalization

ERIC Educational Resources Information Center

McCarty, Teresa L.; Romero, Mary Eunice; Zepeda, Ofelia

2006-01-01

In this article, the authors explore the personal, familial, and academic stakes of Native language loss for youth, drawing on narrative data from the Native Language Shift and Retention Project, a five year (2001-06), federally funded study of the nature and impacts of Native language shift and retention on American Indian students' language…

How Native American Success and Leadership Is Cultivated at the Corporate Level: A Native American Employee Perspective.

ERIC Educational Resources Information Center

One Feather, Sandra

2003-01-01

A Chippewa-Cree engineer helps educate Native American college students on how to adjust to the corporate environment and become successful employees and leaders. Issues include differences between Native and corporate cultures, impact of cultural differences on group dynamics, business etiquette, and the importance of workplace mentors. Corporate…

Irrigation to enhance native seed production for Great Basin restoration

Treesearch

Clinton C. Shock; Erik B. G. Feibert; Nancy L. Shaw; Myrtle P. Shock; Lamont D. Saunders

2015-01-01

Native shrublands and their associated grasses and forbs have been disappearing from the Great Basin as a result of grazing practices, exotic weed invasions, altered fire regimes, climate change and other human impacts. Native forb seed is needed to restore these areas. The irrigation requirements for maximum seed production of four key native forb species (Eriogonum...

Your worst enemy could be your best friend: predator contributions to invasion resistance and persistence of natives

PubMed Central

Lounibos, L. Philip; Nishimura, Naoya; Greene, Krystle

2010-01-01

Native predators are postulated to have an important role in biotic resistance of communities to invasion and community resilience. Effects of predators can be complex, and mechanisms by which predators affect invasion success and impact are understood for only a few well-studied communities. We tested experimentally whether a native predator limits an invasive species' success and impact on a native competitor for a community of aquatic insect larvae in water-filled containers. The native mosquito Aedes triseriatus alone had no significant effect on abundance of the invasive mosquito Aedes albopictus. The native predatory midge Corethrella appendiculata, at low or high density, significantly reduced A. albopictus abundance. This effect was not caused by trait-mediated oviposition avoidance of containers with predators, but instead was a density-mediated effect caused by predator-induced mortality. The presence of this predator significantly reduced survivorship of the native species, but high predator density also significantly increased development rate of the native species when the invader was present, consistent with predator-mediated release from interspecific competition with the invader. Thus, a native predator can indirectly benefit its native prey when a superior competitor invades. This shows the importance of native predators as a component of biodiversity for both biotic resistance to invasion and resilience of a community perturbed by successful invasion. PMID:19841945

Human land use promotes the abundance and diversity of exotic species on caribbean islands.

PubMed

Jesse, Wendy A M; Behm, Jocelyn E; Helmus, Matthew R; Ellers, Jacintha

2018-05-31

Human land use causes major changes in species abundance and composition, yet native and exotic species can exhibit different responses to land use change. Native populations generally decline in human-impacted habitats while exotic species often benefit. In this study, we assessed the effects of human land use on exotic and native reptile diversity, including functional diversity, which relates to the range of habitat use strategies in biotic communities. We surveyed 114 reptile communities from localities that varied in habitat structure and human impact level on two Caribbean islands, and calculated species richness, overall abundance and evenness for every plot. Functional diversity indices were calculated using published trait data, which enabled us to detect signs of trait filtering associated with impacted habitats. Our results show that environmental variation among sampling plots was explained by two PCA ordination axes related to habitat structure (i.e. forest or non-forest) and human impact level (i.e. addition of man-made constructions such as roads and buildings). Several diversity indices were significantly correlated with the two PCA axes, but exotic and native species showed opposing responses. Native species reached the highest abundance in forests, while exotic species were absent in this habitat. Human impact was associated with an increase in exotic abundance and species richness, while native species showed no significant associations. Functional diversity was highest in non-forested environments on both islands, and further increased on St. Martin with the establishment of functionally unique exotic species in non-forested habitat. Habitat structure, rather than human impact, proved to be an important agent for environmental filtering of traits, causing divergent functional trait values across forested and non-forested environments. Our results illustrate the importance of considering various elements of land use when studying its impact on species diversity and the establishment and spread of exotic species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Long-term record of Argentine ant invasions reveals enduring ecological impacts.

PubMed

Menke, Sean B; Ward, Philip S; Holway, David A

2018-05-01

The ecological effects of species introductions can change in magnitude over time, but an understanding of how and why they do so remains incompletely understood. Clarifying this issue requires consideration of how temporal variation in invader traits affects invasion impacts (e.g., through differential effects on the diversity and composition of native species assemblages). We examine the temporal dynamics of Argentine ant invasions in northern California by resurveying 202 sites first sampled 30-40 yr ago. To test how invasion impacts change over time, we estimated native ant richness and species composition at 20 riparian woodland sites that span a 30-yr invasion chronosequence. We then use these data to test how variation in two invader traits (aggression and relative abundance) is related to time since invasion and invasion impact. Native ant assemblages along the chronosequence exhibited reduced native ant richness and altered species composition (compared to uninvaded control sites), but the magnitude of these impacts was independent of time since invasion. These results are corroborated by additional temporal comparisons of native ant assemblages at riparian sites sampled 20-30 yr ago. Our findings together illustrate that the impacts of invasions can persist undiminished over at least a 30-yr time frame and remain evident at regional scales. Although neither invader trait varied with time since invasion, native ant richness declined as the relative abundance of the Argentine ant increased. This latter result supports the hypothesis that factors reducing invader abundance at particular sites can decrease invasion impacts, but also that such changes may be due to site-specific factors (e.g., abiotic conditions) that affect invader abundance rather than time since invasion per se. Future studies should attempt to differentiate factors that are intrinsic to the process of invasion (e.g., changes in invader populations) from long-term environmental changes (e.g., climate change) that represent extrinsic influences on the dynamics of invasion. © 2018 by the Ecological Society of America.

Doublethink and scale mismatch polarize policies for an invasive tree

USGS Publications Warehouse

Roberts, Caleb P.; Uden, Daniel R.; Allen, Craig R.; Twidwell, Dirac

2018-01-01

Mismatches between invasive species management policies and ecological knowledge can lead to profound societal consequences. For this reason, natural resource agencies have adopted the scientifically-based density-impact invasive species curve to guide invasive species management. We use the density-impact model to evaluate how well management policies for a native invader (Juniperus virginiana) match scientific guidelines. Juniperus virginiana invasion is causing a sub-continental regime shift from grasslands to woodlands in central North America, and its impacts span collapses in endemic diversity, heightened wildfire risk, and crashes in grazing land profitability. We (1) use land cover data to identify the stage of Juniperus virginiana invasion for three ecoregions within Nebraska, USA, (2) determine the range of invasion stages at individual land parcel extents within each ecoregion based on the density-impact model, and (3) determine policy alignment and mismatches relative to the density-impact model in order to assess their potential to meet sustainability targets and avoid societal impacts as Juniperus virginiana abundance increases. We found that nearly all policies evidenced doublethink and policy-ecology mismatches, for instance, promoting spread of Juniperus virginiana regardless of invasion stage while simultaneously managing it as a native invader in the same ecoregion. Like other invasive species, theory and literature for this native invader indicate that the consequences of invasion are unlikely to be prevented if policies fail to prioritize management at incipient invasion stages. Theory suggests a more realistic approach would be to align policy with the stage of invasion at local and ecoregion management scales. There is a need for scientists, policy makers, and ecosystem managers to move past ideologies governing native versus non-native invader classification and toward a framework that accounts for the uniqueness of native species invasions, their anthropogenic drivers, and their impacts on ecosystem services.

NESTs, Necessary or Not? Examining the Impact of Native English Speaker Instruction in South Korea

ERIC Educational Resources Information Center

Schenck, Andrew

2018-01-01

Although Native English-Speaking Teachers (NESTs) are extensively utilized, very little is known about the impact of these teachers on speaking or writing in Asian contexts like South Korea. The purpose of this study was to examine the impact of NEST instruction on EFL learners' speech in a South Korean context. First, proficiency level of 100…

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines.

PubMed

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan; Lee, Jun-Heon

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

PubMed Central

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens. PMID:29425208

Improving the Expression and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers by Targeted Sequence Changes

PubMed Central

Ringe, Rajesh P.; Ozorowski, Gabriel; Yasmeen, Anila; Cupo, Albert; Cruz Portillo, Victor M.; Pugach, Pavel; Golabek, Michael; Rantalainen, Kimmo; Holden, Lauren G.; Cottrell, Christopher A.; Wilson, Ian A.; Sanders, Rogier W.; Ward, Andrew B.; Klasse, P. J.

2017-01-01

ABSTRACT Soluble, recombinant native-like envelope glycoprotein (Env) trimers of various human immunodeficiency virus type 1 (HIV-1) genotypes are being developed for structural studies and as vaccine candidates aimed at the induction of broadly neutralizing antibodies (bNAbs). The prototypic design is designated SOSIP.664, but many HIV-1 env genes do not yield fully native-like trimers efficiently. One such env gene is CZA97.012 from a neutralization-resistant (tier 2) clade C virus. As appropriately purified, native-like CZA97.012 SOSIP.664 trimers induce autologous neutralizing antibodies (NAbs) efficiently in immunized rabbits, we sought to improve the efficiency with which they can be produced and to better understand the limitations to the original design. By using structure- and antigenicity-guided mutagenesis strategies focused on the V2 and V3 regions and the gp120-gp41 interface, we developed the CZA97 SOSIP.v4.2-M6.IT construct. Fully native-like, stable trimers that display multiple bNAb epitopes could be expressed from this construct in a stable CHO cell line and purified at an acceptable yield using either a PGT145 or a 2G12 bNAb affinity column. We also show that similar mutagenesis strategies can be used to improve the yields and properties of SOSIP.664 trimers of the DU422, 426c, and 92UG037 genotypes. IMPORTANCE Recombinant trimeric proteins based on HIV-1 env genes are being developed for future vaccine trials in humans. A feature of these proteins is their mimicry of the envelope glycoprotein (Env) structure on virus particles that is targeted by neutralizing antibodies, i.e., antibodies that prevent cells from becoming infected. The vaccine concept under exploration is that recombinant trimers may be able to elicit virus-neutralizing antibodies when delivered as immunogens. Because HIV-1 is extremely variable, a practical vaccine may need to incorporate Env trimers derived from multiple different virus sequences. Accordingly, we need to understand how to make recombinant trimers from many different env genes. Here, we show how to produce trimers from a clade C virus, CZA97.012, by using an array of protein engineering techniques to improve a prototypic construct. We also show that the methods may have wider utility for other env genes, thereby further guiding immunogen design. PMID:28381572

Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

PubMed

Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz; Srivas, Rohith; Licon, Katherine; Kreisberg, Jason; Ng, Cherie T; Krogan, Nevan; Sharan, Roded; Ideker, Trey

2016-02-24

Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by the Gene Ontology or a complementary ontology inferred directly from previously published datasets. Guided by the ontology's hierarchical structure, we organize genotype data into an "ontotype," that is, a hierarchy of perturbations representing the effects of genetic variation at multiple cellular scales. The ontotype is then interpreted using logical rules generated by machine learning to predict phenotype. This approach substantially outperforms previous, non-hierarchical methods for translating yeast genotype to cell growth phenotype, and it accurately predicts the growth outcomes of two new screens of 2,503 double gene knockouts impacting DNA repair or nuclear lumen. Ontotypes also generalize to larger knockout combinations, setting the stage for interpreting the complex genetics of disease.

Impact of Direct Acting Antiviral Therapy for Treatment of Hepatitis C Genotypes 1, 3 and 4: A Real Life Experience from India.

PubMed

Mehta, Varun; Mahajan, Ramit; Midha, Vandana; Narang, Vikram; Kaur, Kirandeep; Singh, Arshdeep; Malhotra, Anand; Parvez, Aslam; Sood, Ajit

2018-03-01

To assess impact of Direct Acting Antiviral (DAA) therapies for treatment of Hepatitis C Virus (HCV) genotypes 1, 3 and 4 in a real-world cohort from India. Adults with chronic HCV infection treated with Sofosbuvir (SOF) and Ledipasvir (LDV) (genotypes 1 and 4) or SOF and Daclatasvir (DCV) (genotype 3), with or without Ribavirin (RBV) between December 2015 and December 2016 were included. The primary endpoint was Sustained Virological Response at Post-treatment Week 12 (SVR12). Of the 648 patients, 181 received SOF/LDV (65 with RBV) and 467 received SOF/DCV (135 with RBV). Most patients were males (65.4%), aged 41-60 years (49.4%) and treatment-naïve (92.6%). Genotype 3 (72.1%) was most common, followed by genotypes 1 (22.4%) and 4 (5.6%). Forty two percent patients ( n  = 271) had cirrhosis (112 patients were decompensated). SVR12 (modified intention-to-treat) was achieved by 98.1% of patients (512/522) (100% in genotypes 1 and 4, and 97.3% (362/372) in genotype 3). On intention to treat analysis, SVR12 was 88.1% (512/581) [genotype 1-96.8% (121/125), genotype 3-85.2%, genotype 4-93.5% (29/31)]. Seventy patients had treatment failure (non response in 6, virological breakthrough in 2, 10 patients relapsed, 2 died and 50 were lost to follow up). High SVR was observed regardless of HCV genotype, presence of cirrhosis or past history of treatment. No major adverse events warranting discontinuation of treatment were noted. DAA therapy for HCV genotypes 1, 3 and 4 achieves high SVR rates in all patients, including those with cirrhosis and previous non-responders.

CALL FOR ABSTRACTS FOR WORKSHOP ON MINING IMPACTED NATIVE AMERICAN LANDS 2003

EPA Science Inventory

This is a Call for Abstracts for a workshop 9/9-11/2003 in Reno, NV, to unite Tribal members and representatives, and other government officials to examine technical and policy issues related to historic, current, and future mining impacts on Native American Lands.

Impact of Non-Native Terrestrial Mammals on the Structure of the Terrestrial Mammal Food Web of Newfoundland, Canada

PubMed Central

Strong, Justin S.; Leroux, Shawn J.

2014-01-01

The island of Newfoundland is unique because it has as many non-native terrestrial mammals as native ones. The impacts of non-native species on native flora and fauna can be profound and invasive species have been identified as one of the primary drivers of species extinction. Few studies, however, have investigated the effects of a non-native species assemblage on community and ecosystem properties. We reviewed the literature to build the first terrestrial mammal food web for the island of Newfoundland and then used network analyses to investigate how the timing of introductions and trophic position of non-native species has affected the structure of the terrestrial mammal food web in Newfoundland. The first non-native mammals (house mouse and brown rat) became established in Newfoundland with human settlement in the late 15th and early 16th centuries. Coyotes and southern red-backed voles are the most recent mammals to establish themselves on the island in 1985 and 1998, respectively. The fraction of intermediate species increased with the addition of non-native mammals over time whereas the fraction of basal and top species declined over time. This increase in intermediate species mediated by non-native species arrivals led to an overall increase in the terrestrial mammal food web connectance and generality (i.e. mean number of prey per predator). This diverse prey base and sources of carrion may have facilitated the natural establishment of coyotes on the island. Also, there is some evidence that the introduction of non-native prey species such as the southern red-backed vole has contributed to the recovery of the threatened American marten. Long-term monitoring of the food web is required to understand and predict the impacts of the diverse novel interactions that are developing in the terrestrial mammal food web of Newfoundland. PMID:25170923

Variation in the establishment of a non-native annual grass influences competitive interactions with Mojave Desert perennials

USGS Publications Warehouse

DeFalco, L.A.; Fernandez, G.C.J.; Nowak, R.S.

2007-01-01

Competition between native and non-native species can change the composition and structure of plant communities, but in deserts, the highly variable timing of resource availability also influences non-native plant establishment, thus modulating their impacts on native species. In a field experiment, we varied densities of the non-native annual grass Bromus madritensis ssp. rubens around individuals of three native Mojave Desert perennials-Larrea tridentata, Achnatherum hymenoides, and Pleuraphis rigida-in either winter or spring. For comparison, additional plots were prepared for the same perennial species and seasons, but with a mixture of native annual species as neighbors. Growth of perennials declined when Bromus was established in winter because Bromus stands had 2-3 months of growth and high water use before perennial growth began. However, water potentials for the perennials were not significantly reduced, suggesting that direct competition for water may not be the major mechanism driving reduced perennial growth. The impact of Bromus on Larrea was lower than for the two perennial grasses, likely because Larrea maintains low growth rates throughout the year, even after Bromus has completed its life cycle. This result contrasts with the perennial grasses, whose phenology completely overlaps with (Achnatherum) or closely follows (Pleuraphis) that of Bromus. In comparison, Bromus plants established in spring were smaller than those established in winter and thus did not effectively reduce growth of the perennials. Growth of perennials with mixed annuals as neighbors also did not differ from those with Bromus neighbors of equivalent biomass, but stands of these native annuals did not achieve the high biomass of Bromus stands that were necessary to reduce perennial growth. Seed dormancy and narrow requirements for seedling survivorship of native annuals produce densities and biomass lower than those achieved by Bromus; thus, impacts of native Mojave Desert annuals on perennials are expected to be lower than those of Bromus. ?? 2006 Springer Science+Business Media B.V.

Resource diversity and landscape-level homogeneity drive native bee foraging.

PubMed

Jha, Shalene; Kremen, Claire

2013-01-08

Given widespread declines in pollinator communities and increasing global reliance on pollinator-dependent crops, there is an acute need to develop a mechanistic understanding of native pollinator population and foraging biology. Using a population genetics approach, we determine the impact of habitat and floral resource distributions on nesting and foraging patterns of a critical native pollinator, Bombus vosnesenskii. Our findings demonstrate that native bee foraging is far more plastic and extensive than previously believed and does not follow a simple optimal foraging strategy. Rather, bumble bees forage further in pursuit of species-rich floral patches and in landscapes where patch-to-patch variation in floral resources is less, regardless of habitat composition. Thus, our results reveal extreme foraging plasticity and demonstrate that floral diversity, not density, drives bee foraging distance. Furthermore, we find a negative impact of paved habitat and a positive impact of natural woodland on bumble bee nesting densities. Overall, this study reveals that natural and human-altered landscapes can be managed for increased native bee nesting and extended foraging, dually enhancing biodiversity and the spatial extent of pollination services.

Identification, Development, and Release of Insect Biocontrol Agents for the Management of Phragmites australis

DTIC Science & Technology

2014-07-01

an important migratory habitat for many birds , the same habitats are nearly devoid of specialized bird species in North America, particularly of...noctuids on P. australis performance in Europe may not be present in North America. However, various North American bird species are increasingly being...and (5) assess the extent of hybridization between native and introduced genotypes. All selected insect species are stem miners that overwinter as

Impact of angiotensin-converting enzyme gene polymorphism on neurohormonal responses to high- versus low-dose enalapril in advanced heart failure.

PubMed

Tang, W H Wilson; Vagelos, Randall H; Yee, Yin-Gail; Fowler, Michael B

2004-11-01

The impact of angiotensin-converting enzyme (ACE) gene polymorphism on neurohormonal dose response to ACE inhibitor therapy is unclear. ACE Insertion (I) or Deletion (D) genotype was determined in 74 patients with chronic heart failure who were randomly assigned to receive either high-dose or low-dose enalapril over a period of 6 months. Monthly pre-enalapril and post-enalapril neurohormone levels (serum ACE activity (sACE), plasma angiotensin II (A-II), plasma renin activity (PRA), and serum aldosterone (ALDO) were compared between genotype subgroups and between patients who received high- or low-dose enalapril within each genotype subgroup. At baseline, predose/postdose sACE and postdose PRA were significantly higher in the DD genotype. At 6-month follow-up, postdose sACE was reduced in a dose-dependent fashion in all three genotypes (P < .05). However, predose and postdose ALDO and A-II levels did not differ between each genotype subgroup at baseline or by enalapril dose within each genotype subgroup. ALDO escape and A-II reactivation were not affected by ACE genotype or enalapril dosage. Predose sACE were consistently higher in the DD genotype when compared with ID or II subgroups. Despite a dose-dependent suppression of sACE, there were no observed statistically significant differences in ALDO and A-II suppression or escape with escalating doses of enalapril within each subgroup.

A KASP Genotyping Method to Identify Northern Watermilfoil, Eurasian Watermilfoil, and Their Interspecific Hybrids

PubMed Central

Patterson, Eric L.; Fleming, Margaret B.; Kessler, Kallie C.; Nissen, Scott J.; Gaines, Todd A.

2017-01-01

The invasive aquatic plant Eurasian watermilfoil (Myriophyllum spicatum L.) can hybridize with the related North American native species northern watermilfoil (M. sibiricum Kom.). Hybrid watermilfoil (M. spicatum × M. sibiricum) populations have higher fitness and reduced sensitivity to some commonly used aquatic herbicides, making management more difficult. There is growing concern that management practices using herbicides in lakes with mixed populations of watermilfoil species may further select for hybrid individuals due to the difference in herbicide sensitivity. Accurate and cost-effective identification of rare hybrid individuals within populations is therefore critical for herbicide management decisions. Here we describe KASP assays for three SNPs in the ITS region to genotype individuals from both parental watermilfoil species and their hybrid, using synthesized plasmids containing the respective sequences as positive controls. Using KASP we genotyped 16 individuals from one lake and 23 individuals from a second lake, giving a highly accurate picture of Myriophyllum species distribution dynamics. We identified one hybrid individual among 16 samples from one lake, a discovery rate of <10%. Discriminant analysis showed that while a single SNP was generally sufficient for genotyping an individual, using multiple SNPs increased the reliability of genotyping. In the future, the ability to genotype many samples will provide the ability to identify the presence of rare individuals, such as a less common parental species or the inter-specific hybrid. Lakes with complex species distribution dynamics, such as a low proportion of hybrids, are where herbicide application must be carefully chosen so as not to select for the more vigorous and less herbicide-sensitive hybrid individuals. PMID:28533795

When the Native Is Also a Non-Native: "Retrodicting" the Complexity of Language Teacher Cognition

ERIC Educational Resources Information Center

Aslan, Erhan

2015-01-01

The impact of native (NS) and non-native speaker (NNS) identities on second or foreign language teachers' cognition and practices in the classroom has mainly been investigated in ESL/EFL contexts. Using complexity theory as a framework, this case study attempts to fill the gap in the literature by presenting a foreign language teacher in the…

Selective herbicide applications for low impact vegetation management of exotic species and enhancement of native plant communities

Treesearch

Max Williamson

1998-01-01

Selective and specific management for the control of exotic (non-native) plants is necessary for preservation of native plant communities. Managers of federal, state, or county land holdings and parks, wildlife areas, recreation areas, and historic sites are frequently charged with selectively managing the enhancement of desirable or native plant communities. In...

Does Immigration Crowd Natives into or out of Higher Education? Working Papers. No. 15-18

ERIC Educational Resources Information Center

Jackson, Osborne

2015-01-01

This paper investigates the impact of immigration on the college enrollment of U.S. natives. Many studies have focused on the effect of increased demand for schooling by immigrants on the enrollment of natives. However, changes in immigrant labor supply may also affect native enrollment by changing local market prices. Using U.S. Census data from…

Predicting invasiveness of species in trade: Climate match, trophic guild and fecundity influence establishment and impact of non-native freshwater fishes

USGS Publications Warehouse

Howeth, Jennifer G.; Gantz, Crysta A.; Angermeier, Paul; Frimpong, Emmanuel A.; Hoff, Michael H.; Keller, Reuben P.; Mandrak, Nicholas E.; Marchetti, Michael P.; Olden, Julian D.; Romagosa, Christina M.; Lodge, David M.

2016-01-01

AimImpacts of non-native species have motivated development of risk assessment tools for identifying introduced species likely to become invasive. Here, we develop trait-based models for the establishment and impact stages of freshwater fish invasion, and use them to screen non-native species common in international trade. We also determine which species in the aquarium, biological supply, live bait, live food and water garden trades are likely to become invasive. Results are compared to historical patterns of non-native fish establishment to assess the relative importance over time of pathways in causing invasions.LocationLaurentian Great Lakes region.MethodsTrait-based classification trees for the establishment and impact stages of invasion were developed from data on freshwater fish species that established or failed to establish in the Great Lakes. Fishes in trade were determined from import data from Canadian and United States regulatory agencies, assigned to specific trades and screened through the developed models.ResultsClimate match between a species’ native range and the Great Lakes region predicted establishment success with 75–81% accuracy. Trophic guild and fecundity predicted potential harmful impacts of established non-native fishes with 75–83% accuracy. Screening outcomes suggest the water garden trade poses the greatest risk of introducing new invasive species, followed by the live food and aquarium trades. Analysis of historical patterns of introduction pathways demonstrates the increasing importance of these trades relative to other pathways. Comparisons among trades reveal that model predictions parallel historical patterns; all fishes previously introduced from the water garden trade have established. The live bait, biological supply, aquarium and live food trades have also contributed established non-native fishes.Main conclusionsOur models predict invasion risk of potential fish invaders to the Great Lakes region and could help managers prioritize efforts among species and pathways to minimize such risk. Similar approaches could be applied to other taxonomic groups and geographic regions.

Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile

PubMed Central

González Silos, Rosa; Marcelain, Katherine; Baez Benavides, Pablo; Barahona Ponce, Carol; Fischer, Christine; Peil, Barbara; Sinsheimer, Janet; Barajas, Olga; Gonzalez-Jose, Rolando; Cátira Bortolini, Maria; Canizales-Quinteros, Samuel; Gallo, Carla; Ruiz Linares, Andres; Rothhammer, Francisco

2017-01-01

Latin Americans are highly heterogeneous regarding the type of Native American ancestry. Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention. Here we investigate possible associations between the type of Native American ancestry and leading causes of death. After an aggregate-data study based on genome-wide genotype data from 1805 admixed Chileans and 639,789 deaths, we validate an identified association with gallbladder cancer relying on individual data from 64 gallbladder cancer patients, with and without a family history, and 170 healthy controls. Native American proportions were markedly underestimated when the two main types of Native American ancestry in Chile, originated from the Mapuche and Aymara indigenous peoples, were combined together. Consideration of the type of Native American ancestry was crucial to identify disease associations. Native American ancestry showed no association with gallbladder cancer mortality (P = 0.26). By contrast, each 1% increase in the Mapuche proportion represented a 3.7% increased mortality risk by gallbladder cancer (95%CI 3.1–4.3%, P = 6×10−27). Individual-data results and extensive sensitivity analyses confirmed the association between Mapuche ancestry and gallbladder cancer. Increasing Mapuche proportions were also associated with an increased mortality due to asthma and, interestingly, with a decreased mortality by diabetes. The mortality due to skin, bladder, larynx, bronchus and lung cancers increased with increasing Aymara proportions. Described methods should be considered in future studies on human population genetics and human health. Complementary individual-based studies are needed to apportion the genetic and non-genetic components of associations identified relying on aggregate-data. PMID:28542165

Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile.

PubMed

Lorenzo Bermejo, Justo; Boekstegers, Felix; González Silos, Rosa; Marcelain, Katherine; Baez Benavides, Pablo; Barahona Ponce, Carol; Müller, Bettina; Ferreccio, Catterina; Koshiol, Jill; Fischer, Christine; Peil, Barbara; Sinsheimer, Janet; Fuentes Guajardo, Macarena; Barajas, Olga; Gonzalez-Jose, Rolando; Bedoya, Gabriel; Cátira Bortolini, Maria; Canizales-Quinteros, Samuel; Gallo, Carla; Ruiz Linares, Andres; Rothhammer, Francisco

2017-05-01

Latin Americans are highly heterogeneous regarding the type of Native American ancestry. Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention. Here we investigate possible associations between the type of Native American ancestry and leading causes of death. After an aggregate-data study based on genome-wide genotype data from 1805 admixed Chileans and 639,789 deaths, we validate an identified association with gallbladder cancer relying on individual data from 64 gallbladder cancer patients, with and without a family history, and 170 healthy controls. Native American proportions were markedly underestimated when the two main types of Native American ancestry in Chile, originated from the Mapuche and Aymara indigenous peoples, were combined together. Consideration of the type of Native American ancestry was crucial to identify disease associations. Native American ancestry showed no association with gallbladder cancer mortality (P = 0.26). By contrast, each 1% increase in the Mapuche proportion represented a 3.7% increased mortality risk by gallbladder cancer (95%CI 3.1-4.3%, P = 6×10-27). Individual-data results and extensive sensitivity analyses confirmed the association between Mapuche ancestry and gallbladder cancer. Increasing Mapuche proportions were also associated with an increased mortality due to asthma and, interestingly, with a decreased mortality by diabetes. The mortality due to skin, bladder, larynx, bronchus and lung cancers increased with increasing Aymara proportions. Described methods should be considered in future studies on human population genetics and human health. Complementary individual-based studies are needed to apportion the genetic and non-genetic components of associations identified relying on aggregate-data.

Clonal growth: invasion or stability? A comparative study of clonal architecture and diversity in native and introduced lineages of Phragmites australis (Poaceae).

PubMed

Douhovnikoff, Vladimir; Hazelton, Eric L G

2014-09-01

• The characteristics of clonal growth that are advantageous in invasive plants can also result in native plants' ability to resist invasion. In Maine, we compared the clonal architecture and diversity of an invasive lineage (introduced Phragmites) and a noninvasive lineage (native Phragmites) present in much of North America. This study is the first on stand-scale diversity using a sample size and systematic spatial-sampling scheme adequate for characterizing clonal structure in Phragmites. Our questions included: (1) Does the structure and extent of clonal growth suggest that the potential for clonal growth contributes to the invasiveness of the introduced lineage? (2) Is clonal growth common in the native lineage, acting as a possible source of ecological resistance and resilience?• Microsatellite markers were used to measure clonal sizes, architecture, and diversity within each lineage in stands within four marshes in Maine.• Clonal diversity measures indicated that clonal growth was significantly greater in stands of the native lineage than in the introduced. While lineage was a consistent predictor of clonal diversity relative ranking, the marsh location was a much stronger predictor of the absolute range of these values.• Our results indicate an important role for clonal growth in the space consolidation of native Phragmites and could explain why the introduced lineage, with stronger competitive traits, has not replaced the native where they co-occur. These results with regard to clone size, size distributions, singleton occurrence, and clonal architecture provide some evidence for stand development that follows a genotypic initial floristics model. © 2014 Botanical Society of America, Inc.

Applying the collective impact approach to address non-native species: A case study of the Great Lakes Phragmites Collaborative

USGS Publications Warehouse

Braun, H. B.; Kowalski, Kurt P.; Hollins, K.

2016-01-01

To address the invasion of non-native Phragmites in the Great Lakes, researchers at the U.S. Geological Survey—Great Lakes Science Center partnered with the Great Lakes Commission in 2012 to establish the Great Lakes Phragmites Collaborative (GLPC). The GLPC is a regional-scale partnership established to improve collaboration among stakeholders and increase the effectiveness of non-native Phragmites management and research. Rather than forming a traditional partnership with a narrowly defined goal, the GLPC follows the principles of collective impact to engage stakeholders, guide progress, and align resources to address this complex, regional challenge. In this paper, the concept and tenets of collective impact are described, the GLPC is offered as a model for other natural resource-focused collective impact efforts, and steps for establishing collaboratives are presented. Capitalizing on the interactive collective impact approach, the GLPC is moving toward a broadly accepted common agenda around which agencies and individuals will be able to better align their actions and generate measureable progress in the regional campaign to protect healthy, diverse ecosystems from damage caused by non-native Phragmites.

CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins

PubMed Central

Londin, Eric R.; Keller, Margaret A.; Maista, Cathleen; Smith, Gretchen; Mamounas, Laura A.; Zhang, Ran; Madore, Steven J.; Gwinn, Katrina; Corriveau, Roderick A.

2010-01-01

Background Genetic ancestry is known to impact outcomes of genotype-phenotype studies that are designed to identify risk for common diseases in human populations. Failure to control for population stratification due to genetic ancestry can significantly confound results of disease association studies. Moreover, ancestry is a critical factor in assessing lifetime risk of disease, and can play an important role in optimizing treatment. As modern medicine moves towards using personal genetic information for clinical applications, it is important to determine genetic ancestry in an accurate, cost-effective and efficient manner. Self-identified race is a common method used to track and control for population stratification; however, social constructs of race are not necessarily informative for genetic applications. The use of ancestry informative markers (AIMs) is a more accurate method for determining genetic ancestry for the purposes of population stratification. Methodology/Principal Findings Here we introduce a novel panel of 36 microsatellite (MSAT) AIMs that determines continental admixture proportions. This panel, which we have named Continental Ancestry Informative Markers or CoAIMs, consists of MSAT AIMs that were chosen based upon their measure of genetic variance (Fst), allele frequencies and their suitability for efficient genotyping. Genotype analysis using CoAIMs along with a Bayesian clustering method (STRUCTURE) is able to discern continental origins including Europe/Middle East (Caucasians), East Asia, Africa, Native America, and Oceania. In addition to determining continental ancestry for individuals without significant admixture, we applied CoAIMs to ascertain admixture proportions of individuals of self declared race. Conclusion/Significance CoAIMs can be used to efficiently and effectively determine continental admixture proportions in a sample set. The CoAIMs panel is a valuable resource for genetic researchers performing case-control genetic association studies, as it can control for the confounding effects of population stratification. The MSAT-based approach used here has potential for broad applicability as a cost effective tool toward determining admixture proportions. PMID:20976178

Crowding in the City: Losing and Winning Competitors of an Invasive Bird

PubMed Central

Hernández-Brito, Dailos; Carrete, Martina; Popa-Lisseanu, Ana G.; Ibáñez, Carlos; Tella, José L.

2014-01-01

Invasive species can take advantage of resources unexploited by natives (opportunism hypothesis) or they can exploit the same resources but more aggressively or efficiently (competition hypothesis), thus impacting native species. However, invasive species tend to exploit anthropogenic habitats that are inefficiently used by natives such as urban environments. Focusing on the ring-necked parakeet (Psittacula krameri), one of the most invasive birds worldwide, we combined observations of interspecific aggressions, species-specific cavity-nest preferences and the spatial distribution of the native cavity-nesting vertebrate community to determine the invasion process as well as its potential impacts on native species in a Mediterranean city. Our results support the competition hypothesis, suggesting that ring-necked parakeets are outcompeting native species sharing nest-site preferences. Parakeets initiated and won most interspecific aggressions, which were directed towards competitors but also towards predators. This behaviour could explain the spatial arrangement of natives, with most bird species breeding close to parakeets possibly to take advantage of their effective antipredatory behaviour. However, temporal and spatial patterns of segregation suggest that a threatened bat species is negatively affected by parakeets. This demonstrates that common species gain benefits and threatened ones (in this study, a bat and possibly a falcon) lose nest sites due to invaders. Therefore, the conservation status of the native species that pay the costs of competition with invaders should be considered. This scenario of winners and losers may, however, shift towards more losers if the ring-necked parakeet population continues to grow, thus requiring close monitoring and control/eradication programs to avoid further impacts. PMID:24945439

Crowding in the city: losing and winning competitors of an invasive bird.

PubMed

Hernández-Brito, Dailos; Carrete, Martina; Popa-Lisseanu, Ana G; Ibáñez, Carlos; Tella, José L

2014-01-01

Invasive species can take advantage of resources unexploited by natives (opportunism hypothesis) or they can exploit the same resources but more aggressively or efficiently (competition hypothesis), thus impacting native species. However, invasive species tend to exploit anthropogenic habitats that are inefficiently used by natives such as urban environments. Focusing on the ring-necked parakeet (Psittacula krameri), one of the most invasive birds worldwide, we combined observations of interspecific aggressions, species-specific cavity-nest preferences and the spatial distribution of the native cavity-nesting vertebrate community to determine the invasion process as well as its potential impacts on native species in a Mediterranean city. Our results support the competition hypothesis, suggesting that ring-necked parakeets are outcompeting native species sharing nest-site preferences. Parakeets initiated and won most interspecific aggressions, which were directed towards competitors but also towards predators. This behaviour could explain the spatial arrangement of natives, with most bird species breeding close to parakeets possibly to take advantage of their effective antipredatory behaviour. However, temporal and spatial patterns of segregation suggest that a threatened bat species is negatively affected by parakeets. This demonstrates that common species gain benefits and threatened ones (in this study, a bat and possibly a falcon) lose nest sites due to invaders. Therefore, the conservation status of the native species that pay the costs of competition with invaders should be considered. This scenario of winners and losers may, however, shift towards more losers if the ring-necked parakeet population continues to grow, thus requiring close monitoring and control/eradication programs to avoid further impacts.

DNA from the Past Informs Ex Situ Conservation for the Future: An “Extinct” Species of Galápagos Tortoise Identified in Captivity

PubMed Central

Russello, Michael A.; Poulakakis, Nikos; Gibbs, James P.; Tapia, Washington; Benavides, Edgar; Powell, Jeffrey R.; Caccone, Adalgisa

2010-01-01

Background Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species (Chelonoidis elephantopus) once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for C. elephantopus add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry. Methodology/Findings We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males) exhibited strong signatures of Floreana ancestry and a high probability of assignment to C. elephantopus as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to C. elephantopus based on microsatellite genotypic data also possessed a “Floreana-like” mitochondrial DNA haplotype. Significance Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed ex situ species recovery efforts. Here, the availability of population-level genotypic data from the extinct C. elephantopus enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of C. elephantopus ancestry currently reside at a centralized breeding facility on Santa Cruz, these findings permit breeding efforts to commence in support of the reestablishment of this extinct species to its native range. PMID:20084268

Direct and Indirect Influence of Non-Native Neighbours on Pollination and Fruit Production of a Native Plant.

PubMed

Montero-Castaño, Ana; Vilà, Montserrat

2015-01-01

Entomophilous non-native plants can directly affect the pollination and reproductive success of native plant species and also indirectly, by altering the composition and abundance of floral resources in the invaded community. Separating direct from indirect effects is critical for understanding the mechanisms underlying the impacts of non-native species on recipient communities. Our aims are: (a) to explore both the direct effect of the non-native Hedysarum coronarium and its indirect effect, mediated by the alteration of floral diversity, on the pollinator visitation rate and fructification of the native Leopoldia comosa and (b) to distinguish whether the effects of the non-native species were due to its floral display or to its vegetative interactions. We conducted field observations within a flower removal experimental setup (i.e. non-native species present, absent and with its inflorescences removed) at the neighbourhood scale. Our study illustrates the complexity of mechanisms involved in the impacts of non-native species on native species. Overall, Hedysarum increased pollinator visitation rates to Leopoldia target plants as a result of direct and indirect effects acting in the same direction. Due to its floral display, Hedysarum exerted a direct magnet effect attracting visits to native target plants, especially those made by the honeybee. Indirectly, Hedysarum also increased the visitation rate of native target plants. Due to the competition for resources mediated by its vegetative parts, it decreased floral diversity in the neighbourhoods, which was negatively related to the visitation rate to native target plants. Hedysarum overall also increased the fructification of Leopoldia target plants, even though such an increase was the result of other indirect effects compensating for the observed negative indirect effect mediated by the decrease of floral diversity.

Direct and Indirect Influence of Non-Native Neighbours on Pollination and Fruit Production of a Native Plant

PubMed Central

Montero-Castaño, Ana; Vilà, Montserrat

2015-01-01

Background Entomophilous non-native plants can directly affect the pollination and reproductive success of native plant species and also indirectly, by altering the composition and abundance of floral resources in the invaded community. Separating direct from indirect effects is critical for understanding the mechanisms underlying the impacts of non-native species on recipient communities. Objectives Our aims are: (a) to explore both the direct effect of the non-native Hedysarum coronarium and its indirect effect, mediated by the alteration of floral diversity, on the pollinator visitation rate and fructification of the native Leopoldia comosa and (b) to distinguish whether the effects of the non-native species were due to its floral display or to its vegetative interactions. Methods We conducted field observations within a flower removal experimental setup (i.e. non-native species present, absent and with its inflorescences removed) at the neighbourhood scale. Results Our study illustrates the complexity of mechanisms involved in the impacts of non-native species on native species. Overall, Hedysarum increased pollinator visitation rates to Leopoldia target plants as a result of direct and indirect effects acting in the same direction. Due to its floral display, Hedysarum exerted a direct magnet effect attracting visits to native target plants, especially those made by the honeybee. Indirectly, Hedysarum also increased the visitation rate of native target plants. Due to the competition for resources mediated by its vegetative parts, it decreased floral diversity in the neighbourhoods, which was negatively related to the visitation rate to native target plants. Hedysarum overall also increased the fructification of Leopoldia target plants, even though such an increase was the result of other indirect effects compensating for the observed negative indirect effect mediated by the decrease of floral diversity. PMID:26110630

QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice.

PubMed

Senthilvel, Senapathy; Vinod, Kunnummal Kurungara; Malarvizhi, Palaniappan; Maheswaran, Marappa

2008-09-01

Agricultural environments deteriorate due to excess nitrogen application. Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input. Rice genotypes respond variably to soil available nitrogen. The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits. Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena. Three nitrogen regimes namely, native (0 kg/ha; no nitrogen applied), optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments. The parents and DH lines were significantly varying for all traits under different nitrogen regimes. All traits except plant height recorded significant genotype x environment interaction. Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake. Sixteen QTLs were detected by composite interval mapping. Eleven QTLs showed significant QTL x environment interactions. On chromosome 3, seven QTLs were detected associated with nitrogen use, plant yield and associated traits. A QTL region between markers RZ678, RZ574 and RZ284 was associated with nitrogen use and yield. This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.

Microgeographic patterns of genetic divergence and adaptation across environmental gradients in Boechera stricta (Brassicaceae)

PubMed Central

Anderson, Jill T.; Perera, Nadeesha; Chowdhury, Bashira; Mitchell-Olds, Thomas

2015-01-01

Abiotic and biotic conditions often vary continuously across the landscape, imposing divergent selection on local populations. We used a provenance trial approach to examine microgeographic variation in local adaptation in Boechera stricta (Brassicaceae), a perennial forb native to the Rocky Mountains. In montane ecosystems, environmental conditions change considerably over short spatial scales, such that neighboring populations can be subject to different selective pressures. Using accessions from southern (Colorado) and northern (Idaho) populations, we characterized spatial variation in genetic similarity via microsatellite markers. We then transplanted genotypes from multiple local populations into common gardens in both regions. Continuous variation in local adaptation emerged for several components of fitness. In Idaho, genotypes from warmer environments (low elevation or south facing sites) were poorly adapted to the north-facing garden. In high and low elevation Colorado gardens, susceptibility to insect herbivory increased with source elevation. In the high elevation Colorado garden, germination success peaked for genotypes that evolved at similar elevations as the garden, and declined for genotypes from higher and lower elevations. We also found evidence for local maladaptation in survival and fecundity components of fitness in the low elevation Colorado garden. This approach is a necessary first step in predicting how global change could affect evolutionary dynamics. PMID:26656218

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider

PubMed Central

Krehenwinkel, Henrik; Pekar, Stano

2015-01-01

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population. PMID:26309219

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider.

PubMed

Krehenwinkel, Henrik; Pekar, Stano

2015-01-01

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen's age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.

The impacts of climate change on tribal traditional foods

Treesearch

Kathy Lynn; John Daigle; Jennie Hoffman; Frank Lake; Natalie Michelle; Darren Ranco; Carson Viles; Garrit Voggesser; Paul Williams

2013-01-01

American Indian and Alaska Native tribes are uniquely affected by climate change. Indigenous peoples have depended on a wide variety of native fungi, plant and animal species for food, medicine, ceremonies, community and economic health for countless generations. Climate change stands to impact the species and ecosystems that constitute tribal traditional foods that...

Screening of whole genome sequences identified high-impact variants for stallion fertility.

PubMed

Schrimpf, Rahel; Gottschalk, Maren; Metzger, Julia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

2016-04-14

Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes predicted to participate in the regulation of male reproduction. The corresponding equine orthologous genes were searched in whole genome sequence data of seven stallions and four mares and filtered for high-impact genetic variants using SnpEFF, SIFT and Polyphen 2 software. All genetic variants with the missing homozygous mutant genotype were genotyped on 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. Mixed linear model analysis was employed for an association analysis with de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). We screened next generation sequenced data of whole genomes from 11 horses for equine genetic variants in 1194 human and mice genes involved in male fertility and linked through common gene ontology (GO) with male reproductive processes. Variants were filtered for high-impact on protein structure and validated through SIFT and Polyphen 2. Only those genetic variants were followed up when the homozygote mutant genotype was missing in the detection sample comprising 11 horses. After this filtering process, 17 single nucleotide polymorphism (SNPs) were left. These SNPs were genotyped in 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. An association analysis in 216 Hanoverian stallions revealed a significant association of the splice-site disruption variant g.37455302G>A in NOTCH1 with the de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). For 9 high-impact variants within the genes CFTR, OVGP1, FBXO43, TSSK6, PKD1, FOXP1, TCP11, SPATA31E1 and NOTCH1 (g.37453246G>C) absence of the homozygous mutant genotype in the validation sample of all 337 fertile stallions was obvious. Therefore, these variants were considered as potentially deleterious factors for stallion fertility. In conclusion, this study revealed 17 genetic variants with a predicted high damaging effect on protein structure and missing homozygous mutant genotype. The g.37455302G>A NOTCH1 variant was identified as a significant stallion fertility locus in Hanoverian stallions and further 9 candidate fertility loci with missing homozygous mutant genotypes were validated in a panel including 19 horse breeds. To our knowledge this is the first study in horses using next generation sequencing data to uncover strong candidate factors for stallion fertility.

Co-occurring nonnative woody shrubs have additive and non-additive soil legacies.

PubMed

Kuebbing, Sara E; Patterson, Courtney M; Classen, Aimée T; Simberloff, Daniel

2016-09-01

To maximize limited conservation funds and prioritize management projects that are likely to succeed, accurate assessment of invasive nonnative species impacts is essential. A common challenge to prioritization is a limited knowledge of the difference between the impacts of a single nonnative species compared to the impacts of nonnative species when they co-occur, and in particular predicting when impacts of co-occurring nonnative species will be non-additive. Understanding non-additivity is important for management decisions because the management of only one co-occurring invader will not necessarily lead to a predictable reduction in the impact or growth of the other nonnative plant. Nonnative plants are frequently associated with changes in soil biotic and abiotic characteristics, which lead to plant-soil interactions that influence the performance of other species grown in those soils. Whether co-occurring nonnative plants alter soil properties additively or non-additively relative to their effects on soils when they grow in monoculture is rarely addressed. We use a greenhouse plant-soil feedback experiment to test for non-additive soil impacts of two common invasive nonnative woody shrubs, Lonicera maackii and Ligustrum sinense, in deciduous forests of the southeastern United States. We measured the performance of each nonnative shrub, a native herbaceous community, and a nonnative woody vine in soils conditioned by each shrub singly or together in polyculture. Soils conditioned by both nonnative shrubs had non-additive impacts on native and nonnative performance. Root mass of the native herbaceous community was 1.5 times lower and the root mass of the nonnative L. sinense was 1.8 times higher in soils conditioned by both L. maackii and L. sinense than expected based upon growth in soils conditioned by either shrub singly. This result indicates that when these two nonnative shrubs co-occur, their influence on soils disproportionally favors persistence of the nonnative L. sinense relative to this native herbaceous community, and could provide an explanation of why native species abundance is frequently depressed in these communities. Additionally, the difference between native and nonnative performance demonstrates that invasive impact studies focusing on the impact only of single species can be insufficient for determining the impact of co-occurring invasive plant species. © 2016 by the Ecological Society of America.

CBR1 rs9024 genotype status impacts the bioactivation of loxoprofen in human liver.

PubMed

Lombraña, Adolfo Quiñones; Li, Nasi; Del Solar, Virginia; Ekin Atilla-Gokcumen, G; Blanco, Javier G

2018-05-31

Loxoprofen is an anti-inflammatory drug that requires bioactivation into the trans-OH metabolite to exert pharmacological activity. Evidence suggests that carbonyl reductase 1 (CBR1) is important during the bioactivation of loxoprofen. Here, we examined the impact of the functional single nucleotide polymorphism CBR1 rs9024 on the bioactivation of loxoprofen in a collection of human liver samples. The synthesis ratios of trans-OH loxoprofen/cis-OH loxoprofen were 33% higher in liver cytosols from donors homozygous for the CBR1 rs9024 G allele in comparison to the ratios in samples from donors with heterozygous GA genotypes. Complementary studies examined the impact of CBR1 rs9024 on the bioactivation of loxoprofen in lymphoblastoid cell lines. CBR1 rs9024 genotype status impacts the synthesis of the bioactive trans-OH metabolite of loxoprofen in human liver. This article is protected by copyright. All rights reserved.

Fatty acid composition of goose meat depending on genotype and sex.

PubMed

Uhlířová, Linda; Tůmová, Eva; Chodová, Darina; Volek, Zdeněk; Machander, Vlastislav

2018-04-12

The aim of this study was to compare male and female geese of two contrasting genotypes in terms of fatty acid composition, indexes related to human health, lipid metabolism and oxidative stability of the meat. The experiment was carried out on total of 120 geese of two different genotypes; the native breed Czech Goose (CG) and commercial hybrid Novohradska Goose (NG). One-d-old goslings were divided into 4 groups according to genotype and sex, and 8 birds from each group were slaughtered at 8 weeks of age. The effects of the interactions between genotype and sex were observed on growth performance and carcass traits. Final live weight (P < 0.001), daily weight gain (P < 0.001), daily feed intake (P < 0.001), slaughter weight (P < 0.001) and cold carcass weight (P < 0.001) were highest in NG males and lowest in CG females. The meat fatty acid composition results showed effects of both genotype and sex on the total n-6 and the total PUFA content, as well as the PUFA n-6/PUFA n-3 ratio. Regarding genotype, the total n-6, the total PUFA content and the PUFA n-6/PUFA n-3 ratio were higher in CG, and higher values were found in females. In terms of the lipid metabolism, Δ5 - Δ6 desaturase (P = 0.006) was higher in males. The meat oxidative stability results revealed an interaction between genotype, sex and storage time (P < 0.001). The highest (13.85 mg/kg) malondialdehyde content was measured in the meat of CG females after 5 days of storage and was presumably related to a higher PUFA content. NG had a relatively higher growth rate and meat oxidative stability, whereas the advantage of CG meat is its favourable fatty acid profile characterized by a higher PUFA content.

Jack of all trades masters novel host plants: positive genetic correlations in specialist and generalist insect herbivores expanding their diets to novel hosts

PubMed Central

GARCÍA-ROBLEDO, CARLOS; HORVITZ, CAROL C.

2011-01-01

One explanation for the widespread host specialization of insect herbivores is the “Jack of all trades-master of none” principle, which states that genotypes with high performance on one host will perform poorly on other hosts. This principle predicts that cross-host correlation in performance of genotypes will be negative. In this study we experimentally explored cross-host correlations and performance among families in four species (two generalist and two specialist) of leaf beetles (Cephaloleia spp.) that are currently expanding their diets from native to exotic plants. All four species displayed similar responses in body size, developmental rates and mortality rates to experimentally controlled diets. When raised on novel hosts, body size of larvae, pupae and adults were reduced. Development times were longer and larval mortality was higher on novel hosts. Genotype × host plant interactions were not detected for most traits. All significant cross-host correlations were positive. These results indicate very different ecological and evolutionary dynamics than those predicted by the “Jack of all trades-master of none” principle. PMID:22022877

Why segmentation matters: experience-driven segmentation errors impair “morpheme” learning

PubMed Central

Finn, Amy S.; Hudson Kam, Carla L.

2015-01-01

We ask whether an adult learner’s knowledge of their native language impedes statistical learning in a new language beyond just word segmentation (as previously shown). In particular, we examine the impact of native-language word-form phonotactics on learners’ ability to segment words into their component morphemes and learn phonologically triggered variation of morphemes. We find that learning is impaired when words and component morphemes are structured to conflict with a learner’s native-language phonotactic system, but not when native-language phonotactics do not conflict with morpheme boundaries in the artificial language. A learner’s native-language knowledge can therefore have a cascading impact affecting word segmentation and the morphological variation that relies upon proper segmentation. These results show that getting word segmentation right early in learning is deeply important for learning other aspects of language, even those (morphology) that are known to pose a great difficulty for adult language learners. PMID:25730305

Weed-biocontrol insects reduce native-plant recruitment through second-order apparent competition.

PubMed

Pearson, Dean E; Callaway, Ragan M

2008-09-01

Small-mammal seed predation is an important force structuring native-plant communities that may also influence exotic-plant invasions. In the intermountain West, deer mice (Peromyscus maniculatus) are prominent predators of native-plant seeds, but they avoid consuming seeds of certain widespread invasives like spotted knapweed (Centaurea maculosa). These mice also consume the biological-control insects Urophora spp. introduced to control C. maculosa, and this food resource substantially increases deer mouse populations. Thus, mice may play an important role in the invasion and management of C. maculosa through food-web interactions. We examined deer mouse seed predation and its effects on seedling emergence and establishment of a dominant native grass, Pseudoroegneria spicata, and forb, Balsamorhiza sagittata, in C. maculosa-invaded grasslands that were treated with herbicide to suppress C. maculosa or left untreated as controls. Deer mice readily took seeds of both native plants but removed 2-20 times more of the larger B. sagittata seeds than the smaller P. spicata seeds. Seed predation reduced emergence and establishment of both species but had greater impacts on B. sagittata. The intensity of seed predation corresponded with annual and seasonal changes in deer mouse abundance, suggesting that abundance largely determined mouse impacts on native-plant seeds. Accordingly, herbicide treatments that reduced mouse abundance by suppressing C. maculosa and its associated biocontrol food subsidies to mice also reduced seed predation and decreased the impact of deer mice on B. sagittata establishment. These results provide evidence that Urophora biocontrol agents may exacerbate the negative effects of C. maculosa on native plants through a form of second-order apparent competition-a biocontrol indirect effect that has not been previously documented. Herbicide suppressed C. maculosa and Urophora, reducing mouse populations and moderating seed predation on native plants, but the herbicide's direct negative effects on native forb seedlings overwhelmed the indirect positive effect of reducing deer mouse seed predation. By manipulating this four-level food chain, we illustrate that host-specific biological control agents may impact nontarget plant species through food-web interactions, and herbicides may influence management outcomes through indirect trophic interactions in addition to their direct effects on plants.

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

PubMed

Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

2016-07-01

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana.

PubMed

Postma, Froukje M; Ågren, Jon

2015-02-01

The genetic basis of seed dormancy, a key life history trait important for adaptive evolution in plant populations, has yet been studied only using seeds produced under controlled conditions in greenhouse environments. However, dormancy is strongly affected by maternal environmental conditions, and interactions between seed genotype and maternal environment have been reported. Consequently, the genetic basis of dormancy of seeds produced under natural field conditions remains unclear. We examined the effect of maternal environment on the genetic architecture of seed dormancy using a recombinant inbred line (RIL) population derived from a cross between two locally adapted populations of Arabidopsis thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL) for dormancy of seeds produced in the greenhouse and at the native field sites of the parental genotypes. The Italian genotype produced seeds with stronger dormancy at fruit maturation than did the Swedish genotype in all three environments, and the maternal field environments induced higher dormancy levels compared to the greenhouse environment in both genotypes. Across the three maternal environments, a total of nine dormancy QTL were detected, three of which were only detected among seeds matured in the field, and six of which showed significant QTL × maternal environment interactions. One QTL had a large effect on dormancy across all three environments and colocalized with the candidate gene DOG1. Our results demonstrate the importance of studying the genetic basis of putatively adaptive traits under relevant conditions. © 2015 John Wiley & Sons Ltd.

Native American Recipes for the Classroom.

ERIC Educational Resources Information Center

Harvey, Karen D., Comp.

This collection of recipes is intended to assist teachers in using food in the classroom to enhance the study of Native American people. Several concepts are identified to guide teachers in developing instructional units centering around food as a means of understanding the Native American culture: (1) the impact of physical environment and…

(Non)native Speakered: Rethinking (Non)nativeness and Teacher Identity in TESOL Teacher Education

ERIC Educational Resources Information Center

Aneja, Geeta A.

2016-01-01

Despite its imprecision, the native-nonnative dichotomy has become the dominant paradigm for examining language teacher identity development. The nonnative English speaking teacher (NNEST) movement in particular has considered the impact of deficit framings of nonnativeness on "NNEST" preservice teachers. Although these efforts have…

Cardiovascular Deaths among Alaskan Natives, 1980-86.

ERIC Educational Resources Information Center

Middaugh, John P.

1990-01-01

Analyzes death certificate data to discover the number of deaths of Alaskan natives caused by cardiovascular disease. Rates from cardiovascular diseases and atherosclerosis from 1980-86 among Alaskan natives were lower than rates among other Alaskans, while death rates from other causes were higher. Discusses the possible impact of diet. (JS)

Impact of HIV infection on sustained virological response to treatment against hepatitis C virus with pegylated interferon plus ribavirin.

PubMed

Monje-Agudo, P; Castro-Iglesias, A; Rivero-Juárez, A; Martínez-Marcos, F; Ortega-González, E; Real, L M; Pernas, B; Merchante, N; Cid, P; Macías, J; Merino, M D; Rivero, A; Mena, A; Neukam, K; Pineda, J A

2015-10-01

It is commonly accepted that human immunodeficiency (HIV) coinfection negatively impacts on the rates of sustained virological response (SVR) to therapy with pegylated interferon plus ribavirin (PR). However, this hypothesis is derived from comparing different studies. The aim of this study was to determine the impact of HIV coinfection on SVR to PR in one single population. In a multicentric, prospective study conducted between 2000 and 2013, all previously naïve hepatitis C virus (HCV)-infected patients who started PR in five Spanish hospitals were analyzed. SVR was evaluated 24 weeks after the scheduled end of therapy. Of the 1046 patients included in this study, 413 (39%) were coinfected with HIV. Three hundred and forty-one (54%) HCV-monoinfected versus 174 (42%) HIV/HCV-coinfected patients achieved SVR (p < 0.001). The corresponding figures for undetectable HCV RNA at treatment week 4 were 86/181 (47%) versus 59/197 (30%), p < 0.001. SVR was observed in 149 (69%) HCV genotype 2/3-monoinfected subjects versus 91 (68%) HIV/HCV genotype 2/3-coinfected subjects (p = 0.785). In the HCV genotype 1/4-infected population, 188 (46%) monoinfected patients versus 82 (30%) with HIV coinfection (p < 0.001) achieved SVR. In this subgroup, absence of HIV coinfection was independently associated with higher SVR [adjusted odds ratio (95% confidence interval): 2.127 (1.135-3.988); p = 0.019] in a multivariate analysis adjusted for age, sex, baseline HCV RNA load, IL28B genotype, fibrosis stage, and type of pegylated interferon. HIV coinfection impacts on the rates of SVR to PR only in HCV genotype 1/4-infected patients, while it has no effect on SVR in the HCV genotype 2/3-infected subpopulation.

Impact of Maternal Serotonin Transporter Genotype on Placental Serotonin, Fetal Forebrain Serotonin, and Neurodevelopment

PubMed Central

Muller, Christopher L; Anacker, Allison MJ; Rogers, Tiffany D; Goeden, Nick; Keller, Elizabeth H; Forsberg, C Gunnar; Kerr, Travis M; Wender, Carly LA; Anderson, George M; Stanwood, Gregg D; Blakely, Randy D; Bonnin, Alexandre; Veenstra-VanderWeele, Jeremy

2017-01-01

Biomarker, neuroimaging, and genetic findings implicate the serotonin transporter (SERT) in autism spectrum disorder (ASD). Previously, we found that adult male mice expressing the autism-associated SERT Ala56 variant have altered central serotonin (5-HT) system function, as well as elevated peripheral blood 5-HT levels. Early in gestation, before midbrain 5-HT projections have reached the cortex, peripheral sources supply 5-HT to the forebrain, suggesting that altered maternal or placenta 5-HT system function could impact the developing embryo. We therefore used different combinations of maternal and embryo SERT Ala56 genotypes to examine effects on blood, placenta and embryo serotonin levels and neurodevelopment at embryonic day E14.5, when peripheral sources of 5-HT predominate, and E18.5, when midbrain 5-HT projections have reached the forebrain. Maternal SERT Ala56 genotype was associated with decreased placenta and embryonic forebrain 5-HT levels at E14.5. Low 5-HT in the placenta persisted, but forebrain levels normalized by E18.5. Maternal SERT Ala56 genotype effects on forebrain 5-HT levels were accompanied by a broadening of 5-HT-sensitive thalamocortical axon projections. In contrast, no effect of embryo genotype was seen in concepti from heterozygous dams. Blood 5-HT levels were dynamic across pregnancy and were increased in SERT Ala56 dams at E14.5. Placenta RNA sequencing data at E14.5 indicated substantial impact of maternal SERT Ala56 genotype, with alterations in immune and metabolic-related pathways. Collectively, these findings indicate that maternal SERT function impacts offspring placental 5-HT levels, forebrain 5-HT levels, and neurodevelopment. PMID:27550733

Native species richness buffers invader impact in undisturbed but not disturbed grassland assemblages

Treesearch

Sarah M. Pinto; Yvette K. Ortega

2016-01-01

Many systems are prone to both exotic plant invasion and frequent natural disturbances. Native species richness can buffer the effects of invasion or disturbance when imposed in isolation, but it is largely unknown whether richness provides substantial resistance against invader impact in the face of disturbance. We experimentally examined how disturbance (...

Are Adult Educators and Learners "Digital Immigrants"? Examining the Evidence and Impacts for Continuing Education

ERIC Educational Resources Information Center

Smith, Erika

2013-01-01

Over the past decade, Prensky's distinctions between "digital immigrants" and "digital natives" have been oft-referenced. Much has been written about digital native students as a part of the Net generation or as Millennials. However, little work fully considers the impact of digital immigrant discourse within the fields of…

Decoding noises in HIV computational genotyping.

PubMed

Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

2017-11-01

Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

Symbols of pride or prejudice? Examining the impact of Native American sports mascots on stereotype application.

PubMed

Burkley, Melissa; Burkley, Edward; Andrade, Angela; Bell, Angela C

2017-01-01

For over 50 years, a debate has existed over the use of Native American sports mascots; however, few empirical studies on the topic exist. The present study examined if supraliminal exposure to Native American mascots results in the application of negative stereotypes toward Native American people. Results indicated that the effect of Native American mascots was moderated by people's racial attitudes toward Native people. When exposed to Native mascots, people with a prejudiced attitude rated a Native American individual more stereotypically aggressive than those with a non-prejudiced attitude. However, this pattern did not occur when people were exposed to White mascots or neutral images. Furthermore, this pattern was not evident when people evaluated a non-Native individual. This overall pattern of results indicates that Native American mascots selectively facilitate the application of negative stereotypes, resulting in harmful evaluations of Native American people.

Alaska Natives assessing the health of their environment.

PubMed

Garza, D

2001-11-01

The changes in Alaska's ecosystems caused by pollution, contaminants and global climate change are negatively impacting Alaska Natives and rural residents who rely on natural resources for food, culture and community identity. While Alaska commerce has contributed little to these global changes and impacts, Alaska and its resources are nonetheless affected by the changes. While Alaska Natives have historically relied on Alaska's land, water and animals for survival and cultural identity, today their faith in the safety and quality of these resources has decreased. Alaska Natives no longer believe that these wild resources are the best and many are turning to alternative store-bought foods. Such a change in diet and activity may be contributing to a decline in traditional activities and a decline in general health. Contaminants are showing up in the animals, fish and waters that Alaska Natives use. Efforts need to be expanded to empower Alaska Native Tribes to collect and analyze local wild foods for various contaminants. In addition existing information on contaminants and pollution should be made readily available to Alaska residents. Armed with this type of information Alaska Native residents will be better prepared to make informed decisions on using wild foods and materials.

Possible Impacts of the Invasive Plant Rubus niveus on the Native Vegetation of the Scalesia Forest in the Galapagos Islands

PubMed Central

Rentería, Jorge Luis; Gardener, Mark R.; Panetta, F. Dane; Atkinson, Rachel; Crawley, Mick J.

2012-01-01

Originally from Asia, Rubus niveus has become one of the most widespread invasive plant species in the Galapagos Islands. It has invaded open vegetation, shrubland and forest alike. It forms dense thickets up to 4 m high, appearing to displace native vegetation, and threaten the integrity of several native communities. This study used correlation analysis between a R. niveus cover gradient and a number of biotic (vascular plant species richness, cover and vegetation structure) and abiotic (light and soil properties) parameters to help understand possible impacts in one of the last remaining fragments of the Scalesia forest in Santa Cruz Island, Galapagos. Higher cover of R. niveus was associated with significantly lower native species richness and cover, and a different forest structure. Results illustrated that 60% R. niveus cover could be considered a threshold for these impacts. We suggest that a maximum of 40% R. niveus cover could be a suitable management target. PMID:23118934

Climate warming increases biological control agent impact on a non-target species

PubMed Central

Lu, Xinmin; Siemann, Evan; He, Minyan; Wei, Hui; Shao, Xu; Ding, Jianqing

2015-01-01

Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming affects impacts of a multivoltine introduced biocontrol beetle on the non-target native plant Alternanthera sessilis in China. In field surveys across a latitudinal gradient covering their full distributions, we found beetle damage on A. sessilis increased with rising temperature and plant life history changed from perennial to annual. Experiments showed that elevated temperature changed plant life history and increased insect overwintering, damage and impacts on seedling recruitment. These results suggest that warming can shift phenologies, increase non-target effect magnitude and increase non-target effect occurrence by beetle range expansion to additional areas where A. sessilis occurs. This study highlights the importance of understanding how climate change affects species interactions for future biological control of invasive species and conservation of native species. PMID:25376303

Climate warming increases biological control agent impact on a non-target species.

PubMed

Lu, Xinmin; Siemann, Evan; He, Minyan; Wei, Hui; Shao, Xu; Ding, Jianqing

2015-01-01

Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming affects impacts of a multivoltine introduced biocontrol beetle on the non-target native plant Alternanthera sessilis in China. In field surveys across a latitudinal gradient covering their full distributions, we found beetle damage on A. sessilis increased with rising temperature and plant life history changed from perennial to annual. Experiments showed that elevated temperature changed plant life history and increased insect overwintering, damage and impacts on seedling recruitment. These results suggest that warming can shift phenologies, increase non-target effect magnitude and increase non-target effect occurrence by beetle range expansion to additional areas where A. sessilis occurs. This study highlights the importance of understanding how climate change affects species interactions for future biological control of invasive species and conservation of native species. © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies.

PubMed

Criollo-Rayo, Angel A; Bohórquez, Mabel; Prieto, Rodrigo; Howarth, Kimberley; Culma, Cesar; Carracedo, Angel; Tomlinson, Ian; Echeverry de Polnaco, Maria M; Carvajal Carmona, Luis G

2018-06-07

Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers. Nasa and Pijao had a predominant Native American ancestry at the autosomal (92%), maternal (97%) and paternal (70%) level. The admixed groups had a predominant Native American mtDNA ancestry (90%), a substantial frequency of European NRY haplotypes (72%) and similar autosomal contributions from Europeans (51%) and Amerindians (45%). Pijao and nearby Ortega were indistinguishable at the mtDNA and autosomal level, suggesting a genetic continuity between them. Comparisons with multiple Native American populations throughout the Americas revealed that Pijao, had close similarities with Carib-speakers from distant parts of the continent, suggesting an ancient correlation between language and genes. In summary, our study aimed to understand Hispanic patterns of migration, settlement and admixture, supporting an extensive contribution of local Amerindian women to the gene pool of admixed groups and consistent with previous reports of European-male driven admixture in Colombia. Copyright © 2018 Elsevier B.V. All rights reserved.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions.

PubMed

Zenni, Rafael Dudeque; Dickie, Ian A; Wingfield, Michael J; Hirsch, Heidi; Crous, Casparus J; Meyerson, Laura A; Burgess, Treena I; Zimmermann, Thalita G; Klock, Metha M; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J

2016-12-30

Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics, and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand, and manage biological invasions. Published by Oxford University Press on behalf of the Annals of Botany Company.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions

PubMed Central

Dickie, Ian A.; Wingfield, Michael J.; Hirsch, Heidi; Crous, Casparus J.; Meyerson, Laura A.; Burgess, Treena I.; Zimmermann, Thalita G.; Klock, Metha M.; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J.

2017-01-01

Abstract Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand and manage biological invasions. PMID:28039118

Measles Virus Hemagglutinin epitopes immunogenic in natural infection and vaccination are targeted by broad or genotype-specific neutralizing monoclonal antibodies.

PubMed

Muñoz-Alía, Miguel Angel; Casasnovas, José M; Celma, María Luisa; Carabaña, Juan; Liton, Paloma B; Fernandez-Muñoz, Rafael

2017-05-15

Measles virus (MV) remains a leading cause of vaccine-preventable deaths in children. Protection against MV is associated with neutralizing antibodies that preferentially recognize the viral hemagglutinin (MV-H), and to a lesser extent, the fusion protein (MV-F). Although MV is serologically monotypic, 24 genotypes have been identified. Here we report three neutralization epitopes conserved in the more prevalent circulating MV genotypes, two located in the MV-H receptor binding site (RBS) (antigenic site III) and a third in MV-H/MV-F interphase (antigenic site Ia) which are essential for MV multiplication. In contrast, two MV-H neutralization epitopes, showed a genotype-specific neutralization escape due to a single amino acid change, that we mapped in the "noose" antigenic site, or an enhanced neutralization epitope (antigenic site IIa). The monoclonal antibody (mAb) neutralization potency correlated with its binding affinity and was mainly driven by kinetic dissociation rate (k off ). We developed an immunoassay for mAb binding to MV-H in its native hetero-oligomeric structure with MV-F on the surface of a MV productive steady-state persistently infected (p.i.) human cell lines, and a competitive-binding assay with serum from individuals with past infection by different MV genotypes. Binding assays revealed that a broad neutralization epitope, in RBS antigenic site, a genotype specific neutralization epitopes, in noose and IIa sites, were immunogenic in natural infection and vaccination and may elicit long-lasting humoral immunity that might contribute to explain MV immunogenic stability. These results support the design of improved measles vaccines, broad-spectrum prophylactic or therapeutic antibodies and MV-used in oncolytic therapies. Copyright © 2017 Elsevier B.V. All rights reserved.

Soluble and cell wall-bound phenolic acids and ferulic acid dehydrodimers in rye flour and five bread model systems: insight into mechanisms of improved availability

PubMed Central

Dynkowska, Wioletta M; Cyran, Malgorzata R; Ceglińska, Alicja

2015-01-01

Background The bread-making process influences bread components, including phenolics that significantly contribute to its antioxidant properties. Five bread model systems made from different rye cultivars were investigated to compare their impact on concentration of ethanol-soluble (free and ester-bound) and insoluble phenolics. Results Breads produced by a straight dough method without acid addition (A) and three-stage sourdough method with 12 h native starter preparation (C) exhibited the highest, genotype-dependent concentrations of free phenolic acids. Dough acidification by direct acid addition (method B) or by gradual production during prolonged starter fermentation (24 and 48 h, for methods D and E) considerably decreased their level. However, breads B were enriched in soluble ester-bound fraction. Both direct methods, despite substantial differences in dough pH, caused a similar increase in the amount of insoluble ester-bound fraction. The contents of phenolic fractions in rye bread were positively related to activity level of feruloyl esterase and negatively to those of arabinoxylan-hydrolysing enzymes in wholemeal flour. Conclusion The solubility of rye bread phenolics may be enhanced by application of a suitable bread-making procedure with respect to rye cultivar, as the mechanisms of this process are also governed by a response of an individual genotype with specific biochemical profile. © 2014 Plant Breeding and Acclimatization Institute, National Research Institute. © 2014 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:25410263

Practical implementation of cost-effective genomic selection in commercial pig breeding using imputation.

PubMed

Cleveland, M A; Hickey, J M

2013-08-01

Genomic selection can be implemented in pig breeding at a reduced cost using genotype imputation. Accuracy of imputation and the impact on resulting genomic breeding values (gEBV) was investigated. High-density genotype data was available for 4,763 animals from a single pig line. Three low-density genotype panels were constructed with SNP densities of 450 (L450), 3,071 (L3k) and 5,963 (L6k). Accuracy of imputation was determined using 184 test individuals with no genotyped descendants in the data but with parents and grandparents genotyped using the Illumina PorcineSNP60 Beadchip. Alternative genotyping scenarios were created in which parents, grandparents, and individuals that were not direct ancestors of test animals (Other) were genotyped at high density (S1), grandparents were not genotyped (S2), dams and granddams were not genotyped (S3), and dams and granddams were genotyped at low density (S4). Four additional scenarios were created by excluding Other animal genotypes. Test individuals were always genotyped at low density. Imputation was performed with AlphaImpute. Genomic breeding values were calculated using the single-step genomic evaluation. Test animals were evaluated for the information retained in the gEBV, calculated as the correlation between gEBV using imputed genotypes and gEBV using true genotypes. Accuracy of imputation was high for all scenarios but decreased with fewer SNP on the low-density panel (0.995 to 0.965 for S1) and with reduced genotyping of ancestors, where the largest changes were for L450 (0.965 in S1 to 0.914 in S3). Exclusion of genotypes for Other animals resulted in only small accuracy decreases. Imputation accuracy was not consistent across the genome. Information retained in the gEBV was related to genotyping scenario and thus to imputation accuracy. Reducing the number of SNP on the low-density panel reduced the information retained in the gEBV, with the largest decrease observed from L3k to L450. Excluding Other animal genotypes had little impact on imputation accuracy but caused large decreases in the information retained in the gEBV. These results indicate that accuracy of gEBV from imputed genotypes depends on the level of genotyping in close relatives and the size of the genotyped dataset. Fewer high-density genotyped individuals are needed to obtain accurate imputation than are needed to obtain accurate gEBV. Strategies to optimize development of low-density panels can improve both imputation and gEBV accuracy.

Are native songbird populations affected by non-native plant invasion?

Treesearch

Amanda M. Conover; Christopher K. Williams; Vincent. D' Amico

2011-01-01

Development into forested areas is occurring rapidly across the United States, and many of the remnant forests within suburban landscapes are being fragmented into smaller patches, impacting the quality of this habitat for avian species. An ecological effect linked to forest fragmentation is the invasion of non-native plants into the ecosystem.

Indigenizing Leadership Concepts through Perspectives of Native American College Students

ERIC Educational Resources Information Center

Williams, Robin Starr

2012-01-01

The findings from this study were that the Native student leaders in Native student organization (NSO) have been impacted by their experiences in ways that were rewarding, supportive and increased participation. The benefits found from being in a NSO included communicating and networking, building a community on campus, representing Native…

The Digital Native Debate in Higher Education: A Comparative Analysis of Recent Literature

ERIC Educational Resources Information Center

Smith, Erika E.

2012-01-01

More than a decade after Prensky's influential articulation of digital natives and immigrants, disagreement exists around these characterizations of students and the impact of such notions within higher education. Perceptions of today's undergraduate learners as tech-savvy "digital natives" (Prensky, 2001a), who both want and need the…

Native Students with Problems of Addiction. A Manual for Adult Educators.

ERIC Educational Resources Information Center

Hale, Janet Campbell; And Others

This manual's purpose is to help adult-education instructors to deal with addictive or preaddictive behavior in their Native American students. The impact of alcohol and drug-related social problems has been devastating to Native communities. It is essential to examine broader issues such as cultural identity, ethnic pride, self-confidence, and…

The invasive Red-vented bulbul (Pycnonotus cafer) outcompetes native birds in a tropical biodiversity hotspot.

PubMed

Thibault, Martin; Vidal, Eric; Potter, Murray Alan; Sanchez, Thierry; Brescia, Fabrice

2018-01-01

Invasive alien species are a major cause of biodiversity loss globally, but especially on islands where high species richness and levels of endemism accentuate their impacts. The Red vented bulbul (Pycnonotus cafer), a tropical passerine bird that has been introduced widely across locations of high conservation value, is considered an extreme pest. It is currently expanding its range in New Caledonia, one of the world's biodiversity hotspots. Decisive recommendations on management strategies are required urgently to inform local managers and policy makers, but they should be based on quantitative local evidence, not just on expert opinion. The Red-vented bulbul is widely blamed for its impacts on biodiversity, especially through competition. We used data from 2,472 point counts to explore the abundance relationships between the Red-vented bulbul and 14 other species of bird. Our results revealed a negative relationship between the occurrence of the bulbul and the mean abundance of nine species, all native (or endemic, n = 3) to the New Caledonia archipelago. In contrast, the abundance of other introduced species such as Acridotheres tristis (Common myna), Passer domesticus (House sparrow) and Spilopelia chinensis (Spotted dove) were not affected by the Red-vented bulbul. Moreover, temporal trends in the abundance of impacted species suggest that the Red-vented bulbul may cause niche contractions rather than mortality for native species in man-modified habitats. Monitoring and control of the Red-vented bulbul is recommended to prevent on-going impacts on native bird communities throughout New Caledonia, and its impact on native bird communities elsewhere should be quantified.

The invasive Red-vented bulbul (Pycnonotus cafer) outcompetes native birds in a tropical biodiversity hotspot

PubMed Central

Vidal, Eric; Potter, Murray Alan; Sanchez, Thierry; Brescia, Fabrice

2018-01-01

Invasive alien species are a major cause of biodiversity loss globally, but especially on islands where high species richness and levels of endemism accentuate their impacts. The Red vented bulbul (Pycnonotus cafer), a tropical passerine bird that has been introduced widely across locations of high conservation value, is considered an extreme pest. It is currently expanding its range in New Caledonia, one of the world’s biodiversity hotspots. Decisive recommendations on management strategies are required urgently to inform local managers and policy makers, but they should be based on quantitative local evidence, not just on expert opinion. The Red-vented bulbul is widely blamed for its impacts on biodiversity, especially through competition. We used data from 2,472 point counts to explore the abundance relationships between the Red-vented bulbul and 14 other species of bird. Our results revealed a negative relationship between the occurrence of the bulbul and the mean abundance of nine species, all native (or endemic, n = 3) to the New Caledonia archipelago. In contrast, the abundance of other introduced species such as Acridotheres tristis (Common myna), Passer domesticus (House sparrow) and Spilopelia chinensis (Spotted dove) were not affected by the Red-vented bulbul. Moreover, temporal trends in the abundance of impacted species suggest that the Red-vented bulbul may cause niche contractions rather than mortality for native species in man-modified habitats. Monitoring and control of the Red-vented bulbul is recommended to prevent on-going impacts on native bird communities throughout New Caledonia, and its impact on native bird communities elsewhere should be quantified. PMID:29390027

A voyage to Terra Australis: human-mediated dispersal of cats.

PubMed

Koch, K; Algar, D; Searle, J B; Pfenninger, M; Schwenk, K

2015-12-04

Cats have been transported as human commensals worldwide giving rise to many feral populations. In Australia, feral cats have caused decline and extinction of native mammals, but their time of introduction and origin is unclear. Here, we investigate hypotheses of cat arrival pre- or post-European settlement, and the potential for admixture between cats of different invasion events. We analyse the genetic structure and diversity of feral cats from six locations on mainland Australia, seven Australian islands and samples from Southeast Asia and Europe using microsatellite and mitochondrial DNA data. Our results based on phylogeographic model selection are consistent with a European origin of cats in Australia. We find genetic distinctiveness of Australian mainland samples compared with Dirk Hartog Island, Flinders Island, Tasman Island and Cocos (Keeling) Island samples, and genetic similarities between some of the island populations. Historical records suggest that introduction of cats to these islands occurred at the time of European exploration and/or in connection with the pearling, whaling and sealing trades early in the 19th century. On-going influx of domestic cats into the feral cat population is apparently causing the Australian mainland populations to be genetically differentiated from those island populations, which likely are remnants of the historically introduced cat genotypes. A mainly European origin of feral cats in Australia, with possible secondary introductions from Asia following the initial establishment of cats in Australia is reasonable. The islands surrounding Australia may represent founding populations and are of particular interest. The results of the study provide an important timeframe for the impact of feral cats on native species in Australia.

Comparing manager and visitor perceptions of llama use in wilderness

Treesearch

Alan E. Watson; Neal A. Christensen; Dale J. Blahna; Kari S. Archibald

1998-01-01

Llama use in wilderness is projected to increase over the next 5 years. While the greatest concerns about this increase in use are unexpected impacts to native flora, impacts to native fauna, and conflicts with other user types, there is also concern about how prepared managers are to deal with this increasing recreation demand. This research compares manager attitudes...

Toward an Ideal Democracy: The Impact of Standardization Policies on the American Indian/Alaska Native Community and Language Revitalization Efforts

ERIC Educational Resources Information Center

Cohen, Erik; Allen, Ann

2013-01-01

This article explores the impact of standardization policies of the No Child Left Behind Act (NCLB) of 2001 on the American Indian/Alaska Native community and the ability of educational policy to promote sovereignty, liberty and equity within indigenous communities. Examining current research and data generated from the National Indian Education…

Influence of silicon treatment on antimony uptake and translocation in rice genotypes with different radial oxygen loss.

PubMed

Zhang, Liping; Yang, Qianqian; Wang, Shiliang; Li, Wanting; Jiang, Shaoqing; Liu, Yan

2017-10-01

Antimony (Sb) pollution in soil may have a negative impact on the health of people consuming rice. This study investigated the effect of silicon (Si) application on rice biomass, iron plaque formation, and Sb uptake and speciation in rice plants with different radial oxygen loss (ROL) using pot experiments. The results demonstrated that Si addition increased the biomass of straw and grain, but had no obvious impact on the root biomass. Indica genotypes with higher ROL underwent greater iron plaque formation and exhibited more Sb sequestration in iron plaque. Silicon treatments increased iron levels in iron plaque from the different genotypes but decreased the total Sb concentration in root, straw, husk, and grain. In addition, Si treatment reduced the inorganic Sb concentrations but slightly increased the trimethylantimony (TMSb) concentrations in rice straw. Moreover, rice straw from hybrid genotypes accumulated higher concentrations of TMSb and inorganic Sb than that from indica genotypes. The conclusions from this study indicate that Sb contamination in rice can be efficiently reduced by applying Si treatment and selecting genotypes with high ROL. Copyright © 2017 Elsevier Inc. All rights reserved.

Paraoxonase 1 (PON1) Q192R genotypes and their interaction with smoking strongly increase atherogenicity and the Framingham risk score.

PubMed

Souza-Nogueira, Andre de; Camargo, Alissana Ester; Remondi, Felipe Assan; Paoliello, Monica Maria Bastos; Richter, Rebecca J; Furlong, Clement E; Barbosa, Decio Sabbatini; Maes, Michael; Moreira, Estefania Gastaldello

2016-10-01

Paraoxonase 1 (PON1) polymorphisms are associated with an increased susceptibility to cardiovascular disease. PON1 Q192R polymorphism (rs662) partially determine PON1 hydrolytic activity and protect against oxidation of LDL and HDL. This study aimed to delineate the association of PON1 status (functional 192 genotype and plasma activity levels) and atherogenicity in urbans residents aged 40 years or more. Anthropometric data, lipid profiles, the atherogenic index of the plasma (AIP) and Framingham score risk were measured. Three kinetic assays were conducted to assay PON1 status using phenylacetate and 4-(chloromethyl)phenyl acetate as substrates. Smoking per se did not significantly impact the AIP but the interaction PON1 genotype by smoking significantly increased the AIP. In subjects with the RR genotype smoking increased the AIP index from (estimated mean ± SEM) -0.038 ± 0.039 to 0.224 ± 0.094. The QR genotype increased the Framingham risk index by around 1.3 points. Smoking by RR genotype carriers significantly increased the Framingham risk score (17.23 ± 2.04) as compared to smoking (13.00 ± 1.06) and non-smoking (7.79 ± 0.70) by QQ+QR genotype carriers. The interaction RR genotype by smoking was a more important predictor (odds ratio = 7.90) of an increased Framingham risk score (> 20) than smoking per se (odds ratio = 2.73). The interaction smoking by RR genotype carriers significantly increased triglycerides and lowered HDL cholesterol. Smoking per se has no (AIP) or a mild (Framingham risk score) effect on atherogenicity, while the interaction smoking by PON1 RR genotype has a clinically highly significant impact on atherogenicity.

Revisiting policy on chronic HCV treatment under the Thai Universal Health Coverage: An economic evaluation and budget impact analysis.

PubMed

Rattanavipapong, Waranya; Anothaisintawee, Thunyarat; Teerawattananon, Yot

2018-01-01

Thailand is encountering challenges to introduce the high-cost sofosbuvir for chronic hepatitis C treatment as part of the Universal Health Care's benefit package. This study was conducted in respond to policy demand from the Thai government to assess the value for money and budget impact of introducing sofosbuvir-based regimens in the tax-based health insurance scheme. The Markov model was constructed to assess costs and benefits of the four treatment options that include: (i) current practice-peginterferon alfa (PEG) and ribavirin (RBV) for 24 weeks in genotype 3 and 48 weeks for other genotypes; (ii) Sofosbuvir plus peginterferon alfa and ribavirin (SOF+PEG-RBV) for 12 weeks; (iii) Sofosbuvir and daclatasvir (SOF+DCV) for 12 weeks; (iv) Sofosbuvir and ledipasvir (SOF+LDV) for 12 weeks for non-3 genotypes and SOF+PEG-RBV for 12 weeks for genotype 3 infection. Given that policy options (ii) and (iii) are for pan-genotypic infection, the cost of genotype testing was applied only for policy options (i) and (iv). Results reveal that all sofosbuvir-based regimens had greater quality adjusted life years (QALY) gains compared with the current treatment, therefore associated with lower lifetime costs and more favourable health outcomes. Additionally, among the three regimens of sofosbuvir, SOF+PEG-RBV for genotype 3 and SOF+LDV for non-3 genotype are the most cost-effective treatment option with the threshold of 160,000 THB per QALY gained. The results of this study had been used in policy discussion which resulted in the recent inclusion of SOF+PEG-RBV for genotype 3 and SOF+LDV for non-3 genotype in the Thailand's benefit package.

Ethanol production from poplar wood through enzymatic saccharification and fermentation by dilute acid and SPORL pretreatments

Treesearch

Z.J. Wang; J.Y. Zhu; Ronald S. Jr. Zalesny; K.F. Chen

2012-05-01

Dilute acid (DA) and Sulfite Pretreatment to Overcome Recalcitrance of Lignocelluloses (SPORL) pretreatments were directly applied to wood chips of four poplar wood samples of different genotypes (hereafter referred to as poplars; Populus tremuloides Michx. ‘native aspen collection’; Populus deltoides Bartr. ex Marsh x Populus nigra L. ‘NE222’ and ‘DN5’; P. nigra x...

Molecular characterisation of Theileria orientalis in imported and native bovines from Pakistan.

PubMed

Gebrekidan, Hagos; Abbas, Tariq; Wajid, Muhammad; Ali, Aamir; Gasser, Robin B; Jabbar, Abdul

2017-01-01

The epidemiological aspects of Theileria orientalis in Pakistan are unknown; therefore, investigations using sensitive and precise molecular techniques are required. This study reports the first molecular characterisation of T. orientalis detected from imported (Bos taurus) and native cattle (Bos indicus×Bos taurus) and buffaloes (Bubalus bubalis) selected from four districts of Punjab, Pakistan. DNA samples from blood (n=246) were extracted and tested using conventional PCR utilising the major piroplasm surface protein (MPSP) gene and multiplexed tandem PCR (MT-PCR). Theileria orientalis DNA was detected (15%; 22/147) only in imported cattle by conventional PCR, whereas 24.5% (36/147), 6% (3/50) and 6.1% (3/49) of the imported cattle and native Pakistani cattle and buffaloes, respectively were test-positive for T. orientalis using MT-PCR. Using MT-PCR, the prevalence of T. orientalis was significantly higher (P<0.0001) in imported cattle compared to that of detected in native Pakistani bovines. The prevalence of T. orientalis and DNA copies of chitose and ikeda were significantly higher (P<0.05) in imported cattle than those detected in native Pakistani bovines. DNA sequencing of amplicons of the conventional PCR revealed the presence of buffeli, chitose and ikeda genotypes of T. orientalis. Phylogenetic analysis revealed that the MPSP sequences of buffeli, chitose and ikeda from imported cattle were closely related to those sequences reported previously from Australia and other regions. This study provides the first survey of T. orientalis infection in imported and native bovines in Pakistan, and highlights the need for future studies to understand the spread of transboundary animal diseases. Copyright © 2016. Published by Elsevier B.V.

Experimental Test of Preferences for an Invasive Prey by an Endangered Predator: Implications for Conservation.

PubMed

Wilcox, Rebecca C; Fletcher, Robert J

2016-01-01

Identifying impacts of exotic species on native populations is central to ecology and conservation. Although the effects of exotic predators on native prey have received much attention, the role of exotic prey on native predators is poorly understood. Determining if native predators actively prefer invasive prey over native prey has implications for interpreting invasion impacts, identifying the presence of evolutionary traps, and predator persistence. One of the world's most invasive species, Pomacea maculata, has recently established in portions of the endangered Everglade snail kite's (Rostrhamus sociabilis plumbeus) geographic range. Although these exotic snails could provide additional prey resources, they are typically much larger than the native snail, which can lead to lower foraging success and the potential for diminished energetic benefits in comparison to native snails. Nonetheless, snail kites frequently forage on exotic snails. We used choice experiments to evaluate snail kite foraging preference in relation to exotic species and snail size. We found that snail kites do not show a preference for native or exotic snails. Rather, snail kites generally showed a preference for medium-sized snails, the sizes reflective of large native snails. These results suggest that while snail kites frequently forage on exotic snails in the wild, this behavior is likely driven simply by the abundance of exotic snails rather than snail kites preferring exotics. This lack of preference offers insights to hypotheses regarding effects of exotic species, guidance regarding habitat and invasive species management, and illustrates how native-exotic relationships can be misleading in the absence of experimental tests of such interactions.

Why Not Non-Native Varieties of English as Listening Comprehension Test Input?

ERIC Educational Resources Information Center

Abeywickrama, Priyanvada

2013-01-01

The existence of different varieties of English in target language use (TLU) domains calls into question the usefulness of listening comprehension tests whose input is limited only to a native speaker variety. This study investigated the impact of non-native varieties or accented English speech on test takers from three different English use…

Biotic resistance: Exclusion of native rodent consumers releases populations of a weak invader

Treesearch

Dean E. Pearson; Teal Potter; John L. Maron

2012-01-01

Biotic resistance is a commonly invoked hypothesis to explain why most exotic plant species naturalize at low abundance. Although numerous studies have documented negative impacts of native consumers on exotic plant performance, longer-term multi-generation studies are needed to understand how native consumer damage to exotics translates to their population-level...

Non-native plants and adaptive collaborative approaches to ecosystem restoration [Chapter 8

Treesearch

John Schelhas; James H. Miller; Jeanne C. Chambers

2012-01-01

Non-native invasive plant species (NNIPS) pose a serious socio-ecological challenge due to their potential to replace and damage critical human-sustaining ecosystems (OTA 1993; Mack et al. 2000; Pimentel 2002). The impacts of non-native species are widespread and significant - altering ecosystem structure and function, threatening other species, and imposing human...

Impact of native grasses and cheatgrass (Bromus tectorum) on Great Basin forb seedling growth

Treesearch

Hilary Parkinson; Cathy Zabinski; Nancy Shaw

2013-01-01

Re-establishing native communities that resist exotic weed invasion and provide diverse habitat for wildlife are high priorities for restoration in sagebrush ecosystems. Native forbs are an important component of healthy rangelands in this system, but they are rarely included in seedings. Understanding competitive interactions between forb and grass seedlings is...

Why I Can't Read Wallace Stegner and Other Essays: A Tribal Voice.

ERIC Educational Resources Information Center

Cook-Lynn, Elizabeth

In this collection of essays, a Native American feminist intellectual, poet, and literary scholar grapples with issues she encountered as a Native American in academia. The essays examine and criticize the enormous impact of America's media culture and ask questions about who is telling Native peoples' stories, where cultural authority lies, and…

Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

PubMed

Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

2013-01-01

Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies.

Commonly Rare and Rarely Common: Comparing Population Abundance of Invasive and Native Aquatic Species

PubMed Central

Hansen, Gretchen J. A.; Vander Zanden, M. Jake; Blum, Michael J.; Clayton, Murray K.; Hain, Ernie F.; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S.; McIntyre, Peter B.; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D.; Papeş, Monica; Sharma, Sapna

2013-01-01

Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

Community Impacts of Prosopis juliflora Invasion: Biogeographic and Congeneric Comparisons

PubMed Central

Kaur, Rajwant; Gonzáles, Wilfredo L.; Llambi, Luis Daniel; Soriano, Pascual J.; Callaway, Ragan M.; Rout, Marnie E.; Gallaher, Timothy J.; Inderjit

2012-01-01

We coordinated biogeographical comparisons of the impacts of an exotic invasive tree in its native and non-native ranges with a congeneric comparison in the non-native range. Prosopis juliflora is taxonomically complicated and with P. pallida forms the P. juliflora complex. Thus we sampled P. juliflora in its native Venezuela, and also located two field sites in Peru, the native range of Prosopis pallida. Canopies of Prosopis juliflora, a native of the New World but an invader in many other regions, had facilitative effects on the diversity of other species in its native Venezuela, and P. pallida had both negative and positive effects depending on the year, (overall neutral effects) in its native Peru. However, in India and Hawaii, USA, where P. juliflora is an aggressive invader, canopy effects were consistently and strongly negative on species richness. Prosopis cineraria, a native to India, had much weaker effects on species richness in India than P. juliflora. We carried out multiple congeneric comparisons between P. juliflora and P. cineraria, and found that soil from the rhizosphere of P. juliflora had higher extractable phosphorus, soluble salts and total phenolics than P. cineraria rhizosphere soils. Experimentally applied P. juliflora litter caused far greater mortality of native Indian species than litter from P. cineraria. Prosopis juliflora leaf leachate had neutral to negative effects on root growth of three common crop species of north-west India whereas P. cineraria leaf leachate had positive effects. Prosopis juliflora leaf leachate also had higher concentrations of total phenolics and L-tryptophan than P. cineraria, suggesting a potential allelopathic mechanism for the congeneric differences. Our results also suggest the possibility of regional evolutionary trajectories among competitors and that recent mixing of species from different trajectories has the potential to disrupt evolved interactions among native species. PMID:22984595

Local biotic adaptation of trees and shrubs to plant neighbors

USGS Publications Warehouse

Grady, Kevin C.; Wood, Troy E.; Kolb, Thomas E.; Hersch-Green, Erika; Shuster, Stephen M.; Gehring, Catherine A.; Hart, Stephen C.; Allan, Gerard J.; Whitham, Thomas G.

2017-01-01

Natural selection as a result of plant–plant interactions can lead to local biotic adaptation. This may occur where species frequently interact and compete intensely for resources limiting growth, survival, and reproduction. Selection is demonstrated by comparing a genotype interacting with con- or hetero-specific sympatric neighbor genotypes with a shared site-level history (derived from the same source location), to the same genotype interacting with foreign neighbor genotypes (from different sources). Better genotype performance in sympatric than allopatric neighborhoods provides evidence of local biotic adaptation. This pattern might be explained by selection to avoid competition by shifting resource niches (differentiation) or by interactions benefitting one or more members (facilitation). We tested for local biotic adaptation among two riparian trees, Populus fremontii and Salix gooddingii, and the shrub Salix exigua by transplanting replicated genotypes from multiple source locations to a 17 000 tree common garden with sympatric and allopatric treatments along the Colorado River in California. Three major patterns were observed: 1) across species, 62 of 88 genotypes grew faster with sympatric neighbors than allopatric neighbors; 2) these growth rates, on an individual tree basis, were 44, 15 and 33% higher in sympatric than allopatric treatments for P. fremontii, S. exigua and S. gooddingii, respectively, and; 3) survivorship was higher in sympatric treatments for P. fremontiiand S. exigua. These results support the view that fitness of foundation species supporting diverse communities and dominating ecosystem processes is determined by adaptive interactions among multiple plant species with the outcome that performance depends on the genetic identity of plant neighbors. The occurrence of evolution in a plant-community context for trees and shrubs builds on ecological evolutionary research that has demonstrated co-evolution among herbaceous taxa, and evolution of native species during exotic plants invasion, and taken together, refutes the concept that plant communities are always random associations.

Molecular identification of the Cryptosporidium deer genotype in the Hokkaido sika deer (Cervus nippon yesoensis) in Hokkaido, Japan.

PubMed

Kato, Satomi; Yanagawa, Yojiro; Matsuyama, Ryota; Suzuki, Masatsugu; Sugimoto, Chihiro

2016-04-01

The protozoan Cryptosporidium occurs in a wide range of animal species including many Cervidae species. Fecal samples collected from the Hokkaido sika deer (Cervus nippon yesoensis), a native deer of Hokkaido, in the central, western, and eastern areas of Hokkaido were examined by polymerase chain reaction (PCR) to detect infections with Cryptosporidium and for sequence analyses to reveal the molecular characteristics of the amplified DNA. DNA was extracted from 319 fecal samples and examined with PCR using primers for small-subunit ribosomal RNA (SSU-rRNA), actin, and 70-kDa heat shock protein (HSP70) gene loci. PCR-amplified fragments were sequenced and phylogenetic trees were created. In 319 fecal samples, 25 samples (7.8 %) were positive with SSU-rRNA PCR that were identified as the Cryptosporidium deer genotype. Among Cryptosporidium-positive samples, fawns showed higher prevalence (16.1 %) than yearlings (6.4 %) and adults (4.7 %). The result of Fisher's exact test showed a statistical significance in the prevalence of the Cryptosporidium deer genotype between fawn and other age groups. Sequence analyses with actin and HSP70 gene fragments confirmed the SSU-rRNA result, and there were no sequence diversities observed. The Cryptosporidium deer genotype appears to be the prevalent Cryptosporidium species in the wild sika deer in Hokkaido, Japan.

Effect of co-inoculation with mycorrhiza and rhizobia on the nodule trehalose content of different bean genotypes.

PubMed

Ballesteros-Almanza, L; Altamirano-Hernandez, J; Peña-Cabriales, J J; Santoyo, G; Sanchez-Yañez, J M; Valencia-Cantero, E; Macias-Rodriguez, L; Lopez-Bucio, J; Cardenas-Navarro, R; Farias-Rodriguez, R

2010-08-17

Studies on Rhizobium-legume symbiosis show that trehalose content in nodules under drought stress correlates positively with an increase in plant tolerance to this stress. Fewer reports describe trehalose accumulation in mycorrhiza where, in contrast with rhizobia, there is no flux of carbohydrates from the microsymbiont to the plant. However, the trehalose dynamics in the Mycorrhiza-Rhizobium-Legume tripartite symbiosis is unknown. The present study explores the role of this tripartite symbiosis in the trehalose content of nodules grown under contrasting moisture conditions. Three wild genotypes (P. filiformis, P. acutifolis and P. vulgaris) and two commercial genotypes of Phaseolus vulgaris (Pinto villa and Flor de Mayo) were used. Co-inoculation treatments were conducted with Glomus intraradices and a mixture of seven native rhizobial strains, and trehalose content was determined by GC/MS. The results showed a negative effect of mycorrhizal inoculation on nodule development, as mycorrhized plants showed fewer nodules and lower nodule dry weight compared to plants inoculated only with Rhizobium. Mycorrhizal colonization was also higher in plants inoculated only with Glomus as compared to plants co-inoculated with both microsymbionts. In regard to trehalose, co-inoculation negatively affects its accumulation in the nodules of each genotype tested. However, the correlation analysis showed a significantly positive correlation between mycorrhizal colonization and nodule trehalose content.

Short-term impacts of soil amendments on belowground C cycling and soil nutrition in two contrasting Pinus taeda L. genotypes

Treesearch

Michael C Tyree; John R Seiler; Christopher Maier

2011-01-01

We monitored two Pinus taeda L. genotypes, planted in 170 L lysimeters, subjected to different combinations of fertilization and logging residue (LR) incorporation for 1 year. The objectives were to elucidate how soil amendments modified soil biological properties and belowground C cycling, and secondly, to determine if planting of contrasting genotypes have a...

Effects on nonnative fishes on wilderness lake ecosystems in the Sierra Nevada and recommendations for reducing impacts

Treesearch

R. A. Knapp; Kathleen R. Matthews

2000-01-01

Wilderness areas of the Sierra Nevada, California contain thousands of lakes and ponds, nearly all of which were historically fishless. After more than a century of fish stocking, introduced trout are now present in up to 80% of larger lakes. These nonnative fishes have had profound impacts on native fishes, amphibians, and invertebrates. Several of these native...

[Differential impact of social capital on mental health in the native-born and immigrant populations living in Catalonia (Spain)].

PubMed

Stoyanova, Alexandrina; Díaz-Serrano, Luis

2009-12-01

This study attempts to create a bridge between the literature on immigration and on social capital and health. The objectives were two-fold: firstly, to provide new empirical evidence on the association between social capital and health, using data from Catalonia for the first time and, secondly, to explore the possible existence of a differential impact of social capital on health between native-born residents and immigrants. We also distinguished between individual and community-level social capital. We used the 2006 Catalan Health Survey (ESCA 2006). To assess the relationship between social capital and mental health, we used multilevel models, estimated separately for native-born and immigrant residents. The results revealed a positive link between social capital and good mental health in Catalonia. However, this effect was stronger for individual than for community-level social capital. The results did not support the hypothesis of a differential impact between immigrants and native-born Catalans, but did indicate differences with respect to Spaniards born outside Catalonia. Geographic heterogeneity in the effect of individual social capital on mental health in both immigrants and native-born residents was also detected. We believe that enhancing social capital could potentially be an effective policy tool to achieve objectives related to health status improvement.

A critical functional missense mutation (H173R) in the bovine PROP1 gene significantly affects growth traits in cattle.

PubMed

Pan, Chuanying; Wu, Chongyang; Jia, Wenchao; Xu, Yao; Lei, Chuzhao; Hu, Shenrong; Lan, Xianyong; Chen, Hong

2013-12-01

The PROP1 protein, encoded by the prophet of Pit-1 (PROP1) gene, exhibits both DNA-binding and transcriptional activation abilities. Its expression leads to the ontogenesis of growth hormone (GH), prolactin (PRL), thyroid-stimulating hormone (TSH), and pituitary hormone. The missense mutation H173R in PROP1 may result in deficiencies of GH, PRL, TSH, and Pit-1, thereby affecting growth traits. The objective of this study was to characterize the H173R mutation within the PROP1 gene and examine its associations with growth traits in cattle. Accordingly, the H173R mutation was genotyped in 1207 cows belonging to five Chinese native breeds. Three genotypes were identified among the specimens, with genotype AA being the major one. Consequently, the "G" allele was the minor allele. Association testing revealed that the H173R mutation was significantly associated with body weight, average daily weight gain and physical parameters in the analyzed breeds. Interestingly, the cows with genotype AG and/or AA had superior growth traits compared with those expressing the GG genotype, in all tested breeds. These findings revealed that the "A" allele had positive effects on growth traits, which was consistent with the increasing binding ability and enhanced activation capacity associated with the bovine isoform PROP1-173H, representing the "A" allele. Therefore, the H173R mutation can be considered as a DNA marker for selecting individuals with superior growth traits, thereby contributing to research on breeding and genetics in the beef industry. © 2013.

Genotype-by-environment interactions leads to variable selection on life-history strategy in Common Evening Primrose (Oenothera biennis).

PubMed

Johnson, M T J

2007-01-01

Monocarpic plant species, where reproduction is fatal, frequently exhibit variation in the length of their prereproductive period prior to flowering. If this life-history variation in flowering strategy has a genetic basis, genotype-by-environment interactions (G x E) may maintain phenotypic diversity in flowering strategy. The native monocarpic plant Common Evening Primrose (Oenothera biennis L., Onagraceae) exhibits phenotypic variation for annual vs. biennial flowering strategies. I tested whether there was a genetic basis to variation in flowering strategy in O. biennis, and whether environmental variation causes G x E that imposes variable selection on flowering strategy. In a field experiment, I randomized more than 900 plants from 14 clonal families (genotypes) into five distinct habitats that represented a natural productivity gradient. G x E strongly affected the lifetime fruit production of O. biennis, with the rank-order in relative fitness of genotypes changing substantially between habitats. I detected genetic variation in annual vs. biennial strategies in most habitats, as well as a G x E effect on flowering strategy. This variation in flowering strategy was correlated with genetic variation in relative fitness, and phenotypic and genotypic selection analyses revealed that environmental variation resulted in variable directional selection on annual vs. biennial strategies. Specifically, a biennial strategy was favoured in moderately productive environments, whereas an annual strategy was favoured in low-productivity environments. These results highlight the importance of variable selection for the maintenance of genetic variation in the life-history strategy of a monocarpic plant.

Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs.

PubMed

Hao, Wei-Qi; Liu, Jing; Jiang, Li; Han, Jun-Ping; Wang, Ling; Li, Jiu-Ling; Ma, Quan; Liu, Chao; Wang, Hui-Jun; Li, Cai-Xia

2018-06-07

Inferring an unknown DNA's ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.

The impact of the catechol-O-methyltransferase genotype on vascular function and blood pressure after acute green tea ingestion.

PubMed

Miller, Rosalind J; Jackson, Kim G; Dadd, Tony; Mayes, Andrew E; Brown, A Louise; Lovegrove, Julie A; Minihane, Anne M

2012-06-01

Evidence for the benefits of green tea catechins on vascular function is inconsistent, with genotype potentially contributing to the heterogeneity in response. Here, the impact of the catechol-O-methyltransferase (COMT) genotype on vascular function and blood pressure (BP) after green tea extract ingestion are reported. Fifty subjects (n = 25 of the proposed low-activity [AA] and of the high-activity [GG] COMT rs4680 genotype), completed a randomized, double-blind, crossover study. Peripheral arterial tonometry, digital volume pulse (DVP), and BP were assessed at baseline and 90 min after 1.06 g of green tea extract or placebo. A 5.5 h and subsequent 18.5 h urine collection was performed to assess green tea catechin excretion. A genotype × treatment interaction was observed for DVP reflection index (p = 0.014), with green tea extract in the AA COMT group attenuating the increase observed with placebo. A tendency for a greater increase in diastolic BP was evident at 90 min after the green tea extract compared to placebo (p = 0.07). A genotypic effect was observed for urinary methylated epigallocatechin during the first 5.5 h, with the GG COMT group demonstrating a greater concentration (p = 0.049). Differences in small vessel tone according to COMT genotype were evident after acute green tea extract. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional Variants in MBL2 Are Associated With Type 2 Diabetes and Pre-Diabetes Traits in Pima Indians and the Old Order Amish

PubMed Central

Muller, Yunhua L.; Hanson, Robert L.; Bian, Li; Mack, Janel; Shi, Xiaolian; Pakyz, Ruth; Shuldiner, Alan R.; Knowler, William C.; Bogardus, Clifton; Baier, Leslie J.

2010-01-01

OBJECTIVE MBL2 encodes the mannose-binding lectin, which is a key player in the innate immune system and has recently been found to play a role in insulin resistance and development of type 1 diabetes and gestational diabetes mellitus. To assess the role of MBL2 in diabetes susceptibility, this gene was analyzed in the Pima Indian population, which has a high prevalence of type 2 diabetes. RESEARCH DESIGN AND METHODS Nineteen tag single nucleotide polymorphisms (SNPs) were genotyped in a population-based sample of 3,501 full-heritage Pima Indians, and selected SNPs were further genotyped in independent samples of Native American (n = 3,723) and Old Order Amish (n = 486) subjects. RESULTS Two variants, a promoter SNP (rs11003125) at −550 bp with a risk allele frequency of 0.77 and a Gly54Asp (rs1800450) with a risk allele frequency of 0.83, were associated with type 2 diabetes in the full-heritage Pima Indians (odds ratio 1.30 per copy of the G allele for rs1103125, P = 0.0007, and 1.30 per copy of the glycine allele for rs1800450, P = 0.002, adjusted for age, sex, birth year, and family membership). These associations replicated in an independent Native American sample (1.19, P = 0.04, for rs11003125) and a Caucasian sample, the Old Order Amish (1.51, P = 0.004, for rs1103125 and 2.38, P = 0.003, for rs1800450). Among Pima Indians with normal glucose tolerance, the diabetes risk allele glycine of Gly54Asp was associated with a decreased acute insulin response to an intravenous glucose bolus infusion (P = 0.004, adjusted for age, sex, percent body fat, glucose disposal under physiological insulin stimulation, and family membership). CONCLUSIONS Our data suggest that the functional variants in MBL2 contribute to type 2 diabetes susceptibility in both Native Americans and the Old Order Amish. PMID:20522590

Self-reinforcing impacts of plant invasions change over time.

PubMed

Yelenik, Stephanie G; D'Antonio, Carla M

2013-11-28

Returning native species to habitats degraded by biological invasions is a critical conservation goal. A leading hypothesis poses that exotic plant dominance is self-reinforced by impacts on ecosystem processes, leading to persistent stable states. Invaders have been documented to modify fire regimes, alter soil nutrients or shift microbial communities in ways that feed back to benefit themselves over competitors. However, few studies have followed invasions through time to ask whether ecosystem impacts and feedbacks persist. Here we return to woodland sites in Hawai'i Volcanoes National Park that were invaded by exotic C4 grasses in the 1960s, the ecosystem impacts of which were studied intensively in the 1990s. We show that positive feedbacks between exotic grasses and soil nitrogen cycling have broken down, but rather than facilitating native vegetation, the weakening feedbacks facilitate new exotic species. Data from the 1990s showed that exotic grasses increased nitrogen-mineralization rates by two- to fourfold, but were nitrogen-limited. Thus, the impacts of the invader created a positive feedback early in the invasion. We now show that annual net soil nitrogen mineralization has since dropped to pre-invasion levels. In addition, a seedling outplanting experiment that varied soil nitrogen and grass competition demonstrates that the changing impacts of grasses do not favour native species re-establishment. Instead, decreased nitrogen availability most benefits another aggressive invader, the nitrogen-fixing tree Morella faya. Long-term studies of invasions may reveal that ecosystem impacts and feedbacks shift over time, but that this may not benefit native species recovery.

Development of ten microsatellite loci in the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822

USGS Publications Warehouse

Morrison, Cheryl L.; Springmann, Marcus J.; Iwanowicz, Deborah D.; Wade, Christopher M.

2015-01-01

A suite of tetra-nucleotide microsatellite loci were developed for the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822, from Ion Torrent next-generation sequencing data. Ten of the 96 primer sets tested amplified consistently in 30 snails from Miami, Florida, plus 12 individuals representative of their native East Africa, Indian and Pacific Ocean regions. The loci displayed moderate levels of allelic diversity (average 5.6 alleles/locus) and heterozygosity (average 42 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring among regional samples. The invasive A. fulica can cause extensive damage to important food crops and natural resources, including native flora and fauna. The loci characterized here will be useful for determining the origins and tracking the spread of invasions, detecting fine-scale spatial structuring and estimating demographic parameters.

Phytoremediation potential and ecological and phenological changes of native pioneer plants from weathered oil spill-impacted sites at tropical wetlands.

PubMed

Palma-Cruz, Felipe de J; Pérez-Vargas, Josefina; Rivera Casado, Noemí Araceli; Gómez Guzmán, Octavio; Calva-Calva, Graciano

2016-08-01

Pioneer native plant species from weathered oil spill-affected sites were selected to study their potential for phytoremediation on the basis of their ecological and phenological changes during the phytoremediation process. Experiments were conducted in field and in greenhouse. In field, native plants from aged oil spill-impacted sites with up 400 g of weathered petroleum hydrocarbons per kilogram soil were selected. In the impacted sites, the principal dominant plant species with potential for hydrocarbons removal were Cyperus laxus, Cyperus esculentus, and Ludwigia peploides. In greenhouse, the phenology of the selected plant species was drastically affected by the hydrocarbons level above 325 g total petroleum hydrocarbons (TPH) per kilogram soil after 2 years of phytoremediation of soils from the aged oil spill-impacted sites. From the phytoremediation treatments, a mix-culture of C. laxus, C. esculentus, and L. peploides in soil containing 325 g TPH/kg soil, from which 20.3 % were polyaromatic hydrocarbons (PAH) and 34.2 % were asphaltenes (ASF), was able to remove up 93 % of the TPH, while in unvegetated soil the TPH removal was 12.6 %. Furthermore, evaluation of the biodiversity and life forms of plant species in the impacted sites showed that phytoremediation with C. esculentus, alone or in a mix-culture with C. laxus and L. peploides, reduces the TPH to such extent that the native plant community was progressively reestablished by replacing the cultivated species resulting in the ecological recovery of the affected soil. These results demonstrate that native Cyperus species from weathered oil spill-affected sites, specifically C. esculentus and C. laxus, alone or in a mix-culture, have particular potential for phytoremediation of soils from tropical wetlands contaminated with weathered oil hydrocarbons.

Environmental Impact and Relative Invasiveness of Free-Roaming Domestic Carnivores—a North American Survey of Governmental Agencies

PubMed Central

Lepe, Ana; Kaplan, Valerie; Arreaza, Alirio; Szpanderfer, Robert; Bristol, David; Sinclair, M. Scott

2017-01-01

Simple Summary This paper reports on a survey that explores the impact of three non-native domestic carnivores—dogs, cats, and ferrets—on the native wildlife of the United States (US) and Canada. Government agencies were asked to document the number and frequency of sightings, and the degree of concern resulting from free-roaming animals on urban, suburban, rural, recreational areas, and wildlands in their jurisdictions. Results confirm the existence of free-roaming cats and dogs throughout North America, as well as their profound impact on native wildlife, with cats being the major offenders. Except for an occasional stray, free-roaming ferrets were “never” or “rarely seen”; no agency reported that ferrets caused environmental harm. This is the first study to compare the relative impact of free-roaming dogs, cats, and ferrets. It shows differences in how these three animals react to novel environments. For the US and Canada, free roaming cats and dogs meet the definition of an “invasive” species, whereas ferrets do not. However, the way we as a society view these animals, our attitudes and perceptions, may influence how governmental agencies manage and control them. Abstract A survey of the United States and Canadian governmental agencies investigated the environmental impact and relative invasiveness of free-roaming domestic non-native carnivores—dogs, cats, and ferrets. Agencies represented wildlife, fish, game, natural or environmental resources, parks and recreation, veterinary and human health, animal control, and agriculture. Respondents were asked to document the number and frequency of sightings of unconfined animals, evidence for environmental harm, and the resulting “degree of concern” in their respective jurisdictions. Results confirmed the existence of feral (breeding) cats and dogs, documenting high levels of concern regarding the impact of these animals on both continental and surrounding insular habitats. Except for occasional strays, no free-roaming or feral ferrets were reported; nor were there reports of ferrets impacting native wildlife, including ground-nesting birds, or sensitive species. This is the first study to report the relative impact of free-roaming domestic carnivores. Dogs and cats meet the current definition of “invasive” species, whereas ferrets do not. Differences in how each species impacts the North American environment highlights the complex interaction between non-native species and their environment. Public attitudes and perceptions regarding these species may be a factor in their control and agency management priorities. PMID:29036923

An invasive foundation species enhances multifunctionality in a coastal ecosystem.

PubMed

Ramus, Aaron P; Silliman, Brian R; Thomsen, Mads S; Long, Zachary T

2017-08-08

While invasive species often threaten biodiversity and human well-being, their potential to enhance functioning by offsetting the loss of native habitat has rarely been considered. We manipulated the abundance of the nonnative, habitat-forming seaweed Gracilaria vermiculophylla in large plots (25 m 2 ) on southeastern US intertidal landscapes to assess impacts on multiple ecosystem functions underlying coastal ecosystem services. We document that in the absence of native habitat formers, this invasion has an overall positive, density-dependent impact across a diverse set of ecosystem processes (e.g., abundance and richness of nursery taxa, flow attenuation). Manipulation of invader abundance revealed both thresholds and saturations in the provisioning of ecosystem functions. Taken together, these findings call into question the focus of traditional invasion research and management that assumes negative effects of nonnatives, and emphasize the need to consider context-dependence and integrative measurements when assessing the impact of an invader, including density dependence, multifunctionality, and the status of native habitat formers. This work supports discussion of the idea that where native foundation species have been lost, invasive habitat formers may be considered as sources of valuable ecosystem functions.

Ectotherms in Variable Thermal Landscapes: A Physiological Evaluation of the Invasive Potential of Fruit Flies Species

PubMed Central

Boher, Francisca; Trefault, Nicole; Estay, Sergio A.; Bozinovic, Francisco

2016-01-01

Climate change and biological invasions pose one of the greatest threats to biodiversity. Most analyses of the potential biological impacts have focused on changes in mean temperature, but changes in thermal variance may also impact native and invasive organisms, although differentially. We assessed the combined effects of the mean and the variance of temperature on the expression of heat shock protein (hsp90) in adults of the invasive fruit fly Drosophila melanogaster and the native Drosophila gaucha in Mediterranean habitats of central Chile. We observed that, under these experimental conditions, hsp90 mRNA expression was higher in the invasive species but absent in the native one. Apparently, the biogeographic origin and niche conservatisms are playing a role in the heat shock response of these species under different putative scenarios of climate change. We suggest that in order to develop more realistic predictions about the biological impact of climate change and biological invasions, one must consider the interactions between the mean and variance of climatic variables, as well as the evolutionary original conditions of the native and invasive species. PMID:27486407

Genomic replacement of native Cobitis lutheri with introduced C. tetralineata through a hybrid swarm following the artificial connection of river systems

PubMed Central

Kwan, Ye-Seul; Ko, Myeong-Hun; Won, Yong-Jin

2014-01-01

River connections via artificial canals will bring about secondary contacts between previously isolated fish species. Here, we present a genetic consequence of such a secondary contact between Cobitis fish species, C. lutheri in the Dongjin River, and C. tetralineata in the Seomjin River in Korea. The construction of water canals about 80 years ago has unidirectionally introduced C. tetralineata into the native habitat of C. lutheri, and then these species have hybridized in the main stream section of the Dongjin River. According to the divergence population genetic analyses of DNA sequence data, the two species diverged about 3.3 million years ago, which is interestingly coincident with the unprecedented paleoceanographic change that caused isolations of the paleo-river systems in northeast Asia due to sea-level changes around the late Pliocene. Multilocus genotypic data of nine microsatellites and three nuclear loci revealed an extensively admixed structure in the hybrid zone with a high proportion of various post-F1 hybrids. Surprisingly, pure native C. lutheri was absent in the hybrid zone in contrast to the 7% of pure C. tetralineata. Such a biased proportion must have resulted from the dominant influence of continually introducing C. tetralineata on the native C. lutheri which has no supply of natives from other tributaries to the hybrid zone due to numerous low-head dams. In addition, mating experiments indicated that there is no discernible reproductive isolation between them. All the results suggest that the gene pool of native C. lutheri is being rapidly replaced by that of continually introducing C. tetralineata through a hybrid swarm for the last 80 years, which will ultimately lead to the genomic extinction of natives in this hybrid zone. PMID:24834340

Analysis of Plant Growth-Promoting Effects of Fluorescent Pseudomonas Strains Isolated from Mentha piperita Rhizosphere and Effects of Their Volatile Organic Compounds on Essential Oil Composition

PubMed Central

Santoro, Maricel V.; Bogino, Pablo C.; Nocelli, Natalia; Cappellari, Lorena del Rosario; Giordano, Walter F.; Banchio, Erika

2016-01-01

Many species or strains of the genus Pseudomonas have been characterized as plant growth promoting rhizobacteria (PGPR). We used a combination of phenotypic and genotypic techniques to analyze the community of fluorescent Pseudomonas strains in the rhizosphere of commercially grown Mentha piperita (peppermint). Biochemical techniques, Amplified rDNA Restriction Analysis (ARDRA), and 16S rRNA gene sequence analysis revealed that the majority of the isolated native fluorescent strains were P. putida. Use of two Repetitive Sequence-based PCR (rep-PCR) techniques, BOX-PCR and ERIC-PCR, allowed us to evaluate diversity among the native strains and to more effectively distinguish among them. PGPR activity was tested for the native strains and reference strain P. fluorescens WCS417r. Micropropagated M. piperita plantlets were exposed to microbial volatile organic compounds (mVOCs) emitted by the bacterial strains, and plant biomass parameters and production of essential oils (EOs) were measured. mVOCs from 11 of the native strains caused an increase in shoot fresh weight. mVOCs from three native strains (SJ04, SJ25, SJ48) induced changes in M. pierita EO composition. The mVOCs caused a reduction of metabolites in the monoterpene pathway, for example menthofuran, and an increase in menthol production. Menthol production is the primary indicator of EO quality. The mVOCs produced by native strains SJ04, SJ25, SJ48, and strain WCS417r were analyzed. The obtained mVOC chromatographic profiles were unique for each of the three native strains analyzed, containing varying hydrocarbon, aromatic, and alogenic compounds. The differential effects of the strains were most likely due to the specific mixtures of mVOCs emitted by each strain, suggesting a synergistic effect occurs among the compounds present. PMID:27486441

Environmentally induced development costs underlie fitness tradeoffs.

PubMed

Walter, Greg M; Wilkinson, Melanie J; Aguirre, J David; Blows, Mark W; Ortiz-Barrientos, Daniel

2018-06-01

Local adaptation can lead to genotype-by-environment interactions, which can create fitness tradeoffs in alternative environments, and govern the distribution of biodiversity across geographic landscapes. Exploring the ecological circumstances that promote the evolution of fitness tradeoffs requires identifying how natural selection operates and during which ontogenetic stages natural selection is strongest. When organisms disperse to areas outside their natural range, tradeoffs might emerge when organisms struggle to reach key life history stages, or alternatively, die shortly after reaching life history stages if there are greater risks of mortality associated with costs to developing in novel environments. We used multiple populations from four ecotypes of an Australian native wildflower (Senecio pinnatifolius) in reciprocal transplants to explore how fitness tradeoffs arise across ontogeny. We then assessed whether the survival probability for plants from native and foreign populations was contingent on reaching key developmental stages. We found that fitness tradeoffs emerged as ontogeny progressed when native plants were more successful than foreign plants at reaching seedling establishment and maturity. Native and foreign plants that failed to reach seedling establishment died at the same rate, but plants from foreign populations died quicker than native plants after reaching seedling establishment, and died quicker regardless of whether they reached sexual maturity or not. Development rates were similar for native and foreign populations, but changed depending on the environment. Together, our results suggest that natural selection for environment-specific traits early in life history created tradeoffs between contrasting environments. Plants from foreign populations were either unable to develop to seedling establishment, or they suffered increased mortality as a consequence of reaching seedling establishment. The observation of tradeoffs together with environmentally dependent changes in development rate suggest that foreign environments induce organisms to develop at a rate different from their native habitat, incurring consequences for lifetime fitness and population divergence. © 2018 by the Ecological Society of America.

Mitigating exotic impacts: restoring native deer mouse populations elevated by an exotic food subsidy

Treesearch

Dean E. Pearson; Robert J. Fletcher

2008-01-01

The threat posed by exotic organisms to native systems has led to extensive research on exotic invaders, yet management of invasives has progressed relatively slowly. This is partly due to poor understanding of how exotic species management influences native organisms. To address this shortfall, we experimentally evaluated the efficacy of an invasives management tool...

Significant Impact of Environment Regarding Eligibility of Native American and Alaskan Native Students for ESEA Title VII Regulations.

ERIC Educational Resources Information Center

Travis, Michael

Early Russian religious and educational influences on the 20 various Alaskan Native languages are described, followed by those of American origin in schools and religious groups after the American purchase in 1867, all of which show the development of diglossia and language shifts. The present dual educational system, which includes state schools…

The Power of Protection: A Population-Based Comparison of Native and Non-Native Youth Suicide Attempters

ERIC Educational Resources Information Center

Mackin, Juliette; Perkins, Tamara; Furrer, Carrie

2012-01-01

This study provides actionable information about intervening with American Indian/Alaska Native (AI/AN) youth to prevent suicide. Statewide school survey data were used to model the impact of risk and protective factors on self-reported suicide attempts (both AI/AN and non-AI/AN). The cumulative risk and protective model worked similarly for both…

Maynard Participation in Alaska Forum on the Environment Panel Discussion on Increasing Input to the US National Climate Assessment (NCA) and the Intergovernmental Panel on Climate Change (IPCC) Processes from Alaska, with Emphasis on Indigenous Peoples Issues

NASA Technical Reports Server (NTRS)

Maynard, Nancy G.

2012-01-01

Dr. Nancy Maynard was invited by the Alaska Forum on the Environment to participate in a Panel Discussion to discuss (1) background about what the US NCA and International IPCC assessments are, (2) the impact the assessments have on policy-making, (3) the process for participation in both assessments, (4) how we can increase participation by Indigenous Peoples such as Native Americans and Alaska Natives, (5) How we can increase historical and current impacts input from Native communities through stories, oral history, "grey" literature, etc. The session will be chaired by Dr. Bull Bennett, a cochair of the US NCA's chapter on "Native and Tribal Lands and Resources" and Dr. Maynard is the other co-chair of that chapter and they will discuss the latest activities under the NCA process relevant to Native Americans and Alaska Natives. Dr. Maynard is also a Lead Author of the "Polar Regions" chapter of the IPCC WG2 (5th Assessment) and she will describes some of the latest approaches by the IPCC to entrain more Indigenous peoples into the IPCC process.

Apolipoprotein E isoforms 3/3 and 3/4 differentially interact with circulating stearic, palmitic, and oleic fatty acids and lipid levels in Alaskan Natives.

PubMed

Castellanos-Tapia, Lyssia; López-Alvarenga, Juan Carlos; Ebbesson, Sven O E; Ebbesson, Lars O E; Tejero, M Elizabeth

2015-04-01

Lifestyle changes in Alaskan Natives have been related to the increase of cardiovascular disease and metabolic syndrome in the last decades. Variation of the apolipoprotein E (Apo E) genotype may contribute to the diverse response to diet in lipid metabolism and influence the association between fatty acids in plasma and risk factors for cardiovascular disease. The aim of this investigation was to analyze the interaction between Apo E isoforms and plasma fatty acids, influencing phenotypes related to metabolic diseases in Alaskan Natives. A sample of 427 adult Siberian Yupik Alaskan Natives was included. Fasting glucose, total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglycerides, Apo A1, and Apo B plasma concentrations were measured using reference methods. Concentrations of 13 fatty acids in fasting plasma were analyzed by gas chromatography, and Apo E variants were identified. Analyses of covariance were conducted to identify Apo E isoform and fatty acid main effects and multiplicative interactions. The means for body mass index and age were 26 ± 5.2 and 47 ± 1.5, respectively. Significant main effects were observed for variation in Apo E and different fatty acids influencing Apo B levels, triglycerides, and total cholesterol. Significant interactions were found between Apo E isoform and selected fatty acids influencing total cholesterol, triglycerides, and Apo B concentrations. In summary, Apo E3/3 and 3/4 isoforms had significant interactions with circulating levels of stearic, palmitic, oleic fatty acids, and phenotypes of lipid metabolism in Alaskan Natives. Copyright © 2015 Elsevier Inc. All rights reserved.

Association between endothelial nitric oxide synthase (ENOS) G894T polymorphism and high altitude (HA) adaptation: a meta-analysis.

PubMed

Lu, Hong-xiang; Wang, Yu-xiao; Chen, Yu; Luo, Yong-jun

2015-11-01

Highland natives adapt well to the hypoxic environment at high altitude (HA). Several genes have been reported to be linked to HA adaptation. Previous studies showed that the endothelial ni- tric oxide synthase (ENOS) G894T polymorphism contributed to the physiology and pathophysiology of hu- mans at HA by regulating the production of NO. In this meta-analysis, we evaluate the association between the ENOS G894T polymorphism and HA adaptation through analyzing the published data. We searched all relevant literature about the ENOS G894T polymorphism and HA adaptation in PubMed, Med- line, and Embase before Step 2015. A random-effects model was applied (Revman 5.0), and study quality was assessed in duplicate. Six studies with 634 HA native cases and 621 low-altitude controls were included in this meta-analysis. From the results, we observed that the wild-type allele G was significantly overrepresented in the HA groups (OR = 1.85; 95% Cl, 1.47-2.33; P < 0.0001). In addition, the GG genotype was significantly associated with HA adaptation (OR = 1.99; 95% Cl, 1.54-2.57; P < 0.0001). Our results showed that in 894 G allele carriers, the GG genotype might be a beneficial factor for HA adaptation through enhancing the level of NO. However, more studies were needed to confirm our findings due to the limited sample size.

Interactive effects of deer exclusion and exotic plant removal on deciduous forest understory communities

USGS Publications Warehouse

Bourg, Norman; McShea, William J.; Herrmann, Valentine; Stewart, Chad M.

2017-01-01

Mammalian herbivory and exotic plant species interactions are an important ongoing research topic, due to their presumed impacts on native biodiversity. The extent to which these interactions affect forest understory plant community composition and persistence was the subject of our study. We conducted a 5-year, 2 × 2 factorial experiment in three mid-Atlantic US deciduous forests with high densities of white-tailed deer (Odocoileus virginianus) and exotic understory plants. We predicted: (i) only deer exclusion and exotic plant removal in tandem would increase native plant species metrics; and (ii) deer exclusion alone would decrease exotic plant abundance over time. Treatments combining exotic invasive plant removal and deer exclusion for plots with high initial cover, while not differing from fenced or exotic removal only plots, were the only ones to exhibit positive richness responses by native herbaceous plants compared to control plots. Woody seedling metrics were not affected by any treatments. Deer exclusion caused significant increases in abundance and richness of native woody species >30 cm in height. Abundance changes in two focal members of the native sapling community showed that oaks (Quercus spp.) increased only with combined exotic removal and deer exclusion, while shade-tolerant maples (Acer spp.) showed no changes. We also found significant declines in invasive Japanese stiltgrass (Microstegium vimineum) abundance in deer-excluded plots. Our study demonstrates alien invasive plants and deer impact different components and life-history stages of the forest plant community, and controlling both is needed to enhance understory richness and abundance. Alien plant removal combined with deer exclusion will most benefit native herbaceous species richness under high invasive cover conditions while neither action may impact native woody seedlings. For larger native woody species, only deer exclusion is needed for such increases. Deer exclusion directly facilitated declines in invasive species abundance. Resource managers should consider addressing both factors to achieve their forest management goals.

No universal scale-dependent impacts of invasive species on native plant species richness.

PubMed

Stohlgren, Thomas J; Rejmánek, Marcel

2014-01-01

A growing number of studies seeking generalizations about the impact of plant invasions compare heavily invaded sites to uninvaded sites. But does this approach warrant any generalizations? Using two large datasets from forests, grasslands and desert ecosystems across the conterminous United States, we show that (i) a continuum of invasion impacts exists in many biomes and (ii) many possible species-area relationships may emerge reflecting a wide range of patterns of co-occurrence of native and alien plant species. Our results contradict a smaller recent study by Powell et al. 2013 (Science 339, 316-318. (doi:10.1126/science.1226817)), who compared heavily invaded and uninvaded sites in three biomes and concluded that plant communities invaded by non-native plant species generally have lower local richness (intercepts of log species richness-log area regression lines) but steeper species accumulation with increasing area (slopes of the regression lines) than do uninvaded communities. We conclude that the impacts of plant invasions on plant species richness are not universal.

Impacts of the Invasive European Red Ant (Myrmica rubra (L.): Hymenoptera; Formicidae) on a Myrmecochorous System in the Northeastern United States.

PubMed

Gammans, Nicola; Drummond, Frank; Groden, Eleanor

2018-05-16

We investigated the impact of an invasive ant species from Europe, Myrmica rubra (L.), on a myrmecochorous system (seeds dispersed by ants) in its invaded range in North America. We assessed: 1) how M. rubra process the myrmecochorous diapsores (seeds and elaiosome as a single dispersal unit transported by ants) in comparison with native ants; 2) its preference for common native and invasive diaspore species relative to native ants; 3) how far they disperse diaspores in the field; and 4) the diaspore removal rate by invertebrates and vertebrates in infested areas compared to noninvaded sites. Field experiments demonstrated higher diaspore removal rates over a 10-min and 24-h period by M. rubra compared to native ants. M. rubra's diaspore dispersal distance was 40% greater compared to native ants. In two of three laboratory studies and one field study, there was no significant difference between the seed species which M. rubra and native ants selected. Our data suggest no long-term deleterious effects of M. rubra's invasion on diaspore dispersal in the Maine plant community that is comprised of both native and invasive species. This implies that M. rubra benefits from the myrmechorous plant species' diaspores by increasing their dispersal range away from the parent plant and potentially reducing seed predation. However, it is not known whether the fact that the native ant fauna and M. rubra are attracted to the same plant species' diaspores creates a high level of competition between the ants with deleterious effects on the native ant community.

Reconstructing Native American population history.

PubMed

Reich, David; Patterson, Nick; Campbell, Desmond; Tandon, Arti; Mazieres, Stéphane; Ray, Nicolas; Parra, Maria V; Rojas, Winston; Duque, Constanza; Mesa, Natalia; García, Luis F; Triana, Omar; Blair, Silvia; Maestre, Amanda; Dib, Juan C; Bravi, Claudio M; Bailliet, Graciela; Corach, Daniel; Hünemeier, Tábita; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, María Luiza; Acuña-Alonzo, Victor; Aguilar-Salinas, Carlos; Canizales-Quinteros, Samuel; Tusié-Luna, Teresa; Riba, Laura; Rodríguez-Cruz, Maricela; Lopez-Alarcón, Mardia; Coral-Vazquez, Ramón; Canto-Cetina, Thelma; Silva-Zolezzi, Irma; Fernandez-Lopez, Juan Carlos; Contreras, Alejandra V; Jimenez-Sanchez, Gerardo; Gómez-Vázquez, Maria José; Molina, Julio; Carracedo, Angel; Salas, Antonio; Gallo, Carla; Poletti, Giovanni; Witonsky, David B; Alkorta-Aranburu, Gorka; Sukernik, Rem I; Osipova, Ludmila; Fedorova, Sardana A; Vasquez, René; Villena, Mercedes; Moreau, Claudia; Barrantes, Ramiro; Pauls, David; Excoffier, Laurent; Bedoya, Gabriel; Rothhammer, Francisco; Dugoujon, Jean-Michel; Larrouy, Georges; Klitz, William; Labuda, Damian; Kidd, Judith; Kidd, Kenneth; Di Rienzo, Anna; Freimer, Nelson B; Price, Alkes L; Ruiz-Linares, Andrés

2012-08-16

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia.

PubMed

Burgos-Paz, William; Cerón-Muñoz, Mario; Solarte-Portilla, Carlos

2011-10-01

The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.

Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia

PubMed Central

Burgos-Paz, William; Cerón-Muñoz, Mario; Solarte-Portilla, Carlos

2011-01-01

The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations. PMID:22215979

A regional assessment of white-tailed deer effects on plant invasion

PubMed Central

Mortensen, David A; Smithwick, Erica A H; Kalisz, Susan; McShea, William J; Bourg, Norman A; Parker, John D; Royo, Alejandro A; Abrams, Marc D; Apsley, David K; Blossey, Bernd; Boucher, Douglas H; Caraher, Kai L; DiTommaso, Antonio; Johnson, Sarah E; Masson, Robert; Nuzzo, Victoria A

2018-01-01

Abstract Herbivores can profoundly influence plant species assembly, including plant invasion, and resulting community composition. Population increases of native herbivores, e.g. white-tailed deer (Odocoileus virginianus), combined with burgeoning plant invasions raise concerns for native plant diversity and forest regeneration. While individual researchers typically test for the impact of deer on plant invasion at a few sites, the overarching influence of deer on plant invasion across regional scales is unclear. We tested the effects of deer on the abundance and diversity of introduced and native herbaceous and woody plants across 23 white-tailed deer research sites distributed across the east-central and north-eastern USA and representing a wide range of deer densities and invasive plant abundance and identity. Deer access/exclusion or deer population density did not affect introduced plant richness or community-level abundance. Native and total plant species richness, abundance (cover and stem density) and Shannon diversity were lower in deer-access vs. deer-exclusion plots. Among deer-access plots, native species richness, native and total cover, and Shannon diversity (cover) declined as deer density increased. Deer access increased the proportion of introduced species cover (but not of species richness or stem density). As deer density increased, the proportion of introduced species richness, cover and stem density all increased. Because absolute abundance of introduced plants was unaffected by deer, the increase in proportion of introduced plant abundance is likely an indirect effect of deer reducing native cover. Indicator species analysis revealed that deer access favoured three introduced plant species, including Alliaria petiolata and Microstegium vimineum, as well as four native plant species. In contrast, deer exclusion favoured three introduced plant species, including Lonicera japonica and Rosa multiflora, and 15 native plant species. Overall, native deer reduced community diversity, lowering native plant richness and abundance, and benefited certain invasive plants, suggesting pervasive impacts of this keystone herbivore on plant community composition and ecosystem services in native forests across broad swathes of the eastern USA. PMID:29340133

DOE Office of Scientific and Technical Information (OSTI.GOV)

Averill, Kristine M.; Mortensen, David A.; Smithwick, Erica A. H.

Herbivores can profoundly influence plant species assembly, including plant invasion, and resulting community composition. Population increases of native herbivores, e.g., white-tailed deer (Odocoileus virginianus), combined with burgeoning plant invasions raise concerns for native plant diversity and forest regeneration. While individual researchers typically test for the impact of deer on plant invasion at a few sites, the overarching influence of deer on plant invasion across regional scales is unclear. We tested the effects of deer on the abundance and diversity of introduced and native herbaceous and woody plants across 23 white-tailed deer research sites distributed across the east central and northeasternmore » United States and representing a wide range of deer densities and invasive plant abundance and identity. Deer access/exclusion or deer population density did not affect introduced plant richness or community-level abundance. Native and total plant species richness, abundance (cover and stem density), and Shannon diversity were lower in deer-access vs. deer-exclusion plots. Among deer access plots, native species richness, native and total cover, and Shannon diversity (cover) declined as deer density increased. Deer access increased the proportion of introduced species cover (but not of species richness or stem density). As deer density increased, the proportion of introduced species richness, cover, and stem density all increased. Because absolute abundance of introduced plants was unaffected by deer, the increase in proportion of introduced plant abundance is likely an indirect effect of deer reducing native cover. Indicator species analysis revealed that deer access favored three introduced plant species, including Alliaria petiolata and Microstegium vimineum, as well as four native plant species. In contrast, deer exclusion favored three introduced plant species, including Lonicera japonica and Rosa multiflora, and fifteen native plant species. Overall, native deer reduced community diversity, lowering native plant richness and abundance, and benefited certain invasive plants, suggesting pervasive impacts of this keystone herbivore on plant community composition and ecosystem services in native forests across broad swathes of the eastern US.« less

A regional assessment of white-tailed deer effects on plant invasion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Averill, Kristine M.; Mortensen, David A.; Smithwick, Erica A. H.

Herbivores can profoundly influence plant species assembly, including plant invasion, and resulting community composition. Population increases of native herbivores, e.g., white-tailed deer ( Odocoileus virginianus), combined with burgeoning plant invasions raise concerns for native plant diversity and forest regeneration. While individual researchers typically test for the impact of deer on plant invasion at a few sites, the overarching influence of deer on plant invasion across regional scales is unclear. We tested the effects of deer on the abundance and diversity of introduced and native herbaceous and woody plants across 23 white-tailed deer research sites distributed across the east central andmore » northeastern United States and representing a wide range of deer densities and invasive plant abundance and identity. Deer access/exclusion or deer population density did not affect introduced plant richness or community-level abundance. Native and total plant species richness, abundance (cover and stem density), and Shannon diversity were lower in deer-access vs. deer-exclusion plots. Among deer access plots, native species richness, native and total cover, and Shannon diversity (cover) declined as deer density increased. Deer access increased the proportion of introduced species cover (but not of species richness or stem density). As deer density increased, the proportion of introduced species richness, cover, and stem density all increased. Because absolute abundance of introduced plants was unaffected by deer, the increase in proportion of introduced plant abundance is likely an indirect effect of deer reducing native cover. Indicator species analysis revealed that deer access favored three introduced plant species, including Alliaria petiolata and Microstegium vimineum, as well as four native plant species. In contrast, deer exclusion favored three introduced plant species, including Lonicera japonica and Rosa multiflora, and fifteen native plant species. Altogether, native deer reduced community diversity, lowering native plant richness and abundance, and benefited certain invasive plants, suggesting pervasive impacts of this keystone herbivore on plant community composition and ecosystem services in native forests across broad swathes of the eastern US.« less

A regional assessment of white-tailed deer effects on plant invasion

DOE PAGES

Averill, Kristine M.; Mortensen, David A.; Smithwick, Erica A. H.; ...

2017-12-07

Herbivores can profoundly influence plant species assembly, including plant invasion, and resulting community composition. Population increases of native herbivores, e.g., white-tailed deer ( Odocoileus virginianus), combined with burgeoning plant invasions raise concerns for native plant diversity and forest regeneration. While individual researchers typically test for the impact of deer on plant invasion at a few sites, the overarching influence of deer on plant invasion across regional scales is unclear. We tested the effects of deer on the abundance and diversity of introduced and native herbaceous and woody plants across 23 white-tailed deer research sites distributed across the east central andmore » northeastern United States and representing a wide range of deer densities and invasive plant abundance and identity. Deer access/exclusion or deer population density did not affect introduced plant richness or community-level abundance. Native and total plant species richness, abundance (cover and stem density), and Shannon diversity were lower in deer-access vs. deer-exclusion plots. Among deer access plots, native species richness, native and total cover, and Shannon diversity (cover) declined as deer density increased. Deer access increased the proportion of introduced species cover (but not of species richness or stem density). As deer density increased, the proportion of introduced species richness, cover, and stem density all increased. Because absolute abundance of introduced plants was unaffected by deer, the increase in proportion of introduced plant abundance is likely an indirect effect of deer reducing native cover. Indicator species analysis revealed that deer access favored three introduced plant species, including Alliaria petiolata and Microstegium vimineum, as well as four native plant species. In contrast, deer exclusion favored three introduced plant species, including Lonicera japonica and Rosa multiflora, and fifteen native plant species. Altogether, native deer reduced community diversity, lowering native plant richness and abundance, and benefited certain invasive plants, suggesting pervasive impacts of this keystone herbivore on plant community composition and ecosystem services in native forests across broad swathes of the eastern US.« less

The loss-of-allele assay for ES cell screening and mouse genotyping.

PubMed

Frendewey, David; Chernomorsky, Rostislav; Esau, Lakeisha; Om, Jinsop; Xue, Yingzi; Murphy, Andrew J; Yancopoulos, George D; Valenzuela, David M

2010-01-01

Targeting vectors used to create directed mutations in mouse embryonic stem (ES) cells consist, in their simplest form, of a gene for drug selection flanked by mouse genomic sequences, the so-called homology arms that promote site-directed homologous recombination between the vector and the target gene. The VelociGene method for the creation of targeted mutations in ES cells employs targeting vectors, called BACVecs, that are based on bacterial artificial chromosomes. Compared with conventional short targeting vectors, BacVecs provide two major advantages: (1) their much larger homology arms promote high targeting efficiencies without the need for isogenicity or negative selection strategies; and (2) they enable deletions and insertions of up to 100kb in a single targeting event, making possible gene-ablating definitive null alleles and other large-scale genomic modifications. Because of their large arm sizes, however, BACVecs do not permit screening by conventional assays, such as long-range PCR or Southern blotting, that link the inserted targeting vector to the targeted locus. To exploit the advantages of BACVecs for gene targeting, we inverted the conventional screening logic in developing the loss-of-allele (LOA) assay, which quantifies the number of copies of the native locus to which the mutation was directed. In a correctly targeted ES cell clone, the LOA assay detects one of the two native alleles (for genes not on the X or Y chromosome), the other allele being disrupted by the targeted modification. We apply the same principle in reverse as a gain-of-allele assay to quantify the copy number of the inserted targeting vector. The LOA assay reveals a correctly targeted clone as having lost one copy of the native target gene and gained one copy of the drug resistance gene or other inserted marker. The combination of these quantitative assays makes LOA genotyping unequivocal and amenable to automated scoring. We use the quantitative polymerase chain reaction (qPCR) as our method of allele quantification, but any method that can reliably distinguish the difference between one and two copies of the target gene can be used to develop an LOA assay. We have designed qPCR LOA assays for deletions, insertions, point mutations, domain swaps, conditional, and humanized alleles and have used the insert assays to quantify the copy number of random insertion BAC transgenics. Because of its quantitative precision, specificity, and compatibility with high throughput robotic operations, the LOA assay eliminates bottlenecks in ES cell screening and mouse genotyping and facilitates maximal speed and throughput for knockout mouse production. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Impact of Austropuccinia psidii (myrtle rust) on Myrtaceae-rich wet sclerophyll forests in south east Queensland.

PubMed

Pegg, Geoff; Taylor, Tamara; Entwistle, Peter; Guymer, Gordon; Giblin, Fiona; Carnegie, Angus

2017-01-01

In April 2010, Austropuccinia psidii (formerly Puccinia psidii) was detected for the first time in Australia on the central coast of New South Wales. The fungus spread rapidly along the east coast and can now be found infecting vegetation in a range of native forest ecosystems with disease impacts ranging from minor leaf spots to severe shoot and stem blight and tree dieback. Localised extinction of some plant species has been recorded. In 2014, the impact of A. psidii was observed for the first time in a wet sclerophyll site with a rainforest understory, dominated by species of Myrtaceae, in Tallebudgera Valley, south east Queensland, Australia. This study aimed to determine the impact of A. psidii on individual species and species composition. Here we provide quantitative and qualitative evidence on the significant impact A. psidii has in native ecosystems, on a broader range of species than previously reported. Archirhodomyrtus beckleri, Decaspermum humile, Gossia hillii and Rhodamnia maideniana are in serious decline, with significant increases in tree mortality over the period of our study. This research further highlights the potential of this invasive pathogen to negatively impact native ecosystems and biodiversity.

Impact of Austropuccinia psidii (myrtle rust) on Myrtaceae-rich wet sclerophyll forests in south east Queensland

PubMed Central

Taylor, Tamara; Entwistle, Peter; Guymer, Gordon; Giblin, Fiona; Carnegie, Angus

2017-01-01

In April 2010, Austropuccinia psidii (formerly Puccinia psidii) was detected for the first time in Australia on the central coast of New South Wales. The fungus spread rapidly along the east coast and can now be found infecting vegetation in a range of native forest ecosystems with disease impacts ranging from minor leaf spots to severe shoot and stem blight and tree dieback. Localised extinction of some plant species has been recorded. In 2014, the impact of A. psidii was observed for the first time in a wet sclerophyll site with a rainforest understory, dominated by species of Myrtaceae, in Tallebudgera Valley, south east Queensland, Australia. This study aimed to determine the impact of A. psidii on individual species and species composition. Here we provide quantitative and qualitative evidence on the significant impact A. psidii has in native ecosystems, on a broader range of species than previously reported. Archirhodomyrtus beckleri, Decaspermum humile, Gossia hillii and Rhodamnia maideniana are in serious decline, with significant increases in tree mortality over the period of our study. This research further highlights the potential of this invasive pathogen to negatively impact native ecosystems and biodiversity. PMID:29161305

American foulbrood of the honey bee: occurrence and distribution of different genotypes of Paenibacillus larvae in the administrative district of Arnsberg (North Rhine-Westphalia).

PubMed

Peters, M; Kilwinski, J; Beringhoff, A; Reckling, D; Genersch, E

2006-03-01

Between March 2003 and October 2004, Paenibacillus larvae, the aetiological agent of American foulbrood disease of the honey bee, was isolated from broodcombs and honey samples of 54 apiaries in the administrative district of Arnsberg (North Rhine-Westphalia, Germany). Genotyping of 176 P. larvae isolates with repetitive element polymerase chain reaction fingerprinting (rep-PCR) using BOX A1R and MBO REP1 primers revealed five different genotypes (AB, Ab, ab, ass, Acapital BE, Cyrillic). In samples of three apiaries, more than one genotype was detected. A combination of two genotypes was isolated from honey samples of the same hive two times (ab/ass and Ab/ab). The five genotypes were not randomly distributed in the district, but revealed a certain geographical clustering. Possible factors with impact on the genotype diversity and the distribution pattern are discussed.

Integrating regeneration, genetic resistance, and timing of intervention for the long-term sustainability of ecosystems challenged by non-native pests - a novel proactive approach

Treesearch

A. W Schoettle; J. G. Klutsch; R. A. Sniezko

2012-01-01

Global trade increases the likelihood of introduction of non-native, invasive species which can threaten native species and their associated ecosystems. This has led to significant impacts to forested landscapes, including extensive tree mortality, shifts in ecosystem composition, and vulnerabilities to other stresses. With the increased appreciation of the importance...

Impacts of erosion control treatments on native vegetation recovery after severe wildfire in the Eastern Cascades, USA

Treesearch

Erich Kyle Dodson; David W. Peterson; Richy J. Harrod

2010-01-01

Slope stabilization treatments like mulching and seeding are used to increase soil cover and reduce runoff and erosion following severe wildfires, but may also retard native vegetation recovery. We evaluated the effects of seeding and fertilization on the cover and richness of native and exotic plants and on individual plant species following the 2004 Pot Peak wildfire...

Sociocultural Variables That Impact High School Students' Perceptions of Native Fauna: A Study on the Species Component of the Biodiversity Concept

ERIC Educational Resources Information Center

Bermudez, Gonzalo M.; Battistón, Luisina V.; García Capocasa, María C.; De Longhi, Ana L.

2017-01-01

This study investigates the influence of school sector (private versus state schools) and student gender on knowledge of native fauna. Our main objectives were (a) to describe the knowledge of high school students from the province of Cordoba, Argentina with respect to native animal species, (b) to determine if any exotic species (introduced or…

Culturally scarred trees in the Bob Marshall Wilderness, Montana, USA - Interpreting Native American historical forest use in a wilderness area

Treesearch

Lars Ostlund; Bob Keane; Steve Arno; Rikard Andersson

2005-01-01

Wilderness areas are primarily set aside to protect natural ecosystems and processes. However, most protected areas have a long history of native peoples' land use predating their protection. The general paucity of evidence in the form of historical records, in combination with romantic views of native peoples' effects on nature, often leads to their impact...

Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

PubMed

Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

2012-01-01

Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

Considering the unintentional consequences of pollinator gardens for urban native plants: is the road to extinction paved with good intentions?

PubMed

Johnson, Anna L; Fetters, Andrea M; Ashman, Tia-Lynn

2017-09-01

Urban centers are important foci for plant biodiversity and yet widespread planting of wildflower gardens in cities to sustain pollinator biodiversity is on the rise, without full consideration of potential ecological consequences. The impact of intentional wildflower plantings on remnant native plant diversity in urban and peri-urban settings has not received attention, although shared pollinators are likely to mediate several types of biotic interactions between human-introduced plants and remnant native ones. Additionally, if wildflower species escape gardens these indirect effects may be compounded with direct ones. We review the potential positive and negative impacts of wildflower gardens on urban native flowering plants, and we reveal substantial gaps in our knowledge. We present a roadmap for research to address whether wildflower gardens, while benefiting pollinators, could also hasten the extinction of native remnant plants in urban settings, or whether they could have other effects that enrich urban biodiversity. Goals of future wildflower mixes should consider the totality of potential interactions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Predicting invasive species impacts: a community module functional response approach reveals context dependencies.

PubMed

Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

2015-03-01

Predatory functional responses play integral roles in predator-prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator-prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Historical thermal regimes define limits to coral acclimatization.

PubMed

Howells, Emily J; Berkelmans, Ray; van Oppen, Madeleine J H; Willis, Bette L; Bay, Line K

2013-05-01

Knowledge of the degree to which corals undergo physiological acclimatization or genetic adaptation in response to changes in their thermal environment is crucial to the success of coral reef conservation strategies. The potential of corals to acclimatize to temperatures exceeding historical thermal regimes was investigated by reciprocal transplantation of Acropora millepora colonies between the warm central and cool southern regions of the Great Barrier Reef (GBR) for a duration of 14 months. Colony fragments retained at native sites remained healthy, whereas transplanted fragments, although healthy over initial months when temperatures remained within native thermal regimes, subsequently bleached and suffered mortality during seasonal temperature extremes. Corals hosting Symbiodinium D transplanted to the southern GBR bleached in winter and the majority suffered whole (40%; n=20 colonies) or partial (50%) mortality at temperatures 1.1 degrees C below their 15-year native minimum. In contrast, corals hosting Symbiodinium C2 transplanted to the central GBR bleached in summer and suffered whole (50%; n=10 colonies) or partial (42%) mortality at temperatures 2.5 degrees C above their 15-year native maximum. During summer bleaching, the dominant Symbiodinium type changed from C2 to D within corals transplanted to the central GBR. Corals transplanted to the cooler, southern GBR grew 74-80% slower than corals at their native site, and only 50% of surviving colonies reproduced, at least partially because of cold water bleaching of transplants. Despite the absence of any visual signs of stress, corals transplanted to the warmer, central GBR grew 52-59% more slowly than corals at their native site before the summer bleaching (i.e., from autumn to spring). Allocation of energy to initial acclimatization or reproduction may explain this pattern, as the majority (65%) of transplants reproduced one month earlier than portions of the same colonies retained at the southern native site. All parameters investigated (bleaching, mortality, Symbiodinium type fidelity, reproductive timing) demonstrated strong interactions between genotype and environment, indicating that the acclimatization potential of A. millepora populations may be limited by adaptation of the holobiont to native thermal regimes.

Species traits and network structure predict the success and impacts of pollinator invasions.

PubMed

Valdovinos, Fernanda S; Berlow, Eric L; Moisset de Espanés, Pablo; Ramos-Jiliberto, Rodrigo; Vázquez, Diego P; Martinez, Neo D

2018-05-31

Species invasions constitute a major and poorly understood threat to plant-pollinator systems. General theory predicting which factors drive species invasion success and subsequent effects on native ecosystems is particularly lacking. We address this problem using a consumer-resource model of adaptive behavior and population dynamics to evaluate the invasion success of alien pollinators into plant-pollinator networks and their impact on native species. We introduce pollinator species with different foraging traits into network models with different levels of species richness, connectance, and nestedness. Among 31 factors tested, including network and alien properties, we find that aliens with high foraging efficiency are the most successful invaders. Networks exhibiting high alien-native diet overlap, fraction of alien-visited plant species, most-generalist plant connectivity, and number of specialist pollinator species are the most impacted by invaders. Our results mimic several disparate observations conducted in the field and potentially elucidate the mechanisms responsible for their variability.

Genetic moderation of the effects of cannabis: catechol-O-methyltransferase (COMT) affects the impact of Δ9-tetrahydrocannabinol (THC) on working memory performance but not on the occurrence of psychotic experiences.

PubMed

Tunbridge, Elizabeth M; Dunn, Graham; Murray, Robin M; Evans, Nicole; Lister, Rachel; Stumpenhorst, Katharina; Harrison, Paul J; Morrison, Paul D; Freeman, Daniel

2015-11-01

Cannabis use can induce cognitive impairments and psychotic experiences. A functional polymorphism in the catechol-O-methyltransferase (COMT) gene (Val(158)Met) appears to influence the immediate cognitive and psychotic effects of cannabis, or ∆(9)-tetrahydrocannabinol (THC), its primary psychoactive ingredient. This study investigated the moderation of the impact of experimentally administered THC by COMT. Cognitive performance and psychotic experiences were studied in participants without a psychiatric diagnosis, using a between-subjects design (THC vs. placebo). The effect of COMT Val(158)Met genotype on the cognitive and psychotic effects of THC, administered intravenously in a double-blind, placebo-controlled manner to 78 participants who were vulnerable to paranoia, was examined. The results showed interactive effects of genotype and drug group (THC or placebo) on working memory, assayed using the Digit Span Backwards task. Specifically, THC impaired performance in COMT Val/Val, but not Met, carriers. In contrast, the effect of THC on psychotic experiences, measured using the Community Assessment of Psychic Experiences (CAPE) positive dimension, was unaffected by COMT genotype. This study is the largest to date examining the impact of COMT genotype on response to experimentally administered THC, and the first using a purely non-clinical cohort. The data suggest that COMT genotype moderates the cognitive, but not the psychotic, effects of acutely administered THC. © The Author(s) 2015.

Occurrence and molecular characterization of Cryptosporidium spp. and Enterocytozoon bieneusi in dairy cattle, beef cattle and water buffaloes in China.

PubMed

Ma, Jingbo; Li, Pei; Zhao, Xiaoping; Xu, Hailing; Wu, Wenxian; Wang, Yuanfei; Guo, Yaqiong; Wang, Lin; Feng, Yaoyu; Xiao, Lihua

2015-01-30

Cryptosporidium spp. and Enterocytozoon bieneusi are important protists in a wide range of vertebrate hosts, causing diarrheal diseases. Cattle are considered potential reservoirs of Cryptosporidium infection in humans, although their role in the transmission of E. bieneusi is not clear. In the present work, 793 fecal specimens from dairy cattle, native beef cattle, and water buffaloes on 11 farms in China were examined for the presence of Cryptosporidium spp. and E. bieneusi using nested PCR targeting the small subunit (SSU) rRNA gene of Cryptosporidium spp. and the internal transcribed spacer (ITS) of E. bieneusi. For Cryptosporidium, 144/446 (32.3%) dairy cattle, 44/166 (26.5%) beef cattle, and 43/181 (23.8%) water buffaloes were PCR-positive. Sequence analysis was successful for 213 of the 231 Cryptosporidium-positive isolates; among them 94 had Cryptosporidium andersoni, 61 had Cryptosporidium bovis, 54 had Cryptosporidium ryanae, 2 had a Cryptosporidium suis-like genotype, and 2 had mixed infections of C. bovis and C. ryanae. In dairy and beef cattle, C. andersoni and C. bovis were the most common species, whereas C. ryanae was the dominant species in water buffaloes. The latter species produced SSU rRNA sequences different between cattle and water buffaloes. For E. bieneusi, the infection rate of E. bieneusi in dairy cattle, beef cattle and water buffaloes was 4.9%, 5.4% and 2.2%, respectively. All 35 E. bieneusi-positive specimens were successfully sequenced, revealing the presence of four genotypes: three Group 2 genotypes previously reported in cattle as well as humans (I, J and BEB4) and one Group 1 genotype recently reported in yaks (CHN11). Genotypes I and J were the most common genotypes in dairy and beef cattle, while genotype CHN11 was the only genotype seen in water buffaloes. Thus, the distribution of Cryptosporidium spp. and E. bieneusi in water buffaloes might be different from in dairy and beef cattle in China. These findings indicate that some of the Cryptosporidium species and all four E. bieneusi genotypes identified in bovine animals in the study areas may have zoonotic potential. Copyright © 2014 Elsevier B.V. All rights reserved.

Biology and impacts of Pacific island invasive species 9. Capra hircus, the feral goat, (Mammalia: Bovidae)

USGS Publications Warehouse

Chynoweth, Mark W.; Litton, Creighton M.; Lepczyk, Christopher A.; Hess, Steve A.; Cordell, Susan

2013-01-01

Domestic goats, Capra hircus, were intentionally introduced to numerous oceanic islands beginning in the sixteenth century. The remarkable ability of C. hircus to survive in a variety of conditions has enabled this animal to become feral and impact native ecosystems on islands throughout the world. Direct ecological impacts include consumption and trampling of native plants, leading to plant community modification and transformation of ecosystem structure. While the negative impacts of feral goats are well-known and effective management strategies have been developed to control this invasive species, large populations persist on many islands. This review summarizes the impacts of feral goats on Pacific island ecosystems, and the management strategies available to control this invasive species.

The density and spatial arrangement of the invasive oyster Crassostrea gigas determines its impact on settlement of native oyster larvae

PubMed Central

Wilkie, Emma M; Bishop, Melanie J; O'Connor, Wayne A

2013-01-01

Understanding how the density and spatial arrangement of invaders is critical to developing management strategies of pest species. The Pacific oyster, Crassostrea gigas, has been translocated around the world for aquaculture and in many instances has established wild populations. Relative to other species of bivalve, it displays rapid suspension feeding, which may cause mortality of pelagic invertebrate larvae. We compared the effect on settlement of Sydney rock oyster, Saccostrea glomerata, larvae of manipulating the spatial arrangement and density of native S. glomerata, and non-native C. gigas. We hypothesized that while manipulations of dead oysters would reveal the same positive relationship between attachment surface area and S. glomerata settlement between the two species, manipulations of live oysters would reveal differing density-dependent effects between the native and non-native oyster. In the field, whether oysters were live or dead, more larvae settled on C. gigas than S. glomerata when substrate was arranged in monospecific clumps. When, however, the two species were interspersed, there were no differences in larval settlement between them. By contrast, in aquaria simulating a higher effective oyster density, more larvae settled on live S. glomerata than C. gigas. When C. gigas was prevented from suspension feeding, settlement of larvae on C. gigas was enhanced. By contrast, settlement was similar between the two species when dead. While the presently low densities of the invasive oyster C. gigas may enhance S. glomerata larval settlement in east Australian estuaries, future increases in densities could produce negative impacts on native oyster settlement. Synthesis and applications: Our study has shown that both the spatial arrangement and density of invaders can influence their impact. Hence, management strategies aimed at preventing invasive populations reaching damaging sizes should not only consider the threshold density at which impacts exceed some acceptable limit, but also how patch formation modifies this. PMID:24455120

Transferrin saturation phenotype and HFE genotype screening for hemochromatosis and primary iron overload: predictions from a model based on national, racial, and ethnic group composition in central Alabama.

PubMed

Barton, J C; Acton, R T

2000-01-01

There is interest in general population screening for hemochromatosis and other primary iron overload disorders, although not all persons are at equal risk. We developed a model to estimate the numbers of persons in national, racial, or ethnic population subgroups in Jefferson County, Alabama, who would be detected using transferrin saturation (phenotype) or HFE mutation analysis (genotype) screening. Approximately 62% are Caucasians, 37% are African Americans, and the remainder are Hispanics, Asians, or Native Americans. The predicted phenotype frequencies are greatest in a Caucasian subgroup, ethnicity unspecified, which consists predominantly of persons of Scotch and Irish descent (0.0065 men, 0.0046 women), and in African Americans (0.0089 men, 0.0085 women). Frequencies of the HFE genotype C282Y/C282Y > or = 0.0001 are predicted to occur only among Caucasians; the greatest frequency (0.0080) was predicted to occur in the ethnicity-unspecified Caucasian population. C282Y/C282Y frequency estimates were lower in Italian, Greek, and Jewish subgroups. There is excellent agreement in the numbers of the ethnicity-unspecified Caucasians who would be detected using phenotype and genotype criteria. Our model also indicates that phenotyping would identify more persons with primary iron overload than would genotyping in our Italian Caucasian, Hispanic, and African American subgroups. This is consistent with previous observations that indicate that primary iron overload disorders in persons of southern Italian descent and African Americans are largely attributable to non-HFE alleles. Because the proportions of population subgroups and their genetic constitution may differ significantly in other geographic regions, we suggest that models similar to the present one be constructed to predict optimal screening strategies for primary iron overload disorders.

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

USGS Publications Warehouse

Hohenlohe, Paul A.; Day, Mitch D.; Amish, Stephen J.; Miller, Michael R.; Kamps-Hughes, Nick; Boyer, Matthew C.; Muhlfeld, Clint C.; Allendorf, Fred W.; Johnson, Eric A.; Luikart, Gordon

2013-01-01

Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.

Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution

PubMed Central

2011-01-01

Background In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing. Results Three multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses. Conclusions We introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestry-sensitive DNA markers. PMID:21429198

Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker

NASA Astrophysics Data System (ADS)

Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

2008-01-01

Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

Neighbour tolerance, not suppression, provides competitive advantage to non-native plants.

PubMed

Golivets, Marina; Wallin, Kimberly F

2018-05-01

High competitive ability has often been invoked as a key determinant of invasion success and ecological impacts of non-native plants. Yet our understanding of the strategies that non-natives use to gain competitive dominance remains limited. Particularly, it remains unknown whether the two non-mutually exclusive competitive strategies, neighbour suppression and neighbour tolerance, are equally important for the competitive advantage of non-native plants. Here, we analyse data from 192 peer-reviewed studies on pairwise plant competition within a Bayesian multilevel meta-analytic framework and show that non-native plants outperform their native counterparts due to high tolerance of competition, as opposed to strong suppressive ability. Competitive tolerance ability of non-native plants was driven by neighbour's origin and was expressed in response to a heterospecific native but not heterospecific non-native neighbour. In contrast to natives, non-native species were not more suppressed by hetero- vs. conspecific neighbours, which was partially due to higher intensity of intraspecific competition among non-natives. Heterogeneity in the data was primarily associated with methodological differences among studies and not with phylogenetic relatedness among species. Altogether, our synthesis demonstrates that non-native plants are competitively distinct from native plants and challenges the common notion that neighbour suppression is the primary strategy for plant invasion success. © 2018 John Wiley & Sons Ltd/CNRS.

Impact of native plants on bird and butterfly biodiversity in suburban landscapes.

PubMed

Burghardt, Karin T; Tallamy, Douglas W; Gregory Shriver, W

2009-02-01

Managed landscapes in which non-native ornamental plants are favored over native vegetation now dominate the United States, particularly east of the Mississippi River. We measured how landscaping with native plants affects the avian and lepidopteran communities on 6 pairs of suburban properties in southeastern Pennsylvania. One property in each pair was landscaped entirely with native plants and the other exhibited a more conventional suburban mixture of plants--a native canopy with non-native groundcover and shrubs. Vegetation sampling confirmed that total plant cover and plant diversity did not differ between treatments, but non-native plant cover was greater on the conventional sites and native plant cover was greater on the native sites. Several avian (abundance, species richness, biomass, and breeding-bird abundance) and larval lepidopteran (abundance and species richness) community parameters were measured from June 2006 to August 2006. Native properties supported significantly more caterpillars and caterpillar species and significantly greater bird abundance, diversity, species richness, biomass, and breeding pairs of native species. Of particular importance is that bird species of regional conservation concern were 8 times more abundant and significantly more diverse on native properties. In our study area, native landscaping positively influenced the avian and lepidopteran carrying capacity of suburbia and provided a mechanism for reducing biodiversity losses in human-dominated landscapes.

Evaluation of the contribution of D9S1120 to anthropological studies in Native American populations.

PubMed

Aguilar-Velázquez, J A; Martínez-Sevilla, V Manuel; Sosa-Macías, M; González-Martin, A; Muñoz-Valle, J F; Rangel-Villalobos, H

2017-12-01

The D9S1120 locus exhibits a population-specific allele of 9 repeats (9RA) in all Native American and two Siberian populations currently studied, but it is absent in other worldwide populations. Although this feature has been used in anthropological genetic studies, its impact on the evaluation of the structure and genetic relations among Native American populations has been scarcely assessed. Consequently, the aim of this study was to evaluate the anthropological impact of D9S1120 when it was added to STR population datasets in Mexican Native American groups. We analyzed D9S1120 by PCR and capillary electrophoresis (CE) in 1117 unrelated individuals from 13 native groups from the north and west of Mexico. Additional worldwide populations previously studied with D9S1120 and/or 15 autosomal STRs (Identifier kit) were included for interpopulation analyses. We report statistical results of forensic importance for D9S1120. On average, the modal alleles were the Native American-specific allele 9RA (0.3254) and 16 (0.3362). Genetic distances between Native American and worldwide populations were estimated. When D9S1120 was included in the 15 STR population dataset, we observed improvements for admixture estimation in Mestizo populations and for representing congruent genetic relationships in dendrograms. Analysis of molecular variance (AMOVA) based on D9S1120 confirms that most of the genetic variability in the Mexican population is attributable to their Native American backgrounds, and allows the detection of significant intercontinental differentiation attributed to the exclusive presence of 9RA in America. Our findings demonstrate the contribution of D9S1120 to a better understanding of the genetic relationships and structure among Mexican Native groups. Copyright © 2017 Elsevier GmbH. All rights reserved.

Trophic Strategies of a Non-Native and a Native Amphibian Species in Shared Ponds

PubMed Central

San Sebastián, Olatz; Navarro, Joan; Llorente, Gustavo A.; Richter-Boix, Álex

2015-01-01

One of the critical factors for understanding the establishment, success and potential impact on native species of an introduced species is a thorough knowledge of how these species manage trophic resources. Two main trophic strategies for resource acquisition have been described: competition and opportunism. In the present study our objective was to identify the main trophic strategies of the non-native amphibian Discoglossus pictus and its potential trophic impact on the native amphibian Bufo calamita. We determine whether D. pictus exploits similar trophic resources to those exploited by the native B. calamita (competition hypothesis) or alternative resources (opportunistic hypothesis). To this end, we analyzed the stable isotope values of nitrogen and carbon in larvae of both species, in natural ponds and in controlled laboratory conditions. The similarity of the δ15N and δ13C values in the two species coupled with isotopic signal variation according to pond conditions and niche partitioning when they co-occurred indicated dietary competition. Additionally, the non-native species was located at higher levels of trophic niches than the native species and B. calamita suffered an increase in its standard ellipse area when it shared ponds with D. pictus. These results suggest niche displacement of B. calamita to non-preferred resources and greater competitive capacity of D. pictus in field conditions. Moreover, D. pictus showed a broader niche than the native species in all conditions, indicating increased capacity to exploit the diversity of resources; this may indirectly favor its invasiveness. Despite the limitations of this study (derived from potential variability in pond isotopic signals), the results support previous experimental studies. All the studies indicate that D. pictus competes with B. calamita for trophic resources with potential negative effects on the fitness of the latter. PMID:26101880

Lake Michigan: Man's effects on native fish stocks and other biota

USGS Publications Warehouse

Wells, LaRue; McLain, Alberton L.

1973-01-01

Exploitation was largely responsible for the changes in Lake Michigan fish stocks before the invasion of the smelt, and probably before the invasion of the sea lamprey. The lamprey and alewife, however, have exerted a greater impact than the fishery on native fish populations in recent decades. Accelerated eutrophication and other pollution, although important, have not equalled the other factors in causing changes in native fish populations.

78 FR 60309 - Draft Environmental Impact Statement for the Restoration of Native Species in High Elevation...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-01

... prevent the extinction of two species of mountain yellow-legged frogs (Rana muscosa and Rana sierrae; MYLF... enable the NPS to fulfill its mission and policy directives to conserve native animals, plants and...

Native bees buffer the negative impact of climate warming on honey bee pollination of watermelon crops.

PubMed

Rader, Romina; Reilly, James; Bartomeus, Ignasi; Winfree, Rachael

2013-10-01

If climate change affects pollinator-dependent crop production, this will have important implications for global food security because insect pollinators contribute to production for 75% of the leading global food crops. We investigate whether climate warming could result in indirect impacts upon crop pollination services via an overlooked mechanism, namely temperature-induced shifts in the diurnal activity patterns of pollinators. Using a large data set on bee pollination of watermelon crops, we predict how pollination services might change under various climate change scenarios. Our results show that under the most extreme IPCC scenario (A1F1), pollination services by managed honey bees are expected to decline by 14.5%, whereas pollination services provided by most native, wild taxa are predicted to increase, resulting in an estimated aggregate change in pollination services of +4.5% by 2099. We demonstrate the importance of native biodiversity in buffering the impacts of climate change, because crop pollination services would decline more steeply without the native, wild pollinators. More generally, our study provides an important example of how biodiversity can stabilize ecosystem services against environmental change. © 2013 John Wiley & Sons Ltd.

Avian malaria Plasmodium relictum in native Hawaiian forest birds: epizootiology and demographic impacts on ‵apapane Himatione sanguinea

USGS Publications Warehouse

Atkinson, Carter T.; Samuel, Michael D.

2010-01-01

The role of introduced avian malaria Plasmodium relictum in the decline and extinction of native Hawaiian forest birds has become a classic example of the potential effect of invasive diseases on biological diversity of naïve populations. However, empirical evidence describing the impact of avian malaria on fitness of Hawai‵i's endemic forest birds is limited, making it difficult to determine the importance of disease among the suite of potential limiting factors affecting the distribution and abundance of this threatened avifauna. We combined epidemiological force-of-infection with multistate capture––recapture models to evaluate a 7-year longitudinal study of avian malaria in ‵apapane, a relatively common native honeycreeper within mid-elevation Hawaiian forests. We found that malaria transmission was seasonal in this mid-elevation forest; transmission peaked during fall and during some years produced epizootic mortality events. Estimated annual mortality of hatch-year birds typically exceeded 50% and mortality of adults exceeded 25% during epizootics. The substantial impact of avian malaria on this relatively common native species demonstrates the key role this disease has played in the decline and extinction of Hawaiian forest birds.

Allelopathic interference of alfalfa (Medicago sativa L.) genotypes to annual ryegrass (Lolium rigidum).

PubMed

Zubair, Hasan Muhammad; Pratley, James E; Sandral, G A; Humphries, A

2017-07-01

Alfalfa (Medicago sativa L.) genotypes at varying densities were investigated for allelopathic impact using annual ryegrass (Lolium rigidum) as the target species in a laboratory bioassay. Three densities (15, 30, and 50 seedlings/beaker) and 40 alfalfa genotypes were evaluated by the equal compartment agar method (ECAM). Alfalfa genotypes displayed a range of allelopathic interference in ryegrass seedlings, reducing root length from 5 to 65%. The growth of ryegrass decreased in response to increasing density of alfalfa seedlings. At the lowest density, Q75 and Titan9 were the least allelopathic genotypes. An overall inhibition index was calculated to rank each alfalfa genotype. Reduction in seed germination of annual ryegrass occurred in the presence of several alfalfa genotypes including Force 10, Haymaster7 and SARDI Five. A comprehensive metabolomic analysis using Quadruple Time of Flight (Q-TOF), was conducted to compare six alfalfa genotypes. Variation in chemical compounds was found between alfalfa root extracts and exudates and also between genotypes. Further individual compound assessments and quantitative study at greater chemical concentrations are needed to clarify the allelopathic activity. Considerable genetic variation exists among alfalfa genotypes for allelopathic activity creating the opportunity for its use in weed suppression through selection.

Use of partial least squares regression to impute SNP genotypes in Italian cattle breeds.

PubMed

Dimauro, Corrado; Cellesi, Massimo; Gaspa, Giustino; Ajmone-Marsan, Paolo; Steri, Roberto; Marras, Gabriele; Macciotta, Nicolò P P

2013-06-05

The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used. Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content. In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip. Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available.

The negative ecological impacts of a globally introduced species decrease with time since introduction.

PubMed

Závorka, Libor; Buoro, Mathieu; Cucherousset, Julien

2018-05-25

While there is a long-history of biological invasions and their ecological impacts have been widely demonstrated across taxa and ecosystems, our knowledge on the temporal dynamic of these impacts remains extremely limited. Using a meta-analytic approach, we investigated how the ecological impacts of non-native brown trout (Salmo trutta), a model species with a 170-year long and well-documented history of intentional introductions across the globe, vary with time since introduction. We first observed significant negative ecological impacts immediately after the species introduction. Second, we found that the negative ecological impacts decrease with time since introduction and that the average ecological impacts become non-significant more than one century after introduction. This pattern was consistent across other ecological contexts (i.e. geographical location, levels of biological organisation, and methodological approach). However, overall negative ecological impacts were more pronounced at the individual and population levels and in experimental studies. While the mechanisms leading to this decrease remain to be determined, our results indicate that rapid response of native organisms (e.g. adaptation, but also local extinction) may play an important role in this dynamic. Changes in native species traits and local extinction can have important conservation implications. Therefore, we argue that the decline of the negative ecological impacts over time should not be used as an argument to neglect the negative impacts of biological invasions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Relationships between Genetic Variations of PNPLA3, TM6SF2 and Histological Features of Nonalcoholic Fatty Liver Disease in Japan.

PubMed

Akuta, Norio; Kawamura, Yusuke; Arase, Yasuji; Suzuki, Fumitaka; Sezaki, Hitomi; Hosaka, Tetsuya; Kobayashi, Masahiro; Kobayashi, Mariko; Saitoh, Satoshi; Suzuki, Yoshiyuki; Ikeda, Kenji; Kumada, Hiromitsu

2016-05-23

It is important to determine the noninvasive parameters of histological features in nonalcoholic fatty liver disease (NAFLD). The aim of this study was to investigate the value of genetic variations as surrogate markers of histological features. The parameters that affected the histological features of NAFLD were investigated in 211 Japanese patients with biopsy-proven NAFLD. The relationships between genetic variations in PNPLA3 rs738409 or TM6SF2 rs58542926 and histological features were analyzed. Furthermore, the impact of genetic variations that affected the pathological criteria for the diagnosis of nonalcoholic steatohepatitis (NASH) (Matteoni classification and NAFLD activity score) was evaluated. The fibrosis stage of PNPLA3 GG was significantly more progressive than that of CG by multiple comparisons. Multivariate analysis identified PNPLA3 genotypes as predictors of fibrosis of stage 2 or more, but the impact tended to decrease at stage 3 or greater. There were no significant differences among the histological features of the three genotypes of TM6SF2. PNPLA3 genotypes partly affected the definition of NASH by the NAFLD activity score, but TM6SF2 genotypes did not affect the definition of NASH. In Japanese patients with biopsy-proven NAFLD, PNPLA3 genotypes may partly affect histological features, including stage of fibrosis, but the TM6SF2 genotype does not affect histological features.

Competitive Interactions between Invasive Nile Tilapia and Native Fish: The Potential for Altered Trophic Exchange and Modification of Food Webs

PubMed Central

Martin, Charles W.; Valentine, Marla M.; Valentine, John F.

2010-01-01

Recent studies have highlighted both the positive and negative impacts of species invasions. Most of these studies have been conducted on either immobile invasive plants or sessile fauna found at the base of food webs. Fewer studies have examined the impacts of vagile invasive consumers on native competitors. This is an issue of some importance given the controlling influence that consumers have on lower order plants and animals. Here, we present results of laboratory experiments designed to assess the impacts of unintended aquaculture releases of the Nile tilapia (Oreochromis niloticus), in estuaries of the Gulf of Mexico, on the functionally similar redspotted sunfish (Lepomis miniatus). Laboratory choice tests showed that tilapia prefer the same structured habitat that native sunfish prefer. In subsequent interspecific competition experiments, agonistic tilapia displaced sunfish from their preferred structured habitats. When a piscivore (largemouth bass) was present in the tank with both species, the survival of sunfish decreased. Based on these findings, if left unchecked, we predict that the proliferation of tilapia (and perhaps other aggressive aquaculture fishes) will have important detrimental effects on the structure of native food webs in shallow, structured coastal habitats. While it is likely that the impacts of higher trophic level invasive competitors will vary among species, these results show that consequences of unintended releases of invasive higher order consumers can be important. PMID:21200433

Cryptic invasion of Northern Leopard Frogs (Rana pipiens) across phylogeographic boundaries and a dilemma for conservation of a declining amphibian

USGS Publications Warehouse

O'Donnell, Ryan P.; Drost, Charles A.; Mock, Karen E.

2017-01-01

Anthropogenic introduction of species is a major contributor to loss of biodiversity. Translocations within the range of a species are less frequently recognized, but have the potential for negative effects as well. Genetic mixing may lead to loss of local adaptations or further decline through outbreeding depression. These cryptic invasions may be quite difficult to recognize, but genetic tools can be used to recognize and monitor such intraspecific introductions. Conversely, translocations within species can be an important conservation tool to reduce inbreeding depression and replace lost genetic diversity. Thus, cryptic invasions can be either an aid or a hindrance to conservation efforts. We tested for the presence of non-native genotypes and assessed the extent and nature of introgression in populations of Northern Leopard Frog (Rana pipiens) in the southwestern US, where populations have declined to a few remnant populations. The most abundant and diverse complex of populations in the region contained a mitochondrial haplotype that was not native to the western US, probably resulting from the introduction of released pets, laboratory animals, or release during fish stocking. These non-native haplotypes were well integrated into a large complex of ponds and lakes, contributing to high genetic diversity in this area. Logistically, the geographic extent of non-native genetic influence within this population precludes eliminating or controlling the non-native component of this population. We recommend assessing the progress and fate of the introgression over time—along with population fitness parameters—to determine whether this introduction is beneficial or detrimental to population persistence. Meanwhile, translocations from nearby locations with similar environmental conditions have the best prospects for avoiding problems with outbreeding depression in other declining populations and will also most effectively preserve regional genetic diversity.

Establishment of non-native plant species after wildfires: Effects of fuel treatments, abiotic and biotic factors, and post-fire grass seeding treatments

USGS Publications Warehouse

Hunter, M.E.; Omi, Philip N.; Martinson, E.J.; Chong, G.W.

2006-01-01

Establishment and spread of non-native species following wildfires can pose threats to long-term native plant recovery. Factors such as disturbance severity, resource availability, and propagule pressure may influence where non-native species establish in burned areas. In addition, pre- and post-fire management activities may influence the likelihood of non-native species establishment. In the present study we examine the establishment of non-native species after wildfires in relation to native species richness, fire severity, dominant native plant cover, resource availability, and pre- and post-fire management actions (fuel treatments and post-fire rehabilitation treatments). We used an information-theoretic approach to compare alternative hypotheses. We analysed post-fire effects at multiple scales at three wildfires in Colorado and New Mexico. For large and small spatial scales at all fires, fire severity was the most consistent predictor of non-native species cover. Non-native species cover was also correlated with high native species richness, low native dominant species cover, and high seeded grass cover. There was a positive, but non-significant, association of non-native species with fuel-treated areas at one wildfire. While there may be some potential for fuels treatments to promote non-native species establishment, wildfire and post-fire seeding treatments seem to have a larger impact on non-native species. ?? IAWF 2006.

Impacts of feral horses on a desert environment

PubMed Central

2009-01-01

Background Free-ranging horses (Equus caballus) in North America are considered to be feral animals since they are descendents of non-native domestic horses introduced to the continent. We conducted a study in a southern California desert to understand how feral horse movements and horse feces impacted this arid ecosystem. We evaluated five parameters susceptible to horse trampling: soil strength, vegetation cover, percent of nonnative vegetation, plant species diversity, and macroinvertebrate abundance. We also tested whether or not plant cover and species diversity were affected by the presence of horse feces. Results Horse trailing resulted in reduced vegetation cover, compacted soils, and in cases of intermediate intensity disturbance, increased plant species diversity. The presence of horse feces did not affect plant cover, but it did increase native plant diversity. Conclusion Adverse impacts, such as soil compaction and increased erosion potential, were limited to established horse trails. In contrast, increased native plant diversity near trails and feces could be viewed as positive outcomes. Extensive trailing can result in a surprisingly large impact area: we estimate that < 30 horses used > 25 km2 of trails in our study area. PMID:19903355

Impacts of feral horses on a desert environment.

PubMed

Ostermann-Kelm, Stacey D; Atwill, Edward A; Rubin, Esther S; Hendrickson, Larry E; Boyce, Walter M

2009-11-10

Free-ranging horses (Equus caballus) in North America are considered to be feral animals since they are descendents of non-native domestic horses introduced to the continent. We conducted a study in a southern California desert to understand how feral horse movements and horse feces impacted this arid ecosystem. We evaluated five parameters susceptible to horse trampling: soil strength, vegetation cover, percent of nonnative vegetation, plant species diversity, and macroinvertebrate abundance. We also tested whether or not plant cover and species diversity were affected by the presence of horse feces. Horse trailing resulted in reduced vegetation cover, compacted soils, and in cases of intermediate intensity disturbance, increased plant species diversity. The presence of horse feces did not affect plant cover, but it did increase native plant diversity. Adverse impacts, such as soil compaction and increased erosion potential, were limited to established horse trails. In contrast, increased native plant diversity near trails and feces could be viewed as positive outcomes. Extensive trailing can result in a surprisingly large impact area: we estimate that < 30 horses used > 25 km2 of trails in our study area.

Trichothecene-Genotypes Play a Role in Fusarium Head Blight Disease Spread and Trichothecene Accumulation in Wheat

USDA-ARS?s Scientific Manuscript database

In the current study, we evaluated the impact of the observed North American evolutionary shift in the Fusarium graminearum complex on disease spread, kernel damage, and trichothecene accumulation in resistant and susceptible wheat genotypes. Four inocula were prepared using composites of F. gramin...

Growth and physiological plasticity among differentially adapted genotypes of a widespread C4 grass under altered precipitation

USDA-ARS?s Scientific Manuscript database

Background/Question/Methods Variation in precipitation expected with climate change may impact plant fitness and alter ecosystem dynamics by modifying species phenology, productivity, and physiology. Species responses to varied precipitation will depend in part on plastic responses of genotypes ad...

The impact of genotype x environment effects on runner type peanut seed vigor response to temperature

USDA-ARS?s Scientific Manuscript database

Experiments were conducted from 2007 to 2012 to evaluate the genotype-by-environment effects on germination and vigor of eight peanut (Arachis hypogaea L.) runner-type cultivars from University of Georgia research trials conducted under the same production practices each year. Irrigated experiments...

Biology of the invasive ascidian Ascidiella aspersa in its native habitat: Reproductive patterns and parasite load

NASA Astrophysics Data System (ADS)

Lynch, Sharon A.; Darmody, Grainne; O'Dwyer, Katie; Gallagher, Mary Catherine; Nolan, Sinead; McAllen, Rob; Culloty, Sarah C.

2016-11-01

The European sea squirt Ascidiella aspersa is a solitary tunicate native to the northeastern Atlantic, commonly found in shallow and sheltered marine ecosystems where it is capable of forming large clumps and outcompeting other invertebrate fauna at settlement. To date, there have been relatively few studies looking at the reproductive biology and health status of this invasive species. Between 2006 and 2010 sampling of a native population took place to investigate gametogenesis and reproductive cycle and to determine the impact of settlement depth on reproduction. In addition, parasite diversity and impact was assessed. A staging system to assess reproductive development was determined. The study highlighted that from year to year the tunicate could change its reproductive strategy from single sex to hermaphrodite, with spawning possible throughout the year. Depth did not impact on sex determination, however, gonad maturation and spawning occurred earlier in individuals in deeper waters compared to shallow depth and it also occurred later in A. aspersa at sites further away from the open sea. Four significant parasite groups including eugregarines, ciliates, trematodes and turbellarians were detected and prevalence of parasite infections increased in A. aspersa at sites with a reduced water flow rate. This study demonstrates the high biotic potential of this ascidian bioinvader to have a negative impact on native fauna in an introduced ecosystem, due to its highly efficient reproductive and resource allocation strategies. Artificial structures such as mooring lines can harbour large aggregations of A. aspersa, however, these manmade habitats may facilitate the colonisation and establishment of this invasive species in the benthos. Additionally, the parasite communities that A. aspersa harbour may also exacerbate its negative impact, both ecologically and economically, in an introduced area by possibly leading to the emergence of new disease in native species i.e. pathogen spillover.

Modeling prey consumption by native and non-native piscivorous fishes: implications for competition and impacts on shared prey in an ultraoligotrophic lake in Patagonia

USGS Publications Warehouse

Juncos, Romina; Beauchamp, David A.; Viglianoc, Pablo H.

2013-01-01

We examined trophic interactions of the nonnative salmonids Rainbow Trout Oncorhynchus mykiss, Brown Trout Salmo trutta, and Brook Trout Salvelinus fontinalisand the main native predator Creole Perch Percichthys trucha in Lake Nahuel Huapi (Patagonia, Argentina) to determine the relative impact of each predator on their forage base and to evaluate the potential vulnerability of each predator to competitive impacts by the others. Using bioenergetics simulations, we demonstrated the overall importance of galaxiids and decapods to the energy budgets of nonnative salmonids and Creole Perch. Introduced salmonids, especially Rainbow Trout, exerted considerably heavier predatory demands on shared resources than did the native Creole Perch on both a per capita basis and in terms of relative population impacts. Rainbow Trout consumed higher quantities and a wider size range of Small Puyen (also known as Inanga) Galaxias maculatus than the other predators, including early pelagic life stages of that prey; as such, this represents an additional source of mortality for the vulnerable early life stages of Small Puyen before and during their transition from pelagic to benthic habitats. All predators were generally feeding at high feeding rates (above 40% of their maximum physiological rates), suggesting that competition for prey does not currently limit either Creole Perch or the salmonids in this lake. This study highlights the importance of keystone prey for the coexistence of native species with nonnative top predators. It provides new quantitative and qualitative evidence of the high predation pressure exerted on Small Puyen, the keystone prey species, during the larval to juvenile transition from pelagic to littoral-benthic habitat in Patagonian lakes. This study also emphasizes the importance of monitoring salmonid and Creole Perch population dynamics in order to detect signs of potential impacts through competition and shows the need to carefully consider the rationale behind any additional trout stocking.

Potential impacts of sea level rise on native plant communities and associated cultural sites in coastal areas of the main Hawaiian Islands

USGS Publications Warehouse

Jacobi, James D.; Warshauer, Frederick R.

2017-01-01

Hawaiian coastal vegetation is comprised of plant species that are adapted to growing in extremely harsh conditions (salt spray, wave wash, wind, and substrates with limited nutrients) found in this habitat zone. Prior to human colonization of Hawai‘i coastal vegetation extended as a continuous ring around each of the islands, broken only by stretches of recent lava flows or unstable cliff faces. However, since humans arrived in Hawai‘i many areas that originally supported native coastal plant communities have been highly altered or the native vegetation totally removed for agriculture, housing, or resort development, destroyed by fire, displaced by invasive plants, eaten by introduced mammals, or damaged by recreational use. This study was focused on identifying sites that still retain relatively intact and highly diverse native coastal plant communities throughout the main Hawaiian Islands that may be further impacted by projected sea level rise. Approximately 40 percent of Hawai‘i’s coastlines were found to still contain high quality native coastal plant communities. Most of these sites were located in areas where the coastal vegetation can still migrate inshore in response to rising sea level and associated inundation by waves. However, six sites with high-quality native coastal vegetation were found on low-lying offshore islets that will be totally inundated with a one meter increase in sea level and thirty sites were found to have some type of fixed barrier, such as a paved road or structure, which would restrict the plants from colonizing the adjacent inland areas. Many of these sites also have other cultural resources that are fixed in place and will definitely be impacted by rising sea level. The results of this study can help refine our understanding of Hawai‘i’s remaining native coastal vegetation and aid with the development of management and restoration strategies to ensure the long-term survival of these unique plant communities.

Body mass index and C-174G interleukin-6 promoter polymorphism interact in predicting type 2 diabetes.

PubMed

Möhlig, Matthias; Boeing, Heiner; Spranger, Joachim; Osterhoff, Martin; Kroke, Anja; Fisher, Eva; Bergmann, Manuela M; Ristow, Michael; Hoffmann, Kurt; Pfeiffer, Andreas F H

2004-04-01

Increased levels of IL-6 add further risk to the impact of obesity in respect to the development of type 2 diabetes mellitus (T2DM). A C-174G polymorphism within the IL-6 promoter region was shown to influence transcription rate of IL-6. We made use of a nested case-control study within the European Prospective Investigation into Cancer and Nutrition-Potsdam cohort of 27,548 individuals, selecting 188 T2DM cases and 376 controls to investigate this polymorphism in respect to development of T2DM. This polymorphism was found to modify the correlation between body mass index (BMI) and IL-6 by showing a much stronger increase of IL-6 at increased BMI for CC genotypes compared with GG genotypes. Interestingly, C-174G polymorphism was found to be an effect modifier for the impact of BMI regarding T2DM. Whereas BMI greater than or equal to 28 kg/m(2) increased the risk of T2DM 3.44-fold [95% confidence interval (CI), 1.34- to 8.24-fold] for GG genotypes and 2.94-fold (95% CI, 1.56- to 5.56-fold) for GC genotypes, we found a 17.68-fold (95% CI, 3.57- to 87.66-fold) increase in risk for CC genotypes. In conclusion, obese individuals with BMI greater than or equal to 28 kg/m(2) carrying the CC genotype showed a more than 5-fold increased risk of developing T2DM compared with the remaining genotypes and, hence, might profit most from weight reduction.

Multiple norovirus infections in a birth cohort in a Peruvian Periurban community.

PubMed

Saito, Mayuko; Goel-Apaza, Sonia; Espetia, Susan; Velasquez, Daniel; Cabrera, Lilia; Loli, Sebastian; Crabtree, Jean E; Black, Robert E; Kosek, Margaret; Checkley, William; Zimic, Mirko; Bern, Caryn; Cama, Vitaliano; Gilman, Robert H

2014-02-01

Human noroviruses are among the most common enteropathogens globally, and are a leading cause of infant diarrhea in developing countries. However, data measuring the impact of norovirus at the community level are sparse. We followed a birth cohort of children to estimate norovirus infection and diarrhea incidence in a Peruvian community. Stool samples from diarrheal episodes and randomly selected nondiarrheal samples were tested by polymerase chain reaction for norovirus genogroup and genotype. Excretion duration and rotavirus coinfection were evaluated in a subset of episodes. Two hundred twenty and 189 children were followed to 1 and 2 years of age, respectively. By 1 year, 80% (95% confidence interval [CI], 75%-85%) experienced at least 1 norovirus infection and by 2 years, 71% (95% CI, 65%-77%) had at least 1 episode of norovirus-associated diarrhea. Genogroup II (GII) infections were 3 times more frequent than genogroup 1 (GI) infections. Eighteen genotypes were found; GII genotype 4 accounted for 41%. Median excretion duration was 34.5 days for GII vs 8.5 days for GI infection (P = .0006). Repeat infections by the same genogroup were common, but repeat infections by the same genotype were rare. Mean length-for-age z score at 12 months was lower among children with prior norovirus infection compared to uninfected children (coefficient: -0.33 [95% CI, -.65 to -.01]; P = .04); the effect persisted at 24 months. Norovirus infection occurs early in life and children experience serial infections with multiple genotypes, suggesting genotype-specific immunity. An effective vaccine would have a substantial impact on morbidity, but may need to target multiple genotypes.

Phenotype, Genotype, and Drug Resistance in Subtype C HIV-1 Infection.

PubMed

Derache, Anne; Wallis, Carole L; Vardhanabhuti, Saran; Bartlett, John; Kumarasamy, Nagalingeswaran; Katzenstein, David

2016-01-15

Virologic failure in subtype C is characterized by high resistance to first-line antiretroviral (ARV) drugs, including efavirenz, nevirapine, and lamivudine, with nucleoside resistance including type 2 thymidine analog mutations, K65R, a T69del, and M184V. However, genotypic algorithms predicting resistance are mainly based on subtype B viruses and may under- or overestimate drug resistance in non-B subtypes. To explore potential treatment strategies after first-line failure, we compared genotypic and phenotypic susceptibility of subtype C human immunodeficiency virus 1 (HIV-1) following first-line ARV failure. AIDS Clinical Trials Group 5230 evaluated patients failing an initial nonnucleoside reverse-transcriptase inhibitor (NNRTI) regimen in Africa and Asia, comparing the genotypic drug resistance and phenotypic profile from the PhenoSense (Monogram). Site-directed mutagenesis studies of K65R and T69del assessed the phenotypic impact of these mutations. Genotypic algorithms overestimated resistance to etravirine and rilpivirine, misclassifying 28% and 32%, respectively. Despite K65R with the T69del in 9 samples, tenofovir retained activity in >60%. Reversion of the K65R increased susceptibility to tenofovir and other nucleosides, while reversion of the T69del showed increased resistance to zidovudine, with little impact on other NRTI. Although genotype and phenotype were largely concordant for first-line drugs, estimates of genotypic resistance to etravirine and rilpivirine may misclassify subtype C isolates compared to phenotype. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

An invasive plant alters phenotypic selection on the vegetative growth of a native congener.

PubMed

Beans, Carolyn M; Roach, Deborah A

2015-02-01

The ecological consequences of plant competition have frequently been tested, but the evolutionary outcomes of these interactions have gone largely unexplored. The study of species invasions can make an important contribution to this field of research by allowing us to watch ecological and evolutionary processes unfold as a novel species is integrated into a plant community. We explored the ecological and evolutionary impact of an invasive jewelweed, Impatiens glandulifera, on a closely related native congener, I. capensis and asked: (1) Does the presence of the invasive jewelweed alter the fitness of native jewelweed populations? (2) Does the invasive jewelweed affect the vegetative growth of the native congener? and (3) Does the invasive jewelweed alter phenotypic selection on the vegetative traits of the native congener? We used a greenhouse competition experiment, an invasive species removal field experiment, and a survey of natural populations. We show that when the invasive jewelweed is present, phenotypic selection favors native jewelweed individuals investing less in rapid upward growth and more in branching and fruiting potential through the production of nodes. This research demonstrates that invasive plants have the potential to greatly alter natural selection on native competitors. Studies investigating altered selection in invaded communities can reveal the potential evolutionary impact of invasive competitors, while deepening our understanding of the more general role of competition in driving plant evolution and permitting species coexistence. © 2015 Botanical Society of America, Inc.

Confronting the Impact of Alcohol Labeling and Marketing on Native American Health and Culture. Hearing before the Select Committee on Children, Youth and Families. House of Representatives, One Hundred Second Congress, Second Session.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. House Select Committee on Children, Youth, and Families.

A congressional hearing examined the effects of alcohol labeling and marketing on Native American health and culture. The focus of the hearing was on "Crazy Horse" malt liquor, a product named for the spiritual and political leader of the Native American Sioux. Following opening remarks by presiding committee chairwoman, Patricia…

Favorable climate change response explains non-native species' success in Thoreau's woods.

PubMed

Willis, Charles G; Ruhfel, Brad R; Primack, Richard B; Miller-Rushing, Abraham J; Losos, Jonathan B; Davis, Charles C

2010-01-26

Invasive species have tremendous detrimental ecological and economic impacts. Climate change may exacerbate species invasions across communities if non-native species are better able to respond to climate changes than native species. Recent evidence indicates that species that respond to climate change by adjusting their phenology (i.e., the timing of seasonal activities, such as flowering) have historically increased in abundance. The extent to which non-native species success is similarly linked to a favorable climate change response, however, remains untested. We analyzed a dataset initiated by the conservationist Henry David Thoreau that documents the long-term phenological response of native and non-native plant species over the last 150 years from Concord, Massachusetts (USA). Our results demonstrate that non-native species, and invasive species in particular, have been far better able to respond to recent climate change by adjusting their flowering time. This demonstrates that climate change has likely played, and may continue to play, an important role in facilitating non-native species naturalization and invasion at the community level.

Effects of Using Personal Genotype Data on Student Learning and Attitudes in a Pharmacogenomics Course

PubMed Central

McDonough, Caitrin W.; Elsey, Amanda R.; Burkley, Benjamin; Cavallari, Larisa H.; Johnson, Julie A.

2016-01-01

Objective. To evaluate the impact of personal genotyping and a novel educational approach on student attitudes, knowledge, and beliefs regarding pharmacogenomics and genomic medicine. Methods. Two online elective courses (pharmacogenomics and genomic medicine) were offered to student pharmacists at the University of Florida using a flipped-classroom, patient-centered teaching approach. In the pharmacogenomics course, students could be genotyped and apply results to patient cases. Results. Thirty-four and 19 student pharmacists completed the pharmacogenomics and genomic medicine courses, respectively, and 100% of eligible students (n=34) underwent genotyping. Student knowledge improved after the courses. Seventy-four percent (n=25) of students reported better understanding of pharmacogenomics based on having undergone genotyping. Conclusions. Completion of a novel pharmacogenomics elective course sequence that incorporated personal genotyping and genomic medicine was associated with increased student pharmacist knowledge and improved clinical confidence with pharmacogenomics. PMID:27756930

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES)

PubMed Central

2009-01-01

Background Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD) risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP), formed from a sample from the Multiethnic Cohort (MEC) study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians). Sensitivity of ancestry estimates to relative sample size was considered. Results We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. Conclusion These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that it will be important to assess this heterogeneity within future association studies on Latino populations. Our study raises awareness of the diversity within "Latinos" and the necessity to assess appropriate risk and treatment management. PMID:19903357

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

PubMed

Shtir, Corina J; Marjoram, Paul; Azen, Stanley; Conti, David V; Le Marchand, Loic; Haiman, Christopher A; Varma, Rohit

2009-11-10

Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD) risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP), formed from a sample from the Multiethnic Cohort (MEC) study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians). Sensitivity of ancestry estimates to relative sample size was considered. We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that it will be important to assess this heterogeneity within future association studies on Latino populations. Our study raises awareness of the diversity within "Latinos" and the necessity to assess appropriate risk and treatment management.

Reconstructing Native American migrations from whole-genome and whole-exome data.

PubMed

Gravel, Simon; Zakharia, Fouad; Moreno-Estrada, Andres; Byrnes, Jake K; Muzzio, Marina; Rodriguez-Flores, Juan L; Kenny, Eimear E; Gignoux, Christopher R; Maples, Brian K; Guiblet, Wilfried; Dutil, Julie; Via, Marc; Sandoval, Karla; Bedoya, Gabriel; Oleksyk, Taras K; Ruiz-Linares, Andres; Burchard, Esteban G; Martinez-Cruzado, Juan Carlos; Bustamante, Carlos D

2013-01-01

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.

Unexpected inverse correlation between Native American ancestry and Asian American variants of HPV16 in admixed Colombian cervical cancer cases.

PubMed

Lopera, Esteban A; Baena, Armando; Florez, Victor; Montiel, Jehidys; Duque, Constanza; Ramirez, Tatiana; Borrero, Mauricio; Cordoba, Carlos M; Rojas, Fredy; Pareja, Rene; Bedoya, Astrid M; Bedoya, Gabriel; Sanchez, Gloria I

2014-12-01

European (E) variants of HPV 16 are evenly distributed among world regions, meanwhile Non-European variants such as European-Asian (EAs), Asian American (AA) and African (Af) are mostly confined to Eastern Asia, The Americas and African regions respectively. Several studies have shown that genetic variation of HPV 16 is associated with the risk of cervical cancer, which also seems to be dependent on the population. This relationship between ethnicity and variants have led to the suggestion that there is co-evolution of variants with humankind. Our aim was to evaluate the relationship between the individual ancestry proportion and infection with HPV 16 variants in cervical cancer. We examined the association between ancestry and HPV 16 variants in samples of 82 cervical cancer cases from different regions of Colombia. Individual ancestry proportions (European, African and Native American) were estimated by genotyping 106 ancestry informative markers. Variants were identified by PCR amplification of the E6 gene, followed by reverse line blot hybridization (RLB) with variants specific probes. Overall European (E) and Asian American (AA) variants frequency was 66.5% and 33.5% respectively. Similar distribution was observed in cases with higher proportions of European or African ancestry. A higher Native American ancestry was significantly associated with higher frequency of E variants (median ancestry>23.6%, Age and place of birth adjusted OR: 3.55, 95% CI: 1.26-10.03, p=0.01). Even further, an inverse geographic correlation between Native American ancestry and frequency of infections with AA variants was observed (ρ=-0.825, p=0.008). Regions with higher proportion of Native American ancestry had a lower frequency of AA variants of HPV 16. This study suggests replacement of AA variants by E variants of human papillomavirus 16 in cervical cancer cases with high Native American ancestry. Copyright © 2014 Elsevier B.V. All rights reserved.

Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

PubMed Central

Gravel, Simon; Muzzio, Marina; Rodriguez-Flores, Juan L.; Kenny, Eimear E.; Gignoux, Christopher R.; Maples, Brian K.; Guiblet, Wilfried; Dutil, Julie; Via, Marc; Sandoval, Karla; Bedoya, Gabriel; Oleksyk, Taras K.; Ruiz-Linares, Andres; Burchard, Esteban G.; Martinez-Cruzado, Juan Carlos; Bustamante, Carlos D.

2013-01-01

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations. PMID:24385924

Modulation of the COMT Val(158)Met polymorphism on resting-state EEG power.

PubMed

Solís-Ortiz, Silvia; Pérez-Luque, Elva; Gutiérrez-Muñoz, Mayra

2015-01-01

The catechol-O-methyltransferase (COMT) Val(158)Met polymorphism impacts cortical dopamine (DA) levels and may influence cortical electrical activity in the human brain. This study investigated whether COMT genotype influences resting-state electroencephalogram (EEG) power in the frontal, parietal and midline regions in healthy volunteers. EEG recordings were conducted in the resting-state in 13 postmenopausal healthy woman carriers of the Val/Val genotype and 11 with the Met/Met genotype. The resting EEG spectral absolute power in the frontal (F3, F4, F7, F8, FC3 and FC4), parietal (CP3, CP4, P3 and P4) and midline (Fz, FCz, Cz, CPz, Pz and Oz) was analyzed during the eyes-open and eyes-closed conditions. The frequency bands considered were the delta, theta, alpha1, alpha2, beta1 and beta2. EEG data of the Val/Val and Met/Met genotypes, brain regions and conditions were analyzed using a general linear model analysis. In the individuals with the Met/Met genotype, delta activity was increased in the eyes-closed condition, theta activity was increased in the eyes-closed and in the eyes-open conditions, and alpha1 band, alpha2 band and beta1band activity was increased in the eyes-closed condition. A significant interaction between COMT genotypes and spectral bands was observed. Met homozygote individuals exhibited more delta, theta and beta1 activity than individuals with the Val/Val genotype. No significant interaction between COMT genotypes and the resting-state EEG regional power and conditions were observed for the three brain regions studied. Our findings indicate that the COMT Val(158)Met polymorphism does not directly impact resting-state EEG regional power, but instead suggest that COMT genotype can modulate resting-state EEG spectral power in postmenopausal healthy women.

Modulation of the COMT Val158Met polymorphism on resting-state EEG power

PubMed Central

Solís-Ortiz, Silvia; Pérez-Luque, Elva; Gutiérrez-Muñoz, Mayra

2015-01-01

The catechol-O-methyltransferase (COMT) Val158Met polymorphism impacts cortical dopamine (DA) levels and may influence cortical electrical activity in the human brain. This study investigated whether COMT genotype influences resting-state electroencephalogram (EEG) power in the frontal, parietal and midline regions in healthy volunteers. EEG recordings were conducted in the resting-state in 13 postmenopausal healthy woman carriers of the Val/Val genotype and 11 with the Met/Met genotype. The resting EEG spectral absolute power in the frontal (F3, F4, F7, F8, FC3 and FC4), parietal (CP3, CP4, P3 and P4) and midline (Fz, FCz, Cz, CPz, Pz and Oz) was analyzed during the eyes-open and eyes-closed conditions. The frequency bands considered were the delta, theta, alpha1, alpha2, beta1 and beta2. EEG data of the Val/Val and Met/Met genotypes, brain regions and conditions were analyzed using a general linear model analysis. In the individuals with the Met/Met genotype, delta activity was increased in the eyes-closed condition, theta activity was increased in the eyes-closed and in the eyes-open conditions, and alpha1 band, alpha2 band and beta1band activity was increased in the eyes-closed condition. A significant interaction between COMT genotypes and spectral bands was observed. Met homozygote individuals exhibited more delta, theta and beta1 activity than individuals with the Val/Val genotype. No significant interaction between COMT genotypes and the resting-state EEG regional power and conditions were observed for the three brain regions studied. Our findings indicate that the COMT Val158Met polymorphism does not directly impact resting-state EEG regional power, but instead suggest that COMT genotype can modulate resting-state EEG spectral power in postmenopausal healthy women. PMID:25883560

Genetic variants of APOC3 promoter and HLA-B genes in an HIV infected cohort in northern South Africa: a pilot study.

PubMed

Masebe, Tracy; Bessong, Pascal Obong; Ndip, Roland Ndip; Meyer, Debra

2014-06-26

Metabolic disorders and hypersensitivities affect tolerability and impact adherence to highly active antiretroviral therapy (HAART). The aim of this study was to determine the prevalence of C-482T/T-455C variants in the Apolipoprotein C3 (APOC3) promoter gene and Human leukocyte antigen (HLA)-B*57:01, known to impact lipid metabolic disorders and hypersensitivity respectively; and to correlate genotypes with gender, CD4+ cell count and viral load in an HIV infected cohort in northern South Africa. Frequencies of C-482 and T-455 polymorphisms in APOC3 were determined by restriction fragment length polymorphism analysis. Allele determination for HLA-B was performed with Assign SBT software in an HLA library. Analysis of APOC3 C-482 site revealed a prevalence of 196/199 (98.5%) for CC, 1/199 (0.5%) for CT and 2/199 (1.0%) for TT genotype (p = 0.000 with 1° of freedom; χ2 = 126.551). For the T-455 site, prevalences were: 69/199 (35%) for TT and 130/199 (65%) for the CC genotype (p = 0.000 with 1° of freedom; χ2 = 199). There was no association between gender and the presence of -482 (p = 1; χ2 = 0.00001) or -455 genotypes (p = 0.1628; χ2 = 1.9842). There was no significant difference in the increase in CD4+ cell count irrespective of genotypes. Significant increases in CD4+ cell count were observed in males and females considering the -455C genotype, but not in males for the -455T genotype. Viral load decreases were significant with the -455C and -482C genotypes irrespective of gender. HLA-B*57:01 was not identified in the study cohort. The apparently high prevalence of APOC3 T-455CC genotype needs confirmation with a larger samples size and triglyceride measurements to support screening of patients to pre-empt HAART associated lipid disorders.

A trial of two trouts: Comparing the impacts of rainbow and brown trout on a native galaxiid

USGS Publications Warehouse

Young, K.A.; Dunham, J.B.; Stephenson, J.F.; Terreau, A.; Thailly, A.F.; Gajardo, G.; de Leaniz, C. G.

2010-01-01

Rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta are the world's two most widespread exotic fishes, dominate the fish communities of most cold-temperate waters in the southern hemisphere and are implicated in the decline and extirpation of native fish species. Here, we provide the first direct comparison of the impacts of rainbow and brown trout on populations of a native fish by quantifying three components of exotic species impact: range, abundance and effect. We surveyed 54 small streams on the island of Chilo?? in Chilean Patagonia and found that the rainbow trout has colonized significantly more streams and has a wider geographic range than brown trout. The two species had similar post-yearling abundances in allopatry and sympatry, and their abundances depended similarly on reach-level variation in the physical habitat. The species appeared to have dramatically different effects on native drift-feeding Aplochiton spp., which were virtually absent from streams invaded by brown trout but shared a broad sympatric range with rainbow trout. Within this range, the species' post-yearling abundances varied independently before and after controlling for variation in the physical habitat. In the north of the island, Aplochiton spp. inhabited streams uninvaded by exotic trouts. Our results provide a context for investigating the mechanisms responsible for apparent differences in rainbow and brown trout invasion biology and can help inform conservation strategies for native fishes in Chilo?? and elsewhere. ?? 2010 The Authors. Journal compilation ?? 2010 The Zoological Society of London.

Parasites and genetic diversity in an invasive bumblebee.

PubMed

Jones, Catherine M; Brown, Mark J F

2014-11-01

Biological invasions are facilitated by the global transportation of species and climate change. Given that invasions may cause ecological and economic damage and pose a major threat to biodiversity, understanding the mechanisms behind invasion success is essential. Both the release of non-native populations from natural enemies, such as parasites, and the genetic diversity of these populations may play key roles in their invasion success. We investigated the roles of parasite communities, through enemy release and parasite acquisition, and genetic diversity in the invasion success of the non-native bumblebee, Bombus hypnorum, in the United Kingdom. The invasive B. hypnorum had higher parasite prevalence than most, or all native congeners for two high-impact parasites, probably due to higher susceptibility and parasite acquisition. Consequently parasites had a higher impact on B. hypnorum queens' survival and colony-founding success than on native species. Bombus hypnorum also had lower functional genetic diversity at the sex-determining locus than native species. Higher parasite prevalence and lower genetic diversity have not prevented the rapid invasion of the United Kingdom by B. hypnorum. These data may inform our understanding of similar invasions by commercial bumblebees around the world. This study suggests that concerns about parasite impacts on the small founding populations common to re-introduction and translocation programs may be less important than currently believed. © 2014 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability.

PubMed

Drummond, Emily B M; Vellend, Mark

2012-01-01

Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass) clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects), whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture). Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations.

CYP2C9 Genotype-Dependent Warfarin Pharmacokinetics: Impact of CYP2C9 Genotype on R- and S-Warfarin and Their Oxidative Metabolites.

PubMed

Flora, Darcy R; Rettie, Allan E; Brundage, Richard C; Tracy, Timothy S

2017-03-01

Multiple factors can impact warfarin therapy, including genetic variations in the drug-metabolizing enzyme cytochrome P450 2C9 (CYP2C9). Compared with individuals with the wild-type allele, CYP2C9*1, carriers of the common *3 variant have significantly impaired CYP2C9 metabolism. Genetic variations in CYP2C9, the primary enzyme governing the metabolic clearance of the more potent S-enantiomer of the racemic anticoagulant warfarin, may impact warfarin-drug interactions. To establish a baseline for such studies, plasma and urine concentrations of R- and S-warfarin and 10 warfarin metabolites were monitored for up to 360 hours following a 10-mg warfarin dose in healthy subjects with 4 different CYP2C9 genotypes: CYP2C9*1/*1 (n = 8), CYP2C9*1/*3 (n = 9), CYP2C9*2/*3 (n = 3), and CYP2C9*3/*3 (n = 4). Plasma clearance of S-warfarin, but not R-warfarin, decreased multiexponentially and in a CYP2C9 gene-dependent manner: 56%, 70%, and 75% for CYP2C9*1/*3, CYP2C9*2/*3, and CYP2C9*3/*3 genotypes, respectively, compared with CYP2C9*1/*1, resulting in pronounced differences in the S:R ratio that identified warfarin-sensitive genotypes. CYP2C9 was the primary P450 enzyme contributing to S-warfarin metabolism and a minor contributor to R-warfarin metabolism. In the presence of a defective CYP2C9 allele, switching of warfarin metabolism to other oxidative pathways and P450 enzymes for the metabolic elimination of S-warfarin was not observed. The 10-hydroxywarfarin metabolites, whose detailed pharmacokinetics are reported for the first time, exhibited a prolonged half-life with no evidence of renal excretion and displayed elimination rate-limited kinetics. Understanding the impact of CYP2C9 genetics on warfarin pharmacokinetics lays the foundation for future genotype-dependent warfarin-drug interaction studies. © 2016, The American College of Clinical Pharmacology.

Comparison of parasitological and productive traits of Criollo lambs native to the central Mexican Plateau and Suffolk lambs experimentally infected with Haemonchus contortus.

PubMed

Alba-Hurtado, F; Romero-Escobedo, E; Muñoz-Guzmán, M A; Torres-Hernández, G; Becerril-Pérez, C M

2010-09-20

The study compares the parasitological and productive traits of Criollo lambs native to the central Mexican Plateau (CNCMP) and Suffolk (SU) lambs experimentally infected with Haemonchus contortus. CNCMP lambs (n=20) and SU lambs (n=15) were infected with L3 of H. contortus while five lambs of each genotype were kept as controls. Fecal egg count (FEC), packed cell volume (PCV), blood eosinophil number (BEN), ocular mucous membrane color (as measured by the FAMACHA index), changes in body condition score (BCS) and cumulative live weight gain (CLWG) were measured weekly during a 20-week period. On week 20, all animals were euthanized and the number of adult worms (AW) in the abomasum was counted. Infected SU lambs had higher (p<0.05) FEC and AW mean values compared to CNCMP lambs, which had a higher mean BEN count (p<0.05). Infected lambs had lower PCV values than controls, regardless of genotype, and had a negative correlation (r=-0.84, p<0.05) with the FAMACHA index. BCS tended to decline for infected SU lambs and increased slightly for infected CNCMP lambs. CLWG differed in all groups (p<0.05); infected SU lambs gained 12.1+/-1.9kg, infected CNCMP lambs gained 18.8+/-0.7kg, control SU lambs gained 34.6+/-1.6kg, and control CNCMP lambs gained 26.9+/-0.8kg. In conclusion, CNCMP lambs had a smaller worm burden, a better ability to maintain their productive traits, and were less affected by infection with Haemonchus contortus.

Two colonisation stages generate two different patterns of genetic diversity within native and invasive ranges of Ulex europaeus

PubMed Central

Hornoy, B; Atlan, A; Roussel, V; Buckley, Y M; Tarayre, M

2013-01-01

Genetic diversity and the way a species is introduced influence the capacity of populations of invasive species to persist in, and adapt to, their new environment. The diversity of introduced populations affects their evolutionary potential, which is particularly important for species that have invaded a wide range of habitats and climates, such as European gorse, Ulex europaeus. This species originated in the Iberian peninsula and colonised Europe in the Neolithic; over the course of the past two centuries it was introduced to, and has become invasive in, other continents. We characterised neutral genetic diversity and its structure in the native range and in invaded regions. By coupling these results with historical data, we have identified the way in which gorse populations were introduced and the consequences of introduction history on genetic diversity. Our study is based on the genotyping of individuals from 18 populations at six microsatellite loci. As U. europaeus is an allohexaploid species, we used recently developed tools that take into account genotypic ambiguity. Our results show that genetic diversity in gorse is very high and mainly contained within populations. We confirm that colonisation occurred in two stages. During the first stage, gorse spread out naturally from Spain towards northern Europe, losing some genetic diversity. During the second stage, gorse was introduced by humans into different regions of the world, from northern Europe. These introductions resulted in the loss of rare alleles but did not significantly reduce genetic diversity and thus the evolutionary potential of this invasive species. PMID:23759725

Two colonisation stages generate two different patterns of genetic diversity within native and invasive ranges of Ulex europaeus.

PubMed

Hornoy, B; Atlan, A; Roussel, V; Buckley, Y M; Tarayre, M

2013-11-01

Genetic diversity and the way a species is introduced influence the capacity of populations of invasive species to persist in, and adapt to, their new environment. The diversity of introduced populations affects their evolutionary potential, which is particularly important for species that have invaded a wide range of habitats and climates, such as European gorse, Ulex europaeus. This species originated in the Iberian peninsula and colonised Europe in the Neolithic; over the course of the past two centuries it was introduced to, and has become invasive in, other continents. We characterised neutral genetic diversity and its structure in the native range and in invaded regions. By coupling these results with historical data, we have identified the way in which gorse populations were introduced and the consequences of introduction history on genetic diversity. Our study is based on the genotyping of individuals from 18 populations at six microsatellite loci. As U. europaeus is an allohexaploid species, we used recently developed tools that take into account genotypic ambiguity. Our results show that genetic diversity in gorse is very high and mainly contained within populations. We confirm that colonisation occurred in two stages. During the first stage, gorse spread out naturally from Spain towards northern Europe, losing some genetic diversity. During the second stage, gorse was introduced by humans into different regions of the world, from northern Europe. These introductions resulted in the loss of rare alleles but did not significantly reduce genetic diversity and thus the evolutionary potential of this invasive species.

Risk and pathway assessment for the introduction of exotic insects and pathogens that could affect Hawai'i's native forests

Treesearch

Gregg A. DeNitto; Philip Cannon; Andris Eglitis; Jessie A. Glaeser; Helen Maffei; Sheri Smith

2015-01-01

The unmitigated risk potential of the introduction of exotic insects and pathogens to Hawai'i was evaluated for its impact on native plants, specifically Acacia koa, Cibotium spp., Dicranopteris linearis, Diospyros sandwicensis, Dodonaea viscosa, ...

A large indel mutation of the bovine ADD1/SREBP1c gene and its effects on growth traits in some native cattle breeds from China.

PubMed

Huang, Yong-Zhen; Zhang, En-Ping; Wang, Jing; Huai, Yong-Tao; Ma, Liang; Chen, Fu-Ying; Lan, Xian-Yong; Lei, Chu-Zhao; Fang, Xing-Tang; Wang, Ju-Qiang; Chen, Hong

2011-03-01

Adipocyte determination and differentiation-dependent factor 1/sterol regulatory element-binding protein-1c (ADD1/SREBP1c) is a major determinant of tissue differential lipogenic capacity in mammalian and avian species. The objectives of the present study were to focus on insertion-deletion polymorphism (indel) in the bovine ADD1/SREBP1c gene, and analyzing its effect on growth traits in a sample of 1035 cattle belonging to four Chinese cattle breeds. PCR-SSCP, DNA sequencing and agarose electrophoresis methods were used. The 778 bp PCR products of ADD1/SREBP1c gene exhibited three genotypes and two alleles were revealed: W and D. Frequencies of the W allele varied from 0.8651 to 1.000. The associations of the 84 bp indel mutation of ADD1/SREBP1c gene with growth traits of 265 Nanyang cows were analyzed. The animals with genotype WD had significantly higher birth weight, body weight, average daily gain than those with genotype WW at birth, 6-, 12-, 18-, and 24-month old (P < 0.05 or P < 0.01). These results suggest that the indel mutation of bovine ADD1/SREBP1c gene may influence the growth traits in cattle.

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.

PubMed

Yurchenko, Andrey; Yudin, Nikolay; Aitnazarov, Ruslan; Plyusnina, Alexandra; Brukhin, Vladimir; Soloshenko, Vladimir; Lhasaranov, Bulat; Popov, Ruslan; Paronyan, Ivan A; Plemyashov, Kirill V; Larkin, Denis M

2018-01-01

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies.

PubMed

Fondevila, M; Phillips, C; Santos, C; Freire Aradas, A; Vallone, P M; Butler, J M; Lareu, M V; Carracedo, A

2013-01-01

A revision of an established 34 SNP forensic ancestry test has been made by swapping the under-performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for the revised SNP set in 66 reference populations from 1000 Genomes and HGDP-CEPH panels and used this as reference data to analyse four U.S. populations showing a range of admixture patterns. The U.S. Hispanics sample in particular displayed heterogeneous values of co-ancestry between European, Native American and African contributors, likely to reflect in part, the way this disparate group is defined using cultural as well as population genetic parameters. The genotyping of over 700 U.S. population samples also provided the opportunity to thoroughly gauge peak mobility variation and peak height ratios observed from routine use of the single base extension chemistry of the 34-plex test. Finally, the genotyping of the widely used DNA profiling Standard Reference Material samples plus other control DNAs completes the audit of the 34-plex assay to allow forensic practitioners to apply this test more readily in their own laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Native American casino gambling in Arizona: A case study of the Fort McDowell reservation.

PubMed

Anders, G C

1996-09-01

Since Congress passed the American Indian Gambling Regulatory Act (IGRA) in 1988, there has been an explosion in the number of gambling casinos located on Native American reservations. It is estimated that in 1994 the total net revenue from 81 Native American casinos exceeded $2.3 billion dollars. As the number of Native American casinos grows along with the volume of gambling activity, opposition increases from states, the established gambling industry hurt by lost revenues, and groups with moral objections to gambling. This article reports on an effort to measure the economic impact of the Fort McDowell casino located near Phoenix, Arizona. The article discusses the casino's history and current operations. Next, it explains the use of an input-output model to compute the impact of casino's income and employment effects on the economy of Maricopa County. It is estimated that the casino is responsible for 2,483 new jobs, and an increase of approximately $80.35 million in regional output. Additional information is necessary to more accurately assess both the benefits and costs of the casino. Unfortunately, subsequent efforts to collect additional data have been unsuccessful. The conclusion discusses why, and raises questions regarding Native American gaming.

Invasion of non-native grasses causes a drop in soil carbon storage in California grasslands

NASA Astrophysics Data System (ADS)

Koteen, Laura E.; Baldocchi, Dennis D.; Harte, John

2011-10-01

Vegetation change can affect the magnitude and direction of global climate change via its effect on carbon cycling among plants, the soil and the atmosphere. The invasion of non-native plants is a major cause of land cover change, of biodiversity loss, and of other changes in ecosystem structure and function. In California, annual grasses from Mediterranean Europe have nearly displaced native perennial grasses across the coastal hillsides and terraces of the state. Our study examines the impact of this invasion on carbon cycling and storage at two sites in northern coastal California. The results suggest that annual grass invasion has caused an average drop in soil carbon storage of 40 Mg/ha in the top half meter of soil, although additional mechanisms may also contribute to soil carbon losses. We attribute the reduction in soil carbon storage to low rates of net primary production in non-native annuals relative to perennial grasses, a shift in rooting depth and water use to primarily shallow sources, and soil respiratory losses in non-native grass soils that exceed production rates. These results indicate that even seemingly subtle land cover changes can significantly impact ecosystem functions in general, and carbon storage in particular.

Interference competition between an invasive parakeet and native bird species at feeding sites.

PubMed

Le Louarn, Marine; Couillens, Bertrand; Deschamps-Cottin, Magali; Clergeau, Philippe

2016-01-01

Interference competition has proved to be a factor of successful establishment of invasive species. This type of competition may have a stronger impact when native species have temporal niche overlap with the invasive species. The ring-necked parakeet Psittacula krameri has been successfully introduced in many countries and its interspecific agonistic behavior has already been reported. The purpose of this study is to analyze the territorial and preemptive interference competition between the ring-necked parakeet and native bird species in a recently colonized area. We used an empirical approach by recording video sequences in gardens equipped with bird feeders in winter. Our results showed that the ring-necked parakeet was the most frequent species at the feeders. Several native species showed temporal niche overlap with the ring-necked parakeet, the highest overlap being with the starling Sturnus vulgaris . The starling was also the species most impacted by interference competition with the parakeet. Our study suggests that, by being most frequently present at the feeders, by demonstrating the most agonistic behavior and by hindering access to food of the other species, the ring-necked parakeet is a superior competitor and may compete with native bird species.

Native Peoples-Native Homelands Climate Change Workshop: Lessons Learned

NASA Technical Reports Server (NTRS)

Maynard, Nancy G.

2003-01-01

The Native Peoples-Native Homelands Climate Change Workshop was held on October 28 through November 01,1998, as part of a series of workshops being held around the U.S. to improve the understanding of the potential consequences of climate variability and change for the Nation. This workshop was specifically designed by Native Peoples to examine the impacts of climate change and extreme weather variability on Native Peoples and Native Homelands from an indigenous cultural and spiritual perspective and to develop recommendations as well as identify potential response actions. The workshop brought together interested Native Peoples, representatives of Tribal governments, traditional elders, Tribal leaders, natural resource managers, Tribal College faculty and students, and climate scientists fiom government agencies and universities. It is clear that Tribal colleges and universities play a unique and critical role in the success of these emerging partnerships for decision-making in addition to the important education function for both Native and non-Native communities such as serving as a culturally-appropriate vehicle for access, analysis, control, and protection of indigenous cultural and intellectual property. During the discussions between scientists and policy-makers from both Native and non-Native communities, a number of important lessons emerged which are key to building more effective partnerships between Native and non-Native communities for collaboration and decision-making for a more sustainable future. This talk summarizes the key issues, recommendations, and lessons learned during this workshop.

A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

PubMed

Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

2014-01-01

Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

North American Birds as Potential Amplifying Hosts of Japanese Encephalitis Virus

PubMed Central

Nemeth, Nicole; Bosco-Lauth, Angela; Oesterle, Paul; Kohler, Dennis; Bowen, Richard

2012-01-01

Japanese encephalitis virus (JEV) is an emerging arbovirus, and inter-continental spread is an impending threat. The virus is maintained in a transmission cycle between mosquito vectors and vertebrate hosts, including birds. We detected variation in interspecies responses among North American birds to infection with strains of two different JEV genotypes (I and III). Several native North American passerine species and ring-billed gulls had the highest average peak viremia titers after inoculation with a Vietnamese (genotype I) JEV strain. Oral JEV shedding was minimal and cloacal shedding was rarely detected. The majority of birds, both viremic (72 of 74; 97.3%) and non-viremic (31 of 37; 83.8%), seroconverted by 14 days post-inoculation and West Nile virus-immune individuals had cross-protection against JEV viremia. Reservoir competence and serologic data for a variety of avian taxa are important for development of JEV surveillance and control strategies and will aid in understanding transmission ecology in the event of JEV expansion to North America. PMID:22927494

Toxoplasma gondii antibody prevalence and two new genotypes of the parasite in endangered Hawaiian Geese (nene: Branta sandvicensis)

USGS Publications Warehouse

Work, Thierry M.; Verma, Shiv K.; Su, Chunlei; Medeiros, John; Kaiakapu, Thomas; Kwok, Oliver C.; Dubey, Jitender P.

2016-01-01

Toxoplasma gondii is a protozoan parasite transmitted by domestic cats (Felis catus) that has historically caused mortality in native Hawaiian birds. To estimate how widespread exposure to the parasite is in nene (Hawaiian Geese, Branta sandvicensis), we did a serologic survey for T. gondii antibody and genetically characterized parasite DNA from the tissues of dead birds that had confirmed infections by immunohistochemistry. Of 94 geese sampled, prevalence on the island of Kauai, Maui, and Molokai was 21% (n=42), 23% (n=31), and 48% (n=21), respectively. Two new T. gondii genotypes were identified by PCR-restriction fragment length polymorphism from four geese, and these appeared segregated geographically. Exposure to T. gondii in wild nene is widespread and, while the parasite is not a major cause of death, it could have sublethal or behavioral effects. How to translate such information to implement effective ways to manage feral cats in Hawaii poses challenges.

Genotype Specification Language.

PubMed

Wilson, Erin H; Sagawa, Shiori; Weis, James W; Schubert, Max G; Bissell, Michael; Hawthorne, Brian; Reeves, Christopher D; Dean, Jed; Platt, Darren

2016-06-17

We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.

Impacts of invasive plants on carbon pools depend on both species' traits and local climate.

PubMed

Martin, Philip A; Newton, Adrian C; Bullock, James M

2017-04-01

Invasive plants can alter ecosystem properties, leading to changes in the ecosystem services on which humans depend. However, generalizing about these effects is difficult because invasive plants represent a wide range of life forms, and invaded ecosystems differ in their plant communities and abiotic conditions. We hypothesize that differences in traits between the invader and native species can be used to predict impacts and so aid generalization. We further hypothesize that environmental conditions at invaded sites modify the effect of trait differences and so combine with traits to predict invasion impacts. To test these hypotheses, we used systematic review to compile data on changes in aboveground and soil carbon pools following non-native plant invasion from studies across the World. Maximum potential height (H max ) of each species was drawn from trait databases and other sources. We used meta-regression to assess which of invasive species' H max , differences in this height trait between native and invasive plants, and climatic water deficit, a measure of water stress, were good predictors of changes in carbon pools following invasion. We found that aboveground biomass in invaded ecosystems relative to uninvaded ones increased as the value of H max of invasive relative to native species increased, but that this effect was reduced in more water stressed ecosystems. Changes in soil carbon pools were also positively correlated with the relative H max of invasive species, but were not altered by water stress. This study is one of the first to show quantitatively that the impact of invasive species on an ecosystem may depend on differences in invasive and native species' traits, rather than solely the traits of invasive species. Our study is also the first to show that the influence of trait differences can be altered by climate. Further developing our understanding of the impacts of invasive species using this framework could help researchers to identify not only potentially dangerous invasive species, but also the ecosystems where impacts are likely to be greatest. © 2017 by the Ecological Society of America.

Impact of hepatitis C virus recombinant form RF1_2k/1b on treatment outcomes within the Georgian national hepatitis C elimination program.

PubMed

Karchava, Marine; Chkhartishvili, Nikoloz; Sharvadze, Lali; Abutidze, Akaki; Dvali, Natia; Gatserelia, Lana; Dzigua, Lela; Bolokadze, Natalia; Dolmazashvili, Ekaterine; Kotorashvili, Adam; Imnadze, Paata; Gamkrelidze, Amiran; Tsertsvadze, Tengiz

2018-01-01

Hepatitis C virus (HCV) recombinant form RF1_2k/1b is common in ethnic Georgians. This chimera virus contains genomic fragments of genotype 2 and genotype 1 and is misclassified as genotype 2 by standard genotyping. We aimed to identify RF1_2k/1b strains among genotype 2 patients and assess its impact on treatment outcomes. The study included 148 patients with HCV genotype 2 as determined by 5-untranslated region/core genotyping assay. RF1_2k/1b was identified by sequencing the non-structural protein 5B region. Patients were treated within the national hepatitis C elimination program with sofosbuvir/ribavirin (SOF/RBV), interferon (IFN)/SOF/RBV, or ledipasvir (LDV)/SOF/RBV. Of 148 patients, 103 (69.5%) had RF1_ 2k/1b. Sustained virologic response (SVR) data was available for 136 patients (RF1_ 2k/1b, n = 103; genotype 2, n = 33). Sustained virologic response was achieved in more genotype 2 patient than in RF1_2k/1b patients (97.0% vs. 76.7%, P = 0.009). Twelve weeks of LDV/SOF/RBV treatment was highly effective (100% SVR) in both genotypes. Among RF1_2k/1b patients, LDV/SOF/RBV for 12 weeks was superior (100% SVR) to SOF/RBV for 12 weeks (56.4%, P < 0.0001) or 20 weeks (79.2%, P = 0.05). Twelve weeks of IFN/SOF/RBV also showed better response than SOF/RBV for 12 weeks (88.9% vs. 56.4%, P = 0.02) in these patients. High prevalence of the RF1_2k/1b strain can significantly affect treatment outcomes. Treatment with IFN/SOF/RBV and especially LDV/SOF/RBV ensured significantly higher SVR in patients infected with RF1_2k/1b strain compared to standard HCV genotype 2 treatment with SOF/RBV. There is a need to reassess existing methods for the management of HCV genotype 2 infections, especially in areas with high prevalence of the RF1_2k/1b strain. © 2017 The Japan Society of Hepatology.

75 FR 38540 - Notice of Availability of Final Supplemental Environmental Impact Statement Updating Cumulative...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-02

... cumulative impacts including potential impacts to air quality, minerals, Native American and cultural... additional 350 feet below what had been previously authorized, to expand waste rock disposal facilities and...

The forensic use of behavioral genetics in criminal proceedings: Case of the MAOA-L genotype.

PubMed

McSwiggan, Sally; Elger, Bernice; Appelbaum, Paul S

The role of behavioral genetic evidence in excusing and mitigating criminal behavior is unclear. Research has suggested that a low activity genotype of the enzyme monoamine oxidase (MAOA-L) may increase the risk for aggressive and antisocial behavior. By examining criminal proceedings in which MAOA-L genotype evidence was introduced, we explored the forensic uses of behavioral genetic science. Westlaw and LexisNexis legal databases were electronically searched for cases from 1995 to 2016 to identify court documents from cases involving the MAOA-L genotype. Evidence of the MAOA-L genotype was included in records from 11 criminal cases (9 U.S. and 2 Italian). In the guilt phase, genotype evidence was ruled admissible in one of two cases, and may have contributed to a conviction on a lesser charge. In the sentencing phase, genotype evidence was admissible in four of five cases, one of which ended with a lesser sentence. Five cases used genotype evidence for post-conviction appeals, two of which resulted in sentence reductions. Even when charges or sentences are reduced it is difficult to gauge the effect of evidence of the MAOA-L genotype. Genotype evidence may lack persuasive effect because the impact of the allele on a particular accused is difficult to establish. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Forensic Use of Behavioral Genetics in Criminal Proceedings: Case of the MAOA-L Genotype

PubMed Central

McSwiggan, Sally; Elger, Bernice; Appelbaum, Paul S.

2016-01-01

The role of behavioral genetic evidence in excusing and mitigating criminal behavior is unclear. Research has suggested that a low activity genotype of the enzyme monoamine oxidase (MAOA-L) may increase the risk for aggressive and antisocial behavior. By examining criminal proceedings in which MAOA-L genotype evidence was introduced, we explored the forensic uses of behavioral genetic science. Westlaw and LexisNexis legal databases were electronically searched for cases from 1995–2016 to identify court documents from cases involving the MAOA-L genotype. Evidence of the MAOA-L genotype was included in records from 11 criminal cases (9 U.S. and 2 Italian). In the guilt phase, genotype evidence was ruled admissible in one of two cases, and may have contributed to a conviction on a lesser charge. In the sentencing phase, genotype evidence was admissible in four of five cases, one of which ended with a lesser sentence. Five cases used genotype evidence for post-conviction appeals, two of which resulted in sentence reductions. Even when charges or sentences are reduced it is difficult to gauge the effect of evidence of the MAOA-L genotype. Genotype evidence may lack persuasive effect because the impact of the allele on a particular accused is difficult to establish. PMID:27823806

Reconstructing Native American Population History

PubMed Central

Reich, David; Patterson, Nick; Campbell, Desmond; Tandon, Arti; Mazieres, Stéphane; Ray, Nicolas; Parra, Maria V.; Rojas, Winston; Duque, Constanza; Mesa, Natalia; García, Luis F.; Triana, Omar; Blair, Silvia; Maestre, Amanda; Dib, Juan C.; Bravi, Claudio M.; Bailliet, Graciela; Corach, Daniel; Hünemeier, Tábita; Bortolini, Maria-Cátira; Salzano, Francisco M.; Petzl-Erler, María Luiza; Acuña-Alonzo, Victor; Aguilar-Salinas, Carlos; Canizales-Quinteros, Samuel; Tusié-Luna, Teresa; Riba, Laura; Rodríguez-Cruz, Maricela; Lopez-Alarcón, Mardia; Coral-Vazquez, Ramón; Canto-Cetina, Thelma; Silva-Zolezzi, Irma; Fernandez-Lopez, Juan Carlos; Contreras, Alejandra V.; Jimenez-Sanchez, Gerardo; Gómez-Vázquez, María José; Molina, Julio; Carracedo, Ángel; Salas, Antonio; Gallo, Carla; Poletti, Giovanni; Witonsky, David B.; Alkorta-Aranburu, Gorka; Sukernik, Rem I.; Osipova, Ludmila; Fedorova, Sardana; Vasquez, René; Villena, Mercedes; Moreau, Claudia; Barrantes, Ramiro; Pauls, David; Excoffier, Laurent; Bedoya, Gabriel; Rothhammer, Francisco; Dugoujon, Jean Michel; Larrouy, Georges; Klitz, William; Labuda, Damian; Kidd, Judith; Kidd, Kenneth; Rienzo, Anna Di; Freimer, Nelson B.; Price, Alkes L.; Ruiz-Linares, Andrés

2013-01-01

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America. PMID:22801491

Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations.

PubMed

Cubillos, Francisco A; Vásquez, Claudia; Faugeron, Sylvain; Ganga, Angélica; Martínez, Claudio

2009-01-01

Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding (F(is)) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.

Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

PubMed

Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

2005-01-01

In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas

PubMed Central

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible. PMID:24671218

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.

PubMed

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.

Native and agricultural forests at risk to a changing climate in the Northern Plains

USDA-ARS?s Scientific Manuscript database

Native and agricultural forests in the Northern Plains provide ecosystem services that benefit human society—diversified agricultural systems, forest-based products, and rural vitality. The impacts of recent trends in temperature and disturbances are impairing the delivery of these services. Climate...

Community-based research as a mechanism to reduce environmental health disparities in American Indian and Alaska Native communities

EPA Science Inventory

Racial and ethnic minority communities, including American Indian and Alaska Natives, have been disproportionately impacted by environmental pollution and contamination. This includes siting and location of point sources of pollution, legacies of contamination of drinking and re...

Particle exposure and the historical loss of Native American lives to infections

EPA Science Inventory

This is a letter to the editor-excerpt: An alternative reason for the devastating loss of Native American lives to infectious diseases introduced through interactions with Europeans could include an impact of exposure to particulate matter (PM) associated with the preparation of...

Evaluating winter/spring seeding of a native perennial bunchgrass in the sagebrush steppe

USDA-ARS?s Scientific Manuscript database

Sagebrush (Artemisia tridentata Nutt.) plant communities in the US Great Basin region are being severely impacted by increasingly frequent wildfires in association with the expansion of exotic annual grasses. Maintenance of native perennial bunchgrasses is key to controlling annual grass expansion,...

Biological control of Botrytis cinerea: interactions with native vineyard yeasts from Washington State

USDA-ARS?s Scientific Manuscript database

Native fermentations are of increasing interest to Washington and US winemakers and consumers. This, and environmental impact concerns, warrant the exploration of biological control as an alternative to chemical fungicides. The objective of this study was to characterize the biological control activ...

36 CFR 251.123 - Most directly affected Native Corporation determination.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the only opportunity to apply for most directly affected status for that particular CSU. (1) At a... assessment of the socioeconomic impacts (including changes in historical and traditional use and... Native Corporation's population centers and/or business address to the applicable CSU; (2) Socioeconomic...

A review of Ruffe (Gymnocephalus cernuus) life history in its native versus non-native range

EPA Science Inventory

Invasive Ruffe (Gymnocephalus cernuus) have caused or have the potential to cause negative economic and ecological impacts in North America (particularly the Laurentian Great Lakes), the European Union, Scandinavian countries, and the United Kingdom. To better predict potential f...

Expansion of an exotic species and concomitant disease outbreaks: pigeon paramyxovirus in free-ranging Eurasian collared doves.

PubMed

Schuler, Krysten L; Green, David E; Justice-Allen, Anne E; Jaffe, Rosemary; Cunningham, Mark; Thomas, Nancy J; Spalding, Marilyn G; Ip, Hon S

2012-06-01

Eurasian collared doves (Streptopelia decaocto) have expanded their range across the United States since their introduction several decades ago. Recent mortality events in Eurasian collared doves in Arizona and Montana, USA, during the winter of 2009-2010 were the result of pigeon paramyxovirus (PPMV), a novel disease agent. The first instance of mortality by this emerging infectious disease in this species occurred in Florida in 2001 with subsequent disease events in 2006 and 2008. Full diagnostic necropsies were performed on carcasses from the three states. PPMV was identified by RT-PCR and virus isolation and was sequenced to the VIb genotype of avian paramyxovirus-1 (APMV). Other APMVs are common in a variety of free-ranging birds, but concern is warranted because of the potential for commingling of this species with native birds, virus evolution, and threats to domestic poultry. Improved surveillance for wildlife mortality events and efforts to prevent introduction of non-native animals could reduce the threat of introducing new pathogens.

Genetic patterns across multiple introductions of the globally invasive crab genus Carcinus.

PubMed

Darling, John A; Bagley, Mark J; Roman, Joe; Tepolt, Carolyn K; Geller, Jonathan B

2008-12-01

The European green crab Carcinus maenas is one of the world's most successful aquatic invaders, having established populations on every continent with temperate shores. Here we describe patterns of genetic diversity across both the native and introduced ranges of C. maenas and its sister species, C. aestuarii, including all known non-native populations. The global data set includes sequences from the mitochondrial cytochrome c oxidase subunit I gene, as well as multilocus genotype data from nine polymorphic nuclear microsatellite loci. Combined phylogeographic and population genetic analyses clarify the global colonization history of C. maenas, providing evidence of multiple invasions to Atlantic North America and South Africa, secondary invasions to the northeastern Pacific, Tasmania, and Argentina, and a strong likelihood of C. maenas x C. aestuarii hybrids in South Africa and Japan. Successful C. maenas invasions vary broadly in the degree to which they retain genetic diversity, although populations with the least variation typically derive from secondary invasions or from introductions that occurred more than 100 years ago.

Expansion of an exotic species and concomitant disease outbreaks: pigeon paramyxovirus in free-ranging Eurasian collared doves

USGS Publications Warehouse

Schuler, Krysten L.; Green, David E.; Justice-Allen, Anne E.; Jaffe, Rosemary; Cunningham, Mark; Thomas, Nancy J.; Spalding, Marilyn G.; Ip, Hon S.

2012-01-01

Eurasian collared doves (Streptopelia decaocto) have expanded their range across the United States since their introduction several decades ago. Recent mortality events in Eurasian collared doves in Arizona and Montana, USA, during the winter of 2009-2010 were the result of pigeon paramyxovirus (PPMV), a novel disease agent. The first instance of mortality by this emerging infectious disease in this species occurred in Florida in 2001 with subsequent disease events in 2006 and 2008. Full diagnostic necropsies were performed on carcasses from the three states. PPMV was identified by RT-PCR and virus isolation and was sequenced to the VIb genotype of avian paramyxovirus-1 (APMV). Other APMVs are common in a variety of free-ranging birds, but concern is warranted because of the potential for commingling of this species with native birds, virus evolution, and threats to domestic poultry. Improved surveillance for wildlife mortality events and efforts to prevent introduction of non-native animals could reduce the threat of introducing new pathogens.

Cumulative Impact of HIV and Multiple Concurrent Human Papillomavirus Infections on the Risk of Cervical Dysplasia

PubMed Central

Adler, David H.; Wallace, Melissa; Bennie, Thola; Abar, Beau; Meiring, Tracy L.; Williamson, Anna-Lise; Bekker, Linda-Gail

2016-01-01

Infection with HIV is known to increase the risk of cervical cancer. In addition, evidence suggests that concurrent infection with multiple human papillomavirus (HPV) genotypes increases the risk of cervical dysplasia more than infection with a single HPV genotype. However, the impact of the combination of HIV coinfection and presence of multiple concurrent HPV infections on the risk of cervical dysplasia is uncertain. We compared the results of HPV testing and Pap smears between HIV-infected and HIV-uninfected young women to assess the cumulative impact of these two conditions. We found that both HIV and the presence of multiple concurrent HPV infections are associated with increased risk of associated Pap smear abnormality and that the impact of these two risk factors may be additive. PMID:26997954

Columbia River System Operation Review : Final Environmental Impact Statement, Appendix D: Cultural Resources.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Columbia River System Operation Review

1995-11-01

This study attempts to identify and analyze the impacts of the System Operating Strategy (SOS) alternatives on cultural resources. The impacts include effects on Native American traditional cultural values, properties and practices. They also include effects on archeological or historic properties meeting the criteria of the National Register of Historic Places. In addition to responding to the requirements of the National Environmental Policy Act (NEPA), this analysis addresses the requirements of the National Historic Preservation Act (NHPA), the Archeological Resources Protection Act (ARPA), the Native American Graves Protection and Repatriation Act (NAGPRA), the Native American Religious Freedom Act (NARFA), andmore » other relevant legislation. To meet their legally mandated cultural resources requirements, the SOR agencies will develop agreements and Implementation Plans with the appropriate State Historic Preservation Officers (SHPOs), Tribes, and the Advisory Council on Historic Preservation (ACHP) detailing the measures necessary to best manage the resource. The planning and implementation activities will be staged over a number of years in consultation with affected Tribes.« less

The impact of invasive grasses on the population growth of Anemone patens, a long-lived native forb.

PubMed

Williams, Jennifer L; Crone, Elizabeth E

2006-12-01

Negative impacts of invasive plants on natives have been well documented, but much less is known about whether invasive plants can cause population level declines. We used demographic models to investigate the effects of two invasive grasses on the demography and population growth of Anemone patens, a long-lived native perennial of North American grasslands. Demographic data of A. patens growing in patches characterized by Bromus inermis, Poa pratensis, or native grasses were used to parameterize integral projection models. Models based on both average conditions and those allowing for environmental stochasticity indicate that A. patens is slowly increasing in patches of native grass (lambda = 1.02) and declining in patches of invasive grasses, particularly those dominated by B. inermis (lambda = 0.93). Extinction probabilities indicate that A. patens should persist in native grass patches, but has a much higher probability of extinction in Bromus patches compared to Poa patches. While sensitivity analyses showed that survival had the biggest effect on population growth rates in all habitats, results of a Life Table Response Experiment (LTRE) revealed that slower individual growth rates in patches of invasive grasses contributed the most to the observed reduction in population growth. These results suggest that invasive grasses may cause slow declines in A. patens, despite short-term coexistence, and that controlling B. inermis only would not be sufficient to ensure A. patens persistence.

Impacts of fire on non-native plant recruitment in black spruce forests of interior Alaska.

PubMed

Walker, Xanthe J; Frey, Matthew D; Conway, Alexandra J; Jean, Mélanie; Johnstone, Jill F

2017-01-01

Climate change is expected to increase the extent and severity of wildfires throughout the boreal forest. Historically, black spruce (Picea mariana (Mill.) B.S.P.) forests in interior Alaska have been relatively free of non-native species, but the compounding effects of climate change and an altered fire regime could facilitate the expansion of non-native plants. We tested the effects of wildfire on non-native plant colonization by conducting a seeding experiment of non-native plants on different substrate types in a burned black spruce forest, and surveying for non-native plants in recently burned and mature black spruce forests. We found few non-native plants in burned or mature forests, despite their high roadside presence, although invasion of some burned sites by dandelion (Taraxacum officinale) indicated the potential for non-native plants to move into burned forest. Experimental germination rates were significantly higher on mineral soil compared to organic soil, indicating that severe fires that combust much of the organic layer could increase the potential for non-native plant colonization. We conclude that fire disturbances that remove the organic layer could facilitate the invasion of non-native plants providing there is a viable seed source and dispersal vector.

Efficient use of historical data for genomic selection: a case study of rust resistance in wheat

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) is a new methodology that can improve wheat breeding efficiency. To implement GS, a training population (TP) with both phenotypic and genotypic data is required to train a statistical model used to predict genotyped selection candidates (SCs). Several factors impact prediction...

Genome-wide interaction of genotype by erythrocyte n-3 PUFAs contributes to phenotypic variance of diabetes-related traits

USDA-ARS?s Scientific Manuscript database

While genome-wide association studies (GWAS) and candidate gene approach have identified many genetic variants that contribute to disease risk as main effects, the impact of genotype by environment (GxE) interactions remains rather under-surveyed. The present study aimed to examine variance contribu...

Dissecting genotype × environment interactions and trait correlations present in the Pee Dee cotton germplasm collection following seventy years of plant breeding

USDA-ARS?s Scientific Manuscript database

Genotype × environment interactions and trait correlations significantly impact efforts to develop high yield, high quality, and environmentally stable Upland cotton (Gossypium hirsutum L.) cultivars. Knowledge of both can and should be used to design optimal breeding programs and effective selectio...

Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008-2012.

PubMed

Prabdial-Sing, N; Chirwa, T; Thaver, J; Smuts, H; Vermeulen, M; Suchard, M; Puren, A J

2016-11-01

There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease. © 2016 John Wiley & Sons Ltd.

Conservation on International Boundaries: The Impact of Security Barriers on Selected Terrestrial Mammals in Four Protected Areas in Arizona, USA

PubMed Central

McCallum, Jamie W.; Rowcliffe, J. Marcus; Cuthill, Innes C.

2014-01-01

Several thousand terrestrial protected areas (PAs) lie on international boundaries. Because international boundaries can be focal points for trade, illegal activity and development, such PAs can be vulnerable to a range of anthropogenic threats. There is an increasing trend towards the erection of international boundary infrastructure (including fences, barriers and ditches) in many parts of the world, which may reduce the risk of these anthropogenic threats to some PAs. However this may restrict home range and access to resources for some native species. We sought to understand the impacts of these two different types of threat by using camera traps to measure the activity level of humans, native and invasive mammals in four US PAs on the Mexican international boundary. Comparisons were made between treatment areas with barriers and those without. Results showed that puma and coati were more likely to appear in treatment areas without barriers, whereas humans were not observed more frequently in one treatment area over another. The suggestion is that the intermittent fencing present in this part of the world does affect some native species, but does not necessarily restrict the movement of humans (including illegal migrants), who may negatively impact native species. PMID:24717982

Impact of PNPLA3 variants on liver histology of 168 patients with HIV infection and chronic hepatitis C.

PubMed

Sagnelli, C; Merli, M; Uberti-Foppa, C; Hasson, H; Cirillo, G; Grandone, A; Salpietro, S; Minichini, C; Del Giudice, E M; Lazzarin, A; Sagnelli, E; Coppola, N

2016-04-01

This study analysed the impact of PNPLA3 variants on liver histology of 168 HIV/hepatitis C virus (HCV)-coinfected patients who were naïve for HCV treatment. A athologist unaware of the patients' condition graded liver fibrosis and necroinflammation (Ishak) and steatosis (Kleiner). Patients were tested for PNPLA3 variants and genotyped for the PNPLA3 rs738409 C to G variant underlying the I148M substitution. All were hepatitis B surface antigen negative and stated no alcohol abuse. The mean age was 40.6 (37.6-44.1) years, 72.6% were males, 42% had HCV genotype 3, 38.9% HCV genotype 1 and 79.2% were receiving highly active antiretroviral therapy. The 79 patients with the PNPLA3 p.148I/M or M/M variants more frequently showed severe steatosis (score 3-4) than the 89 with PNPLA3 p.148I/I (43% vs. 24.7%, p 0.001), whereas no difference was observed in the degree of necroinflammation or fibrosis. Compared with 112 patients with lower scores, 56 with severe steatosis showed higher body mass index (p 0.03), higher rate of HCV genotype 3 (55.6% vs. 35.2%, p 0.01), PNPLA3 p.148I/M or M/M (60.7% vs. 39.3%, p 0.01) and lower CD4(+) cells/mm(3) (514.00 (390.5-673.0) vs. 500.00 (399.0-627.0); p 0.002). At multivariate analysis, body mass index (p 0.01), HCV genotype 3 (p 0.006), CD4(+) cell count (p 0.005) and PNPLA3 p.148I/M or M/M variants (p 0.01) were found to be independent predictors of severe liver steatosis. The PNPLA3 p.148 I/M or M/M variants and CD4(+) cell count were the only independent predictors of severe steatosis in patients with HCV non-3 genotypes. This is the first study to show that among HIV/HCV-coinfected patients the PNPLA3 p.148I/M or M/M variant have substantially less impact on steatosis for those with HCV genotype 3 than non-genotype 3. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Changes in Physical Activity Following a Genetic-Based Internet-Delivered Personalized Intervention: Randomized Controlled Trial (Food4Me)

PubMed Central

Livingstone, Katherine M; Fallaize, Rosalind; Kolossa, Silvia; Hallmann, Jacqueline; San-Cristobal, Rodrigo; Navas-Carretero, Santiago; O'Donovan, Clare B; Woolhead, Clara; Forster, Hannah; Moschonis, George; Lambrinou, Christina-Paulina; Surwillo, Agnieszka; Godlewska, Magdalena; Hoonhout, Jettie; Goris, Annelies; Macready, Anna L; Walsh, Marianne C; Gibney, Eileen R; Brennan, Lorraine; Manios, Yannis; Traczyk, Iwona; Drevon, Christian A; Lovegrove, Julie A; Martinez, J Alfredo; Daniel, Hannelore; Gibney, Michael J; Mathers, John C; Saris, Wim HM

2016-01-01

Background There is evidence that physical activity (PA) can attenuate the influence of the fat mass- and obesity-associated (FTO) genotype on the risk to develop obesity. However, whether providing personalized information on FTO genotype leads to changes in PA is unknown. Objective The purpose of this study was to determine if disclosing FTO risk had an impact on change in PA following a 6-month intervention. Methods The single nucleotide polymorphism (SNP) rs9939609 in the FTO gene was genotyped in 1279 participants of the Food4Me study, a four-arm, Web-based randomized controlled trial (RCT) in 7 European countries on the effects of personalized advice on nutrition and PA. PA was measured objectively using a TracmorD accelerometer and was self-reported using the Baecke questionnaire at baseline and 6 months. Differences in baseline PA variables between risk (AA and AT genotypes) and nonrisk (TT genotype) carriers were tested using multiple linear regression. Impact of FTO risk disclosure on PA change at 6 months was assessed among participants with inadequate PA, by including an interaction term in the model: disclosure (yes/no) × FTO risk (yes/no). Results At baseline, data on PA were available for 874 and 405 participants with the risk and nonrisk FTO genotypes, respectively. There were no significant differences in objectively measured or self-reported baseline PA between risk and nonrisk carriers. A total of 807 (72.05%) of the participants out of 1120 in the personalized groups were encouraged to increase PA at baseline. Knowledge of FTO risk had no impact on PA in either risk or nonrisk carriers after the 6-month intervention. Attrition was higher in nonrisk participants for whom genotype was disclosed (P=.01) compared with their at-risk counterparts. Conclusions No association between baseline PA and FTO risk genotype was observed. There was no added benefit of disclosing FTO risk on changes in PA in this personalized intervention. Further RCT studies are warranted to confirm whether disclosure of nonrisk genetic test results has adverse effects on engagement in behavior change. Trial Registration ClinicalTrials.gov NCT01530139; http://clinicaltrials.gov/show/NCT01530139 (Archived by WebCite at: http://www.webcitation.org/6XII1QwHz) PMID:26851191

Changes in Physical Activity Following a Genetic-Based Internet-Delivered Personalized Intervention: Randomized Controlled Trial (Food4Me).

PubMed

Marsaux, Cyril F M; Celis-Morales, Carlos; Livingstone, Katherine M; Fallaize, Rosalind; Kolossa, Silvia; Hallmann, Jacqueline; San-Cristobal, Rodrigo; Navas-Carretero, Santiago; O'Donovan, Clare B; Woolhead, Clara; Forster, Hannah; Moschonis, George; Lambrinou, Christina-Paulina; Surwillo, Agnieszka; Godlewska, Magdalena; Hoonhout, Jettie; Goris, Annelies; Macready, Anna L; Walsh, Marianne C; Gibney, Eileen R; Brennan, Lorraine; Manios, Yannis; Traczyk, Iwona; Drevon, Christian A; Lovegrove, Julie A; Martinez, J Alfredo; Daniel, Hannelore; Gibney, Michael J; Mathers, John C; Saris, Wim H M

2016-02-05

There is evidence that physical activity (PA) can attenuate the influence of the fat mass- and obesity-associated (FTO) genotype on the risk to develop obesity. However, whether providing personalized information on FTO genotype leads to changes in PA is unknown. The purpose of this study was to determine if disclosing FTO risk had an impact on change in PA following a 6-month intervention. The single nucleotide polymorphism (SNP) rs9939609 in the FTO gene was genotyped in 1279 participants of the Food4Me study, a four-arm, Web-based randomized controlled trial (RCT) in 7 European countries on the effects of personalized advice on nutrition and PA. PA was measured objectively using a TracmorD accelerometer and was self-reported using the Baecke questionnaire at baseline and 6 months. Differences in baseline PA variables between risk (AA and AT genotypes) and nonrisk (TT genotype) carriers were tested using multiple linear regression. Impact of FTO risk disclosure on PA change at 6 months was assessed among participants with inadequate PA, by including an interaction term in the model: disclosure (yes/no) × FTO risk (yes/no). At baseline, data on PA were available for 874 and 405 participants with the risk and nonrisk FTO genotypes, respectively. There were no significant differences in objectively measured or self-reported baseline PA between risk and nonrisk carriers. A total of 807 (72.05%) of the participants out of 1120 in the personalized groups were encouraged to increase PA at baseline. Knowledge of FTO risk had no impact on PA in either risk or nonrisk carriers after the 6-month intervention. Attrition was higher in nonrisk participants for whom genotype was disclosed (P=.01) compared with their at-risk counterparts. No association between baseline PA and FTO risk genotype was observed. There was no added benefit of disclosing FTO risk on changes in PA in this personalized intervention. Further RCT studies are warranted to confirm whether disclosure of nonrisk genetic test results has adverse effects on engagement in behavior change. ClinicalTrials.gov NCT01530139; http://clinicaltrials.gov/show/NCT01530139 (Archived by WebCite at: http://www.webcitation.org/6XII1QwHz).

Andean potato cultivars (Solanum tuberosum L.) as a source of antioxidant and mineral micronutrients.

PubMed

Andre, Christelle M; Ghislain, Marc; Bertin, Pierre; Oufir, Mouhssin; Herrera, María del Rosario; Hoffmann, Lucien; Hausman, Jean-François; Larondelle, Yvan; Evers, Danièle

2007-01-24

Potato tubers were evaluated as a source of antioxidants and minerals for the human diet. A genetically diverse sample of Solanum tuberosum L. cultivars native to the Andes of South America was obtained from a collection of nearly 1000 genotypes using microsatellite markers. This size-manageable collection of 74 landraces, representing at best the genetic diversity among potato germplasm, was analyzed for iron, zinc, calcium, total phenolic, total carotenoid, and total vitamin C contents. The hydrophilic antioxidant capacity of each genotype was also measured using the oxygen radical absorbance capacity (ORAC) assay. The iron content ranged from 29.87 to 157.96 microg g-1 of dry weight (DW), the zinc content from 12.6 to 28.83 microg g-1 of DW, and the calcium content from 271.09 to 1092.93 microg g-1 of DW. Total phenolic content varied between 1.12 and 12.37 mg of gallic acid equiv g-1 of DW, total carotenoid content between 2.83 and 36.21 microg g-1 of DW, and total vitamin C content between 217.70 and 689.47 microg g-1 of DW. The range of hydrophilic ORAC values was 28.25-250.67 micromol of Trolox equiv g-1 of DW. The hydrophilic antioxidant capacity and the total phenolic content were highly and positively correlated (r = 0.91). A strong relationship between iron and calcium contents was also found (r = 0.67). Principal component analysis on the studied nutritional contents of the core collection revealed that most potato genotypes were balanced in terms of antioxidant and mineral contents, but some of them could be distinguished by their high level in distinct micronutrients. Correlations between the micronutrient contents observed in the sample and the genetic distances assessed by microsatellites were weakly significant. However, this study demonstrated the wide variability of health-promoting micronutrient levels within the native potato germplasm as well as the significant contribution that distinct potato tubers may impart to the intake in dietary antioxidants, zinc, and iron.

Economic Impacts of Non-Native Forest Insects in the Continental United States

PubMed Central

Aukema, Juliann E.; Leung, Brian; Kovacs, Kent; Chivers, Corey; Britton, Kerry O.; Englin, Jeffrey; Frankel, Susan J.; Haight, Robert G.; Holmes, Thomas P.; Liebhold, Andrew M.; McCullough, Deborah G.; Von Holle, Betsy

2011-01-01

Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United States but estimates of broad-scale economic impacts associated with these species are largely unavailable. We developed a novel modeling approach that maximizes the use of available data, accounts for multiple sources of uncertainty, and provides cost estimates for three major feeding guilds of non-native forest insects. For each guild, we calculated the economic damages for five cost categories and we estimated the probability of future introductions of damaging pests. We found that costs are largely borne by homeowners and municipal governments. Wood- and phloem-boring insects are anticipated to cause the largest economic impacts by annually inducing nearly $1.7 billion in local government expenditures and approximately $830 million in lost residential property values. Given observations of new species, there is a 32% chance that another highly destructive borer species will invade the U.S. in the next 10 years. Our damage estimates provide a crucial but previously missing component of cost-benefit analyses to evaluate policies and management options intended to reduce species introductions. The modeling approach we developed is highly flexible and could be similarly employed to estimate damages in other countries or natural resource sectors. PMID:21931766

A native plant competitor mediates the impact of above- and belowground damage on an invasive tree.

PubMed

Carrillo, Juli; Siemann, Evan

2016-10-01

Plant competition may mediate the impacts of herbivory on invasive plant species through effects on plant growth and defense. This may predictably depend on whether herbivory occurs above or below ground and on relative plant competitive ability. We simulated the potential impact of above- or belowground damage by biocontrol agents on the growth of a woody invader (Chinese tallow tree, Triadica sebifera) through artificial herbivory, with or without competition with a native grass, little bluestem (Schizachyrium scoparium). We measured two defense responses of Triadica through quantifying constitutive and induced extrafloral nectar production and tolerance of above- and belowground damage (root and shoot biomass regrowth). We examined genetic variation in plant growth and defense across native (China) and invasive (United States) Triadica populations. Without competition, aboveground damage had a greater impact than belowground damage on Triadica performance, whereas with competition and above- and belowground damage impacted Triadica similarly. Whole plant tolerance to damage below ground was negatively associated with tolerance to grass competitors indicating tradeoffs in the ability to tolerate herbivory vs. compete. Competition reduced investment in defensive extrafloral nectar (EFN) production. Aboveground damage inhibited rather than induced EFN production while belowground plant damage did not impact aboveground nectar production. We found some support for the evolution of increased competitive ability hypothesis for invasive plants as United States plants were larger than native China plants and were more plastic in their response to biotic stressors than China plants (they altered their root to shoot ratios dependent on herbivory and competition treatments). Our results indicate that habitat type and the presence of competitors may be a larger determinant of herbivory impact than feeding mode and suggest that integrated pest management strategies including competitive dynamics of recipient communities should be incorporated into biological control agent evaluation at earlier stages. © 2016 by the Ecological Society of America.

Impacts of invading alien plant species on water flows at stand and catchment scales.

PubMed

Le Maitre, D C; Gush, M B; Dzikiti, S

2015-05-01

There have been many studies of the diverse impacts of invasions by alien plants but few have assessed impacts on water resources. We reviewed the information on the impacts of invasions on surface runoff and groundwater resources at stand to catchment scales and covering a full annual cycle. Most of the research is South African so the emphasis is on South Africa's major invaders with data from commercial forest plantations where relevant. Catchment studies worldwide have shown that changes in vegetation structure and the physiology of the dominant plant species result in changes in surface runoff and groundwater discharge, whether they involve native or alien plant species. Where there is little change in vegetation structure [e.g. leaf area (index), height, rooting depth and seasonality] the effects of invasions generally are small or undetectable. In South Africa, the most important woody invaders typically are taller and deeper rooted than the native species. The impacts of changes in evaporation (and thus runoff) in dryland settings are constrained by water availability to the plants and, thus, by rainfall. Where the dryland invaders are evergreen and the native vegetation (grass) is seasonal, the increases can reach 300-400 mm/year. Where the native vegetation is evergreen (shrublands) the increases are ∼200-300 mm/year. Where water availability is greater (riparian settings or shallow water tables), invading tree water-use can reach 1.5-2.0 times that of the same species in a dryland setting. So, riparian invasions have a much greater impact per unit area invaded than dryland invasions. The available data are scattered and incomplete, and there are many gaps and issues that must be addressed before a thorough understanding of the impacts at the site scale can be gained and used in extrapolating to watershed scales, and in converting changes in flows to water supply system yields. Published by Oxford University Press on behalf of the Annals of Botany Company.

Impacts of invading alien plant species on water flows at stand and catchment scales

PubMed Central

Le Maitre, D. C.; Gush, M. B.; Dzikiti, S.

2015-01-01

There have been many studies of the diverse impacts of invasions by alien plants but few have assessed impacts on water resources. We reviewed the information on the impacts of invasions on surface runoff and groundwater resources at stand to catchment scales and covering a full annual cycle. Most of the research is South African so the emphasis is on South Africa's major invaders with data from commercial forest plantations where relevant. Catchment studies worldwide have shown that changes in vegetation structure and the physiology of the dominant plant species result in changes in surface runoff and groundwater discharge, whether they involve native or alien plant species. Where there is little change in vegetation structure [e.g. leaf area (index), height, rooting depth and seasonality] the effects of invasions generally are small or undetectable. In South Africa, the most important woody invaders typically are taller and deeper rooted than the native species. The impacts of changes in evaporation (and thus runoff) in dryland settings are constrained by water availability to the plants and, thus, by rainfall. Where the dryland invaders are evergreen and the native vegetation (grass) is seasonal, the increases can reach 300–400 mm/year. Where the native vegetation is evergreen (shrublands) the increases are ∼200–300 mm/year. Where water availability is greater (riparian settings or shallow water tables), invading tree water-use can reach 1.5–2.0 times that of the same species in a dryland setting. So, riparian invasions have a much greater impact per unit area invaded than dryland invasions. The available data are scattered and incomplete, and there are many gaps and issues that must be addressed before a thorough understanding of the impacts at the site scale can be gained and used in extrapolating to watershed scales, and in converting changes in flows to water supply system yields. PMID:25935861

The divergent impact of catechol-O-methyltransferase (COMT) Val158Met genetic polymorphisms on executive function in adolescents with discrete patterns of childhood adversity.

PubMed

Zhang, Huihui; Li, Jie; Yang, Bei; Ji, Tao; Long, Zhouting; Xing, Qiquan; Shao, Di; Bai, Huayu; Sun, Jiwei; Cao, Fenglin

2018-02-01

Catechol-O-methyltransferase (COMT) Val 158 Met functional polymorphisms play a crucial role in the development of executive function (EF), but their effect may be moderated by environmental factors such as childhood adversity. The present study aimed at testing the divergent impact of the COMT Val 158 Met genotype on EF in non-clinical adolescents with discrete patterns of childhood adversity. A total of 341 participants completed the Childhood Trauma Questionnaire, the self-reported version of the Behavior Rating Inventory of Executive Function, and self-administered questionnaires on familial function. The participants' COMT Val 158 Met genotype was determined. Associations among the variables were explored using latent class analysis and general linear models. We found that Val/Val homozygotes showed significantly worse performance on behavioral shift, relative to Met allele carriers (F=5.921, p=0.015, Partial η 2 =0.018). Moreover, three typical patterns of childhood adversity, namely, low childhood adversity (23.5%), childhood neglect (59.8%), and high childhood adversity (16.7%), were found. Both childhood neglect and high childhood adversity had a negative impact on each aspect of EF and on global EF performance. Importantly, these results provided evidence for significant interaction effects, as adolescents with the Val/Val genotype showed inferior behavioral shift performance than Met carriers (F=6.647, p=0.010, Partial η 2 =0.020) in the presence of high childhood adversity. Furthermore, there were no differences between the genotypes for childhood neglect and low childhood adversity. Overall, this is the first study to show that an interaction between the COMT genotype and childhood adversity affects EF in non-clinical adolescents. These results suggest that the COMT genotype may operate as a susceptibility gene vulnerable to an adverse environment. Copyright © 2017 Elsevier Inc. All rights reserved.

Soil sterilization alters interactions between the native grass Bouteloua gracilis and invasive Bromus tectorum

USDA-ARS?s Scientific Manuscript database

Aims: The invasive grass Bromus tectorum negatively impacts grassland communities throughout the western U.S. We asked whether soil biota growing in association with a native grass (Bouteloua gracilis) increase growth and competitive ability of Bromus, and whether responses vary between soils collec...

78 FR 7450 - Final Environmental Impact Statement for Protecting and Restoring Native Ecosystems by Managing...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-01

...-Native Ungulates, Hawaii Volcanoes National Park, HI AGENCY: National Park Service, Interior. ACTION..., HI 96718, and in local libraries (locations noted on above Web site). A limited number of compact... 52, Hawaii Volcanoes National Park, HI 96718-0052; (808) 985-6098. SUPPLEMENTARY INFORMATION: The...

The Emotional Impact of Being Myself: Emotions and Foreign-Language Processing

ERIC Educational Resources Information Center

Ivaz, Lela; Costa, Albert; Duñabeitia, Jon Andoni

2016-01-01

Native languages are acquired in emotionally rich contexts, whereas foreign languages are typically acquired in emotionally neutral academic environments. As a consequence of this difference, it has been suggested that bilinguals' emotional reactivity in foreign-language contexts is reduced as compared with native language contexts. In the current…

Water use efficiency by switchgrass compared to a native grass or a native grass alfalfa mixture

USDA-ARS?s Scientific Manuscript database

Development of sustainable cellulosic biofuel systems requires knowing the water use efficiency (WUE) of potential bioenergy crops. Impact of early and late season droughts on WUE and soil water deficits were evaluated in switchgrass (Panicum virgatum L.), western wheatgrass (Pascopyrum smithii (Ry...

Introduced and Native Parasitoid Wasps Associated With Larch Casebearer (Lepidoptera: Coleophoridae) in Western Larch

Treesearch

M. Miller-Pierce; D. C. Shaw; A. Demarco; P. T. Oester

2015-01-01

The larch casebearer [Coleophora laricella (Hubner)], a non-native insect, continues to impact western larch (Larix occidentalis Nutt.) through defoliation events in the Pacific Northwest. Biological control programs starting in the 1960s released seven species of parasitoid wasps to control C. laricella...

The effects of an invasive seaweed on native communities vary along a gradient of land-based human impacts

PubMed Central

Badalamenti, Fabio; Iveša, Ljiljana; Mikac, Barbara; Musco, Luigi; Jaklin, Andrej; Rattray, Alex; Vega Fernández, Tomás; Benedetti-Cecchi, Lisandro

2016-01-01

The difficulty in teasing apart the effects of biological invasions from those of other anthropogenic perturbations has hampered our understanding of the mechanisms underpinning the global biodiversity crisis. The recent elaboration of global-scale maps of cumulative human impacts provides a unique opportunity to assess how the impact of invaders varies among areas exposed to different anthropogenic activities. A recent meta-analysis has shown that the effects of invasive seaweeds on native biota tend to be more negative in relatively pristine than in human-impacted environments. Here, we tested this hypothesis through the experimental removal of the invasive green seaweed, Caulerpa cylindracea, from rocky reefs across the Mediterranean Sea. More specifically, we assessed which out of land-based and sea-based cumulative impact scores was a better predictor of the direction and magnitude of the effects of this seaweed on extant and recovering native assemblages. Approximately 15 months after the start of the experiment, the removal of C. cylindracea from extant assemblages enhanced the cover of canopy-forming macroalgae at relatively pristine sites. This did not, however, result in major changes in total cover or species richness of native assemblages. Preventing C. cylindracea re-invasion of cleared plots at pristine sites promoted the recovery of canopy-forming and encrusting macroalgae and hampered that of algal turfs, ultimately resulting in increased species richness. These effects weakened progressively with increasing levels of land-based human impacts and, indeed, shifted in sign at the upper end of the gradient investigated. Thus, at sites exposed to intense disturbance from land-based human activities, the removal of C. cylindracea fostered the cover of algal turfs and decreased that of encrusting algae, with no net effect on species richness. Our results suggests that competition from C. cylindracea is an important determinant of benthic assemblage diversity in pristine environments, but less so in species-poor assemblages found at sites exposed to intense disturbance from land-based human activities, where either adverse physical factors or lack of propagules may constrain the number of potential native colonizers. Implementing measures to reduce the establishment and spread of C. cylindracea in areas little impacted by land-based human activities should be considered a priority for preserving the biodiversity of Mediterranean shallow rocky reefs. PMID:27014513

The effects of an invasive seaweed on native communities vary along a gradient of land-based human impacts.

PubMed

Bulleri, Fabio; Badalamenti, Fabio; Iveša, Ljiljana; Mikac, Barbara; Musco, Luigi; Jaklin, Andrej; Rattray, Alex; Vega Fernández, Tomás; Benedetti-Cecchi, Lisandro

2016-01-01

The difficulty in teasing apart the effects of biological invasions from those of other anthropogenic perturbations has hampered our understanding of the mechanisms underpinning the global biodiversity crisis. The recent elaboration of global-scale maps of cumulative human impacts provides a unique opportunity to assess how the impact of invaders varies among areas exposed to different anthropogenic activities. A recent meta-analysis has shown that the effects of invasive seaweeds on native biota tend to be more negative in relatively pristine than in human-impacted environments. Here, we tested this hypothesis through the experimental removal of the invasive green seaweed, Caulerpa cylindracea, from rocky reefs across the Mediterranean Sea. More specifically, we assessed which out of land-based and sea-based cumulative impact scores was a better predictor of the direction and magnitude of the effects of this seaweed on extant and recovering native assemblages. Approximately 15 months after the start of the experiment, the removal of C. cylindracea from extant assemblages enhanced the cover of canopy-forming macroalgae at relatively pristine sites. This did not, however, result in major changes in total cover or species richness of native assemblages. Preventing C. cylindracea re-invasion of cleared plots at pristine sites promoted the recovery of canopy-forming and encrusting macroalgae and hampered that of algal turfs, ultimately resulting in increased species richness. These effects weakened progressively with increasing levels of land-based human impacts and, indeed, shifted in sign at the upper end of the gradient investigated. Thus, at sites exposed to intense disturbance from land-based human activities, the removal of C. cylindracea fostered the cover of algal turfs and decreased that of encrusting algae, with no net effect on species richness. Our results suggests that competition from C. cylindracea is an important determinant of benthic assemblage diversity in pristine environments, but less so in species-poor assemblages found at sites exposed to intense disturbance from land-based human activities, where either adverse physical factors or lack of propagules may constrain the number of potential native colonizers. Implementing measures to reduce the establishment and spread of C. cylindracea in areas little impacted by land-based human activities should be considered a priority for preserving the biodiversity of Mediterranean shallow rocky reefs.

Multiple Norovirus Infections in a Birth Cohort in a Peruvian Periurban Community

PubMed Central

Saito, Mayuko; Goel-Apaza, Sonia; Espetia, Susan; Velasquez, Daniel; Cabrera, Lilia; Loli, Sebastian; Crabtree, Jean E.; Black, Robert E.; Kosek, Margaret; Checkley, William; Zimic, Mirko; Bern, Caryn; Cama, Vitaliano; Gilman, Robert H.; Xiao, L.; Kelleher, D.; Windle, H. J.; van Doorn, L. J.; Varela, M.; Verastegui, M.; Calderon, M.; Alva, A.; Roman, K.

2014-01-01

Background. Human noroviruses are among the most common enteropathogens globally, and are a leading cause of infant diarrhea in developing countries. However, data measuring the impact of norovirus at the community level are sparse. Methods. We followed a birth cohort of children to estimate norovirus infection and diarrhea incidence in a Peruvian community. Stool samples from diarrheal episodes and randomly selected nondiarrheal samples were tested by polymerase chain reaction for norovirus genogroup and genotype. Excretion duration and rotavirus coinfection were evaluated in a subset of episodes. Results. Two hundred twenty and 189 children were followed to 1 and 2 years of age, respectively. By 1 year, 80% (95% confidence interval [CI], 75%–85%) experienced at least 1 norovirus infection and by 2 years, 71% (95% CI, 65%–77%) had at least 1 episode of norovirus-associated diarrhea. Genogroup II (GII) infections were 3 times more frequent than genogroup 1 (GI) infections. Eighteen genotypes were found; GII genotype 4 accounted for 41%. Median excretion duration was 34.5 days for GII vs 8.5 days for GI infection (P = .0006). Repeat infections by the same genogroup were common, but repeat infections by the same genotype were rare. Mean length-for-age z score at 12 months was lower among children with prior norovirus infection compared to uninfected children (coefficient: −0.33 [95% CI, −.65 to −.01]; P = .04); the effect persisted at 24 months. Conclusions. Norovirus infection occurs early in life and children experience serial infections with multiple genotypes, suggesting genotype-specific immunity. An effective vaccine would have a substantial impact on morbidity, but may need to target multiple genotypes. PMID:24300042

Identifying traits for genotypic adaptation using crop models.

PubMed

Ramirez-Villegas, Julian; Watson, James; Challinor, Andrew J

2015-06-01

Genotypic adaptation involves the incorporation of novel traits in crop varieties so as to enhance food productivity and stability and is expected to be one of the most important adaptation strategies to future climate change. Simulation modelling can provide the basis for evaluating the biophysical potential of crop traits for genotypic adaptation. This review focuses on the use of models for assessing the potential benefits of genotypic adaptation as a response strategy to projected climate change impacts. Some key crop responses to the environment, as well as the role of models and model ensembles for assessing impacts and adaptation, are first reviewed. Next, the review describes crop-climate models can help focus the development of future-adapted crop germplasm in breeding programmes. While recently published modelling studies have demonstrated the potential of genotypic adaptation strategies and ideotype design, it is argued that, for model-based studies of genotypic adaptation to be used in crop breeding, it is critical that modelled traits are better grounded in genetic and physiological knowledge. To this aim, two main goals need to be pursued in future studies: (i) a better understanding of plant processes that limit productivity under future climate change; and (ii) a coupling between genetic and crop growth models-perhaps at the expense of the number of traits analysed. Importantly, the latter may imply additional complexity (and likely uncertainty) in crop modelling studies. Hence, appropriately constraining processes and parameters in models and a shift from simply quantifying uncertainty to actually quantifying robustness towards modelling choices are two key aspects that need to be included into future crop model-based analyses of genotypic adaptation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Probable Zoonotic Leprosy in the Southern United States

PubMed Central

Truman, Richard W.; Singh, Pushpendra; Sharma, Rahul; Busso, Philippe; Rougemont, Jacques; Paniz-Mondolfi, Alberto; Kapopoulou, Adamandia; Brisse, Sylvain; Scollard, David M.; Gillis, Thomas P.; Cole, Stewart T.

2011-01-01

BACKGROUND In the southern region of the United States, such as in Louisiana and Texas, there are autochthonous cases of leprosy among native-born Americans with no history of foreign exposure. In the same region, as well as in Mexico, wild armadillos are infected with Mycobacterium leprae. METHODS Whole-genome resequencing of M. leprae from one wild armadillo and three U.S. patients with leprosy revealed that the infective strains were essentially identical. Comparative genomic analysis of these strains and M. leprae strains from Asia and Brazil identified 51 single-nucleotide polymorphisms and an 11-bp insertion–deletion. We genotyped these polymorphic sites, in combination with 10 variable-number tandem repeats, in M. leprae strains obtained from 33 wild armadillos from five southern states, 50 U.S. outpatients seen at a clinic in Louisiana, and 64 Venezuelan patients, as well as in four foreign reference strains. RESULTS The M. leprae genotype of patients with foreign exposure generally reflected their country of origin or travel history. However, a unique M. leprae genotype (3I-2-v1) was found in 28 of the 33 wild armadillos and 25 of the 39 U.S. patients who resided in areas where exposure to armadillo-borne M. leprae was possible. This genotype has not been reported elsewhere in the world. CONCLUSIONS Wild armadillos and many patients with leprosy in the southern United States are infected with the same strain of M. leprae. Armadillos are a large natural reservoir for M. leprae, and leprosy may be a zoonosis in the region. (Funded by the National Institute of Allergy and Infectious Diseases and others.) PMID:21524213

Climatic-Induced Shifts in the Distribution of Teak ( Tectona grandis) in Tropical Asia: Implications for Forest Management and Planning

NASA Astrophysics Data System (ADS)

Deb, Jiban Chandra; Phinn, Stuart; Butt, Nathalie; McAlpine, Clive A.

2017-09-01

Modelling the future suitable climate space for tree species has become a widely used tool for forest management planning under global climate change. Teak ( Tectona grandis) is one of the most valuable tropical hardwood species in the international timber market, and natural teak forests are distributed from India through Myanmar, Laos and Thailand. The extents of teak forests are shrinking due to deforestation and the local impacts of global climate change. However, the direct impacts of climate changes on the continental-scale distributions of native and non-native teak have not been examined. In this study, we developed a species distribution model for teak across its entire native distribution in tropical Asia, and its non-native distribution in Bangladesh. We used presence-only records of trees and twelve environmental variables that were most representative for current teak distributions in South and Southeast Asia. MaxEnt (maximum entropy) models were used to model the distributions of teak under current and future climate scenarios. We found that land use/land cover change and elevation were the two most important variables explaining the current and future distributions of native and non-native teak in tropical Asia. Changes in annual precipitation, precipitation seasonality and annual mean actual evapotranspiration may result in shifts in the distributions of teak across tropical Asia. We discuss the implications for the conservation of critical teak habitats, forest management planning, and risks of biological invasion that may occur due to its cultivation in non-native ranges.

Spatial and temporal genetic analysis of Walleyes in the Ohio River

USGS Publications Warehouse

Page, Kevin S.; Zweifela, Richard D.; Stott, Wendylee

2017-01-01

Previous genetic analyses have shown that Walleyes Sander vitreus in the upper Ohio River comprise two distinct genetic strains: (1) fish of Great Lakes origin that were stocked into the Ohio River basin and (2) a remnant native strain (Highlands strain). Resource agencies are developing management strategies to conserve and restore the native strain within the upper reaches of the Ohio River. Hybridization between strains has impacted the genetic integrity of the native strain. To better understand the extent and effects of hybridization on the native strain, we used mitochondrial DNA and microsatellite markers to evaluate the spatial (river sections) and temporal (pre- and poststocking) genetic diversity of Ohio River Walleyes. Contemporary Lake Erie Walleyes and archival museum specimens collected from the Ohio River basin were used for comparison to contemporary Ohio River samples. Although there was evidence of hybridization between strains, most of the genetic diversity within the Ohio River was partitioned by basin of origin (Great Lakes versus the Ohio River), with greater similarity among river sections than between strains within the same section. Results also suggested that the native strain has diverged from historical populations. Furthermore, notable decreases in measures of genetic diversity and increased relatedness among native-strain Walleyes within two sections of the Ohio River may be related to stocking aimed at restoration of the Highlands strain. Our results suggest that although the Highlands strain persists within the Ohio River, it has diverged over time, and managers should consider the potential impacts of future management practices on the genetic diversity of this native strain.

Differences in viral load among human respiratory syncytial virus genotypes in hospitalized children with severe acute respiratory infections in the Philippines.

PubMed

Kadji, Francois Marie Ngako; Okamoto, Michiko; Furuse, Yuki; Tamaki, Raita; Suzuki, Akira; Lirio, Irene; Dapat, Clyde; Malasao, Rungnapa; Saito, Mariko; Pedrera-Rico, Gay Anne Granada; Tallo, Veronica; Lupisan, Socorro; Saito, Mayuko; Oshitani, Hitoshi

2016-06-27

Human respiratory syncytial virus (HRSV) is a leading viral etiologic agent of pediatric lower respiratory infections, including bronchiolitis and pneumonia. Two antigenic subgroups, HRSV-A and B, each contain several genotypes. While viral load may vary among HRSV genotypes and affect the clinical course of disease, data are scarce regarding the actual differences among genotypes. Therefore, this study estimated and compared viral load among NA1 and ON1 genotypes of HRSV-A and BA9 of HRSV-B. ON1 is a newly emerged genotype with a 72-nucleotide duplication in the G gene as observed previously with BA genotypes in HRSV-B. Children <5 years of age with an initial diagnosis of severe or very severe pneumonia at a hospital in the Philippines from September 2012 to December 2013 were enrolled. HRSV genotypes were determined and the viral load measured from nasopharyngeal swabs (NPS). The viral load of HRSV genotype NA1 were significantly higher than those of ON1 and BA9. Regression analysis showed that both genotype NA1 and younger age were significantly associated with high HRSV viral load. The viral load of NA1 was higher than that of ON1 and BA9 in NPS samples. HRSV genotypes may be associated with HRSV viral load. The reasons and clinical impacts of these differences in viral load among HRSV genotypes require further evaluation.

First-Principles Study of Native Defects in TlBr: Carrier Trapping, Compensation, and Polarization Phemomenon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Mao-Hua

2010-01-01

First-principles calculations are carried out to study the native defect properties in TlBr. Three important results emerge: (1) the native defects are benign in terms of electron trapping because the low-energy defects do not induce electron traps; (2) the dominant defects in nearly stoichiometric TlBr are Schottky defects that pin the Fermi level near the midgap, leading to high resistivity; and (3) the calculated low diffusion barriers for several native defects show that ionic conductivity can occur at room temperature. The important impacts of these material properties on the room-temperature radiation detection using TlBr are discussed.

First-principles study of native defects in TlBr: Carrier trapping, compensation, and polarization phemomenon

NASA Astrophysics Data System (ADS)

Du, Mao-Hua

2010-09-01

First-principles calculations are carried out to study the native defect properties in TlBr. Three important results emerge: (1) the native defects are benign in terms of electron trapping because the low-energy defects do not induce electron traps; (2) the dominant defects in nearly stoichiometric TlBr are Schottky defects that pin the Fermi level near the midgap, leading to high resistivity; and (3) the calculated low diffusion barriers for several native defects show that ionic conductivity can occur at room temperature. The important impacts of these material properties on the room-temperature radiation detection using TlBr are discussed.

Apparent competition and native consumers exacerbate the strong competitive effect of an exotic plant species.

PubMed

Orrock, John L; Dutra, Humberto P; Marquis, Robert J; Barber, Nicholas

2015-04-01

Direct and indirect effects can play a key role in invasions, but experiments evaluating both are rare. We examined the roles of direct competition and apparent competition by exotic Amur honeysuckle (Lonicera maackii) by manipulating (1) L. maackii vegetation, (2) presence of L. maackii fruits, and (3) access to plants by small mammals and deer. Direct competition with L. maackii reduced the abundance and richness of native and exotic species, and native consumers significantly reduced the abundance and richness of native species. Although effects of direct competition and consumption were more pervasive, richness of native plants was also reduced through apparent competition, as small-mammal consumers reduced richness only when L. maackii fruits were present. Our experiment reveals the multiple, interactive pathways that affect the success and impact of an invasive exotic plant: exotic plants may directly benefit from reduced attack by native consumers, may directly exert strong competitive effects on native plants, and may also benefit from apparent competition.

Introduced species as evolutionary traps

USGS Publications Warehouse

Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

2005-01-01

Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

Response of native insect communities to invasive plants.

PubMed

Bezemer, T Martijn; Harvey, Jeffrey A; Cronin, James T

2014-01-01

Invasive plants can disrupt a range of trophic interactions in native communities. As a novel resource they can affect the performance of native insect herbivores and their natural enemies such as parasitoids and predators, and this can lead to host shifts of these herbivores and natural enemies. Through the release of volatile compounds, and by changing the chemical complexity of the habitat, invasive plants can also affect the behavior of native insects such as herbivores, parasitoids, and pollinators. Studies that compare insects on related native and invasive plants in invaded habitats show that the abundance of insect herbivores is often lower on invasive plants, but that damage levels are similar. The impact of invasive plants on the population dynamics of resident insect species has been rarely examined, but invasive plants can influence the spatial and temporal dynamics of native insect (meta)populations and communities, ultimately leading to changes at the landscape level.

Invasive non-native species' provision of refugia for endangered native species.

PubMed

Chiba, Satoshi

2010-08-01

The influence of non-native species on native ecosystems is not predicted easily when interspecific interactions are complex. Species removal can result in unexpected and undesired changes to other ecosystem components. I examined whether invasive non-native species may both harm and provide refugia for endangered native species. The invasive non-native plant Casuarina stricta has damaged the native flora and caused decline of the snail fauna on the Ogasawara Islands, Japan. On Anijima in 2006 and 2009, I examined endemic land snails in the genus Ogasawarana. I compared the density of live specimens and frequency of predation scars (from black rats [Rattus rattus]) on empty shells in native vegetation and Casuarina forests. The density of land snails was greater in native vegetation than in Casuarina forests in 2006. Nevertheless, radical declines in the density of land snails occurred in native vegetation since 2006 in association with increasing predation by black rats. In contrast, abundance of Ogasawarana did not decline in the Casuarina forest, where shells with predation scars from rats were rare. As a result, the density of snails was greater in the Casuarina forest than in native vegetation. Removal of Casuarina was associated with an increased proportion of shells with predation scars from rats and a decrease in the density of Ogasawarana. The thick and dense litter of Casuarina appears to provide refugia for native land snails by protecting them from predation by rats; thus, eradication of rats should precede eradication of Casuarina. Adaptive strategies, particularly those that consider the removal order of non-native species, are crucial to minimizing the unintended effects of eradication on native species. In addition, my results suggested that in some cases a given non-native species can be used to mitigate the impacts of other non-native species on native species.

Conservation Implications of Changes in Endemic Hawaiian Drosophilidae Diversity across Land Use Gradients

PubMed Central

Leblanc, Luc; Rubinoff, Daniel; Wright, Mark G.

2013-01-01

Endemic Hawaiian Drosophilidae, a radiation of nearly 1000 species including 13 federally listed as endangered, occur mostly in intact native forest, 500–1500 m above sea level. But their persistence in disturbed forest and agricultural areas has not been documented. Thus, control efforts for agricultural pests may impact endemic species if previously undocumented refugia in agricultural areas may play a role in their conservation. To quantify whether invasive plants and agriculture habitats may harbor endemic Drosophilidae, we established standardized trapping arrays, with traps typically designed to control invasive fruit flies (Tephritidae), with 81 sites across native, disturbed and agricultural land use gradients on the islands of Hawai’i and Maui. We collected and identified, to species level, over 22,000 specimens. We found 121 of the possible 292 species expected to occur in the sampled areas, and the majority (91%) of the captured specimens belonged to 24 common species. Species diversity and numbers were greatest in the native forest, but 55% of the species occurred in the invasive strawberry guava belt and plantation forest, adjacent to and almost 500 m from native forest, and 22 species were collected in orchards and nonnative forest as far as 10 km from native habitats. Their persistence outside of native forest suggests that more careful management of disturbed forest and a reassessment of its conservation value are in order. Conservation efforts and assessments of native forest integrity should include the subset of species restricted to intact native forest, since these species are highly localized and particularly sensitive. Additionally, future efforts to control invasive pest fruit flies should consider the nontarget impacts of maintaining traps in and near native forest. This survey project demonstrates the utility of thorough biotic surveys and taxonomic expertise in developing both sensitive species lists and baseline diversity indices for future conservation and monitoring efforts. PMID:23650514

Seed Removal Increased by Scramble Competition with an Invasive Species

PubMed Central

Minor, Rebecca L.; Koprowski, John L.

2015-01-01

Competition for seeds has a major influence on the evolution of granivores and the plants on which they rely. The complexity of interactions and coevolutionary relationships vary across forest types. The introduction of non-native granivores has considerable potential to alter seed dispersal dynamics. Non-native species are a major cause of endangerment for native species, but the mechanisms are often unclear. As biological invasions continue to rise, it is important to understand mechanisms to build up strategies to mitigate the threat. Our field experiment quantified the impact of introduced Abert’s squirrels (Sciurus aberti) on rates of seed removal within the range of critically endangered Mount Graham red squirrels (Tamiasciurus hudsonicus grahamensis), which consumes similar foods. In the presence of invasive Abert’s squirrels, the time cones were removed was faster than when the invasive was excluded, accounting for a median removal time of cones available to red and Abert’s squirrels that is 32.8% less than that of cones available only to the rare native red squirrels. Moreover, in the presence of Abert’s squirrels, removal rates are higher at great distance from a territorial red squirrel larderhoard and in more open portions of the forest, which suggests differential patterns of seed dispersal. The impact on food availability as a result of cone removal by Abert’s squirrels suggests the potential of food competition as a mechanism of endangerment for the Mount Graham red squirrel. Furthermore, the magnitude and differential spatial patterns of seed removal suggest that non-native granivores may have impacts on forest regeneration and structure. PMID:26650073

Seed Removal Increased by Scramble Competition with an Invasive Species.

PubMed

Minor, Rebecca L; Koprowski, John L

2015-01-01

Competition for seeds has a major influence on the evolution of granivores and the plants on which they rely. The complexity of interactions and coevolutionary relationships vary across forest types. The introduction of non-native granivores has considerable potential to alter seed dispersal dynamics. Non-native species are a major cause of endangerment for native species, but the mechanisms are often unclear. As biological invasions continue to rise, it is important to understand mechanisms to build up strategies to mitigate the threat. Our field experiment quantified the impact of introduced Abert's squirrels (Sciurus aberti) on rates of seed removal within the range of critically endangered Mount Graham red squirrels (Tamiasciurus hudsonicus grahamensis), which consumes similar foods. In the presence of invasive Abert's squirrels, the time cones were removed was faster than when the invasive was excluded, accounting for a median removal time of cones available to red and Abert's squirrels that is 32.8% less than that of cones available only to the rare native red squirrels. Moreover, in the presence of Abert's squirrels, removal rates are higher at great distance from a territorial red squirrel larderhoard and in more open portions of the forest, which suggests differential patterns of seed dispersal. The impact on food availability as a result of cone removal by Abert's squirrels suggests the potential of food competition as a mechanism of endangerment for the Mount Graham red squirrel. Furthermore, the magnitude and differential spatial patterns of seed removal suggest that non-native granivores may have impacts on forest regeneration and structure.

Keystone predators (eastern newts, Notophthalmus viridescens) reduce the impacts of an aquatic invasive species

USGS Publications Warehouse

Smith, Kimberly G.

2006-01-01

Predation, competition, and their interaction are known to be important factors that influence the structure of ecological communities. In particular, in those cases where a competitive hierarchy exists among prey species, the presence of certain keystone predators can result in enhanced diversity in the prey community. However, little is known regarding the influence of keystone predator presence on invaded prey communities. Given the widespread occurrence of invasive species and substantial concern regarding their ecological impacts, studies on this topic are needed. In this study I used naturalistic replications of an experimental tadpole assemblage to assess the influence of predatory eastern newts, Notophthalmus viridescens, on the outcome of interspecific competition among native and nonindigenous tadpoles. When newts were absent, the presence of the tadpoles of one invasive species, the Cuban treefrog, Osteopilus septentrionalis, resulted in decreased survival and growth rate of the dominant native species, Bufo terrestris, and dominance of the tadpole assemblage by O. septentrionalis. However, the presence of one adult newt generally reduced or eliminated the negative impacts of O. septentrionalis tadpoles, resulting in comparable survival and performance of native species in invaded and noninvaded treatments. Differential mortality among the tadpole species suggests that newts preyed selectively on O. septentrionalis tadpoles, supporting the hypothesis that newts acted as keystone predators in the invaded assemblage. The presence of nonindigenous larval cane toads, Bufo marinus, did not significantly affect native species, and this species was not negatively affected by the presence of newts. Collectively, these results suggest that eastern newts significantly modified the competitive hierarchy of the invaded tadpole assemblage and reduced the impacts of a competitively superior invasive species. If general, these results suggest that the presence of certain species may be an essential factor regulating the ecological impacts of biological invasions.

Seed wasp invasions promoted by unregulated seed trade affect vegetal and animal biodiversity.

PubMed

Auger-Rozenberg, Marie-Anne; Roques, Alain

2012-09-01

Cone and seed insects are considered the most important predators of tree seeds during the pre-dispersal phase of development. Among them, exotic seed chalcids in the genus Megastigmus invaded Europe as a result of the rapidly-increasing and mostly unregulated seed trade for afforestation and ornamental plantations. Unlike their economic impact in seed orchards, until recently, little attention was paid to the ecological impact of these insects. In the present study, selected case studies of alien Megastigmus spp. were considered to assess their specific impact on the potential of natural regeneration of native woody plants and on the native entomofauna competing for seed resource. We re-analyzed data from former studies that did not focus on these ecological interactions and, here, present previously unpublished results. Seeds of Douglas-fir, true cedars, true firs and wild roses were sampled all over Europe, and the relative importance of the native and invasive chalcid species was assessed as well as their specific impact on seed yield. In most cases, the recent arrival of alien chalcids resulted in a significant decrease in the regeneration potential of the host trees. In the absence of competitors, alien chalcids occupied the entire seed niche in Douglas-fir, but their impact tended to decrease after the arrival of invasive seed bugs. In firs, alien chalcids tended to displace the native chalcids, but not in wild roses and cedars, where their damage was increasing. Different biological traits that might explain invasive success of alien chalcids are discussed. However, no general invasive patterns seem to exist. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Genotypic Diversity Effects on the Performance of Taraxacum officinale Populations Increase with Time and Environmental Favorability

PubMed Central

Drummond, Emily B. M.; Vellend, Mark

2012-01-01

Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass) clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects), whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture). Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations. PMID:22348004

APOL1 Genotype and Kidney Transplantation Outcomes From Deceased African American Donors.

PubMed

Freedman, Barry I; Pastan, Stephen O; Israni, Ajay K; Schladt, David; Julian, Bruce A; Gautreaux, Michael D; Hauptfeld, Vera; Bray, Robert A; Gebel, Howard M; Kirk, Allan D; Gaston, Robert S; Rogers, Jeffrey; Farney, Alan C; Orlando, Giuseppe; Stratta, Robert J; Mohan, Sumit; Ma, Lijun; Langefeld, Carl D; Bowden, Donald W; Hicks, Pamela J; Palmer, Nicholette D; Palanisamy, Amudha; Reeves-Daniel, Amber M; Brown, W Mark; Divers, Jasmin

2016-01-01

Two apolipoprotein L1 gene (APOL1) renal-risk variants in donors and African American (AA) recipient race are associated with worse allograft survival in deceased-donor kidney transplantation (DDKT) from AA donors. To detect other factors impacting allograft survival from deceased AA kidney donors, APOL1 renal-risk variants were genotyped in additional AA kidney donors. The APOL1 genotypes were linked to outcomes in 478 newly analyzed DDKTs in the Scientific Registry of Transplant Recipients. Multivariate analyses accounting for recipient age, sex, race, panel-reactive antibody level, HLA match, cold ischemia time, donor age, and expanded criteria donation were performed. These 478 transplantations and 675 DDKTs from a prior report were jointly analyzed. Fully adjusted analyses limited to the new 478 DDKTs replicated shorter renal allograft survival in recipients of APOL1 2-renal-risk-variant kidneys (hazard ratio [HR], 2.00; P = 0.03). Combined analysis of 1153 DDKTs from AA donors revealed donor APOL1 high-risk genotype (HR, 2.05; P = 3 × 10), older donor age (HR, 1.18; P = 0.05), and younger recipient age (HR, 0.70; P = 0.001) adversely impacted allograft survival. Although prolonged allograft survival was seen in many recipients of APOL1 2-renal-risk-variant kidneys, follow-up serum creatinine concentrations were higher than that in recipients of 0/1 APOL1 renal-risk-variant kidneys. A competing risk analysis revealed that APOL1 impacted renal allograft survival, but not recipient survival. Interactions between donor age and APOL1 genotype on renal allograft survival were nonsignificant. Shorter renal allograft survival is reproducibly observed after DDKT from APOL1 2-renal-risk-variant donors. Younger recipient age and older donor age have independent adverse effects on renal allograft survival.

The role of HFE genotype in macrophage phenotype.

PubMed

Nixon, Anne M; Neely, Elizabeth; Simpson, Ian A; Connor, James R

2018-02-01

Iron regulation is essential for cellular energy production. Loss of cellular iron homeostasis has critical implications for both normal function and disease progression. The H63D variant of the HFE gene is the most common gene variant in Caucasians. The resulting mutant protein alters cellular iron homeostasis and is associated with a number of neurological diseases and cancer. In the brain, microglial and infiltrating macrophages are critical to maintaining iron homeostasis and modulating inflammation associated with the pathogenic process in multiple diseases. This study addresses whether HFE genotype affects macrophage function and the implications of these findings for disease processes. Bone marrow macrophages were isolated from wildtype and H67D HFE knock-in mice. The H67D gene variant in mice is the human equivalent of the H63D variant. Upon differentiation, the macrophages were used to analyze iron regulatory proteins, cellular iron release, migration, phagocytosis, and cytokine expression. The results of this study demonstrate that the H67D HFE genotype significantly impacts a number of critical macrophage functions. Specifically, fundamental activities such as proliferation in response to iron exposure, L-ferritin expression in response to iron loading, secretion of BMP6 and cytokines, and migration and phagocytic activity were all found to be impacted by genotype. Furthermore, we demonstrated that exposure to apo-Tf (iron-poor transferrin) can increase the release of iron from macrophages. In normal conditions, 70% of circulating transferrin is unsaturated. Therefore, the ability of apo-Tf to induce iron release could be a major regulatory mechanism for iron release from macrophages. These studies demonstrate that the HFE genotype impacts fundamental components of macrophage phenotype that could alter their role in degenerative and reparative processes in neurodegenerative disorders.

Impact of transmission intensity on the accuracy of genotyping to distinguish recrudescence from new infection in antimalarial clinical trials.

PubMed

Greenhouse, Bryan; Dokomajilar, Christian; Hubbard, Alan; Rosenthal, Philip J; Dorsey, Grant

2007-09-01

Antimalarial clinical trials use genotyping techniques to distinguish new infection from recrudescence. In areas of high transmission, the accuracy of genotyping may be compromised due to the high number of infecting parasite strains. We compared the accuracies of genotyping methods, using up to six genotyping markers, to assign outcomes for two large antimalarial trials performed in areas of Africa with different transmission intensities. We then estimated the probability of genotyping misclassification and its effect on trial results. At a moderate-transmission site, three genotyping markers were sufficient to generate accurate estimates of treatment failure. At a high-transmission site, even with six markers, estimates of treatment failure were 20% for amodiaquine plus artesunate and 17% for artemether-lumefantrine, regimens expected to be highly efficacious. Of the observed treatment failures for these two regimens, we estimated that at least 45% and 35%, respectively, were new infections misclassified as recrudescences. Increasing the number of genotyping markers improved the ability to distinguish new infection from recrudescence at a moderate-transmission site, but using six markers appeared inadequate at a high-transmission site. Genotyping-adjusted estimates of treatment failure from high-transmission sites may represent substantial overestimates of the true risk of treatment failure.

Genotyping of polyomavirus BK by Real Time PCR for VP1 gene.

PubMed

Gambarino, Stefano; Costa, Cristina; Astegiano, Sara; Piasentin, Elsa Alessio; Segoloni, Giuseppe P; Cavallo, Rossana; Bergallo, Massimiliano

2011-10-01

Polyomavirus BK latently persist in different sites, including the renourinary tract, and may reactivate causing nephropathy in renal transplant recipients or hemorrhagic cystitis in bone marrow recipients. Based on the sequence of the VP1 gene, four genotypes have been described, corresponding to the four serologically differentiated subtypes I-IV, with different prevalence and geographic distribution. In this study, the development and clinical validation of four different Real-Time PCR assays for the detection and discrimination of BKV genotypes as a substitute of DNA sequencing are described. 379 BK VP1 sequences, belonging to the main four genotypes, were aligned and "hot spots" of mutation specific for all the strains or isolates were identified. Specific primers and probes for the detection and discrimination of each genotype by four Real-Time PCR assays were designed and technically validated. Subsequently, the four Real-Time PCR assays were used to test 20 BK-positive urine specimens from renal transplant patients, and evidenced a prevalence of BK genotype I, as previously reported in Europe. Results were confirmed by sequencing. The availability of a rapid and simple genotyping method could be useful for the evaluation of BK genotypes prevalence and studies on the impact of the infecting genotype on viral biological behavior, pathogenic role, and immune evasion strategies.

Leaf-level gas-exchange uniformity and photosynthetic capacity among loblolly pine (Pinus taeda L.) genotypes of contrasting inherent genetic variation

Treesearch

Michael J. Aspinwall; John S. King; Steven E. McKeand; Jean-Christophe Domec

2011-01-01

Variation in leaf-level gas exchange among widely planted genetically improved loblolly pine (Pinus taeda L.) genotypes could impact stand-level water use, carbon assimilation, biomass production, C allocation, ecosystem sustainability and biogeochemical cycling under changing environmental conditions. We examined uniformity in leaf-level light-saturated photosynthesis...

The effects of drought and herbivory on plant–herbivore interactions across 16 soybean genotypes in a field experiment

USDA-ARS?s Scientific Manuscript database

As the Earth’s climate continues to change, drought and insect population outbreaks are predicted to increase in many parts of the world. It is therefore important to understand how changes in such abiotic and biotic stressors might impact agroecosystems. 16 soybean genotypes were tested in a field ...

The ACE/DD genotype is associated with the extent of exercise-induced left ventricular growth in endurance athletes.

PubMed

Hernández, Domingo; de la Rosa, Alejandro; Barragán, Antonio; Barrios, Ysamar; Salido, Eduardo; Torres, Armando; Martín, Basilio; Laynez, Ignacio; Duque, Amelia; De Vera, Antonia; Lorenzo, Victor; González, Antonio

2003-08-06

We studied the impact of the angiotensin-converting enzyme (ACE)/DD genotype on morphologic and functional cardiac changes in adult endurance athletes. Trained athletes usually develop adaptive left ventricular hypertrophy (LVH), and ACE gene polymorphisms may regulate myocardial growth. However, little is known about the impact of the ACE/DD genotype and D allele dose on the cardiac changes in adult endurance athletes. METHODS; Echocardiographic studies (including tissue Doppler) were performed in 61 male endurance athletes ranging in age from 25 to 40 years, with a similar period of training (15.6 +/- 4 h/week for 12.6 +/- 5.7 years). The ACE genotype (insertion [I] or deletion [D] alleles) was ascertained by polymerase chain reaction (DD = 27, ID = 31, and II = 3). Athletes with the DD genotype were compared with their ID counterparts. The DD genotype was associated with a higher left ventricular mass index (LVMI) than the ID genotype (162.6 +/- 36.5 g/m(2) vs. 141.6 +/- 34 g/m(2), p = 0.031), regardless of other confounder variables. As a result, 70.4% of DD athletes and only 42% of ID athletes met the criteria for LVH (p = 0.037). Although systolic and early diastolic myocardial velocities were similar in DD and ID subjects, a more prolonged E-wave deceleration time (DT) was observed in DD as compared with ID athletes, after adjusting for other biologic variables (210 +/- 48 ms vs. 174 +/- 36 ms, respectively; p = 0.008). Finally, a positive association between DT and myocardial systolic peak velocity (medial and lateral peak S(m)) was only observed in DD athletes (p = 0.013, r = 0.481). The ACE/DD genotype is associated with the extent of exercise-induced LVH in endurance athletes, regardless of other known biologic factors.