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Sample records for diverse helicobacter species

  1. Emergence of Diverse Helicobacter Species in the Pathogenesis of Gastric and Enterohepatic Diseases

    PubMed Central

    Solnick, Jay V.; Schauer, David B.

    2001-01-01

    Since Helicobacter pylori was first cultivated from human gastric biopsy specimens in 1982, it has become apparent that many related species can often be found colonizing the mucosal surfaces of humans and other animals. These other Helicobacter species can be broadly grouped according to whether they colonize the gastric or enterohepatic niche. Gastric Helicobacter species are widely distributed in mammalian hosts and are often nearly universally prevalent. In many cases they cause an inflammatory response resembling that seen with H. pylori in humans. Although usually not pathogenic in their natural host, these organisms serve as models of human disease. Enterohepatic Helicobacter species are an equally diverse group of organisms that have been identified in the intestinal tract and the liver of humans, other mammals, and birds. In many cases they have been linked with inflammation or malignant transformation in immunocompetent hosts and with more severe clinical disease in immunocompromised humans and animals. The purpose of this review is to describe these other Helicobacter species, characterize their role in the pathogenesis of gastrointestinal and enterohepatic disease, and discuss their implications for our understanding of H. pylori infection in humans. PMID:11148003

  2. Intestinal Microbiota and Species Diversity of Campylobacter and Helicobacter spp. in Migrating Shorebirds in Delaware Bay

    PubMed Central

    Ryu, Hodon; Grond, Kirsten; Verheijen, Bram; Elk, Michael; Buehler, Deborah M.

    2014-01-01

    Using 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in red knot (Calidris canutus; n = 40), ruddy turnstone (Arenaria interpres; n = 35), and semipalmated sandpiper (Calidris pusilla; n = 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of Campylobacter spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of Bacilli (63.5%), Fusobacteria (12.7%), Epsilonproteobacteria (6.5%), and Clostridia (5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as Campylobacter (82.3%) or Helicobacter (17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as C. lari (>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of Campylobacter, such as C. jejuni and C. coli, were not detected in excreta of any of the three bird species. Most Helicobacter-like sequences identified were closely related to H. pametensis (>99% sequence identity) and H. anseris (92% sequence identity). qPCR results showed that the occurrence and abundance of Campylobacter spp. was relatively high compared to those of fecal indicator bacteria, such as Enterococcus spp., E. faecalis, and Catellicoccus marimammalium. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic Campylobacter species. PMID:24413599

  3. Intestinal Microbiota and Species Diversity of Campylobacter and Helicobacter spp. in Migrating Shorebirds in Delaware Bay

    EPA Science Inventory

    Using rDNA sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in Red Knot (Calidris canutus, n=40), Ruddy Turnstone (Arenaria interpres, n=35), and Semipalmated Sandpiper (Calidris ...

  4. Lethal photosensitization of Helicobacter species

    NASA Astrophysics Data System (ADS)

    Millson, Charles E.; Wilson, Michael; MacRobert, Alexander J.; Thurrell, Wendy; Mlkvy, Peter; Davies, Claire; Bown, Stephen G.

    1995-01-01

    Helicobacter pylori (H. pylori) is associated with a large number of gastroduodenal disorders. Clearance of the bacteria has been shown to benefit patients with duodenal ulcers, gastric ulcers, and certain rare types of gastric tumors. Broad-spectrum antibiotics are the mainstay of current treatment strategies but side-effects, poor compliance, and drug resistance limit their usefulness. We sensitized H. pylori with toluidine blue, haematoporphyrin derivative, aluminum disulphonated phthalocyanine, methylene blue or protoporphyrin IX prior to exposure to low-power laser light from either a gallium aluminum arsenide laser or a helium neon gas laser. All 5 sensitizers caused reductions of greater than 1000-fold in the number of viable bacteria. Light alone had no effect and only HpD caused a significant decrease in bacterial numbers without laser light. Next, we sensitized H. mustelae on explanted ferret gastric mucosa (ex vivo) with the same sensitizers and exposed them to light from a copper vapor pumped dye laser tuned appropriately. MB caused significant reductions in bacterial counts. Successful lethal photosensitization of Helicobacter pylori both in vitro and ex vivo raises the possibility of a local method for eradicating the bacteria, especially as the bacteria are only found in those parts of the upper gastrointestinal tract that are accessible to the endoscope.

  5. Occurrence, diversity, and host association of intestinal Campylobacter, Arcobacter, and Helicobacter in reptiles.

    PubMed

    Gilbert, Maarten J; Kik, Marja; Timmerman, Arjen J; Severs, Tim T; Kusters, Johannes G; Duim, Birgitta; Wagenaar, Jaap A

    2014-01-01

    Campylobacter, Arcobacter, and Helicobacter species have been isolated from many vertebrate hosts, including birds, mammals, and reptiles. Multiple studies have focused on the prevalence of these Epsilonproteobacteria genera in avian and mammalian species. However, little focus has been given to the presence within reptiles, and their potential zoonotic and pathogenic roles. In this study, occurrence, diversity, and host association of intestinal Epsilonproteobacteria were determined for a large variety of reptiles. From 2011 to 2013, 444 cloacal swabs and fecal samples originating from 417 predominantly captive-held reptiles were screened for Epsilonproteobacteria. Campylobacter, Arcobacter, and Helicobacter genus specific PCRs were performed directly on all samples. All samples were also cultured on selective media and screened for the presence of Epsilonproteobacteria. Using a tiered approach of AFLP, atpA, and 16S rRNA sequencing, 432 Epsilonproteobacteria isolates were characterized at the species level. Based on PCR, Campylobacter, Arcobacter, and Helicobacter were detected in 69.3% of the reptiles; 82.5% of the chelonians, 63.8% of the lizards, and 58.0% of the snakes were positive for one or more of these genera. Epsilonproteobacteria were isolated from 22.1% of the reptiles and were isolated most frequently from chelonians (37.0%), followed by lizards (19.6%) and snakes (3.0%). The most commonly isolated taxa were Arcobacter butzleri, Arcobacter skirrowii, reptile-associated Campylobacter fetus subsp. testudinum, and a putative novel Campylobacter taxon. Furthermore, a clade of seven related putative novel Helicobacter taxa was isolated from lizards and chelonians. This study shows that reptiles carry various intestinal Epsilonproteobacteria taxa, including several putative novel taxa.

  6. Helicobacter cetorum sp. nov., a urease-positive Helicobacter species isolated from dolphins and whales.

    PubMed

    Harper, C G; Feng, Y; Xu, S; Taylor, N S; Kinsel, M; Dewhirst, F E; Paster, B J; Greenwell, M; Levine, G; Rogers, A; Fox, J G

    2002-12-01

    A novel helicobacter with the proposed name Helicobacter cetorum, sp. nov. (type strain MIT 99-5656; GenBank accession number AF 292378), was cultured from the main stomach of two wild, stranded Atlantic white-sided dolphins (Lagenorhynchus acutus) and from the feces of three captive cetaceans (a Pacific white-sided dolphin [Lagenorhynchus obliquidens]; an Atlantic bottlenose dolphin [Tursiops truncatus]; and a beluga whale [Delphinapterus leucas]). The infected captive cetaceans were either subclinical, or clinical signs included intermittent regurgitation, inappetance, weight loss, and lethargy. Ulcers were observed in the esophagus and forestomach during endoscopic examination in two of the three captive animals. In the third animal, esophageal linear erosions were visualized endoscopically, and histopathological evaluation of the main stomach revealed multifocal lymphoplasmacytic gastritis with silver-stained spiral-shaped bacteria. Helicobacter cetorum is a fusiform gram-negative bacterium with a single bipolar flagellum. The isolates grow under microaerobic conditions at 37 and 42 degrees C but not at 25 degrees C. H. cetorum is urease, catalase, and oxidase positive, and it is sensitive to cephalothin. The isolates from the wild, stranded dolphins were sensitive to nalidixic acid, whereas the isolates from the collection animals were resistant. By 16S rRNA sequencing it was determined that H. cetorum represented a distinct taxon that clusters most closely with H. pylori. Further studies are necessary to determine the role of H. cetorum in the development of gastric ulcers and gastritis of cetaceans. This is the first description and formal naming of a novel Helicobacter species from a marine mammal.

  7. Use of pulsed-field gel electrophoresis to determine genomic diversity in strains of Helicobacter hepaticus from geographically distant locations.

    PubMed Central

    Saunders, K E; McGovern, K J; Fox, J G

    1997-01-01

    In 1992 a helical microorganism associated with chronic active hepatitis and a high incidence of hepatocellular tumors was identified in the hepatic parenchyma of A/JCr mice. By using biochemical tests, phenotypic characterization, and 16S rRNA gene sequence analysis, the organism was classified as a novel Helicobacter species and named Helicobacter hepaticus. Recent surveys completed in our laboratory indicate that H. hepaticus is widespread in academic and commercial mouse colonies. The aim of this study was to examine the H. hepaticus genome by pulsed-field gel electrophoresis (PFGE) to determine the degree of genomic variation and genomic size. This technique has been used to identify significant genomic diversity among strains of Helicobacter pylori and to demonstrate only slight genomic diversity among strains of Helicobacter mustelae. Genomic DNAs from 11 isolates of H. hepaticus from the United States, Germany, France, and The Netherlands were subjected to PFGE after digestion with SmaI. Isolates from three independent sources within the United States had very similar PFGE patterns, suggesting that the genomic DNAs of these isolates are conserved. Genomic DNA isolated from a fourth source within the United States had a PFGE pattern different from those of the other U.S. isolates. Isolates obtained from Germany, France, and The Netherlands had PFGE patterns that differed markedly from those of the U.S. isolates and from one another. The use of DNA fingerprinting may be useful in subsequent epidemiological studies of H. hepaticus when the source and method of spread of this murine pathogen need to be ascertained. By PFGE, the genomic size of H. hepaticus is estimated to be roughly 1.3 Mb, which compares to 1.67 Mb for H. pylori and 1.7 Mb for H. mustelae. PMID:9350747

  8. Association of Helicobacter species with hepatitis C cirrhosis with or without hepatocellular carcinoma

    PubMed Central

    Rocha, M; Avenaud, P; Ménard, A; Le Bail, B; Balabaud, C; Bioulac-Sage, P; de Magalhães Queiroz, D M; Mégraud, F

    2005-01-01

    Background and aims: Recent studies have suggested that bacterial coinfection with Helicobacter species in patients already infected with hepatitis C virus (HCV) could be involved in the development of cirrhosis and hepatocellular carcinoma (HCC). A retrospective cross sectional study was performed in order to explore the association between Helicobacter species and HCV associated liver diseases. Methods: The presence of Helicobacter species was tested by polymerase chain reaction on liver samples from four groups of patients. Results: Helicobacter 16S rDNA was found in only 4.2% of liver samples from control patients (n = 24) and in 3.5% of liver samples from patients with non-cirrhotic chronic hepatitis C (n = 29) while it was found in 68.0% of liver samples from patients with HCV positive cirrhosis without HCC (n = 25) as well as in 61.3% of cirrhotic liver samples from patients with HCV positive cirrhosis and HCC (n = 31). In addition, when the HCC tumour tissue was tested (n = 21), 90.5% of samples were positive. DNA from Helicobacter pylori- and Helicobacter pullorum-like organisms was found. Conclusions: There is an association between the presence of Helicobacter species DNA in the liver and hepatitis C cirrhosis, with or without HCC. Indeed, the presence of these bacteria could be the result of structural changes in the liver. Alternatively, Helicobacter species could be a co-risk factor in HCV chronic liver diseases. This result warrants prospective studies to determine the possible causal role of these bacteria in the progression of chronic hepatitis C. PMID:15710989

  9. OVERVIEW: DISINFECTION OF HELICOBACTER PYLORI AND AEROMONAS SPECIES

    EPA Science Inventory

    Helicobacter pylori and Aeromonas hydrophila are contaminants listed on the USEPA's 1998 Contaminant Candidate List (CCL).The sensitivity of H. pylori to chlorine and of Aeromonas spp. to inactivation by free chlorine, chloramine and ultraviolet (UV) was examined. Selective and...

  10. Characterization in Helicobacter pylori of a Nickel Transporter Essential for Colonization That Was Acquired during Evolution by Gastric Helicobacter Species

    PubMed Central

    Turlin, Evelyne; Mancuso, Francesco; Michel, Valérie; Richaud, Pierre; Veyrier, Frédéric J.; De Reuse, Hilde; Vinella, Daniel

    2016-01-01

    Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease. Using a genetic screen, we identified an ABC transporter, that we designated NiuBDE, as a novel H. pylori nickel transport system. Unmarked mutants carrying deletions of nixA, niuD and/or niuB, were constructed and used to measure (i) tolerance to toxic nickel exposure, (ii) intracellular nickel content by ICP-OES, (iii) transport of radioactive nickel and (iv) expression of a reporter gene controlled by nickel concentration. We demonstrated that NiuBDE and NixA function separately and are the sole nickel transporters in H. pylori. NiuBDE, but not NixA, also transports cobalt and bismuth, a metal currently used in H. pylori eradication therapy. Both NiuBDE and NixA participate in nickel-dependent urease activation at pH 5 and survival under acidic conditions mimicking those encountered in the stomach. However, only NiuBDE is able to carry out this activity at neutral pH and is essential for colonization of the mouse stomach. Phylogenomic analyses indicated that both nixA and niuBDE genes have been acquired via horizontal gene transfer by the last common ancestor of the gastric Helicobacter species. Our work highlights the importance of this evolutionary event for the emergence of Helicobacter gastric species that are adapted to the hostile environment of the stomach where the capacity of Helicobacter to import nickel and thereby activate urease needs to be optimized. PMID:27923069

  11. Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization

    PubMed Central

    Vorontsov, Egor; Gallaud, Julien; Malosse, Christian; Michel, Valérie; Cavazza, Christine; Robbe-Saule, Marie; Richaud, Pierre; Chamot-Rooke, Julia; Brochier-Armanet, Céline; De Reuse, Hilde

    2015-01-01

    Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. Virulence of the human gastric pathogen Helicobacter pylori is dependent on nickel, cofactor of two enzymes essential for in vivo colonization, urease and [NiFe] hydrogenase. We found that two small paralogous nickel-binding proteins with high content in Histidine (Hpn and Hpn-2) play a central role in maintaining non-toxic intracellular nickel content and in controlling its intracellular trafficking. Measurements of metal resistance, intracellular nickel contents, urease activities and interactomic analysis were performed. We observed that Hpn acts as a nickel-sequestration protein, while Hpn-2 is not. In vivo, Hpn and Hpn-2 form homo-multimers, interact with each other, Hpn interacts with the UreA urease subunit while Hpn and Hpn-2 interact with the HypAB hydrogenase maturation proteins. In addition, Hpn-2 is directly or indirectly restricting urease activity while Hpn is required for full urease activation. Based on these data, we present a model where Hpn and Hpn-2 participate in a common pathway of controlled nickel transfer to urease. Using bioinformatics and top-down proteomics to identify the predicted proteins, we established that Hpn-2 is only expressed by H. pylori and its closely related species Helicobacter acinonychis. Hpn was detected in every gastric Helicobacter species tested and is absent from the enterohepatic Helicobacter species. Our phylogenomic analysis revealed that Hpn acquisition was concomitant with the specialization of Helicobacter to colonization of the gastric environment and the duplication at the origin of hpn-2 occurred in the common ancestor of H. pylori and H. acinonychis. Finally, Hpn and Hpn-2 were found to be required for colonization of the mouse model by H. pylori. Our data show that during evolution of the Helicobacter genus, acquisition of Hpn and Hpn-2 by gastric

  12. The carcinogenic liver fluke Opisthorchis viverrini is a reservoir for species of Helicobacter.

    PubMed

    Deenonpoe, Raksawan; Chomvarin, Chariya; Pairojkul, Chawalit; Chamgramol, Yaowalux; Loukas, Alex; Brindley, Paul J; Sripa, Banchob

    2015-01-01

    There has been a strong, positive correlation between opisthorchiasis-associated cholangiocarcinoma and infection with Helicobacter. Here a rodent model of human infection with Opisthorchis viverrini was utilized to further investigate relationships of apparent co-infections with O. viverrini and H. pylori. A total of 150 hamsters were assigned to five groups: i) Control hamsters not infected with O. viverrini; ii) O. viverrini-infected hamsters; iii) non-O. viverrini infected hamsters treated with antibiotics (ABx); iv) O. viverrini-infected hamsters treated with ABx; and v) O. viverrini-infected hamsters treated both with ABx and praziquantel (PZQ). Stomach, gallbladder, liver, colonic tissue, colorectal feces and O. viverrini worms were collected and the presence of species of Helicobacter determined by PCR-based approaches. In addition, O. viverrini worms were cultured in vitro with and without ABx for four weeks, after which the presence of Helicobacter spp. was determined. In situ localization of H. pylori and Helicobacter-like species was performed using a combination of histochemistry and immunohistochemistry. The prevalence of H. pylori infection in O. viverrini-infected hamsters was significantly higher than that of O. viverrini-uninfected hamsters (p≤0.001). Interestingly, O. viverrini-infected hamsters treated with ABx and PZQ (to remove the flukes) had a significantly lower frequency of H. pylori than either O. viverrini- infected hamsters treated only with ABx or O. viverrini-infected hamsters, respectively (p≤0.001). Quantitative RT-PCR strongly confirmed the correlation between intensity H. pylori infection and the presence of liver fluke infection. In vitro, H. pylori could be detected in the O. viverrini worms cultured with ABx over four weeks. In situ localization revealed H. pylori and other Helicobacter-like bacteria in worm gut. The findings indicate that the liver fluke O. viverrini in the biliary tree of the hamsters harbors H. pylori

  13. Detection of gastric Helicobacter species in free-ranging lynx (Lynx lynx) and red foxes (Vulpes vulpes) in Sweden.

    PubMed

    Mörner, Torsten; Bröjer, Caroline; Ryser-Degiorgis, Marie-Pierre; Gavier-Widén, Dolores; Nilsson, Hans-Olof; Wadström, Torkel

    2008-07-01

    Specimens of gastric mucosa and liver of 25 free-ranging Eurasian lynx (Lynx lynx), and four red foxes (Vulpes vulpes) shot in Sweden during 1999-2000, were investigated for the presence of Helicobacter species. Histopathology, bacteriologic culture and urease test, Helicobacter genus-specific 16S rDNA PCR analysis, and DNA sequence analysis were applied. Numerous Helicobacter-like organisms were observed histologically in the gastric mucosa of one fox. Helicobacter spp. were detected in the stomach by PCR analysis in 17 (68%) of the lynx and in three (75%) of the foxes. Seven of the positive lynx were also positive in the urease test. PCR fragments, amplified from lynx and foxes, were sequenced and compared with those of known Helicobacter species. PCR products from lynx were closely related (>or=98% homology) to H. heilmannii, and PCR fragments from foxes demonstrated close homology to H. heilmannii and H. salomonis. No Helicobacter spp. or Helicobacter-like organisms could be cultured. The PCR analysis of the liver was negative for all animals. The pathologic significance of the presence of Helicobacter spp. in the stomach of free-ranging lynx and foxes remains uncertain.

  14. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure.

    PubMed Central

    Go, M F; Kapur, V; Graham, D Y; Musser, J M

    1996-01-01

    Genetic diversity and relationships in 74 Helicobacter pylori isolates recovered from patients assigned to distinct clinical categories were estimated by examination of allelic variation in six genes encoding metabolic housekeeping enzymes by multilocus enzyme electrophoresis. Seventy-three distinct allele profiles, representing multilocus chromosomal genotypes, were identified. All six loci were highly polymorphic, with an average of 11.2 alleles per locus. The mean genetic diversity in the sample was 0.735, a value that exceeds the level of diversity recorded in virtually all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles (lack of enzyme activity) was identified and warrants further investigation at the molecular level. Lack of linkage disequilibrium (nonrandom association (of alleles over loci) indicates that horizontal transfer and recombination of metabolic enzyme genes have contributed to the generation of chromosomal diversity in H. pylori. In this sample of isolates, there was no statistically significant association of multilocus enzyme electrophoretic types or cluster of related chromosomal types and disease category. PMID:8682800

  15. Species interaction mechanisms maintain grassland plant species diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theory has outpaced empirical research in pursuit of identifying mechanisms maintaining species diversity. Here we demonstrate how data from diversity-ecosystem functioning experiments can be used to test maintenance of diversity theory. We predict that grassland plant diversity can be maintained by...

  16. Helicobacter pylori Genetic Diversity and Gastro-duodenal Diseases in Malaysia

    PubMed Central

    Gunaletchumy, Selva Perumal; Seevasant, Indran; Tan, Mun Hua; Croft, Laurence J.; Mitchell, Hazel M.; Goh, Khean Lee; Loke, Mun Fai; Vadivelu, Jamuna

    2014-01-01

    Helicobacter pylori infection results in diverse clinical conditions ranging from chronic gastritis and ulceration to gastric adenocarcinoma. Among the multiethnic population of Malaysia, Indians consistently have a higher H. pylori prevalence as compared with Chinese and Malays. Despite the high prevalence of H. pylori, Indians have a relatively low incidence of peptic ulcer disease and gastric cancer. In contrast, gastric cancer and peptic ulcer disease incidence is high in Chinese. H. pylori strains from Chinese strains predominantly belong to the hspEAsia subpopulation while Indian/Malay strains mainly belong to the hspIndia subpopulation. By comparing the genome of 27 Asian strains from different subpopulations, we identified six genes associated with risk of H. pylori-induced peptic ulcer disease and gastric cancer. This study serves as an important foundation for future studies aiming to understand the role of bacterial factors in H. pylori-induced gastro-duodenal diseases. PMID:25503415

  17. High-level genetic diversity in the vapD chromosomal region of Helicobacter pylori.

    PubMed Central

    Cao, P; Cover, T L

    1997-01-01

    Helicobacter pylori isolates from different patients are characterized by diversity in the nucleotide sequences of individual genes, variation in genome size, and variation in gene order. Genetic diversity is particularly striking in vacuolating cytotoxin (vacA) alleles. In this study, five open reading frames (ORFs) were identified within a 4.2-kb region downstream from vacA in H. pylori 60190. One of these ORFs was closely related to the virulence-associated protein D (vapD) gene of Dichelobacter nodosus (64.9% nucleotide identity). A probe derived from vapD of H. pylori 60190 hybridized with only 19 (61.3%) of 31 H. pylori strains tested. Sequence analysis of the vapD region in vapD-negative H. pylori strains revealed that there were two different families of approximately 0.5-kb DNA segments, which were both unrelated to vapD. The presence of vapD was not associated with any specific family of vacA alleles. These findings are consistent with a recombinational population structure for H. pylori. PMID:9139899

  18. Species diversity of Trichoderma in Poland

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fifteen species of Trichoderma were identified from among 118 strains originating from different regions and ecological niches in Poland. This low number indicates low species diversity of Trichoderma in this Central European region. Using the ITS1-ITS2 regions, 64 strains were positively identified...

  19. Lipopolysaccharide Diversity Evolving in Helicobacter pylori Communities through Genetic Modifications in Fucosyltransferases

    PubMed Central

    Nilsson, Christina; Skoglund, Anna; Moran, Anthony P.; Annuk, Heidi; Engstrand, Lars; Normark, Staffan

    2008-01-01

    Helicobacter pylori persistently colonizes the gastric mucosa of half the human population. It is one of the most genetically diverse bacterial organisms and subvariants are continuously emerging within an H. pylori population. In this study we characterized a number of single-colony isolates from H. pylori communities in various environmental settings, namely persistent human gastric infection, in vitro bacterial subcultures on agar medium, and experimental in vivo infection in mice. The lipopolysaccharide (LPS) O-antigen chain revealed considerable phenotypic diversity between individual cells in the studied bacterial communities, as demonstrated by size variable O-antigen chains and different levels of Lewis glycosylation. Absence of high-molecular-weight O-antigen chains was notable in a number of experimentally passaged isolates in vitro and in vivo. This phenotype was not evident in bacteria obtained from a human gastric biopsy, where all cells expressed high-molecular-weight O-antigen chains, which thus may be the preferred phenotype for H. pylori colonizing human gastric mucosa. Genotypic variability was monitored in the two genes encoding α1,3-fucosyltransferases, futA and futB, that are involved in Lewis antigen expression. Genetic modifications that could be attributable to recombination events within and between the two genes were commonly detected and created a diversity, which together with phase variation, contributed to divergent LPS expression. Our data suggest that the surrounding environment imposes a selective pressure on H. pylori to express certain LPS phenotypes. Thus, the milieu in a host will select for bacterial variants with particular characteristics that facilitate adaptation and survival in the gastric mucosa of that individual, and will shape the bacterial community structure. PMID:19043574

  20. Detection of Helicobacter species in the gastrointestinal tract of ringtail possum and koala: possible influence of diet, on the gut microbiota.

    PubMed

    Coldham, Thosaporn; Rose, Karrie; O'Rourke, Jani; Neilan, Brett A; Dalton, Helen; Lee, Adrian; Mitchell, Hazel

    2013-10-25

    The presence of Helicobacter spp. was examined in the liver and in different regions of the gastrointestinal tract (GIT) including the stomach, 3 cm above ileum, ileum, caecum, colon and rectum of 10 ringtail possums (RTPs) and 3 koalas using a combination of microscopy, culture and PCR. Helicobacter was detected in the distal end of the GIT of 7 of 10 RTPs by direct PCR and in all (10/10) RTPs by nested PCR. Five 'S' shaped isolates with bipolar sheathed flagella were isolated from the lower bowel of 3 of the 10 RTPs. 16S rRNA sequence analysis of these 5 isolates confirmed them as potentially novel Helicobacter species. No Helicobacter species were cultured from the koalas, however Helicobacter DNA was detected, in the majority of liver and/or stomach samples of the three koalas and in the colonic region of one koala, using nested PCR. The 16S rRNA gene was sequenced directly from DNA extracted from the homogenised livers and mucus scrapings of the stomach from koala 1 and were confirmed to be Helicobacter species. Based on histopathological examination of sections from the liver and intestine no evidence of infection could be related to the presence of helicobacters in either the RTP or koala. Based on our results, it is possible that diet may influence the detection of Helicobacter species; however this required further investigation.

  1. Genotypic and phenotypic variation of Lewis antigen expression in geographically diverse Helicobacter pylori isolates

    PubMed Central

    Pohl, Mary Ann; Zhang, William; Shah, Sunny; Sanabria-Valentín, Edgardo L.; Perez-Perez, Guillermo I.; Blaser, Martin J.

    2011-01-01

    Background Helicobacter pylori is a persistent colonizer of the human gastric mucosa, which can lead to the development peptic ulcer disease and gastric adenocarcinomas. However, H. pylori can asymptomatically colonize a host for years. One factor that has been hypothesized to contribute to such persistence is the production of Lewis (Le) antigens in the lipopolysaccharide layer of the bacterial outer membrane as a form of molecular mimicry, since humans also express these antigens on their gastric mucosa. Humans and H. pylori both are polymorphic for Le expression, which is driven in H. pylori by variation at the Le synthesis loci. In this report we sought to characterize Le genotypic and phenotypic variation in geographically diverse H. pylori isolates. Materials and Methods From patients undergoing endoscopy in 29 countries, we determined Le phenotypes of 78 H. pylori strains, and performed genotyping of the galT and β-(1,3)galT loci in 113 H. pylori strains. Results Le antigen phenotyping revealed a significant (p <0.0001) association between type 1 (Lea and Leb) expression and strains of East-Asian origin. Genotyping revealed a significant correlation between strain origin and the size of the promoter region upstream of the Le synthesis gene, galT (p <0.0001). Conclusion These results indicate that the heterogeneity of human Le phenotypes are reflected in their H. pylori colonizing strains, and suggest new loci that can be studied to assess variation of Le expression. PMID:22059399

  2. Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains.

    PubMed

    Draper, Jenny L; Hansen, Lori M; Bernick, David L; Abedrabbo, Samar; Underwood, Jason G; Kong, Nguyet; Huang, Bihua C; Weis, Allison M; Weimer, Bart C; van Vliet, Arnoud H M; Pourmand, Nader; Solnick, Jay V; Karplus, Kevin; Ottemann, Karen M

    2017-02-21

    Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB α-1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains.IMPORTANCE Although it is well known that many bacterial genomes are highly variable, it is nonetheless traditional to refer to, analyze, and publish "the genome" of a bacterial strain. Variability is usually reduced ("only sequence from a single colony"), ignored ("just publish the consensus

  3. Impact of reactive oxygen species generation on Helicobacter pylori-related extragastric diseases: a hypothesis.

    PubMed

    Kountouras, Jannis; Boziki, Marina; Polyzos, Stergios A; Katsinelos, Panagiotis; Gavalas, Emmanouel; Zeglinas, Christos; Tzivras, Dimitri; Romiopoulos, Iordanis; Giorgakis, Nikolaos; Anastasiadou, Kyriaki; Vardaka, Elizabeth; Kountouras, Constantinos; Kazakos, Evangelos; Xiromerisiou, Georgia; Dardiotis, Efthimios; Deretzi, Georgia

    2017-01-01

    Helicobacter pylori (H. pylori) induces reactive oxygen species (ROS) production that contribute to pathogenesis of a variety of H. pylori-related gastric diseases, as shown in animal and human studies. Helicobacter pylori infection is also associated with variety of systemic extragastric diseases in which H. pylori-related ROS production might also be involved in the pathogenesis of these systemic conditions. We proposed that Hp-related ROS may play a crucial role in the pathophysiology of Hp-related systemic diseases including Alzheimer's disease, multiple sclerosis, glaucoma and other relative neurodegenerative diseases, thereby suggesting introduction of relative ROS scavengers as therapeutic strategies against these diseases which are among the leading causes of disability and are associated with a large public health global burden. Moreover, we postulated that H. pylori-related ROS might also be involved in the pathogenesis of extragastric common malignancies, thereby suggesting that H. pylori eradication might inhibit the development or delay the progression of aforementioned diseases. However, large-scale future studies are warranted to elucidate the proposed pathophysiological mechanisms, including H. pylori-related ROS, involved in H. pylori-associated systemic and malignant conditions.

  4. Plant Functional Diversity and Species Diversity in the Mongolian Steppe

    PubMed Central

    Liu, Guofang; Xie, Xiufang; Ye, Duo; Ye, Xuehua; Tuvshintogtokh, Indree; Mandakh, Bayart; Huang, Zhenying; Dong, Ming

    2013-01-01

    Background The Mongolian steppe is one of the most important grasslands in the world but suffers from aridization and damage from anthropogenic activities. Understanding structure and function of this community is important for the ecological conservation, but has seldom been investigated. Methodology/Principal Findings In this study, a total of 324 quadrats located on the three main types of Mongolian steppes were surveyed. Early-season perennial forbs (37% of total importance value), late-season annual forbs (33%) and late-season perennial forbs (44%) were dominant in meadow, typical and desert steppes, respectively. Species richness, diversity and plant functional type (PFT) richness decreased from the meadow, via typical to desert steppes, but evenness increased; PFT diversity in the desert and meadow steppes was higher than that in typical steppe. However, above-ground net primary productivity (ANPP) was far lower in desert steppe than in the other two steppes. In addition, the slope of the relationship between species richness and PFT richness increased from the meadow, via typical to desert steppes. Similarly, with an increase in species diversity, PFT diversity increased more quickly in both the desert and typical steppes than that in meadow steppe. Random resampling suggested that this coordination was partly due to a sampling effect of diversity. Conclusions/Significance These results indicate that desert steppe should be strictly protected because of its limited functional redundancy, which its ecological functioning is sensitive to species loss. In contrast, despite high potential forage production shared by the meadow and typical steppes, management of these two types of steppes should be different: meadow steppe should be preserved due to its higher conservation value characterized by more species redundancy and higher spatial heterogeneity, while typical steppe could be utilized moderately because its dominant grass genus Stipa is resistant to

  5. Molecular species identification boosts bat diversity

    PubMed Central

    Mayer, Frieder; Dietz, Christian; Kiefer, Andreas

    2007-01-01

    The lack of obvious morphological differences between species impedes the identification of species in many groups of organisms. Meanwhile, DNA-based approaches are increasingly used to survey biological diversity. In this study we show that sequencing the mitochondrial protein-coding gene NADH dehydrogenase, subunit 1 (nd1) from 534 bats of the Western Palaearctic region corroborates the promise of DNA barcodes in two major respects. First, species described with classical taxonomic tools can be genetically identified with only a few exceptions. Second, substantial sequence divergence suggests an unexpected high number of undiscovered species. PMID:17295921

  6. Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains

    PubMed Central

    Hansen, Lori M.; Bernick, David L.; Abedrabbo, Samar; Underwood, Jason G.; Kong, Nguyet; Huang, Bihua C.; Weis, Allison M.; Pourmand, Nader

    2017-01-01

    ABSTRACT Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB α-1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains. PMID:28223462

  7. Toward a trophic theory of species diversity.

    PubMed

    Terborgh, John W

    2015-09-15

    Efforts to understand the ecological regulation of species diversity via bottom-up approaches have failed to yield a consensus theory. Theories based on the alternative of top-down regulation have fared better. Paine's discovery of keystone predation demonstrated that the regulation of diversity via top-down forcing could be simple, strong, and direct, yet ecologists have persistently failed to perceive generality in Paine's result. Removing top predators destabilizes many systems and drives transitions to radically distinct alternative states. These transitions typically involve community reorganization and loss of diversity, implying that top-down forcing is crucial to diversity maintenance. Contrary to the expectations of bottom-up theories, many terrestrial herbivores and mesopredators are capable of sustained order-of-magnitude population increases following release from predation, negating the assumption that populations of primary consumers are resource limited and at or near carrying capacity. Predation sensu lato (to include Janzen-Connell mortality agents) has been shown to promote diversity in a wide range of ecosystems, including rocky intertidal shelves, coral reefs, the nearshore ocean, streams, lakes, temperate and tropical forests, and arctic tundra. The compelling variety of these ecosystems suggests that top-down forcing plays a universal role in regulating diversity. This conclusion is further supported by studies showing that the reduction or absence of predation leads to diversity loss and, in the more dramatic cases, to catastrophic regime change. Here, I expand on the thesis that diversity is maintained by the interaction between predation and competition, such that strong top-down forcing reduces competition, allowing coexistence.

  8. Toward a trophic theory of species diversity

    PubMed Central

    Terborgh, John W.

    2015-01-01

    Efforts to understand the ecological regulation of species diversity via bottom-up approaches have failed to yield a consensus theory. Theories based on the alternative of top-down regulation have fared better. Paine’s discovery of keystone predation demonstrated that the regulation of diversity via top-down forcing could be simple, strong, and direct, yet ecologists have persistently failed to perceive generality in Paine’s result. Removing top predators destabilizes many systems and drives transitions to radically distinct alternative states. These transitions typically involve community reorganization and loss of diversity, implying that top-down forcing is crucial to diversity maintenance. Contrary to the expectations of bottom-up theories, many terrestrial herbivores and mesopredators are capable of sustained order-of-magnitude population increases following release from predation, negating the assumption that populations of primary consumers are resource limited and at or near carrying capacity. Predation sensu lato (to include Janzen–Connell mortality agents) has been shown to promote diversity in a wide range of ecosystems, including rocky intertidal shelves, coral reefs, the nearshore ocean, streams, lakes, temperate and tropical forests, and arctic tundra. The compelling variety of these ecosystems suggests that top-down forcing plays a universal role in regulating diversity. This conclusion is further supported by studies showing that the reduction or absence of predation leads to diversity loss and, in the more dramatic cases, to catastrophic regime change. Here, I expand on the thesis that diversity is maintained by the interaction between predation and competition, such that strong top-down forcing reduces competition, allowing coexistence. PMID:26374788

  9. Functional diversity within the Penicillium roqueforti species.

    PubMed

    Gillot, Guillaume; Jany, Jean-Luc; Poirier, Elisabeth; Maillard, Marie-Bernadette; Debaets, Stella; Thierry, Anne; Coton, Emmanuel; Coton, Monika

    2017-01-16

    Penicillium roqueforti is used as a ripening culture for blue cheeses and largely contributes to their organoleptic quality and typical characteristics. Different types of blue cheeses are manufactured and consumed worldwide and have distinct aspects, textures, flavors and colors. These features are well accepted to be due to the different manufacturing methods but also to the specific P. roqueforti strains used. Indeed, inoculated P. roqueforti strains, via their proteolytic and lipolytic activities, have an effect on both blue cheese texture and flavor. In particular, P. roqueforti produces a wide range of flavor compounds and variations in their proportions influence the flavor profiles of this type of cheese. Moreover, P. roqueforti is also characterized by substantial morphological and genetic diversity thus raising the question about the functional diversity of this species. In this context, 55 representative strains were screened for key metabolic properties including proteolytic activity (by determining free NH2 amino groups) and secondary metabolite production (aroma compounds using HS-Trap GC-MS and mycotoxins via LC-MS/Q-TOF). Mini model cheeses were used for aroma production and proteolysis analyses, whereas Yeast Extract Sucrose (YES) agar medium was used for mycotoxin production. Overall, this study highlighted high functional diversity among isolates. Noteworthy, when only P. roqueforti strains isolated from Protected Designation of Origin (PDO) or Protected Geographical Indication (PGI) blue cheeses were considered, a clear relationship between genetic diversity, population structure and the assessed functional traits was shown.

  10. Seasonality and predictability shape temporal species diversity.

    PubMed

    Tonkin, Jonathan D; Bogan, Michael T; Bonada, Núria; Rios-Touma, Blanca; Lytle, David A

    2017-01-31

    Temporal environmental fluctuations, such as seasonality, exert strong controls on biodiversity. While the effects of seasonality are well known, the predictability of fluctuations across years may influence seasonality in ways that are less well understood. The ability of a habitat to support unique, non-nested assemblages of species at different times of the year should depend on both seasonality (occurrence of events at specific periods of the year) and predictability (the reliability of event recurrence) of characteristic ecological conditions. Drawing on tools from wavelet analysis and information theory, we develop a framework for quantifying both seasonality and predictability of habitats, and applied this using global long-term rainfall data. Our analysis predicted that temporal beta diversity should be maximized in highly-predictable and highly-seasonal climates, and that low degrees of seasonality, predictability, or both would lower diversity in characteristic ways. Using stream invertebrate communities as a case study, we demonstrated that temporal species diversity, as exhibited by community turnover, was determined by a balance between temporal environmental variability (seasonality) and the reliability of this variability (predictability). Communities in highly-seasonal Mediterranean environments exhibited strong oscillations in community structure, with turnover from one unique community type to another across seasons, whereas communities in aseasonal New Zealand environments fluctuated randomly. Understanding the influence of seasonal and other temporal scales of environmental oscillations on diversity is not complete without a clear understanding of their predictability, and our framework provides tools for examining these trends at a variety of temporal scales, seasonal and beyond. Given the uncertainty of future climates, seasonality and predictability are critical considerations for both basic science and management of ecosystems (e.g. dam

  11. Gastric and enterohepatic non-Helicobacter pylori Helicobacters.

    PubMed

    Flahou, Bram; Haesebrouck, Freddy; Smet, Annemieke; Yonezawa, Hideo; Osaki, Takako; Kamiya, Shigeru

    2013-09-01

    A substantial number of reports published in the last year have contributed to a better understanding of both human and animal infection with non-Helicobacter pylori Helicobacter species (NHPH). Gastric infection of humans with Helicobacter suis and Helicobacter felis as well as unidentified NHPH has been described to cause a chronic gastritis and a variety of clinical symptoms, whereas enterohepatic NHPH, including Helicobacter cinaedi, Helicobacter bilis, and Helicobacter canis, have been reported to be associated with human diseases such as bacteremia, cellulitis, cutaneous diseases, and fever of unknown origin in immunocompromised hosts. In various animal species, including dogs and laboratory mice, high rates of infection with NHPH were described. For gastric NHPH, mainly H. suis and H. felis infection was studied, revealing that differences in the immune response evoked in the host do exist when compared to Helicobacter pylori. Pathogenic mechanisms of infection with Helicobacter pullorum, H. bilis, and Helicobacter hepaticus were investigated, as well as immune responses involved in H. bilis-, Helicobacter typhlonius-, and H. hepaticus-induced intestinal inflammation. Complete genome sequences of Helicobacter heilmannii strain ASB1 and a H. cinaedi strain isolated in a case of human bacteremia were published, as well as comparative genomics of a human-derived Helicobacter bizzozeronii strain and proteome or secretome analyses for H. hepaticus and Helicobacter trogontum, respectively. Molecular analysis has revealed a function for type VI secretion systems of H. hepaticus and H. pullorum, the Helicobacter mustelae iron urease, and several other functional components of NHPH. In each section of this chapter, new findings on gastric NHPH will first be discussed, followed by those on enterohepatic Helicobacter species.

  12. Purification and characterization of the urease enzymes of Helicobacter species from humans and animals.

    PubMed Central

    Turbett, G R; Høj, P B; Horne, R; Mee, B J

    1992-01-01

    The urease enzymes of Helicobacter pylori, H. mustelae, H. felis, and H. nemestrinae have been purified to homogeneity by affinity chromatography and characterized. The native urease enzymes of the four organisms were found to be almost identical, with a pI of 6.1 and molecular masses of 480 to 500 kDa, as determined by electrophoretic mobility in nondenaturing polyacrylamide gels. Transmission electron microscopy of the native urease showed it to be a molecule approximately 13 nm in diameter, with hexagonal symmetry. Denaturation studies indicated that each urease enzyme molecule was composed of two nonidentical subunits with molecular masses of approximately 64 and 30 kDa. The subunits were present in a 1:1 ratio, suggesting a hexameric stoichiometry for the native molecule. The predicted molecular mass of H. pylori urease, based on subunit molecular weight and stoichiometry, is 568 kDa. N-terminal amino acid sequencing of the enzyme subunits from the four species revealed high levels of homology. The large subunits (UreB) were found to be 92 to 100% homologous, and the small subunits (UreA) were 75 to 95% homologous over the first 12 to 20 residues. The high degree of homology suggests a common ancestral origin and an important role for the urease enzymes of these organisms. Images PMID:1452359

  13. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    PubMed

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  14. Analysis of Genomic Diversity among Helicobacter pylori Strains Isolated from Iranian Children by Pulsed Field Gel Electrophoresis

    PubMed Central

    Falsafi, Tahereh; Sotoudeh, Nazli; Feizabadi, Mohammad-Mehdi; Mahjoub, Fatemeh

    2014-01-01

    Objective: Presence of genomic diversity among Helicobacter pylori (H. pylori) strains have been suggested by numerous investigators. Little is known about diversity of H. pylori strains isolated from Iranian children and their association with virulence of the strains. Our purpose was to assess the degree of genomic diversity among H. pylori strains isolated from Iranian-children, on the basis of vacA genotype, cagA status of the strains, sex, age as well as the pathological status of the patients. Methods: Genomic DNA from 44 unrelated H. pylori strains isolated during 1997–2009, was examined by pulse-field gel electrophoresis (PFGE). Pathological status of the patients was performed according to the modified Sydney-system and genotype/status of vacA/cagA genes was determined by PCR. PFGE was performed using XbaI restriction-endonuclease and the field inversion-gel electrophoresis system. Findings: No significant relationship was observed between the patterns of PFGE and the cagA/vacA status/genotype. Also no relationship was observed between age, sex, and pathological status of the children and the PFGE patterns of their isolates. Similar conclusion was obtained by Total Lab software. However, more relationship was observed between the strains isolated in the close period (1997–2009, 2001–2003, 2005–2007, and 2007–2009) and more difference was observed among those obtained in the distant periods (1997 and 2009). Conclusion: H. pylori strains isolated from children in Iran are extremely diverse and this diversity is not related to their virulence characteristics. Occurrence of this extreme diversity may be related to adaptation of H. pylori strains to variable living conditions during transmission between various host individuals. PMID:26019775

  15. Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

    PubMed

    Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

  16. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    USGS Publications Warehouse

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  17. Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability

    PubMed Central

    Lu, Qun-Feng; Li, Song-Bo; Wang, Ju-Ping; Chen, Yu-Li

    2016-01-01

    The genus Helicobacter is a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species. Helicobacter pylori (H. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings of H. pylori that are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representative H. pylori and 24 non-pylori Helicobacter genomes. There were 1173 conserved protein families of H. pylori and 673 of all 99 Helicobacter genus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of the H. pylori but lacked in non-pylori Helicobacter species. The operons, genes, and sRNAs within the H. pylori unique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship. PMID:28078297

  18. [Species diversity of floor bryophyte communities in Bogda Mountains, Xinjiang].

    PubMed

    Zhang, Yuanming; Cao, Tong; Pan, Borong

    2003-06-01

    By means of species similarity coefficient and species diversity index, the characteristics of species diversity of floor bryophyte communities in Bogda Mountain, Xinjiang were studied. The results showed that the bryoflora of Bogda Mountain had the characteristics of richness and complexion. There were 186 floor species (including infraspecies taxa) belonging to 73 genera of 32 families. The species similarity between mountain desert and mountain grassland belt was the highest (0.6809), while that between mountain forest and alpine cushion belt was the lowest (0.1342). The bryophyte community in mountain forest was the ominant one among the floor bryophyte communities. The bryophyte community in mountain forest had the richest species diversity, and the mountain forest was the distribution center of bryophyte diversity and the key area for bryophyte diversity conservation in Bogda Mountain area.

  19. Genetic calibration of species diversity among North America's freshwater fishes

    PubMed Central

    April, Julien; Mayden, Richard L.; Hanner, Robert H.; Bernatchez, Louis

    2011-01-01

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required. PMID:21670289

  20. Genetic calibration of species diversity among North America's freshwater fishes.

    PubMed

    April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

    2011-06-28

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

  1. Elevated prevalence of Helicobacter species and virulence factors in opisthorchiasis and associated hepatobiliary disease

    PubMed Central

    Deenonpoe, Raksawan; Mairiang, Eimorn; Mairiang, Pisaln; Pairojkul, Chawalit; Chamgramol, Yaovalux; Rinaldi, Gabriel; Loukas, Alex; Brindley, Paul J.; Sripa, Banchob

    2017-01-01

    Recent reports suggest that Opisthorchis viverrini serves as a reservoir of Helicobacter and implicate Helicobacter in pathogenesis of opisthorchiasis-associated cholangiocarcinoma (CCA). Here, 553 age-sex matched cases and controls, 293 and 260 positive and negative for liver fluke O. viverrini eggs, of residents in Northeastern Thailand were investigated for associations among infection with liver fluke, Helicobacter and hepatobiliary fibrosis. The prevalence of H. pylori infection was higher in O. viverrini-infected than uninfected participants. H. pylori bacterial load correlated positively with intensity of O. viverrini infection, and participants with opisthorchiasis exhibited higher frequency of virulent cagA-positive H. pylori than those free of fluke infection. Genotyping of cagA from feces of both infected and uninfected participants revealed that the AB genotype accounted for 78% and Western type 22%. Participants infected with O. viverrini exhibited higher prevalence of typical Western type (EPIYA ABC) and variant AB’C type (EPIYT B) CagA. Multivariate analyses among H. pylori virulence genes and severity of hepatobiliary disease revealed positive correlations between biliary periductal fibrosis during opisthorchiasis and CagA and CagA with CagA multimerization (CM) sequence-positive H. pylori. These findings support the hypothesis that H. pylori contributes to the pathogenesis of chronic opisthorchiasis and specifically to opisthorchiasis-associated CCA. PMID:28198451

  2. Does plant species co-occurrence influence soil mite diversity?

    PubMed

    St John, Mark G; Wall, Diana H; Behan-Pelletier, Valerie M

    2006-03-01

    Few studies have considered whether plant taxa can be used as predictors of belowground faunal diversity in natural ecosystems. We examined soil mite (Acari) diversity beneath six grass species at the Konza Prairie Biological Station, Kansas, USA. We tested the hypotheses that soil mite species richness, abundance, and taxonomic diversity are greater (1) beneath grasses in dicultures (different species) compared to monocultures (same species), (2) beneath grasses of higher resource quality (lower C:N) compared to lower resource quality, and (3) beneath heterogeneous mixes of grasses (C3 and C4 grasses growing together) compared to homogeneous mixes (C3 or C4 grasses) using natural occurrences of plant species as treatments. This study is the first to examine the interaction between above- and belowground diversity in a natural setting with species-level resolution of a hyper-diverse taxon. Our results indicate that grasses in diculture supported a more species and phylogenetically rich soil mite fauna than was observed for monocultures and that this relationship was significant at depth but not in the upper soil horizon. We noted that mite species richness was not linearly related to grass species richness, which suggests that simple extrapolations of soil faunal diversity based on plant species inventories may underestimate the richness of associated soil mite communities. The distribution of mite size classes in dicultures was considerably different than those for monocultures. There was no difference in soil mite richness between grass combinations of differing resource quality, or resource heterogeneity.

  3. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.

    PubMed

    Taberlet, Pierre; Zimmermann, Niklaus E; Englisch, Thorsten; Tribsch, Andreas; Holderegger, Rolf; Alvarez, Nadir; Niklfeld, Harald; Coldea, Gheorghe; Mirek, Zbigniew; Moilanen, Atte; Ahlmer, Wolfgang; Marsan, Paolo Ajmone; Bona, Enzo; Bovio, Maurizio; Choler, Philippe; Cieślak, Elżbieta; Colli, Licia; Cristea, Vasile; Dalmas, Jean-Pierre; Frajman, Božo; Garraud, Luc; Gaudeul, Myriam; Gielly, Ludovic; Gutermann, Walter; Jogan, Nejc; Kagalo, Alexander A; Korbecka, Grażyna; Küpfer, Philippe; Lequette, Benoît; Letz, Dominik Roman; Manel, Stéphanie; Mansion, Guilhem; Marhold, Karol; Martini, Fabrizio; Negrini, Riccardo; Niño, Fernando; Paun, Ovidiu; Pellecchia, Marco; Perico, Giovanni; Piękoś-Mirkowa, Halina; Prosser, Filippo; Puşcaş, Mihai; Ronikier, Michał; Scheuerer, Martin; Schneeweiss, Gerald M; Schönswetter, Peter; Schratt-Ehrendorfer, Luise; Schüpfer, Fanny; Selvaggi, Alberto; Steinmann, Katharina; Thiel-Egenter, Conny; van Loo, Marcela; Winkler, Manuela; Wohlgemuth, Thomas; Wraber, Tone; Gugerli, Felix; Vellend, Mark

    2012-12-01

    The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.

  4. Geographic diversity of Helicobacter pylori in cadavers: forensic estimation of geographical origin.

    PubMed

    Nagasawa, Sayaka; Motani-Saitoh, Hisako; Inoue, Hiroyuki; Iwase, Hirotaro

    2013-06-10

    A method for determining the geographical origin of unidentified cadavers by determining the genotype of Helicobacter pylori, which is latent in one-half of the world's population, was developed. In the first stage, DNA was extracted from samplings at 5 points in the gastric mucosa of 177 individuals randomly selected from cadavers undergoing medico-legal autopsy. 16S-rDNA of H. pylori DNA was detected by polymerase chain reaction (PCR) in 101 cadavers (57.0%); by sex, 74 of 123 (60.1%) males and 28 of 54 (46.4%) females were positive. There were no significant differences in H. pylori detection rate among the 5 sampling points of the gastric mucosa, cause of death, or age. In the second stage, amplified fragments of H. pylori vacA regions s and m from 17 individuals with the following ethnic backgrounds were sequenced: Japanese, 10; Chinese, 2; South Korean, 1; Taiwanese, 1; Thai, 1; Afghan, 1; and Filipino, 1. A phylogenetic tree constructed with these and 28 previously reported H. pylori strain sequences revealed 3 major gene clusters consisting of East Asian type I (Japanese, South Korean and Chinese), Western type II, and Southeast Asia type III. The Taiwanese and Filipino samples deviated from the clusters type III to which they typically belong. The ultimate aim of the present study was to develop a more accurate method of determining of geographic origin of unidentified cadavers through the combination of the present method with other, virus-based methods H. pylori DNA was detected from over half of the cadavers tested and vacA genotypes showed specificity to geographical origin. Therefore, these results suggest that the H. pylori genome provides valuable additional information for tracing the geographical origin of unidentified cadavers.

  5. Highlighting Astyanax Species Diversity through DNA Barcoding

    PubMed Central

    Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

    2016-01-01

    DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

  6. One species, many terpenes: matching chemical and biological diversity.

    PubMed

    Loreto, Francesco; Bagnoli, Francesca; Fineschi, Silvia

    2009-08-01

    Volatile terpenes have been proposed as chemotaxonomic markers, despite the strong environmental control on their synthesis. To clarify whether chemical profiles match biological diversity, cork oak, a monoterpene-emitting species that has been bred by humans and frequently hybridizes with other oaks, is a useful case-study. Analysis of the available genetic information in cork oak provenances suggests that volatile terpenes might indeed suitably track geographical diversity even at the intraspecific level. Phylogeographical diversity does not reflect chemical diversity in other evergreen oaks that have not been intensively bred. Breeding for productive traits might therefore drive selection for terpene diversity, in turn modulating important adaptive mechanisms against biotic and abiotic stressors.

  7. Plant species loss decreases arthropod diversity and shifts trophic structure.

    PubMed

    Haddad, Nick M; Crutsinger, Gregory M; Gross, Kevin; Haarstad, John; Knops, Johannes M H; Tilman, David

    2009-10-01

    Plant diversity is predicted to be positively linked to the diversity of herbivores and predators in a foodweb. Yet, the relationship between plant and animal diversity is explained by a variety of competing hypotheses, with mixed empirical results for each hypothesis. We sampled arthropods for over a decade in an experiment that manipulated the number of grassland plant species. We found that herbivore and predator species richness were strongly, positively related to plant species richness, and that these relationships were caused by different mechanisms at herbivore and predator trophic levels. Even more dramatic was the threefold increase, from low- to high-plant species richness, in abundances of predatory and parasitoid arthropods relative to their herbivorous prey. Our results demonstrate that, over the long term, the loss of plant species propagates through food webs, greatly decreasing arthropod species richness, shifting a predator-dominated trophic structure to being herbivore dominated, and likely impacting ecosystem functioning and services.

  8. Do Stacked Species Distribution Models Reflect Altitudinal Diversity Patterns?

    PubMed Central

    Mateo, Rubén G.; Felicísimo, Ángel M.; Pottier, Julien; Guisan, Antoine; Muñoz, Jesús

    2012-01-01

    The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed. PMID

  9. Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity.

    PubMed

    Jurasinski, Gerald; Retzer, Vroni; Beierkuhnlein, Carl

    2009-02-01

    Almost half a century after Whittaker (Ecol Monogr 30:279-338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative--depending on the organism(s) or ecosystems investigated--this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term "inventory diversity." Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness ("key concept" vs. "abstruse concept"). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, "differentiation diversity" (first group) and "proportional diversity" (second group). Thus, we propose to use the terms "inventory diversity" for within-sample diversity, "differentiation diversity" for compositional similarity between samples, and "proportional diversity" for the

  10. Effects of topsoil removal on seedling emergence and species diversity

    SciTech Connect

    Winkel, V.K.; Ostler, W.K.

    1994-02-01

    Approximately 800 hectares on the US Department of Energy Nevada Test Site and vicinity are contaminated with Plutonium. As part of a cleanup effort, both the vegetation and the top 5--10 cm of soil may be removed. A study was developed to determine the effects of topsoil removal on seedling emergence and plant species diversity. Trial plots were prepared by removing 5, 10, or 20 cm of topsoil, seeding a mix of nine native species, mulching with straw, and then anchoring the straw with erosion netting. Additional plots (0 topsoil removal treatment) were lightly bladed to remove existing vegetation and then treated as above. Approximately 85 mm of supplemental irrigation was applied to help initiate germination during early spring. Seedling density data of seeded and nonseeded species was collected following emergence, and species diversity was calculated with the Shannon diversity index for the nonseeded species. Densities of seeded species either were unaffected by or increased with increased depth of topsoil removal. In general, densities of nonseeded species decreased with increased depth of topsoil removal. The number of species, species diversity and evenness also decreased with increased depth of topsoil removal. Initial emergence of seeded species is apparently unaffected by topsoil removal at this site.

  11. High Diversity of vacA and cagA Helicobacter pylori Genotypes in Patients with and without Gastric Cancer

    PubMed Central

    López-Vidal, Yolanda; Ponce-de-León, Sergio; Castillo-Rojas, Gonzalo; Barreto-Zúñiga, Rafael; Torre-Delgadillo, Aldo

    2008-01-01

    Background Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. The aim of this study was to assess the topographical distribution of H. pylori in the stomach as well as the vacA and cagA genotypes in patients with and without gastric cancer. Methodology/Principal Findings Three gastric biopsies, from predetermined regions, were evaluated in 16 patients with gastric cancer and 14 patients with dyspeptic symptoms. From cancer patients, additional biopsy specimens were obtained from tumor centers and margins; among these samples, the presence of H. pylori vacA and cagA genotypes was evaluated. Positive H. pylori was 38% and 26% in biopsies obtained from the gastric cancer and non-cancer groups, respectively (p = 0.008), and 36% in tumor sites. In cancer patients, we found a preferential distribution of H. pylori in the fundus and corpus, whereas, in the non-cancer group, the distribution was uniform (p = 0.003). A majority of the biopsies were simultaneously cagA gene-positive and -negative. The fundus and corpus demonstrated a higher positivity rate for the cagA gene in the non-cancer group (p = 0.036). A mixture of cagA gene sizes was also significantly more frequent in this group (p = 0.003). Ninety-two percent of all the subjects showed more than one vacA gene genotype; s1b and m1 vacA genotypes were predominantly found in the gastric cancer group. The highest vacA-genotype signal-sequence diversity was found in the corpus and 5 cm from tumor margins. Conclusion/Significance High H. pylori colonization diversity, along with the cagA gene, was found predominantly in the fundus and corpus of patients with gastric cancer. The genotype diversity observed across systematic whole-organ and tumor sampling was remarkable. We find that there is insufficient evidence to support the association of one isolate with a specific disease, due to the multistrain nature of H. pylori infection shown in this work. PMID:19050763

  12. Genetic diversity analysis in Piper species (Piperaceae) using RAPD markers.

    PubMed

    Sen, Sandeep; Skaria, Reby; Abdul Muneer, P M

    2010-09-01

    The genetic diversity of eight species of Piper (Piperaceae) viz., P. nigrum, P. longum, P. betle, P. chaba, P. argyrophyllum, P. trichostachyon, P. galeatum, and P. hymenophyllum from Kerala state, India were analyzed by Random amplified polymorphic DNA (RAPD). Out of 22 10-mer RAPD primers screened, 11 were selected for comparative analysis of different species of Piper. High genetic variations were found among different Piper species studied. Among the total of 149 RAPD fragments amplified, 12 bands (8.05%) were found monomorphic in eight species. The remaining 137 fragments were found polymorphic (91.95%). Species-specific bands were found in all eight species studied. The average gene diversity or heterozygosity (H) was 0.33 across all the species, genetic distances ranged from 0.21 to 0.69. The results of this study will facilitate germplasm identification, management, and conservation.

  13. Population diversity and the portfolio effect in an exploited species.

    PubMed

    Schindler, Daniel E; Hilborn, Ray; Chasco, Brandon; Boatright, Christopher P; Quinn, Thomas P; Rogers, Lauren A; Webster, Michael S

    2010-06-03

    One of the most pervasive themes in ecology is that biological diversity stabilizes ecosystem processes and the services they provide to society, a concept that has become a common argument for biodiversity conservation. Species-rich communities are thought to produce more temporally stable ecosystem services because of the complementary or independent dynamics among species that perform similar ecosystem functions. Such variance dampening within communities is referred to as a portfolio effect and is analogous to the effects of asset diversity on the stability of financial portfolios. In ecology, these arguments have focused on the effects of species diversity on ecosystem stability but have not considered the importance of biologically relevant diversity within individual species. Current rates of population extirpation are probably at least three orders of magnitude higher than species extinction rates, so there is a pressing need to clarify how population and life history diversity affect the performance of individual species in providing important ecosystem services. Here we use five decades of data from Oncorhynchus nerka (sockeye salmon) in Bristol Bay, Alaska, to provide the first quantification of portfolio effects that derive from population and life history diversity in an important and heavily exploited species. Variability in annual Bristol Bay salmon returns is 2.2 times lower than it would be if the system consisted of a single homogenous population rather than the several hundred discrete populations it currently consists of. Furthermore, if it were a single homogeneous population, such increased variability would lead to ten times more frequent fisheries closures. Portfolio effects are also evident in watershed food webs, where they stabilize and extend predator access to salmon resources. Our results demonstrate the critical importance of maintaining population diversity for stabilizing ecosystem services and securing the economies and livelihoods

  14. Trophic Niche in a Raptor Species: The Relationship between Diet Diversity, Habitat Diversity and Territory Quality

    PubMed Central

    2015-01-01

    Recent research reports that many populations of species showing a wide trophic niche (generalists) are made up of both generalist individuals and individuals with a narrow trophic niche (specialists), suggesting trophic specializations at an individual level. If true, foraging strategies should be associated with individual quality and fitness. Optimal foraging theory predicts that individuals will select the most favourable habitats for feeding. In addition, the “landscape heterogeneity hypothesis” predicts a higher number of species in more diverse landscapes. Thus, it can be predicted that individuals with a wider realized trophic niche should have foraging territories with greater habitat diversity, suggesting that foraging strategies, territory quality and habitat diversity are inter-correlated. This was tested for a population of common kestrels Falco tinnunculus. Diet diversity, territory occupancy (as a measure of territory quality) and habitat diversity of territories were measured over an 8-year period. Our results show that: 1) territory quality was quadratically correlated with habitat diversity, with the best territories being the least and most diverse; 2) diet diversity was not correlated with territory quality; and 3) diet diversity was negatively correlated with landscape heterogeneity. Our study suggests that niche generalist foraging strategies are based on an active search for different prey species within or between habitats rather than on the selection of territories with high habitat diversity. PMID:26047025

  15. Identification of Helicobacter pylori by immunological dot blot method based on reaction of a species-specific monoclonal antibody with a surface-exposed protein.

    PubMed Central

    Bölin, I; Lönroth, H; Svennerholm, A M

    1995-01-01

    Monoclonal antibodies (MAbs) against membrane preparations of Helicobacter pylori were produced. One MAb was found to be specific for H. pylori, because it did not react with a number of other bacterial species, including Helicobacter felis and Campylobacter jejuni. This MAb reacted with a 30-kDa protein found in outer membrane preparations of H. pylori. The protein was also detected on the cell surface on intact bacteria when analyzed by immunoelectron microscopy. To facilitate the identification of H. pylori isolates after culturing of biopsies, an immunodot blot assay based on the reaction of this MAb was developed. This assay was found to be highly specific for H. pylori. Sixty-six clinical isolates typed as H. pylori by conventional biochemical tests were found to be positive, whereas no other bacterial species tested gave a positive result. By this method, reliable and rapid identification of H. pylori could be accomplished. PMID:7714196

  16. Bacterial Community Diversity Harboured by Interacting Species

    PubMed Central

    Bili, Mikaël; Cortesero, Anne Marie; Mougel, Christophe; Gauthier, Jean Pierre; Ermel, Gwennola; Simon, Jean Christophe; Outreman, Yannick; Terrat, Sébastien; Mahéo, Frédérique; Poinsot, Denis

    2016-01-01

    All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts. PMID:27258532

  17. Diverse microbial species survive high ammonia concentrations

    NASA Astrophysics Data System (ADS)

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  18. High-order species interactions shape ecosystem diversity

    PubMed Central

    Bairey, Eyal; Kelsic, Eric D.; Kishony, Roy

    2016-01-01

    Classical theory shows that large communities are destabilized by random interactions among species pairs, creating an upper bound on ecosystem diversity. However, species interactions often occur in high-order combinations, whereby the interaction between two species is modulated by one or more other species. Here, by simulating the dynamics of communities with random interactions, we find that the classical relationship between diversity and stability is inverted for high-order interactions. More specifically, while a community becomes more sensitive to pairwise interactions as its number of species increases, its sensitivity to three-way interactions remains unchanged, and its sensitivity to four-way interactions actually decreases. Therefore, while pairwise interactions lead to sensitivity to the addition of species, four-way interactions lead to sensitivity to species removal, and their combination creates both a lower and an upper bound on the number of species. These findings highlight the importance of high-order species interactions in determining the diversity of natural ecosystems. PMID:27481625

  19. Empirical Relationships between Species Richness, Evenness, and Proportional Diversity.

    PubMed

    Stirling, G; Wilsey, B

    2001-09-01

    Diversity (or biodiversity) is typically measured by a species count (richness) and sometimes with an evenness index; it may also be measured by a proportional statistic that combines both measures (e.g., Shannon-Weiner index or H'). These diversity measures are hypothesized to be positively and strongly correlated, but this null hypothesis has not been tested empirically. We used the results of Caswell's neutral model to generate null relationships between richness (S), evenness (J'), and proportional diversity (H'). We tested predictions of the null model against empirical relationships describing data in a literature survey and in four individual studies conducted across various scales. Empirical relationships between log S or J' and H' differed from the null model when <10 species were tested and in plants, vertebrates, and fungi. The empirical relationships were similar to the null model when >10 and <100 species were tested and in invertebrates. If >100 species were used to estimate diversity, the relation between log S and H' was negative. The strongest predictive models included log S and J'. A path analysis indicated that log S and J' were always negatively related, that empirical observations could not be explained without including indirect effects, and that differences between the partials may indicate ecological effects, which suggests that S and J' act like diversity components or that diversity should be measured using a compound statistic.

  20. Rare species support vulnerable functions in high-diversity ecosystems.

    PubMed

    Mouillot, David; Bellwood, David R; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C E Timothy; Renaud, Julien; Thuiller, Wilfried

    2013-01-01

    Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

  1. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

    PubMed Central

    Yahara, Koji; Furuta, Yoshikazu; Morimoto, Shinpei; Kikutake, Chie; Komukai, Sho; Matelska, Dorota; Dunin-Horkawicz, Stanisław; Bujnicki, Janusz M.; Uchiyama, Ikuo; Kobayashi, Ichizo

    2016-01-01

    Selection has been a central issue in biology in eukaryotes as well as prokaryotes. Inference of selection in recombining bacterial species, compared with clonal ones, has been a challenge. It is not known how codons under diversifying selection are distributed along the chromosome or among functional categories or how frequently such codons are subject to mutual homologous recombination. Here, we explored these questions by analysing genes present in >90% among 29 genomes of Helicobacter pylori, one of the bacterial species with the highest mutation and recombination rates. By a method for recombining sequences, we identified codons under diversifying selection (dN/dS > 1), which were widely distributed and accounted for ∼0.2% of all the codons of the genome. The codons were enriched in genes of host interaction/cell surface and genome maintenance (DNA replication, recombination, repair, and restriction modification system). The encoded amino acid residues were sometimes found adjacent to critical catalytic/binding residues in protein structures. Furthermore, by estimating the intensity of homologous recombination at a single nucleotide level, we found that these codons appear to be more frequently subject to recombination. We expect that the present study provides a new approach to population genomics of selection in recombining prokaryotes. PMID:26961370

  2. Habitat fragmentation may not matter to species diversity

    PubMed Central

    Yaacobi, Gal; Ziv, Yaron; Rosenzweig, Michael L

    2007-01-01

    Conservation biologists worry that fragmenting a bloc of natural habitat might reduce its species diversity. However, they also recognize the difficulty and importance of isolating the effect of fragmentation from that of simple loss of area. Using two different methods (species–area curve and Fisher's α index of diversity) to analyse the species diversities of plants, tenebrionid beetles and carabid beetles in a highly fragmented Mediterranean scrub landscape, we decoupled the effect of degree of fragmentation from that of area loss. In this system, fragmentation by itself seems not to have influenced the number of species. Our results, obtained at the scale of hectares, agree with similar results at island and continent scales. PMID:17666380

  3. Ecological mechanisms underlying arthropod species diversity in grasslands.

    PubMed

    Joern, Anthony; Laws, Angela N

    2013-01-01

    Arthropods are an important component of grassland systems, contributing significantly to biodiversity and ecosystem structure and function. Climate, fire, and grazing by large herbivores are important drivers in grasslands worldwide. Arthropod responses to these drivers are highly variable and clear patterns are difficult to find, but responses are largely indirect with respect to changes in resources, species interactions, habitat structure, and habitat heterogeneity resulting from interactions among fire, grazing, and climate. Here, we review these ecological mechanisms influencing grassland arthropod diversity. We summarize hypotheses describing species diversity at local and regional scales and then discuss specific factors that may affect arthropod diversity in grassland systems. These factors include direct and indirect effects of grazing, fire, and climate, species interactions, above- and belowground interactions, and landscape-level effects.

  4. Global patterns of freshwater species diversity, threat and endemism

    PubMed Central

    Collen, Ben; Whitton, Felix; Dyer, Ellie E; Baillie, Jonathan E M; Cumberlidge, Neil; Darwall, William R T; Pollock, Caroline; Richman, Nadia I; Soulsby, Anne-Marie; Böhm, Monika

    2014-01-01

    Aim Global-scale studies are required to identify broad-scale patterns in the distributions of species, to evaluate the processes that determine diversity and to determine how similar or different these patterns and processes are among different groups of freshwater species. Broad-scale patterns of spatial variation in species distribution are central to many fundamental questions in macroecology and conservation biology. We aimed to evaluate how congruent three commonly used metrics of diversity were among taxa for six groups of freshwater species. Location Global. Methods We compiled geographical range data on 7083 freshwater species of mammals, amphibians, reptiles, fishes, crabs and crayfish to evaluate how species richness, richness of threatened species and endemism are distributed across freshwater ecosystems. We evaluated how congruent these measures of diversity were among taxa at a global level for a grid cell size of just under 1°. Results We showed that although the risk of extinction faced by freshwater decapods is quite similar to that of freshwater vertebrates, there is a distinct lack of spatial congruence in geographical range between different taxonomic groups at this spatial scale, and a lack of congruence among three commonly used metrics of biodiversity. The risk of extinction for freshwater species was consistently higher than for their terrestrial counterparts. Main conclusions We demonstrate that broad-scale patterns of species richness, threatened-species richness and endemism lack congruence among the six freshwater taxonomic groups examined. Invertebrate species are seldom taken into account in conservation planning. Our study suggests that both the metric of biodiversity and the identity of the taxa on which conservation decisions are based require careful consideration. As geographical range information becomes available for further sets of species, further testing will be warranted into the extent to which geographical variation in

  5. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

    PubMed

    Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

    2016-05-01

    A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.

  6. Diversity of Microbial Species Implicated in Keratitis: A Review

    PubMed Central

    Karsten, Elisabeth; Watson, Stephanie Lousie; Foster, Leslie John Ray

    2012-01-01

    Background: Microbial keratitis is an infectious disease of the cornea characterised by inflammation and is considered an ophthalmic emergency requiring immediate attention. While a variety of pathogenic microbes associated with microbial keratitis have been identified, a comprehensive review identifying the diversity of species has not been completed. Methods: A search of peer-reviewed publications including case reports and research articles reporting microorganims implicated in keratitis was conducted. Search engines including PubMed, Scopus and Web of Science with years ranging from 1950-2012 were used. Results: 232 different species from 142 genera, representing 80 families were found to be implicated in microbial keratitis. Fungi exhibited the largest diversity with 144 species from 92 genera. In comparison, 77 species of bacteria from 42 genera, 12 species of protozoa from 4 genera and 4 types of virus were identified as the infectious agents. A comparison of their aetiologies shows reports of similarities between genera. Conclusions: The diversity of microbial species implicated in keratitis has not previously been reported and is considerably greater than suggested by incidence studies. Effective treatment is heavily reliant upon correct identification of the responsible microorganisms. Species identification, the risk factors associated with, and pathogenesis of microbial keratitis will allow the development of improved therapies. This review provides a resource for clinicians and researchers to assist in identification and readily source treatment information. PMID:23248737

  7. Scorpions from Mexico: From Species Diversity to Venom Complexity

    PubMed Central

    Santibáñez-López, Carlos E.; Francke, Oscar F.; Ureta, Carolina; Possani, Lourival D.

    2015-01-01

    Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world’s medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided. PMID:26712787

  8. Scorpions from Mexico: From Species Diversity to Venom Complexity.

    PubMed

    Santibáñez-López, Carlos E; Francke, Oscar F; Ureta, Carolina; Possani, Lourival D

    2015-12-24

    Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world's medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided.

  9. Measuring β-diversity with species abundance data.

    PubMed

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  10. Bird species diversity in the padawan limestone area, sarawak.

    PubMed

    Mansor, Mohammad Saiful; Sah, Shahrul Anuar Mohd; Koon, Lim Chan; Rahman, Mustafa Abdul

    2011-12-01

    Bird surveys were conducted in the Padawan Limestone Area for seven days at each of two study sites, Giam and Danu, from August to December 2008. The purpose of the study was to compare the area's bird species richness and abundance of bird species in other limestone areas and in other forest types. The study also compared the species richness and relative abundance of birds in undisturbed and disturbed areas at both study sites. Twenty mist nets were deployed for 12 hours daily. During this study period, direct observations of birds were also made. In all, 80 species from 34 families were recorded at both sites. At Giam, 120 birds were mist-netted. These birds represented 31 species from 16 families. The direct observations at Giam recorded 13 species from 11 families. In the undisturbed area, 21 species from 13 families were mist-netted, whereas in the disturbed area, 21 species from 10 families were mist-netted. In Danu, a total of 48 birds, representing 25 species from 12 families, were mist-netted. The observations at Danu recorded 34 species from 19 families. Twelve species from 7 families were mist-netted in the undisturbed area, whereas 18 species from 11 families were mist-netted in the disturbed area. Statistical analysis showed that the species diversity index differed significantly between undisturbed and disturbed areas.

  11. Bird Species Diversity in the Padawan Limestone Area, Sarawak

    PubMed Central

    Mansor, Mohammad Saiful; Sah, Shahrul Anuar Mohd; Koon, Lim Chan; Rahman, Mustafa Abdul

    2011-01-01

    Bird surveys were conducted in the Padawan Limestone Area for seven days at each of two study sites, Giam and Danu, from August to December 2008. The purpose of the study was to compare the area’s bird species richness and abundance of bird species in other limestone areas and in other forest types. The study also compared the species richness and relative abundance of birds in undisturbed and disturbed areas at both study sites. Twenty mist nets were deployed for 12 hours daily. During this study period, direct observations of birds were also made. In all, 80 species from 34 families were recorded at both sites. At Giam, 120 birds were mist-netted. These birds represented 31 species from 16 families. The direct observations at Giam recorded 13 species from 11 families. In the undisturbed area, 21 species from 13 families were mist-netted, whereas in the disturbed area, 21 species from 10 families were mist-netted. In Danu, a total of 48 birds, representing 25 species from 12 families, were mist-netted. The observations at Danu recorded 34 species from 19 families. Twelve species from 7 families were mist-netted in the undisturbed area, whereas 18 species from 11 families were mist-netted in the disturbed area. Statistical analysis showed that the species diversity index differed significantly between undisturbed and disturbed areas. PMID:24575218

  12. Divergence between the Highly Virulent Zoonotic Pathogen Helicobacter heilmannii and Its Closest Relative, the Low-Virulence “Helicobacter ailurogastricus” sp. nov.

    PubMed Central

    Joosten, Myrthe; Lindén, Sara; Rossi, Mirko; Skoog, Emma; Padra, Médea; Peters, Fanny; Perkins, Tim; Vandamme, Peter; Van Nieuwerburgh, Filip; D'Herde, Katharina; Van den Broeck, Wim; Flahou, Bram; Deforce, Dieter; Ducatelle, Richard; Marshall, Barry; Haesebrouck, Freddy

    2015-01-01

    Helicobacter heilmannii naturally colonizes the stomachs of dogs and cats and has been associated with gastric disorders in humans. Nine feline Helicobacter strains, classified as H. heilmannii based on ureAB and 16S rRNA gene sequences, were divided into a highly virulent and a low-virulence group. The genomes of these strains were sequenced to investigate their phylogenetic relationships, to define their gene content and diversity, and to determine if the differences in pathogenicity were associated with the presence or absence of potential virulence genes. The capacities of these helicobacters to bind to the gastric mucosa were investigated as well. Our analyses revealed that the low-virulence strains do not belong to the species H. heilmannii but to a novel, closely related species for which we propose the name Helicobacter ailurogastricus. Several homologs of H. pylori virulence factors, such as IceA1, HrgA, and jhp0562-like glycosyltransferase, are present in H. heilmannii but absent in H. ailurogastricus. Both species contain a VacA-like autotransporter, for which the passenger domain is remarkably larger in H. ailurogastricus than in H. heilmannii. In addition, H. ailurogastricus shows clear differences in binding to the gastric mucosa compared to H. heilmannii. These findings highlight the low-virulence character of this novel Helicobacter species. PMID:26527212

  13. Does species diversity limit productivity in natural grassland communities?

    USGS Publications Warehouse

    Grace, J.B.; Anderson, T.M.; Smith, M.D.; Seabloom, E.; Andelman, S.J.; Meche, G.; Weiher, E.; Allain, L.K.; Jutila, H.; Sankaran, M.; Knops, J.; Ritchie, M.; Willig, M.R.

    2007-01-01

    Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where competitive feedbacks and complex environmental influences affect diversity-productivity relationships. In this study, we evaluated diversity-productivity relationships while statistically controlling for environmental influences in 12 natural grassland ecosystems. Because diversity-productivity relationships are conspicuously nonlinear, we developed a nonlinear structural equation modeling (SEM) methodology to separate the effects of diversity on productivity from the effects of productivity on diversity. Meta-analysis was used to summarize the SEM findings across studies. While competitive effects were readily detected, enhancement of production by diversity was not. These results suggest that the influence of small-scale diversity on productivity in mature natural systems is a weak force, both in absolute terms and relative to the effects of other controls on productivity. ?? 2007 Blackwell Publishing Ltd/CNRS.

  14. Determination of the Prevalence of Helicobacter heilmannii-Like Organisms Type 2 (HHLO-2) Infection in Humans and Dogs Using Non-Invasive Genus/Species-Specific PCR in Korea

    PubMed Central

    CHUNG, Tae-Ho; KIM, Hee-Dong; LEE, Young-Sun; HWANG, Cheol-Yong

    2013-01-01

    ABSTRACT Helicobacter spp. may have multiple routes of transmission. It is unclear, however, whether the agent is zoonotic and therefore transmitted from an animal reservoir, including dogs. The aim of this population-based study was to assess the relationship between pet ownership or frequent exposure to dogs and Helicobacter spp. infection, especially focusing on HHLO-2 (Helicobacter heilmannii-like organisms type 2) in saliva and feces samples in Korea, using non-invasive genus/species-specific PCR. One hundred twenty-four eligible human subjects and 39 dogs participated in this study. Relativity of contact with dogs and Helicobacter spp. infection diagnosed by genus-specific PCR showed a statistically significant result (P<0.01), but in the relativity analyses between contact with dogs and H. pylori, H. felis and H. bizzozeronii infections diagnosed using species-specific PCR, only Helicobacter felis showed a statistically significant result. Although H. pylori infection showed a statistically significant relativity, no statistically significant association was found between veterinarian subjects and Helicobacter. spp., H. felis and H. bizzozeronii infections. On performing risk factor analyses of HHLO-2 infection by transmission, using matching species, between HHLO-2-positive dog owners and HHLO-2-positive dogs, Helicobacter felis infection showed an extremely significant relativity (P<0.0001), and Helicobacter bizzozeronii may also be a possible significant risk factor (P<0.01). These results suggest that HHLO-2 infection might be a zoonotic infection, because continuous contact with dogs was proved to be correlated with human H. felis and H. bizzozeronii infections in this study. PMID:24065079

  15. Abundant Microsatellite Diversity and Oil Content in Wild Arachis Species

    PubMed Central

    Ren, Xiaoping; Chen, Yuning; Xiao, Yingjie; Zhao, Xinyan; Tang, Mei; Huang, Jiaquan; Upadhyaya, Hari D.; Liao, Boshou

    2012-01-01

    The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great

  16. Origin matters: diversity affects the performance of alien invasive species but not of native species.

    PubMed

    Sun, Yan; Müller-Schärer, Heinz; Maron, John L; Schaffner, Urs

    2015-06-01

    At local scales, it has often been found that invasibility decreases with increasing resident plant diversity. However, whether resident community diversity similarly resists invasion by alien versus native species is seldom studied. We examined this issue by invading constructed native plant assemblages that varied in species and functional richness with invasive alien or native Asteraceae species. Assemblages were also invaded with spotted knapweed, Centaurea stoebe, a native European aster that has been previously used in diversity-invasibility experiments in North America. We also conducted a field survey to explore the generality of the patterns generated from our experimental study. Both experimental and observational work revealed that increasing diversity reduced the performance of alien but not native invaders. Centaurea stoebe invading its native community performed poorly regardless of resident diversity, whereas in a parallel, previously published study conducted in North America, C. stoebe easily invaded low-diversity but not high-diversity assemblages. Our results suggest that diversity is an attribute of resident communities that makes them more or less susceptible to invasion by novel invasive alien but not native plant species.

  17. Distribution and Molecular Diversity of Arborescent Gossypium Species.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mexico is a center of diversity of Gossypium. As currently circumscribed, arborescent Gossypium species (Section Erioxylum) are widely distributed in dry deciduous forests located from the central state of Sinaloa at the north of its range to the eastern state of Oaxaca in the south. However, extens...

  18. Consumer species richness and nutrients interact in determining producer diversity

    PubMed Central

    Groendahl, Sophie; Fink, Patrick

    2017-01-01

    While it is crucial to understand the factors that determine the biodiversity of primary producer communities, the relative importance of bottom-up and top-down control factors is still poorly understood. Using freshwater benthic algal communities in the laboratory as a model system, we find an unimodal relationship between nutrient availability and producer diversity, and that increasing number of consumer species increases producer diversity, but overall grazing decreases algal biodiversity. Interestingly, these two factors interact strongly in determining producer diversity, as an increase in nutrient supply diminishes the positive effect of consumer species richness on producer biodiversity. This novel and thus-far overlooked interaction of bottom-up and top-down control mechanisms of biodiversity may have a pronounced impact on ecosystem functioning and thus have repercussions for the fields of biodiversity conservation and restoration. PMID:28303953

  19. Orbital forcing of deep-sea benthic species diversity

    USGS Publications Warehouse

    Cronin, T. M.; Raymo, M.E.

    1997-01-01

    Explanations for the temporal and spatial patterns of species biodiversity focus on stability-time, disturbance-mosaic (biogenic microhabitat heterogeneity) and competition-predation (biotic interactions) hypotheses. The stability-time hypothesis holds that high species diversity in the deep sea and in the tropics reflects long-term climatic stability. But the influence of climate change on deep-sea diversity has not been studied and recent evidence suggests that deep-sea environments undergo changes in climatically driven temperature and flux of nutrients and organic-carbon during glacial-interglacial cycles. Here we show that Pliocene (2.85-2.40 Myr) deep-sea North Atlantic benthic ostracod (Crustacea) species diversity is related to solar insolation changes caused by 41,000-yr cycles of Earth's obliquity (tilt). Temporal changes in diversity, as measured by the Shannon- Weiner index, H(S), correlate with independent climate indicators of benthic foraminiferal oxygen-isotope ratios (mainly ice volume) and ostracod Mg:Ca ratios (bottomwater temperature). During glacial periods, H(S) = 0.2-0.6, whereas during interglacials, H(S) = 1.2-1.6, which is three to four times as high. The control of deep-sea benthic diversity by cyclic climate change at timescales of 103-104 yr does not support the stability-time hypothesis because it shows that the deep sea is a temporally dynamic environment. Diversity oscillations reflect large-scale response of the benthic community to climatically driven changes in either thermohaline circulation, bottom temperature (or temperature-related factors) and food, and a coupling of benthic diversity to surface productivity.

  20. Conservation Tillage Affects Species Composition But Not Species Diversity: A Comparative Study in Northern Italy

    NASA Astrophysics Data System (ADS)

    Boscutti, Francesco; Sigura, Maurizia; Gambon, Nadia; Lagazio, Corrado; Krüsi, Bertil O.; Bonfanti, Pierluigi

    2015-02-01

    Conservation tillage (CT) is widely considered to be a practice aimed at preserving several ecosystem functions. In the literature, however, there seems to be no clear pattern with regard to its benefits on species diversity and species composition. In Northern Italy, we compared species composition and diversity of both vascular plants and Carabids under two contrasting tillage systems, i.e., CT and conventional tillage, respectively. We hypothesized a significant positive impact of CT on both species diversity and composition. We also considered the potential influence of crop type. The tillage systems were studied under open field conditions with three types of annual crops (i.e., maize, soybean, and winter cereals), using a split-plot design on pairs of adjacent fields. Linear mixed models were applied to test tillage system, crop, and interaction effects on diversity indices. Plant and Carabids communities were analyzed by multivariate methods (CCA). On the whole, 136 plant and 51 carabid taxa were recorded. The two tillage systems studied did not differ in floristic or carabid diversity. Species composition, by contrast, proved to be characteristic for each combination of tillage system and crop type. In particular, CT fields were characterized by nutrient demanding weeds and the associated Carabids. The differences were especially pronounced in fields with winter cereals. The same was true for the flora and Carabids along the field boundaries. For studying the effects of CT practices on the sustainability of agro-ecosystems, therefore, the focus should be on species composition rather than on diversity measures.

  1. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity

    PubMed Central

    Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

    2014-01-01

    Aim To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to ‘classical’ hotspots based on species richness (SR) only. Location Global Methods SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. Results While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. Main conclusions The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global

  2. Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

    PubMed

    Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

    2016-01-01

    The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the

  3. Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China

    PubMed Central

    Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

    2016-01-01

    The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the

  4. Diversity of Fusarium Species from Highland Areas in Malaysia

    PubMed Central

    Manshor, Nurhazrati; Rosli, Hafizi; Ismail, Nor Azliza; Salleh, Baharuddin; Zakaria, Latiffah

    2012-01-01

    Fusarium is a cosmopolitan and highly diversified genus of saprophytic, phytopathogenic and toxigenic fungi. However, the existence and diversity of a few species of Fusarium are restricted to a certain area or climatic condition. The present study was conducted to determine the occurrence and diversity of Fusarium species in tropical highland areas in Malaysia and to compare with those in temperate and subtropical regions. A series of sampling was carried out in 2005 to 2009 at several tropical highland areas in Malaysia that is: Cameron Highlands, Fraser Hills and Genting Highlands in Pahang; Penang Hill in Penang; Gunung Jerai in Kedah; Kundasang and Kinabalu Park in Sabah; Kubah National Park and Begunan Hill in Sarawak. Sampling was done randomly from various hosts and substrates. Isolation of Fusarium isolates was done by using pentachloronitrobenzene (PCNB) agar and 1449 isolates of Fusarium were successfully recovered. Based on morphological characteristics, 20 species of Fusarium were identified. The most prevalent species occurring on the highlands areas was F. solani (66.1%) followed by F. graminearum (8.5%), F. oxysporum (7.8%), F. semitectum (5.7%), F. subglutinans (3.5%) and F. proliferatum (3.4%). Other Fusarium species, namely F. avenaceum, F. camptoceras, F. chlamydosporum, F. compactum, F. crookwellense, F. culmorum, F. decemcellulare, F. equiseti, F. nygamai, F. poae, F. proliferatum, F. sacchari, F. sporotrichioides, F. sterilihyphosum and F. verticillioides accounted for 1% recoveries. The present study was the first report on the occurrences of Fusarium species on highland areas in Malaysia. PMID:24575229

  5. New species from Ethiopia further expands Middle Pliocene hominin diversity.

    PubMed

    Haile-Selassie, Yohannes; Gibert, Luis; Melillo, Stephanie M; Ryan, Timothy M; Alene, Mulugeta; Deino, Alan; Levin, Naomi E; Scott, Gary; Saylor, Beverly Z

    2015-05-28

    Middle Pliocene hominin species diversity has been a subject of debate over the past two decades, particularly after the naming of Australopithecus bahrelghazali and Kenyanthropus platyops in addition to the well-known species Australopithecus afarensis. Further analyses continue to support the proposal that several hominin species co-existed during this time period. Here we recognize a new hominin species (Australopithecus deyiremeda sp. nov.) from 3.3-3.5-million-year-old deposits in the Woranso-Mille study area, central Afar, Ethiopia. The new species from Woranso-Mille shows that there were at least two contemporaneous hominin species living in the Afar region of Ethiopia between 3.3 and 3.5 million years ago, and further confirms early hominin taxonomic diversity in eastern Africa during the Middle Pliocene epoch. The morphology of Au. deyiremeda also reinforces concerns related to dentognathic (that is, jaws and teeth) homoplasy in Plio-Pleistocene hominins, and shows that some dentognathic features traditionally associated with Paranthropus and Homo appeared in the fossil record earlier than previously thought.

  6. Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

    PubMed

    Campos-Navarrete, María José; Abdala-Roberts, Luis; Munguía-Rosas, Miguel A; Parra-Tabla, Víctor

    2015-01-01

    Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and -within each of these two plot types- mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity.

  7. Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

    PubMed Central

    Campos-Navarrete, María José; Abdala-Roberts, Luis; Munguía-Rosas, Miguel A.; Parra-Tabla, Víctor

    2015-01-01

    Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and –within each of these two plot types– mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity. PMID:26241962

  8. Free recombination within Helicobacter pylori

    PubMed Central

    Suerbaum, Sebastian; Smith, John Maynard; Bapumia, Khairun; Morelli, Giovanna; Smith, Noel H.; Kunstmann, Erdmute; Dyrek, Isabelle; Achtman, Mark

    1998-01-01

    Sequences of three gene fragments (flaA, flaB, and vacA) from Helicobacter pylori strains isolated from patients in Germany, Canada, and South Africa were analyzed for diversity and for linkage equilibrium by using the Homoplasy Test and compatibility matrices. Horizontal genetic exchange in H. pylori is so frequent that different loci and polymorphisms within each locus are all at linkage equilibrium. These results indicate that H. pylori is panmictic. Comparisons with sequences from Escherichia coli, Neisseria meningitidis, and Drosophila melanogaster showed that recombination in H. pylori was much more frequent than in other species. In contrast, when multiple family members infected with H. pylori were investigated, some strains were indistinguishable at all three loci. Thus, H. pylori is clonal over short time periods after natural transmission. PMID:9770535

  9. Conservation priority of global Galliformes species based on phylogenetic diversity.

    PubMed

    Chen, Youhua

    2014-06-01

    In this study, based on phylogenetic diversity (PD), I develop a conservation strategy for Galliformes species around the world. A cladogram of 197 Galliformes species derived from a previous study was used for calculating PD metrics. Branch length is an important aspect of the phylogenetic information a tree can convey, but 2 traditionally-used metrics, the number of phylogenetic groups to which a taxon belongs (I) and the proportion that each taxon contributes to the total diversity of the group (W), are fully node-based and do not take branch length into account. Therefore, to measure PD more appropriately, I combined a branch-related metric, pendant edge (P), in addition to I and W. A final combined rank for Galliformes species was obtained by summing the ranks of the 3 metrics. My results showed that the 5% top priority species for conserving evolutionary potential were Galloperdix lunulata, Haematortyx sanguiniceps, Margaroperdix madagarensis, Syrmaticus soemmerringii, Coturnix pectoralis, Polyplectron napoleonis, Alectoris melanocephala, Xenoperdix udzungwensis, Afropavo congensis and Syrmaticus reevesii. The current species priority ranking based on pylogenetic diversity and the official International Union for Conservation of Nature (IUCN) ranking of Galliformes species was significantly correlated when considering the 5 categories of IUCN (critical endangered, endangered, vulnerable, near threatened and least concern). This indicated the feasibility of introducing the PD index into the network of IUCN regional Red List assessment. The 5% top priority countries selected using the complementarity principle possessing diversified Galliformes genetic resources were China, Indonesia, Mexico, India, Colombia, Australia, Brazil, Angola, Congo and Japan (in descending order). China, Indonesia, Mexico, Brazil, India and Colombia are consistently selected among the 4 top priority sets of richness, rarity, endemicity and PD. This result indicated that the priority

  10. Unrecognized coral species diversity masks differences in functional ecology.

    PubMed

    Boulay, Jennifer N; Hellberg, Michael E; Cortés, Jorge; Baums, Iliana B

    2014-02-07

    Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change.

  11. Unrecognized coral species diversity masks differences in functional ecology

    PubMed Central

    Boulay, Jennifer N.; Hellberg, Michael E.; Cortés, Jorge; Baums, Iliana B.

    2014-01-01

    Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change. PMID:24335977

  12. Diversity and Significance of Mold Species in Norwegian Drinking Water▿

    PubMed Central

    Hageskal, Gunhild; Knutsen, Ann Kristin; Gaustad, Peter; de Hoog, G. Sybren; Skaar, Ida

    2006-01-01

    In order to determine the occurrence, distribution, and significance of mold species in groundwater- and surface water-derived drinking water in Norway, molds isolated from 273 water samples were identified. Samples of raw water, treated water, and water from private homes and hospital installations were analyzed by incubation of 100-ml membrane-filtered samples on dichloran-18% glycerol agar. The total count (number of CFU per 100 ml) of fungal species and the species diversity within each sample were determined. The identification of mold species was based on morphological and molecular methods. In total, 94 mold species belonging to 30 genera were identified. The mycobiota was dominated by species of Penicillium, Trichoderma, and Aspergillus, with some of them occurring throughout the drinking water system. Several of the same species as isolated from water may have the potential to cause allergic reactions or disease in humans. Other species are common contaminants of food and beverages, and some may cause unwanted changes in the taste or smell of water. The present results indicate that the mycobiota of water should be considered when the microbiological safety and quality of drinking water are assessed. In fact, molds in drinking water should possibly be included in the Norwegian water supply and drinking water regulations. PMID:17028226

  13. Sequence diversity, reproductive isolation and species concepts in Saccharomyces.

    PubMed

    Liti, Gianni; Barton, David B H; Louis, Edward J

    2006-10-01

    Using the biological species definition, yeasts of the genus Saccharomyces sensu stricto comprise six species and one natural hybrid. Previous work has shown that reproductive isolation between the species is due primarily to sequence divergence acted upon by the mismatch repair system and not due to major gene differences or chromosomal rearrangements. Sequence divergence through mismatch repair has also been shown to cause partial reproductive isolation among populations within a species. We have surveyed sequence variation in populations of Saccharomyces sensu stricto yeasts and measured meiotic sterility in hybrids. This allows us to determine the divergence necessary to produce the reproductive isolation seen among species. Rather than a sharp transition from fertility to sterility, which may have been expected, we find a smooth monotonic relationship between diversity and reproductive isolation, even as far as the well-accepted designations of S. paradoxus and S. cerevisiae as distinct species. Furthermore, we show that one species of Saccharomyces--S. cariocanus--differs from a population of S. paradoxus by four translocations, but not by sequence. There is molecular evidence of recent introgression from S. cerevisiae into the European population of S. paradoxus, supporting the idea that in nature the boundary between these species is fuzzy.

  14. Foraminifera Species Richness, Abundance, and Diversity Research in Bolinas, California

    NASA Astrophysics Data System (ADS)

    Brunwin, N.; Ingram, Z.; Mendez, M.; Sandoval, K.

    2015-12-01

    Foraminifera are abundant, diverse, respond rapidly to environmental change, and are present in all marine and estuarine environments, making them important indicator species. A survey of occurrence and distribution of foraminifera in the Bolinas Lagoon, Marin County, California was carried out by Hedman in 1975, but no study since has focused on foraminiferal composition within this important ecosystem. In July 2015, the Careers in Science (CiS) Intern Program collected samples at 12 sites previously examined in the 1975 study. Thirty-six samples were collected from the upper few centimeters of sediment from a variety of intertidal and subtidal environments within the lagoon. Foraminifera from each sample were isolated, identified and species richness, abundance and diversity quantified. Furthermore, comparisons of faunal composition represented in our recent collection and that of Hedman's 1975 report are made.

  15. Prevalence and varieties of Helicobacter species in dogs from random sources and pet dogs: animal and public health implications.

    PubMed Central

    Eaton, K A; Dewhirst, F E; Paster, B J; Tzellas, N; Coleman, B E; Paola, J; Sherding, R

    1996-01-01

    Gastric bacteria of a variety of ultrastructural morphologies have been identified in or isolated from domestic carnivores, but their prevalence in different populations of animals and their clinical significance are still unknown. The purposes of this study were (i) to evaluate the prevalence and morphologic types of gastric bacterial in three different populations of dogs; (ii) to determine which of the organisms were culturable, and if the cultured organisms were morphologically similar to the organisms seen in situ; (iii) to identify the isolated organisms; and (iv) to determine if gastric bacteria were associated with gastritis. Three groups of dogs were examined: healthy laboratory dogs, healthy dogs from an animal shelter, and pet dogs with various nongastric illnesses. Of these, 100% of laboratory and shelter dogs and 67% of pet dogs were colonized by large, tightly coiled gastric spiral bacteria morphologically similar to Gastrospirillum hominis or Helicobacter felis (referred to as gastrospirilla). Regardless of the presence or density of gastric bacteria, all of the dogs in the study except one had mild to moderate gastritis. Helicobacter spp. were isolated from only 6 of 39 stomachs cultured, and only three of the organisms isolated were morphologically similar to the bacteria seen in situ. Five helicobacters were identified by 16S rDNA (genes coding for rRNA) sequence analysis. Three were strains of H. felis, one was H. bilis, and one was a novel helicobacter morphologically similar to "Flexispira rappini." Gastrospirilla are almost universal in the stomachs of domestic dogs, and in most infected dogs, they do not appear to be associated with clinical signs or histologic lesions compared with uninfected dogs. Nongastrospirillum helicobacters are rare in dogs and are not histologically detectable. Helicobacter pylori was not isolated from domestic dogs. PMID:8940465

  16. Phylogeny and Species Diversity of Gulf of California Oysters

    EPA Pesticide Factsheets

    Dataset of DNA sequence data from two mitochondrial loci (COI and 16S) used to infer the phylogeny of oysters in the genus Ostrea along the Pacific coast of North America.This dataset is associated with the following publication:Raith, M., D. Zacherl, E. Pilgrim , and D. Eernisse. Phylogeny and species diversity of Gulf of California oysters (Ostreidae) inferred from mitochondrial DNA. American Malacological Bulletin. American Malacological Society, Arlington, VA, USA, 33(2): 263-283, (2016).

  17. Exotic plant species invade hot spots of native plant diversity

    USGS Publications Warehouse

    Stohlgren, T.J.; Binkley, D.; Chong, G.W.; Kalkhan, M.A.; Schell, L.D.; Bull, K.A.; Otsuki, Y.; Newman, G.; Bashkin, M.; Yowhan, S.

    1999-01-01

    Some theories and experimental studies suggest that areas of low plant species richness may be invaded more easily than areas of high plant species richness. We gathered nested-scale vegetation data on plant species richness, foliar cover, and frequency from 200 1-m2 subplots (20 1000-m2 modified-Whittaker plots) in the Colorado Rockies (USA), and 160 1-m2 subplots (16 1000-m2 plots) in the Central Grasslands in Colorado, Wyoming, South Dakota, and Minnesota (USA) to test the generality of this paradigm. At the 1-m2 scale, the paradigm was supported in four prairie types in the Central Grasslands, where exotic species richness declined with increasing plant species richness and cover. At the 1-m2 scale, five forest and meadow vegetation types in the Colorado Rockies contradicted the paradigm; exotic species richness increased with native-plant species richness and foliar cover. At the 1000-m2 plot scale (among vegetation types), 83% of the variance in exotic species richness in the Central Grasslands was explained by the total percentage of nitrogen in the soil and the cover of native plant species. In the Colorado Rockies, 69% of the variance in exotic species richness in 1000-m2 plots was explained by the number of native plant species and the total percentage of soil carbon. At landscape and biome scales, exotic species primarily invaded areas of high species richness in the four Central Grasslands sites and in the five Colorado Rockies vegetation types. For the nine vegetation types in both biomes, exotic species cover was positively correlated with mean foliar cover, mean soil percentage N, and the total number of exotic species. These patterns of invasibility depend on spatial scale, biome and vegetation type, spatial autocorrelation effects, availability of resources, and species-specific responses to grazing and other disturbances. We conclude that: (1) sites high in herbaceous foliar cover and soil fertility, and hot spots of plant diversity (and

  18. The effects of island ontogeny on species diversity and phylogeny.

    PubMed

    Valente, Luis M; Etienne, Rampal S; Phillimore, Albert B

    2014-06-07

    A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological timescales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies.

  19. Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

    NASA Astrophysics Data System (ADS)

    Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

    2016-08-01

    Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and

  20. HELICOBACTER PYLORI

    EPA Science Inventory

    Helicobacter pylori is a pathogenic bacteria which inhabits the human stomach and upper gastrointestinal tract. This encyclopedic entry summarizes the potential role of this organism as a waterborne pathogen. Information is provided on the physiology and morphology of this bacter...

  1. Occurrence and species level diagnostics of Campylobacter spp., enteric Helicobacter spp. and Anaerobiospirillum spp. in healthy and diarrheic dogs and cats.

    PubMed

    Rossi, M; Hänninen, M L; Revez, J; Hannula, M; Zanoni, R G

    2008-06-22

    In order to study the occurrence and co-infection of different species of Campylobacter, enteric Helicobacter and Anaerobiospirillum in dogs and cats and define a possible association between these microrganisms and gastrointestinal disorders, 190 dogs and 84 cats, either healthy or with diarrhea, were sampled between 2002 and 2003. Thirty-three C. upsaliensis, 17 C. jejuni, 2 C. helveticus, 1 C. lari isolates from dogs and 14 C. helveticus, 7 C. jejuni, 6 C. upsaliensis isolates from cats were identified using species-specific PCR and phenotypic tests. Whole cell protein profile analysis, phenotypic tests, PCR-RFLP of gyrB and a phylogenetic study of partial groEL and 16S rRNA sequences were used to identify 37 H. bilis, 22 H. canis and 14 H. cinaedi in dogs and 12 H. canis, 5 H. bilis and 2 H. cinaedi in cats. Whole cell protein profile analysis, phenotypic tests and species-specific PCR of 16S rRNA were used to identify 14 A. succiniciproducens, 12 A. thomasii isolates and one unidentified Anaerobiospirillum sp. isolate in dogs and 3 A. thomasii isolates in cats. Fifty-two animals (19%) were positive for the isolation of more than one genus. No significant statistical correlation was found between any isolates of Campylobacter, Helicobacter or Anaerobiospirillum spp. or the various co-infection rates, and the presence of diarrhea in either dogs or cats. Campylobacter isolates were also tested for antibiotic resistance using the agar dilution method.

  2. SPECIES COMPOSITION AND DIVERSITY AS REGULATORS OF TEMPORAL VARIABILITY IN BIOMASS PRODUCTION OF TALLGRASS PRAIRIE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species diversity is thought to stabilize functioning of plant communities, although diversity-stability studies have focused on species richness to the neglect of the second component of diversity, species evenness (equitability with which biomass or abundances are distributed among species). An a...

  3. Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest

    PubMed Central

    Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

    2016-01-01

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

  4. Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest.

    PubMed

    Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

    2016-02-10

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community.

  5. Resource heterogeneity, soil fertility, and species diversity: effects of clonal species on plant communities.

    PubMed

    Eilts, J Alexander; Mittelbach, Gary G; Reynolds, Heather L; Gross, Katherine L

    2011-05-01

    Spatial heterogeneity in soil resources is widely thought to promote plant species coexistence, and this mechanism figures prominently in resource-ratio models of competition. However, most experimental studies have found that nutrient enhancements depress diversity regardless of whether nutrients are uniformly or heterogeneously applied. This mismatch between theory and empirical pattern is potentially due to an interaction between plant size and the scale of resource heterogeneity. Clonal plants that spread vegetatively via rhizomes or stolons can grow large and may integrate across resource patches, thus reducing the positive effect of small-scale resource heterogeneity on plant species richness. Many rhizomatous clonal species respond strongly to increased soil fertility, and they have been hypothesized to drive the descending arm of the hump-shaped productivity-diversity relationship in grasslands. We tested whether clonals reduce species richness in a grassland community by manipulating nutrient heterogeneity, soil fertility, and the presence of rhizomatous clonal species in a 6-year field experiment. We found strong and consistent negative effects of clonals on species richness. These effects were greatest at high fertility and when soil resources were applied at a scale at which rhizomatous clonals could integrate across resource patches. Thus, we find support for the hypothesis that plant size and resource heterogeneity interact to determine species diversity.

  6. Transposable elements and small RNAs: Genomic fuel for species diversity

    PubMed Central

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us. PMID:26904375

  7. Transposable elements and small RNAs: Genomic fuel for species diversity.

    PubMed

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us.

  8. Discovering the recondite secondary metabolome spectrum of Salinispora species: a study of inter-species diversity.

    PubMed

    Bose, Utpal; Hewavitharana, Amitha K; Vidgen, Miranda E; Ng, Yi Kai; Shaw, P Nicholas; Fuerst, John A; Hodson, Mark P

    2014-01-01

    Patterns of inter-species secondary metabolite production by bacteria can provide valuable information relating to species ecology and evolution. The complex nature of this chemical diversity has previously been probed via directed analyses of a small number of compounds, identified through targeted assays rather than more comprehensive biochemical profiling approaches such as metabolomics. Insights into ecological and evolutionary relationships within bacterial genera can be derived through comparative analysis of broader secondary metabolite patterns, and this can also eventually assist biodiscovery search strategies for new natural products. Here, we investigated the species-level chemical diversity of the two marine actinobacterial species Salinispora arenicola and Salinispora pacifica, isolated from sponges distributed across the Great Barrier Reef (GBR), via their secondary metabolite profiles using LC-MS-based metabolomics. The chemical profiles of these two species were obtained by UHPLC-QToF-MS based metabolic profiling. The resultant data were interrogated using multivariate data analysis methods to compare their (bio)chemical profiles. We found a high level of inter-species diversity in strains from these two bacterial species. We also found rifamycins and saliniketals were produced exclusively by S. arenicola species, as the main secondary metabolites differentiating the two species. Furthermore, the discovery of 57 candidate compounds greatly increases the small number of secondary metabolites previously known to be produced by these species. In addition, we report the production of rifamycin O and W, a key group of ansamycin compounds, in S. arenicola for the first time. Species of the marine actinobacteria harbour a much wider spectrum of secondary metabolites than suspected, and this knowledge may prove a rich field for biodiscovery as well as a database for understanding relationships between speciation, evolution and chemical ecology.

  9. Discovering the Recondite Secondary Metabolome Spectrum of Salinispora Species: A Study of Inter-Species Diversity

    PubMed Central

    Bose, Utpal; Hewavitharana, Amitha K.; Vidgen, Miranda E.; Ng, Yi Kai; Shaw, P. Nicholas; Fuerst, John A.; Hodson, Mark P.

    2014-01-01

    Patterns of inter-species secondary metabolite production by bacteria can provide valuable information relating to species ecology and evolution. The complex nature of this chemical diversity has previously been probed via directed analyses of a small number of compounds, identified through targeted assays rather than more comprehensive biochemical profiling approaches such as metabolomics. Insights into ecological and evolutionary relationships within bacterial genera can be derived through comparative analysis of broader secondary metabolite patterns, and this can also eventually assist biodiscovery search strategies for new natural products. Here, we investigated the species-level chemical diversity of the two marine actinobacterial species Salinispora arenicola and Salinispora pacifica, isolated from sponges distributed across the Great Barrier Reef (GBR), via their secondary metabolite profiles using LC-MS-based metabolomics. The chemical profiles of these two species were obtained by UHPLC-QToF-MS based metabolic profiling. The resultant data were interrogated using multivariate data analysis methods to compare their (bio)chemical profiles. We found a high level of inter-species diversity in strains from these two bacterial species. We also found rifamycins and saliniketals were produced exclusively by S. arenicola species, as the main secondary metabolites differentiating the two species. Furthermore, the discovery of 57 candidate compounds greatly increases the small number of secondary metabolites previously known to be produced by these species. In addition, we report the production of rifamycin O and W, a key group of ansamycin compounds, in S. arenicola for the first time. Species of the marine actinobacteria harbour a much wider spectrum of secondary metabolites than suspected, and this knowledge may prove a rich field for biodiscovery as well as a database for understanding relationships between speciation, evolution and chemical ecology. PMID

  10. Soft Coral Sarcophyton (Cnidaria: Anthozoa: Octocorallia) Species Diversity and Chemotypes

    PubMed Central

    Aratake, Satoe; Tomura, Tomohiko; Saitoh, Seikoh; Yokokura, Ryouma; Kawanishi, Yuichi; Shinjo, Ryuichi; Reimer, James Davis; Tanaka, Junichi; Maekawa, Hideaki

    2012-01-01

    Research on the soft coral genus Sarcophyton extends over a wide range of fields, including marine natural products and the isolation of a number of cembranoid diterpenes. However, it is still unknown how soft corals produce this diverse array of metabolites, and the relationship between soft coral diversity and cembranoid diterpene production is not clear. In order to understand this relationship, we examined Sarcophyton specimens from Okinawa, Japan, by utilizing three methods: morphological examination of sclerites, chemotype identification, and phylogenetic examination of both Sarcophyton (utilizing mitochondrial protein-coding genes MutS homolog: msh1) and their endosymbiotic Symbiodinium spp. (utilizing nuclear internal transcribed spacer of ribosomal DNA: ITS- rDNA). Chemotypes, molecular phylogenetic clades, and sclerites of Sarcophyton trocheliophorum specimens formed a clear and distinct group, but the relationships between chemotypes, molecular phylogenetic clade types and sclerites of the most common species, Sarcophyton glaucum, was not clear. S. glaucum was divided into four clades. A characteristic chemotype was observed within one phylogenetic clade of S. glaucum. Identities of symbiotic algae Symbiodinium spp. had no apparent relation to chemotypes of Sarcophyton spp. This study demonstrates that the complex results observed for S. glaucum are due to the incomplete and complex taxonomy of this species group. Our novel method of identification should help contribute to classification and taxonomic reassessment of this diverse soft coral genus. PMID:22272344

  11. Simple sequence repeat diversity in diploid and tetraploid Coffea species.

    PubMed

    Moncada, Pilar; McCouch, Susan

    2004-06-01

    Thirty-four fluorescently labeled microsatellite markers were used to assess genetic diversity in a set of 30 Coffea accessions from the CENICAFE germplasm bank in Colombia. The plant material included one sample per accession of seven East African accessions representing five diploid species and 23 wild and cultivated tetraploid accessions of Coffea arabica from Africa, Indonesia, and South America. More allelic diversity was detected among the five diploid species than among the 23 tetraploid genotypes. The diploid species averaged 3.6 alleles/locus and had an average polymorphism information content (PIC) value of 0.6, whereas the wild tetraploids averaged 2.5 alleles/locus and had an average PIC value of 0.3 and the cultivated tetraploids (C. arabica cultivars) averaged 1.9 alleles/locus and had an average PIC value of 0.22. Fifty-five percent of the alleles found in the wild tetraploids were not shared with cultivated C. arabica genotypes, supporting the idea that the wild tetraploid ancestors from Ethiopia could be used productively as a source of novel genetic variation to expand the gene pool of elite C. arabica germplasm.

  12. Environmental diversity as a surrogate for species representation.

    PubMed

    Beier, Paul; de Albuquerque, Fábio Suzart

    2015-10-01

    Because many species have not been described and most species ranges have not been mapped, conservation planners often use surrogates for conservation planning, but evidence for surrogate effectiveness is weak. Surrogates are well-mapped features such as soil types, landforms, occurrences of an easily observed taxon (discrete surrogates), and well-mapped environmental conditions (continuous surrogate). In the context of reserve selection, the idea is that a set of sites selected to span diversity in the surrogate will efficiently represent most species. Environmental diversity (ED) is a rarely used surrogate that selects sites to efficiently span multivariate ordination space. Because it selects across continuous environmental space, ED should perform better than discrete surrogates (which necessarily ignore within-bin and between-bin heterogeneity). Despite this theoretical advantage, ED appears to have performed poorly in previous tests of its ability to identify 50 × 50 km cells that represented vertebrates in Western Europe. Using an improved implementation of ED, we retested ED on Western European birds, mammals, reptiles, amphibians, and combined terrestrial vertebrates. We also tested ED on data sets for plants of Zimbabwe, birds of Spain, and birds of Arizona (United States). Sites selected using ED represented European mammals no better than randomly selected cells, but they represented species in the other 7 data sets with 20% to 84% effectiveness. This far exceeds the performance in previous tests of ED, and exceeds the performance of most discrete surrogates. We believe ED performed poorly in previous tests because those tests considered only a few candidate explanatory variables and used suboptimal forms of ED's selection algorithm. We suggest future work on ED focus on analyses at finer grain sizes more relevant to conservation decisions, explore the effect of selecting the explanatory variables most associated with species turnover, and investigate

  13. Differential regulation of urease activity in Helicobacter hepaticus and Helicobacter pylori.

    PubMed

    Belzer, Clara; Stoof, Jeroen; Beckwith, Catherine S; Kuipers, Ernst J; Kusters, Johannes G; van Vliet, Arnoud H M

    2005-12-01

    Helicobacter hepaticus is a pathogen of rodents, which causes diverse enteric and hepatic inflammatory diseases and malignancies. The urease enzyme is an important colonization factor of gastric Helicobacter species like Helicobacter pylori, but little is known about the role and regulation of urease in enterohepatic Helicobacter species. Here it is reported that urease activity of H. hepaticus does not contribute to acid resistance, and that it is nickel-responsive at the post-translational level. H. hepaticus strain ATCC 51449 did not grow or survive at pH 3.0, and supplementation with urea or NiCl2 did not abrogate this acid sensitivity. Furthermore, urease enzyme activity of H. hepaticus was acid-independent, which contrasts with the acid-induced urease system of H. pylori. Nickel supplementation of Brucella medium resulted in a tenfold increase in urease activity in both H. hepaticus and H. pylori, but the maximum level of urease activity in H. hepaticus was still three- to fivefold lower when compared to H. pylori in the same conditions. The increase in urease activity of H. hepaticus was not associated with elevation of urease mRNA or protein levels. Inhibition of protein synthesis by chloramphenicol did not affect nickel-responsive induction of urease activity in H. hepaticus, and confirmed that nickel induction occurs at the post-translational level, probably by activation of preformed apo-enzyme. In conclusion, both the role of the urease enzyme and the regulation of urease activity differ between the enterohepatic pathogen H. hepaticus and the gastric pathogen H. pylori.

  14. The diversity of male nuptial coloration leads to species diversity in Lake Victoria cichlids.

    PubMed

    Miyagi, Ryutaro; Terai, Yohey

    2013-01-01

    The amazing coloration shown by diverse cichlid fish not only fascinates aquarium keepers, but also receives great attention from biologists interested in speciation because of its recently-revealed role in their adaptive radiation in an African lake. We review the important role of coloration in the speciation and adaptive evolution of Lake Victoria cichlids, which have experienced adaptive radiation during a very short evolutionary period. Mature male cichlids display their colors during mate choice. The color of their skin reflects light, and the reflected light forms a color signal that is received by the visual system of females. The adaptive divergence of visual perceptions shapes and diverges colorations, to match the adapted visual perceptions. The divergence of visual perception and coloration indicates that the divergence of color signals causes reproductive isolation between species, and this process leads to speciation. Differences in color signals among coexisting species act to maintain reproductive isolation by preventing hybridization. Thus, the diversity of coloration has caused speciation and has maintained species diversity in Lake Victoria cichlids.

  15. Concordance between genetic and species diversity in coral reef fishes across the Pacific Ocean biodiversity gradient.

    PubMed

    Messmer, Vanessa; Jones, Geoffrey P; Munday, Philip L; Planes, Serge

    2012-12-01

    The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ∼1600 species; New Caledonia: ∼1400 species; French Polynesia: ∼800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential.

  16. Characterization and presumptive identification of Helicobacter pylori isolates from rhesus monkeys.

    PubMed Central

    Drazek, E S; Dubois, A; Holmes, R K

    1994-01-01

    We characterized 38 Helicobacter isolates, including 22 from gastric biopsy samples obtained from 14 rhesus monkeys and single isolates from 16 monkeys in a different colony. Biochemical profiles of these isolates were nearly identical to that of Helicobacter pylori ATCC 43504. Restriction fragment length polymorphism (RFLP) analysis indicated that each infected monkey harbored one to four strains. The 17 RFLP types found among these 22 isolates differed from all seven RFLPs found among the other 16 isolates. Thus, monkeys within a given colony are more likely to be infected by Helicobacter isolates with the same or a similar RFLP than are monkeys from different colonies. A 16S rRNA gene was amplified by PCR and cloned from the Helicobacter isolate from rhesus monkey 85D08. Ribotyping with this probe demonstrated less diversity among isolates from rhesus monkeys than was reported among isolates of H. pylori from humans, as did RFLP analysis of a PCR fragment of the ureA-ureB gene cluster. The DNA sequence of the cloned 16S rRNA gene was determined and compared with sequences reported for H. pylori and other Helicobacter species. Our analysis of 127 nucleotides (corresponding with residues 1240 to 1366 of the Escherichia coli 16S rRNA gene) indicated that the Helicobacter isolate from monkey 85D08 was 99.2 to 100% homologous to isolates of H. pylori from humans but only 83.5 to 96.9% homologous with other Helicobacter species in this region of the 16S rRNA gene. These data provide strong support for the presumptive identification of these isolates as H. pylori. Images PMID:7523441

  17. Characterisation of Species and Diversity of Anopheles gambiae Keele Colony

    PubMed Central

    McGeechan, Sion; Inch, Donald; Smart, Graeme; Richterová, Lenka; Mwangi, Jonathan M.

    2016-01-01

    Anopheles gambiae sensu stricto was recently reclassified as two species, An. coluzzii and An. gambiae s.s., in wild-caught mosquitoes, on the basis of the molecular form, denoted M or S, of a marker on the X chromosome. The An. gambiae Keele line is an outbred laboratory colony strain that was developed around 12 years ago by crosses between mosquitoes from 4 existing An. gambiae colonies. Laboratory colonies of mosquitoes often have limited genetic diversity because of small starting populations (founder effect) and subsequent fluctuations in colony size. Here we describe the characterisation of the chromosomal form(s) present in the Keele line, and investigate the diversity present in the colony using microsatellite markers on chromosome 3. We also characterise the large 2La inversion on chromosome 2. The results indicate that only the M-form of the chromosome X marker is present in the Keele colony, which was unexpected given that 3 of the 4 parent colonies were probably S-form. Levels of diversity were relatively high, as indicated by a mean number of microsatellite alleles of 6.25 across 4 microsatellites, in at least 25 mosquitoes. Both karyotypes of the inversion on chromosome 2 (2La/2L+a) were found to be present at approximately equal proportions. The Keele colony has a mixed M- and S-form origin, and in common with the PEST strain, we propose continuing to denote it as an An. gambiae s.s. line. PMID:28033418

  18. Beyond the zebrafish: diverse fish species for modeling human disease

    PubMed Central

    Schartl, Manfred

    2014-01-01

    ABSTRACT In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research. PMID:24271780

  19. Fingerprinting the Asterid Species Using Subtracted Diversity Array Reveals Novel Species-Specific Sequences

    PubMed Central

    Mantri, Nitin; Olarte, Alexandra; Li, Chun Guang; Xue, Charlie; Pang, Edwin C. K.

    2012-01-01

    Background Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade. Methodology/Principal Findings Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants. Conclusions/Significance Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve

  20. A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

    PubMed

    Barberán, Albert; Casamayor, Emilio O

    2014-12-01

    There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.

  1. Species diversity, structure and dynamics of two populations of an endangered species, Magnolia dealbata (Magnoliaceae).

    PubMed

    Sánchez-Velásquez, Lázaro R; Pineda-López, María del Rosario

    2006-09-01

    Little is known about the ecology and demography of the genus Magnolia. Magnolia dealbata Zucc. is an endangered species endemic to Mexico. Two contrasting populations of M. dealbata (one from the grasslands and other from a secondary cloud forest) were studied. We asked the following questions: (a) Are size structure (diameter at breast height, DBH) and infrutescence production significantly different between the two populations? (b) What are the populations' growth rates (lambda) based on an initial 1987 study? (c) Are the associated species diversity indices of these M. dealbata populations significantly different? The results show no significant differences between the population size structure (p=.094); the growth rates of the populations were 0.992 in grassland and 1.053 in secondary cloud forest. The number of infrutescences produced in year 2001 and DBH relationship were significantly linear (p<.001) in both populations, and there was no significant difference (p>.01) between their slopes. The diversity indices were not significantly different (p>.05), and only 54% of the species were common to both sites. Our study suggests that both populations are relatively stable and that the management history could impact more on the species composition than on the diversity indices.

  2. Diversity of Listeria species in urban and natural environments.

    PubMed

    Sauders, Brian D; Overdevest, Jon; Fortes, Esther; Windham, Katy; Schukken, Ynte; Lembo, Arthur; Wiedmann, Martin

    2012-06-01

    A total of 442 Listeria isolates, including 234 Listeria seeligeri, 80 L. monocytogenes, 74 L. welshimeri, 50 L. innocua, and 4 L. marthii isolates, were obtained from 1,805 soil, water, and other environmental samples collected over 2 years from four urban areas and four areas representing natural environments. Listeria spp. showed similar prevalences in samples from natural (23.4%) and urban (22.3%) environments. While L. seeligeri and L. welshimeri were significantly associated with natural environments (P ≤ 0.0001), L. innocua and L. monocytogenes were significantly associated with urban environments (P ≤ 0.0001). Sequencing of sigB for all isolates revealed 67 allelic types with a higher level of allelic diversity among isolates from urban environments. Some Listeria spp. and sigB allelic types showed significant associations with specific urban and natural areas. Nearest-neighbor analyses also showed that certain Listeria spp. and sigB allelic types were spatially clustered within both natural and urban environments, and there was evidence that these species and allelic types persisted over time in specific areas. Our data show that members of the genus Listeria not only are common in urban and natural environments but also show species- and subtype-specific associations with different environments and areas. This indicates that Listeria species and subtypes within these species may show distinct ecological preferences, which suggests (i) that molecular source-tracking approaches can be developed for Listeria and (ii) that detection of some Listeria species may not be a good indicator for L. monocytogenes.

  3. Landscape corridors can increase invasion by an exotic species and reduce diversity of native species.

    PubMed

    Resasco, Julian; Haddad, Nick M; Orrock, John L; Shoemaker, DeWayne; Brudvig, Lars A; Damschen, Ellen I; Tewksbury, Joshua J; Levey, Douglas J

    2014-08-01

    Landscape corridors are commonly used to mitigate negative effects of habitat fragmentation, but concerns persist that they may facilitate the spread of invasive species. In a replicated landscape experiment of open habitat, we measured effects of corridors on the invasive fire ant, Solenopsis invicta, and native ants. Fire ants have two social forms: polygyne, which tend to disperse poorly but establish at high densities, and monogyne, which disperse widely but establish at lower densities. In landscapes dominated by polygyne fire ants, fire ant abundance was higher and native ant diversity was lower in habitat patches connected by corridors than in unconnected patches. Conversely, in landscapes dominated by monogyne fire ants, connectivity had no influence on fire ant abundance and native ant diversity. Polygyne fire ants dominated recently created landscapes, suggesting that these corridor effects may be transient. Our results suggest that corridors can facilitate invasion and they highlight the importance of considering species' traits when assessing corridor utility.

  4. Helicobacter mesocricetorum sp. nov., a Novel Helicobacter Isolated from the Feces of Syrian Hamsters

    PubMed Central

    Simmons, J. H.; Riley, L. K.; Besch-Williford, C. L.; Franklin, C. L.

    2000-01-01

    A spiral-shaped bacterium with bipolar, single, nonsheathed flagella was isolated from the feces of Syrian hamsters. The bacterium grew as a thin spreading film at 37°C under microaerobic conditions, did not hydrolyze urea, was positive for catalase and alkaline phosphatase, reduced nitrate to nitrite, did not hydrolyze hippurate, and was sensitive to nalidixic acid but resistant to cephalothin. Sequence analysis of the 16S rRNA gene and biochemical and phenotypic criteria indicate that the novel bacterium is a helicobacter. The novel bacterium is most closely related to the recently described mouse enteric helicobacter, Helicobacter rodentium. This is the first urease-negative Helicobacter species with nonsheathed flagella isolated from feces of asymptomatic Syrian hamsters. We propose to name this novel helicobacter Helicobacter mesocricetorum. The type strain is MU 97-1514 (GenBank accession number AF072471). PMID:10790105

  5. Diversity of the cagA gene of Helicobacter pylori strains from patients with gastroduodenal diseases in the Philippines.

    PubMed

    Cortes, Maria Celeste C; Yamakawa, Akiyo; Casingal, Cristine R; Fajardo, Lindsay Sydney N; Juan, Ma Luisa G; De Guzman, Blanquita B; Bondoc, Edgardo M; Mahachai, Varocha; Yamazaki, Yukinao; Yoshida, Masaru; Kutsumi, Hiromu; Natividad, Filipinas F; Azuma, Takeshi

    2010-10-01

    Helicobacter pylori CagA protein is considered a major virulence factor associated with gastric cancer. There are two major types of CagA proteins: the Western and East Asian CagA. The East Asian CagA-positive H. pylori infection is more closely associated with gastric cancer. The prevalence of gastric cancer is quite low in the Philippines, although Philippine populations are considered to originate from an East Asia source. This study investigates the characteristics of the cagA gene and CagA protein in Philippine H. pylori strains and compares them with previously characterized reference strains worldwide. The full-length cagA gene was sequenced from 19 Philippine isolates and phylogenetic relationships between the Philippine and 40 reference strains were analyzed. All Philippine strains examined were cagA positive, and 73.7% (14/19) strains were Western CagA-positive. The phylogenetic tree based on the deduced amino acid sequence of CagA indicated that the Philippine strains were classified into the two major groups of CagA protein: the Western and the East Asian group. These findings suggest that the modern Western influence may have resulted in more Western type H. pylori strains in the Philippines. Therefore, H. pylori-infected Filipinos can be considered to be at a low risk of developing gastric cancer.

  6. The effect of species diversity on metal adsorption onto bacteria

    NASA Astrophysics Data System (ADS)

    Ginn, Brian R.; Fein, Jeremy B.

    2008-08-01

    In this study, we measure proton, Pb, and Cd adsorption onto the bacteria Deinococcus radiodurans, Thermus thermophilus, Acidiphlium angustum, Flavobacterium aquatile, and Flavobacterium hibernum, and we calculate the thermodynamic stability constants for the important surface complexes. These bacterial species represent a wide genetic diversity of bacteria, and they occupy a wide range of habitats. All of the species, except for A. angustum, exhibit similar proton and metal uptake. The only species tested that exhibits significantly different protonation behavior is A. angustum, an acidophile that grows at significantly lower pH than the other species of this study. We demonstrate that a single, metal-specific, surface complexation model can be used to reasonably account for the acid/base and metal adsorption behaviors of each species. We use a four discrete site non-electrostatic model to describe the protonation of the bacterial functional groups, with averaged p Ka values of 3.1 ± 0.3, 4.8 ± 0.2, 6.7 ± 0.1, and 9.2 ± 0.3, and site concentrations of (1.0 ± 0.17) × 10 -4, (9.0 ± 3.0) × 10 -5, (4.6 ± 1.8) × 10 -5, and (6.1 ± 2.3) × 10 -5 mol of sites per gram wet mass of bacteria, respectively. Adsorption of Cd and Pb onto the bacteria can be accounted for by the formation of complexes with each of the bacterial surface sites. The average log stability constants for Cd complexes with Sites 1-4 are 2.4 ± 0.4, 3.2 ± 0.1, 4.4 ± 0.1, and 5.3 ± 0.1, respectively. The average log stability constants for Pb complexes with Sites 1-4 are 3.3 ± 0.2, 4.5 ± 0.3, 6.5 ± 0.1, and 7.9 ± 0.5, respectively. This study demonstrates that a wide range of bacteria exhibit similar proton and metal adsorption behaviors, and that a single set of averaged acidity constants, site concentrations, and stability constants for metal-bacterial surface complexes yields a reasonable model for the adsorption behavior of many of these species. The differences in adsorption

  7. Genomes, diversity and resistance gene analogues in Musa species.

    PubMed

    Azhar, M; Heslop-Harrison, J S

    2008-01-01

    Resistance genes (R genes) in plants are abundant and may represent more than 1% of all the genes. Their diversity is critical to the recognition and response to attack from diverse pathogens. Like many other crops, banana and plantain face attacks from potentially devastating fungal and bacterial diseases, increased by a combination of worldwide spread of pathogens, exploitation of a small number of varieties, new pathogen mutations, and the lack of effective, benign and cheap chemical control. The challenge for plant breeders is to identify and exploit genetic resistances to diseases, which is particularly difficult in banana and plantain where the valuable cultivars are sterile, parthenocarpic and mostly triploid so conventional genetic analysis and breeding is impossible. In this paper, we review the nature of R genes and the key motifs, particularly in the Nucleotide Binding Sites (NBS), Leucine Rich Repeat (LRR) gene class. We present data about identity, nature and evolutionary diversity of the NBS domains of Musa R genes in diploid wild species with the Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), M. textilis (T), M. velutina and M. ornata genomes, and from various cultivated hybrid and triploid accessions, using PCR primers to isolate the domains from genomic DNA. Of 135 new sequences, 75% of the sequenced clones had uninterrupted open reading frames (ORFs), and phylogenetic UPGMA tree construction showed four clusters, one from Musa ornata, one largely from the B and T genomes, one from A and M. velutina, and the largest with A, B, T and S genomes. Only genes of the coiled-coil (non-TIR) class were found, typical of the grasses and presumably monocotyledons. The analysis of R genes in cultivated banana and plantain, and their wild relatives, has implications for identification and selection of resistance genes within the genus which may be useful for plant selection and breeding and also for defining relationships and genome evolution

  8. Regulatory phenotyping reveals important diversity within the species Lactococcus lactis.

    PubMed

    Bachmann, Herwig; Starrenburg, Marjo J C; Dijkstra, Annereinou; Molenaar, Douwe; Kleerebezem, Michiel; Rademaker, Jan L W; van Hylckama Vlieg, Johan E T

    2009-09-01

    The diversity in regulatory phenotypes among a collection of 84 Lactococcus lactis strains isolated from dairy and nondairy origin was explored. The specific activities of five enzymes were assessed in cell extracts of all strains grown in two different media, a nutritionally rich broth and a relatively poor chemically defined medium. The five investigated enzymes, branched chain aminotransferase (BcaT), aminopeptidase N (PepN), X-prolyl dipeptidyl peptidase (PepX), alpha-hydroxyisocaproic acid dehydrogenase (HicDH), and esterase, are involved in nitrogen and fatty acid metabolism and catalyze key steps in the production of important dairy flavor compounds. The investigated cultures comprise 75 L. lactis subsp. lactis isolates (including 7 L. lactis subsp. lactis biovar diacetylactis isolates) and 9 L. lactis subsp. cremoris isolates. All L. lactis subsp. cremoris and 22 L. lactis subsp. lactis (including 6 L. lactis subsp. lactis biovar diacetylactis) cultures originated from a dairy environment. All other cultures originated from (fermented) plant materials and were isolated at different geographic locations. Correlation analysis of specific enzyme activities revealed significantly different regulatory phenotypes for dairy and nondairy isolates. The enzyme activities in the two investigated media were in general poorly correlated and revealed a high degree of regulatory diversity within this collection of closely related strains. To the best of our knowledge, these results represent the most extensive diversity analysis of regulatory phenotypes within a single bacterial species to date. The presented findings underline the importance of the availability of screening procedures for, e.g., industrially relevant enzyme activities in models closely mimicking application conditions. Moreover, they corroborate the notion that regulatory changes are important drivers of evolution.

  9. OryzaGenome: Genome Diversity Database of Wild Oryza Species.

    PubMed

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori

    2016-01-01

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  10. Positive Effects of Plant Genotypic and Species Diversity on Anti-Herbivore Defenses in a Tropical Tree Species

    PubMed Central

    Moreira, Xoaquín; Abdala-Roberts, Luis; Parra-Tabla, Víctor; Mooney, Kailen A.

    2014-01-01

    Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla) and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves). We found that both forms of plant diversity had positive effects on stem (but not leaf) defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s) of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer diversity effects on

  11. Positive effects of plant genotypic and species diversity on anti-herbivore defenses in a tropical tree species.

    PubMed

    Moreira, Xoaquín; Abdala-Roberts, Luis; Parra-Tabla, Víctor; Mooney, Kailen A

    2014-01-01

    Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla) and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves). We found that both forms of plant diversity had positive effects on stem (but not leaf) defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s) of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer diversity effects on

  12. Cryptic diversity in vertebrates: molecular data double estimates of species diversity in a radiation of Australian lizards (Diplodactylus, Gekkota)

    PubMed Central

    Oliver, Paul M.; Adams, Mark; Lee, Michael S.Y.; Hutchinson, Mark N.; Doughty, Paul

    2009-01-01

    A major problem for biodiversity conservation and management is that a significant portion of species diversity remains undocumented (the ‘taxonomic impediment’). This problem is widely acknowledged to be dire among invertebrates and in developing countries; here, we demonstrate that it can be acute even in conspicuous animals (reptiles) and in developed nations (Australia). A survey of mtDNA, allozyme and chromosomal variation in the Australian gecko, genus Diplodactylus, increases overall species diversity estimates from 13 to 29. Four nominal species each actually represent multi-species complexes; three of these species complexes are not even monophyletic. The high proportion of cryptic species discovered emphasizes the importance of continuing detailed assessments of species diversity, even in apparently well-known taxa from industrialized countries. PMID:19324781

  13. Composition of the essential oil of two Nepeta species and in vitro evaluation of their activity against Helicobacter pylori.

    PubMed

    Kalpoutzakis, E; Aligiannis, N; Mentis, A; Mitaku, S; Charvala, C

    2001-12-01

    The chemical composition of the essential oils obtained from the aerial parts of Nepeta camphorata and Nepeta argolica ssp. dirphya were analysed by GC-MS. A total of 52 components were identified and significant differences (qualitative and quantitative) were observed between the two samples. 1,8-Cineol and two nepetalactones were found to be the major components of the oil of N. camphorata and N. argolica ssp. dirphya respectively. The in vitro activity, of the two oils and the three above mentioned isolated compounds, against 25 clinically isolated and commercial strains of Helicobacter pylori was investigated and some activity was found.

  14. Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species

    PubMed Central

    Guo, Wen-Ping; Tian, Jun-Hua; Lin, Xian-Dan; Ni, Xue-Bing; Chen, Xiao-Ping; Liao, Yong; Yang, Si-Yuan; Dumler, J. Stephen; Holmes, Edward C.; Zhang, Yong-Zhen

    2016-01-01

    Rickettsiales are important zoonotic pathogens, causing severe disease in humans globally. Although mosquitoes are an important vector for diverse pathogens, with the exception of members of the genus Wolbachia little is known about their role in the transmission of Rickettsiales. Herein, Rickettsiales were identified by PCR in five species of mosquitoes (Anopheles sinensis, Armigeres subalbatus, Aedes albopictus, Culex quinquefasciatus and Cu. tritaeniorhynchus) collected from three Chinese provinces during 2014–2015. Subsequent phylogenetic analyses of the rrs, groEL and gltA genes revealed the presence of Anaplasma, Ehrlichia, Candidatus Neoehrlichia, and Rickettsia bacteria in mosquitoes, comprising nine documented and five tentative species bacteria, as well as three symbionts/endosybionts. In addition, bacteria were identified in mosquito eggs, larvae, and pupae sampled from aquatic environments. Hence, these data suggest that Rickettsiales circulate widely in mosquitoes in nature. Also of note was that Ehrlichia and Rickettsia bacteria were detected in each life stage of laboratory cultured mosquitoes, suggesting that Rickettsiales may be maintained in mosquitoes through both transstadial and transovarial transmission. In sum, these data indicate that mosquitoes may have played an important role in the transmission and evolution of Rickettsiales in nature. PMID:27934910

  15. Intraspecific functional diversity of common species enhances community stability.

    PubMed

    Wood, Connor M; McKinney, Shawn T; Loftin, Cynthia S

    2017-03-01

    Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles (Myodes gapperi) had greater iFD than deer mice (Peromyscus maniculatus), both among habitats, and within the plant community in which they were most abundant (their "primary habitat"). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperi diet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

  16. Sown species richness and realized diversity can influence functioning of plant communities differently.

    PubMed

    Rychtecká, Terezie; Lanta, Vojtěch; Weiterová, Iva; Lepš, Jan

    2014-08-01

    Biodiversity-ecosystem functioning experiments (BEF) typically manipulate sown species richness and composition of experimental communities to study ecosystem functioning as a response to changes in diversity. If sown species richness is taken as a measure of diversity and aboveground biomass production as a measure of community functioning, then this relationship is usually found to be positive. The sown species richness can be considered the equivalent of a local species pool in natural communities. However, in addition to species richness, realized diversity is also an important community diversity component. Realized diversity is affected by environmental filtering and biotic interactions operating within a community. As both sown species richness and the realized diversity in BEF studies (as well as local species pool vs observed realized richness in natural communities) can differ markedly, so can their effects on the community functioning. We tested this assumption using two data sets: data from a short-term pot experiment and data from the long-term Jena biodiversity plot experiment. We considered three possible predictors of community functioning (aboveground biomass production): sown species richness, realized diversity (defined as inverse of Simpson dominance index), and survivor species richness. Sown species richness affected biomass production positively in all cases. Realized diversity as well as survivor species richness had positive effects on biomass in approximately half of cases. When realized diversity or survivor species richness was tested together with sown species richness, their partial effects were none or negative. Our results suggest that we can expect positive diversity-productivity relationship when the local species pool size is the decisive factor determining realized observed diversity; in other cases, the shape of the diversity-functioning relationship may be quite opposite.

  17. Spatio-temporal change in the relationship between habitat heterogeneity and species diversity

    NASA Astrophysics Data System (ADS)

    González-Megías, Adela; Gómez, José María; Sánchez-Piñero, Francisco

    2011-05-01

    Beta diversity plays an important role in mediating species diversity and therefore improves our understanding of species-diversity patterns. One principal theoretical framework exists for such patterns, the "habitat-heterogeneity hypothesis (HHH)", which postulates a positive relationship between species diversity and habitat heterogeneity. Although HHH is widely accepted, spatial and temporal variability has been found in the relationship between diversity and heterogeneity. Species turnover has been proposed as the main factor explaining spatial variation in the relationship between species diversity and habitat heterogeneity. In this study, we tested the role of species turnover in explaining spatial and temporal variability on diversity-heterogeneity relationship in a Mediterranean ecosystem, using beetles as the study organisms. A hierarchical design including different habitats and years was used to test our hypothesis. Using different multivariate analyses, we tested for spatial and temporal variability in beta diversity, and in the beetle diversity-heterogeneity relationship using two diversity indices. Our study showed that beetle composition changed spatially and temporally, although temporal change was evident only between sampling periods but not between years. Notably, there was spatial and temporal change in the relationship between habitat descriptors and beetle diversity. Nevertheless, there was no correlation between the changes in beetle composition with the changes in the habitat-heterogeneity relationships. In this Mediterranean system, spatial and temporal changes in the diversity-heterogeneity relationships cannot be predicted by species turnover, and other mechanisms need to be explored to satisfactorily explain this variability.

  18. Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau

    PubMed Central

    Jin, Qian; Han, Huilin; Hu, XiMin; Li, XinHai; Zhu, ChaoDong; Ho, Simon Y. W.; Ward, Robert D.; Zhang, Ai-bing

    2013-01-01

    With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of , which is about four times larger than the mean intraspecific distance (). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau. PMID:23741330

  19. Woody species diversity in forest plantations in a mountainous region of Beijing, China: effects of sampling scale and species selection.

    PubMed

    Zhang, Yuxin; Zhang, Shuang; Ma, Keming; Fu, Bojie; Anand, Madhur

    2014-01-01

    The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr.), planted larch (Larix principis-rupprechtii Mayr.), and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer), while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation.

  20. The non-H pylori helicobacters: their expanding role in gastrointestinal and systemic diseases

    PubMed Central

    Fox, J G

    2002-01-01

    The number of species in the genus Helicobacter has rapidly expanded over the past decade. The genus now includes at least 24 formally named species as well as numerous other helicobacters awaiting formal naming. This review highlights the expanding role that other helicobacters, although not as well known as H pylori, play in gastrointestinal and systemic disease in humans. PMID:11788573

  1. Landscape corridors can increase invasion by an exotic species and reduce diversity of native species.

    SciTech Connect

    Resasco, Julian; et al,

    2014-04-01

    Abstract. Landscape corridors are commonly used to mitigate negative effects of habitat fragmentation, but concerns persist that they may facilitate the spread of invasive species. In a replicated landscape experiment of open habitat, we measured effects of corridors on the invasive fire ant, Solenopsis invicta, and native ants. Fire ants have two social forms: polygyne, which tend to disperse poorly but establish at high densities, and monogyne, which disperse widely but establish at lower densities. In landscapes dominated by polygyne fire ants, fire ant abundance was higher and native ant diversity was lower in habitat patches connected by corridors than in unconnected patches. Conversely, in landscapes dominated by monogyne fire ants, connectivity had no influence on fire ant abundance and native ant diversity. Polygyne fire ants dominated recently created landscapes, suggesting that these corridor effects may be transient. Our results suggest that corridors can facilitate invasion and they highlight the importance of considering species’ traits when assessing corridor utility.

  2. The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community, Mexico

    PubMed Central

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as “Endangered” on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions

  3. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    PubMed

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  4. Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

    PubMed Central

    2017-01-01

    While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010–2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon’s landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non

  5. Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

    PubMed

    Lee, Myung-Bok; Martin, James A

    2017-01-01

    While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010-2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon's landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non

  6. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia.

    PubMed

    Degefu, Tulu; Wolde-meskel, Endalkachew; Frostegård, Åsa

    2013-06-01

    The taxonomic diversity of thirty-seven Rhizobium strains, isolated from nodules of leguminous trees and herbs growing in Ethiopia, was studied using multilocus sequence analyses (MLSA) of six core and two symbiosis-related genes. Phylogenetic analysis based on the 16S rRNA gene grouped them into five clusters related to nine Rhizobium reference species (99-100% sequence similarity). In addition, two test strains occupied their own independent branches on the phylogenetic tree (AC86a2 along with R. tibeticum; 99.1% similarity and AC100b along with R. multihospitium; 99.5% similarity). One strain from Milletia ferruginea was closely related (>99%) to the genus Shinella, further corroborating earlier findings that nitrogen-fixing bacteria are distributed among phylogenetically unrelated taxa. Sequence analyses of five housekeeping genes also separated the strains into five well-supported clusters, three of which grouped with previously studied Ethiopian common bean rhizobia. Three of the five clusters could potentially be described into new species. Based on the nifH genes, most of the test strains from crop legumes were closely related to several strains of Ethiopian common bean rhizobia and other symbionts of bean plants (R. etli and R. gallicum sv. phaseoli). The grouping of the test strains based on the symbiosis-related genes was not in agreement with the housekeeping genes, signifying differences in their evolutionary history. Our earlier studies revealing a large diversity of Mesorhizobium and Ensifer microsymbionts isolated from Ethiopian legumes, together with the results from the present analysis of Rhizobium strains, suggest that this region might be a potential hotspot for rhizobial biodiversity.

  7. Cryptic diversity in a fig wasp community-morphologically differentiated species are sympatric but cryptic species are parapatric.

    PubMed

    Darwell, C T; Cook, J M

    2017-02-01

    A key debate in ecology centres on the relative importance of niche and neutral processes in determining patterns of community assembly with particular focus on whether ecologically similar species with similar functional traits are able to coexist. Meanwhile, molecular studies are increasingly revealing morphologically indistinguishable cryptic species with presumably similar ecological roles. Determining the geographic distribution of such cryptic species provides opportunities to contrast predictions of niche vs. neutral models. Discovery of sympatric cryptic species increases alpha diversity and supports neutral models, while documentation of allopatric/parapatric cryptic species increases beta diversity and supports niche models. We tested these predictions using morphological and molecular data, coupled with environmental niche modelling analyses, of a fig wasp community along its 2700-km latitudinal range. Molecular methods increased previous species diversity estimates from eight to eleven species, revealing morphologically cryptic species in each of the four wasp genera studied. Congeneric species pairs that were differentiated by a key morphological functional trait (ovipositor length) coexisted sympatrically over large areas. In contrast, morphologically similar species, with similar ovipositor lengths, typically showed parapatric ranges with very little overlap. Despite parapatric ranges, environmental niche models of cryptic congeneric pairs indicate large regions of potential sympatry, suggesting that competitive processes are important in determining the distributions of ecologically similar species. Niche processes appear to structure this insect community, and cryptic diversity may typically contribute mostly to beta rather than alpha diversity.

  8. GLK gene pairs regulate chloroplast development in diverse plant species.

    PubMed

    Fitter, David W; Martin, David J; Copley, Martin J; Scotland, Robert W; Langdale, Jane A

    2002-09-01

    Chloroplast biogenesis is a complex process that requires close co-ordination between two genomes. Many of the proteins that accumulate in the chloroplast are encoded by the nuclear genome, and the developmental transition from proplastid to chloroplast is regulated by nuclear genes. Here we show that a pair of Golden 2-like (GLK) genes regulates chloroplast development in Arabidopsis. The GLK proteins are members of the GARP superfamily of transcription factors, and phylogenetic analysis demonstrates that the maize, rice and Arabidopsis GLK gene pairs comprise a distinct group within the GARP superfamily. Further phylogenetic analysis suggests that the gene pairs arose through separate duplication events in the monocot and dicot lineages. As in rice, AtGLK1 and AtGLK2 are expressed in partially overlapping domains in photosynthetic tissue. Insertion mutants demonstrate that this expression pattern reflects a degree of functional redundancy as single mutants display normal phenotypes in most photosynthetic tissues. However, double mutants are pale green in all photosynthetic tissues and chloroplasts exhibit a reduction in granal thylakoids. Products of several genes involved in light harvesting also accumulate at reduced levels in double mutant chloroplasts. GLK genes therefore regulate chloroplast development in diverse plant species.

  9. Diverse Thermus species inhabit a single hot spring microbial mat

    NASA Technical Reports Server (NTRS)

    Nold, S. C.; Ward, D. M.

    1995-01-01

    Through an effort to characterize aerobic chemoorganotrophic bacteria in the Octopus Spring cyano-bacterial mat community, we cultivated four Thermus isolates with unique 16S rRNA sequences. Isolates clustered within existing Thermus clades, including those containing Thermus ruber, Thermus aquaticus, and a subgroup closely related to T. aquaticus. One Octopus Spring isolate is nearly identical (99.9% similar) to isolates from Iceland, and two others are closely related to a T. ruber isolated from Russia. Octopus Spring isolates similar to T. aquaticus and T. ruber exhibited optimal growth rates at high (65-70 degrees C) and low (50 degrees C) temperatures, respectively, with the most abundant species best adapted to the temperature of the habitat (50-55 degrees C). Our results display a diversity of Thermus genotypes defined by 16S rRNA within one hot spring microbial community. We suggest that specialization to temperature and perhaps other local environmental features controls the abundance of Thermus populations.

  10. Isolation of Geobacter species from diverse sedimentary environments

    USGS Publications Warehouse

    Coaxes, J.D.; Phillips, E.J.P.; Lonergan, D.J.; Jenter, H.; Lovley, D.R.

    1996-01-01

    In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria. Unlike the type strain, Geobacter metallireducens, three of the five isolates could use H2 as an electron donor fur Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.

  11. RESOURCE-BASED NICHES PROVIDE A BASIS FOR PLANT SPECIES DIVERSITY AND DOMINANCE IN ARCTIC TUNDRA

    EPA Science Inventory

    Ecologists have long been intrigued by the ways co-occurring species divide limiting resources, and have proposed that such resource partitioning, or niche differentiation, promotes species diversity by reducing competition. Although resource partitioning is an important determi...

  12. Patterns of Tree Species Diversity in Relation to Climatic Factors on the Sierra Madre Occidental, Mexico

    PubMed Central

    Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

    2014-01-01

    Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9–14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

  13. Dominant species, rather than diversity, regulates temporal stability of plant communities.

    PubMed

    Sasaki, Takehiro; Lauenroth, William K

    2011-07-01

    A growing body of empirical evidence suggests that the temporal stability of communities typically increases with diversity. The counterview to this is that dominant species, rather than diversity itself, might regulate temporal stability. However, empirical studies that have explicitly examined the relative importance of diversity and dominant species in maintaining community stability have yielded few clear-cut patterns. Here, using a long-term data set, we examined the relative importance of changes in diversity components and dominance hierarchy following the removal of a dominant C4 grass, Bouteloua gracilis, in stabilizing plant communities. We also examined the relationships between the variables of diversity and dominance hierarchy and the statistical components of temporal stability. We found a significant negative relationship between temporal stability and species richness, number of rare species, and relative abundance of rare species, whereas a significant positive relationship existed between temporal stability and relative abundance of the dominant species. Variances and covariances summed over all species significantly increased with increasing species richness, whereas they significantly decreased with increasing relative abundance of dominant species. We showed that temporal stability in a shortgrass steppe plant community was controlled by dominant species rather than by diversity itself. The generality of diversity-stability relationships might be restricted by the dynamics of dominant species, especially when they have characteristics that contribute to stability in highly stochastic systems. A clear implication is that dominance hierarchies and their changes might be among the most important ecological components to consider in managing communities to maintain ecosystem functioning.

  14. Helicobacter pylori CagA: analysis of sequence diversity in relation to phosphorylation motifs and implications for the role of CagA as a virulence factor.

    PubMed

    Evans, D J; Evans, D G

    2001-09-01

    CagA is transported into host target cells and subsequently phosphorylated. Clearly this is a mechanism by which Helicobacter pylori could take control of one or more host cell signal transduction pathways. Presumably the end result of this interaction favors survival of H. pylori, irrespective of eventual damage to the host cell. CagA is noted for its amino acid (AA) sequence diversity, both within and outside the variable region of the molecule. The primary purpose of this review is to examine how variation in the type and number of CagA phosphorylation sites might determine the outcome of infection by different strains of H. pylori. The answer to this question could help to explain the widely disparate results obtained when H. pylori CagA status has been compared to type and severity of disease outcome in different populations, that is in different countries. Analysis of all available CagA sequences revealed that CagA contains both tyrosine phosphorylation motifs (TPMs) and cyclic-AMP-dependent phosphorylation motifs (CPMs). There are two potential CPMs near the N-terminus of CagA and at least two in the repeat region; these are not all equally well conserved. We also defined a 48-residue AA sequence, which includes the N-terminal TPM at tyrosine (Y)-122, which distinguishes between Eastern (Hong Kong-Taiwan-Japan-Thailand) H. pylori isolates and those from the West (Europe-Africa-the Americas-Australia). All 28 of the Eastern type CagA proteins have a functional N-terminal TPM whereas 11 of 47 (23.4%) of the Western type contain an inactive motif, with threonine (T) replacing the critical aspartic acid (D) residue. Only 13 of 24 (54%) known CagA sequences have an active TPM in the repeat region and only one has two TPMs in this region. The potential TPM near the C-terminus of CagA is not likely to be important since only 3 of 24 (12.5%) sequences were found to be intact. Protein database searches revealed that the AA sequence immediately following the TPM at Y

  15. Does population size affect genetic diversity? A test with sympatric lizard species

    PubMed Central

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations. PMID:26306730

  16. Measures of School Integration: Comparing Coleman's Index to Measures of Species Diversity.

    ERIC Educational Resources Information Center

    Mercil, Steven Bray; Williams, John Delane

    This study used species diversity indices developed in ecology as a measure of socioethnic diversity, and compared them to Coleman's Index of Segregation. The twelve indices were Simpson's Concentration Index ("ell"), Simpson's Index of Diversity, Hurlbert's Probability of Interspecific Encounter (PIE), Simpson's Probability of…

  17. Two gut community enterotypes recur in diverse bumblebee species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pollinating insects are key to the evolutionary and ecological success of flowering plants and enable much of the diversity in the human diet. Gut microbial communities likely impact pollinators in diverse ways, from nutrition to defense against disease. Honeybees and bumblebees harbor a simple yet ...

  18. Multivariate analysis of morphological diversity among closely related Daucus species and subspecies in Tunisia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Daucus includes about 20-25 species worldwide. Northern Africa represents a major center of diversity of Daucus, with Tunisia thought to contain 11 species and seven subspecies. We assessed morphological diversity from a Daucus germplasm collection of 103 accessions at the National Gene Ba...

  19. Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest.

    PubMed

    Xu, Wumei; Ci, Xiuqin; Song, Caiyun; He, Tianhua; Zhang, Wenfu; Li, Qiaoming; Li, Jie

    2016-12-01

    The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty-nine plots of 400 m(2) (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.

  20. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa).

    PubMed

    Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A-F; Bruggemann, J Henrich

    2016-12-01

    A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms.

  1. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices.

    PubMed

    Ngo Ngwe, Marie Florence Sandrine; Omokolo, Denis Ndoumou; Joly, Simon

    2015-01-01

    Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

  2. Species pools, community completeness and invasion: disentangling diversity effects on the establishment of native and alien species.

    PubMed

    Bennett, Jonathan A; Riibak, Kersti; Kook, Ene; Reier, Ülle; Tamme, Riin; Guillermo Bueno, C; Pärtel, Meelis

    2016-12-01

    Invasion should decline with species richness, yet the relationship is inconsistent. Species richness, however, is a product of species pool size and biotic filtering. Invasion may increase with richness if large species pools represent weaker environmental filters. Measuring species pool size and the proportion realised locally (completeness) may clarify diversity-invasion relationships by separating environmental and biotic effects, especially if species' life-history stage and origin are accounted for. To test these relationships, we added seeds and transplants of 15 native and alien species into 29 grasslands. Species pool size and completeness explained more variation in invasion than richness alone. Although results varied between native and alien species, seed establishment and biotic resistance to transplants increased with species pool size, whereas transplant growth and biotic resistance to seeds increased with completeness. Consequently, species pools and completeness represent multiple independent processes affecting invasion; accounting for these processes improves our understanding of invasion.

  3. Tree diversity promotes functional dissimilarity and maintains functional richness despite species loss in predator assemblages.

    PubMed

    Schuldt, Andreas; Bruelheide, Helge; Durka, Walter; Michalski, Stefan G; Purschke, Oliver; Assmann, Thorsten

    2014-02-01

    The effects of species loss on ecosystems depend on the community's functional diversity (FD). However, how FD responds to environmental changes is poorly understood. This applies particularly to higher trophic levels, which regulate many ecosystem processes and are strongly affected by human-induced environmental changes. We analyzed how functional richness (FRic), evenness (FEve), and divergence (FDiv) of important generalist predators-epigeic spiders-are affected by changes in woody plant species richness, plant phylogenetic diversity, and stand age in highly diverse subtropical forests in China. FEve and FDiv of spiders increased with plant richness and stand age. FRic remained on a constant level despite decreasing spider species richness with increasing plant species richness. Plant phylogenetic diversity had no consistent effect on spider FD. The results contrast with the negative effect of diversity on spider species richness and suggest that functional redundancy among spiders decreased with increasing plant richness through non-random species loss. Moreover, increasing functional dissimilarity within spider assemblages with increasing plant richness indicates that the abundance distribution of predators in functional trait space affects ecological functions independent of predator species richness or the available trait space. While plant diversity is generally hypothesized to positively affect predators, our results only support this hypothesis for FD-and here particularly for trait distributions within the overall functional trait space-and not for patterns in species richness. Understanding the way predator assemblages affect ecosystem functions in such highly diverse, natural ecosystems thus requires explicit consideration of FD and its relationship with species richness.

  4. Is tree species diversity or tree species identity the most important driver of European forest soil carbon stocks?

    NASA Astrophysics Data System (ADS)

    Vesterdal, Lars; Muhie Dawud, Seid; Raulund-Rasmussen, Karsten; Finér, Leena; Domisch, Timo

    2016-04-01

    Land management includes the selection of specific tree species and tree species mixtures for European forests. Studies of functional species diversity effects have reported positive effects for aboveground carbon (C) sequestration, but the question remains whether higher soil C stocks could also result from belowground niche differentiation including more efficient root exploitation of soils. We studied topsoil C stocks in tree species diversity gradients established within the FunDivEurope project to explore biodiversity-ecosystem functioning relationships in six European forest types in Finland, Poland, Germany, Romania, Spain and Italy. In the Polish forest type we extended the sampling to also include subsoils. We found consistent but modest effects of species diversity on total soil C stocks (forest floor and 0-20 cm) across the six European forest types. Carbon stocks in the forest floor alone and in the combined forest floor and mineral soil layers increased with increasing tree species diversity. In contrast, there was a strong effect of species identity (broadleaf vs. conifer) and its interaction with site-related factors. Within the Polish forest type we sampled soils down to 40 cm and found that species identity was again the main factor explaining total soil C stock. However, species diversity increased soil C stocks in deeper soil layers (20-40 cm), while species identity influenced C stocks significantly within forest floors and the 0-10 cm layer. Root biomass increased with diversity in 30-40 cm depth, and a positive relationship between C stocks and root biomass in the 30-40 cm layer suggested that belowground niche complementarity could be a driving mechanism for higher root carbon input and in turn a deeper distribution of C in diverse forests. We conclude that total C stocks are mainly driven by tree species identity. However, modest positive diversity effects were detected at the European scale, and stronger positive effects on subsoil C stocks

  5. Evaluation of Central North American prairie management based on species diversity, life form, and individual species metrics.

    PubMed

    Brudvig, Lars A; Mabry, Catherine M; Miller, James R; Walker, Tracy A

    2007-06-01

    Reintroduction of fire and grazing, alone or in combination, has increasingly been recognized as central to the restoration of North American mixed-grass and tallgrass prairies. Although ecological studies of these systems are abundant, they have generally been observational, or if experimental, have focused on plant species diversity. Species diversity measures alone are not sufficient to inform management, which often has goals associated with life-form groups and individual species. We examined the effects of prescribed fire, light cattle grazing, and a combination of fire and grazing on three vegetation components: species diversity, groups of species categorized by life-form, and individual species. We evaluated how successful these three treatments were in achieving specific management goals for prairies in the Iowa Loess Hills (U.S.A.). The grazing treatment promoted the greatest overall species richness, whereas grazing and burning and grazing treatments resulted in the lowest cover by woody species. Burning alone best achieved the management goals of increasing the cover and diversity of native species and reducing exotic forb and (predominantly exotic) cool-season grass cover. Species-specific responses to treatments appeared idiosyncratic (i.e., within each treatment there existed a set of species attaining their highest frequency) and nearly half of uncommon species were present in only one treatment. Because all management goals were not achieved by any one treatment, we conclude that management in this region may need refining. We suggest that a mosaic of burning and grazing (alone and in combination) may provide the greatest landscape-level species richness; however, this strategy would also likely promote the persistence of exotic species. Our results support the need to consider multiple measures, including species-specific responses, when planning and evaluating management.

  6. Conserving the Stage: Climate Change and the Geophysical Underpinnings of Species Diversity

    PubMed Central

    Anderson, Mark G.; Ferree, Charles E.

    2010-01-01

    Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R2 = 0.94). To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5–95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001), strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may be a robust

  7. Conserving the stage: climate change and the geophysical underpinnings of species diversity.

    PubMed

    Anderson, Mark G; Ferree, Charles E

    2010-07-14

    Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R(2) = 0.94). To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5-95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001), strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may be a robust

  8. Construction and characterization of an isogenic urease-negative mutant of Helicobacter mustelae.

    PubMed Central

    Solnick, J V; Josenhans, C; Suerbaum, S; Tompkins, L S; Labigne, A

    1995-01-01

    Helicobacter mustelae infects the ferret stomach and provides an opportunity to study pathogenic determinants of a Helicobacter species in its natural host. We constructed an isogenic urease-negative mutant of H. mustelae which produced no detectable urease and showed a reduced acid tolerance. This mutant provides an opportunity to further evaluate the role of urease in the pathogenesis of Helicobacter infection. PMID:7642313

  9. The relationship between regional and local species diversity in marine benthic communities: A global perspective

    PubMed Central

    Witman, Jon D.; Etter, Ron J.; Smith, Franz

    2004-01-01

    The number of species coexisting in ecological communities must be a consequence of processes operating on both local and regional scales. Although a great deal of experimental work has been devoted to local causes of diversity, little is known about the effects of regional processes on local diversity and how they contribute to global diversity patterns in marine systems. We tested the effects of latitude and the richness of the regional species pool on the species richness of local epifaunal invertebrate communities by sampling the diversity of local sites in 12 independent biogeographic regions from 62°S to 63°N latitude. Both regional and local species richness displayed significant unimodal patterns with latitude, peaking at low latitudes and decreasing toward high latitudes. The latitudinal diversity gradient was represented at the scale of local sites because local species richness was positively and linearly related to regional species richness. The richness of the regional species pool explained 73-76% of local species richness. On a global scale, the extent of regional influence on local species richness was nonrandom—the proportion of regional biota represented in local epifaunal communities increased significantly from low to high latitudes. The strong effect of the regional species pool implies that patterns of local diversity in temperate, tropical, and high-latitude marine benthic communities are influenced by processes operating on larger spatiotemporal scales than previously thought. PMID:15501917

  10. Diversity in wild apple species of Chinese origin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Malus collection in the USDA-ARS National Plant Germplasm System has twelve wild species of apple collected from China at the Plant Genetic Resources Unit (PGRU) in Geneva, NY. Between 8 and 148 individual trees represent each species. The assignment of seedling trees to specific species has be...

  11. Gastric and enterohepatic helicobacters other than Helicobacter pylori.

    PubMed

    Ménard, Armelle; Péré-Védrenne, Christelle; Haesebrouck, Freddy; Flahou, Bram

    2014-09-01

    During the past year, research on non-Helicobacter pylori species has intensified. H. valdiviensis was isolated from wild birds, and putative novel species have been isolated from Bengal tigers and Australian marsupials. Various genomes have been sequenced: H. bilis, H. canis, H. macacae, H. fennelliae, H. cetorum, and H. suis. Several studies highlighted the virulence of non-H. pylori species including H. cinaedi in humans and hyperlipidemic mice or H. macacae in geriatric rhesus monkeys with intestinal adenocarcinoma. Not surprisingly, increased attention has been paid to the position of Helicobacter species in the microbiota of children and animal species (mice, chickens, penguins, and migrating birds). A large number of experimental studies have been performed in animal models of Helicobacter induced typhlocolitis, showing that the gastrointestinal microbial community is involved in modulation of host pathways leading to chronic inflammation. Animal models of H. suis, H. heilmannii, and H. felis infection have been used to study the development of severe inflammation-related pathologies, including gastric MALT lymphoma and adenocarcinoma.

  12. Latitudinal species diversity gradient of marine zooplankton for the last three million years

    USGS Publications Warehouse

    Yasuhara, Moriaki; Hunt, Gene; Dowsett, Harry J.; Robinson, Marci M.; Stoll, Danielle K.

    2012-01-01

    High tropical and low polar biodiversity is one of the most fundamental patterns characterising marine ecosystems, and the influence of temperature on such marine latitudinal diversity gradients is increasingly well documented. However, the temporal stability of quantitative relationships among diversity, latitude and temperature is largely unknown. Herein we document marine zooplankton species diversity patterns at four time slices [modern, Last Glacial Maximum (18 000 years ago), last interglacial (120 000 years ago), and Pliocene (~3.3–3.0 million years ago)] and show that, although the diversity-latitude relationship has been dynamic, diversity-temperature relationships are remarkably constant over the past three million years. These results suggest that species diversity is rapidly reorganised as species' ranges respond to temperature change on ecological time scales, and that the ecological impact of future human-induced temperature change may be partly predictable from fossil and paleoclimatological records.

  13. Biotic homogenization and changes in species diversity across human-modified ecosystems

    PubMed Central

    Smart, Simon M; Thompson, Ken; Marrs, Robert H; Le Duc, Mike G; Maskell, Lindsay C; Firbank, Leslie G

    2006-01-01

    Changing land use and the spread of ‘winning’ native or exotic plants are expected to lead to biotic homogenization (BH), in which previously distinct plant communities become progressively more similar. In parallel, many ecosystems have recently seen increases in local species (α-) diversity, yet γ-diversity has continued to decline at larger scales. Using national ecological surveillance data for Great Britain, we quantify relationships between change in α-diversity and between-habitat homogenizations at two levels of organization: species composition and plant functional traits. Across Britain both increases and decreases in α-diversity were observed in small random sampling plots (10–200 m2) located within a national random sample of 1 km square regions. As α-diversity declined (spatially in 1978 or temporally between 1978 and 1998), plant communities became functionally more similar, but species-compositional similarity declined. Thus, different communities converged on a narrower range of winning trait syndromes, but species identities remained historically contingent, differentiating a mosaic of residual species-poor habitat patches within each 1 km square. The reverse trends in β-diversity occurred where α-diversity increased. When impacted by the same type and intensity of environmental change, directions of change in α-diversity are likely to depend upon differences in starting productivity and disturbance. This is one reason why local diversity change and BH across habitats are not likely to be consistently coupled. PMID:17002952

  14. Biotic homogenization and changes in species diversity across human-modified ecosystems.

    PubMed

    Smart, Simon M; Thompson, Ken; Marrs, Robert H; Le Duc, Mike G; Maskell, Lindsay C; Firbank, Leslie G

    2006-10-22

    Changing land use and the spread of 'winning' native or exotic plants are expected to lead to biotic homogenization (BH), in which previously distinct plant communities become progressively more similar. In parallel, many ecosystems have recently seen increases in local species (alpha-) diversity, yet gamma-diversity has continued to decline at larger scales. Using national ecological surveillance data for Great Britain, we quantify relationships between change in alpha-diversity and between-habitat homogenizations at two levels of organization: species composition and plant functional traits. Across Britain both increases and decreases in alpha-diversity were observed in small random sampling plots (10-200m2) located within a national random sample of 1km square regions. As alpha-diversity declined (spatially in 1978 or temporally between 1978 and 1998), plant communities became functionally more similar, but species-compositional similarity declined. Thus, different communities converged on a narrower range of winning trait syndromes, but species identities remained historically contingent, differentiating a mosaic of residual species-poor habitat patches within each 1km square. The reverse trends in beta-diversity occurred where alpha-diversity increased. When impacted by the same type and intensity of environmental change, directions of change in alpha-diversity are likely to depend upon differences in starting productivity and disturbance. This is one reason why local diversity change and BH across habitats are not likely to be consistently coupled.

  15. Species diversity and distribution patterns of the ants of Amazonian Ecuador.

    PubMed

    Ryder Wilkie, Kari T; Mertl, Amy L; Traniello, James F A

    2010-10-01

    Ants are among the most diverse, abundant and ecologically significant organisms on earth. Although their species richness appears to be greatest in the New World tropics, global patterns of ant diversity and distribution are not well understood. We comprehensively surveyed ant diversity in a lowland primary rainforest in Western Amazonia, Ecuador using canopy fogging, pitfall traps, baits, hand collecting, mini-Winkler devices and subterranean probes to sample ants. A total of 489 ant species comprising 64 genera in nine subfamilies were identified from samples collected in only 0.16 square kilometers. The most species-rich genera were Camponotus, Pheidole, Pseudomyrmex, Pachycondyla, Brachymyrmex, and Crematogaster. Camponotus and Pseudomyrmex were most diverse in the canopy, while Pheidole was most diverse on the ground. The three most abundant ground-dwelling ant genera were Pheidole, Solenopsis and Pyramica. Crematogaster carinata was the most abundant ant species in the canopy; Wasmannia auropunctata was most abundant on the ground, and the army ant Labidus coecus was the most abundant subterranean species. Ant species composition among strata was significantly different: 80% of species were found in only one stratum, 17% in two strata, and 3% in all three strata. Elevation and the number of logs and twigs available as nest sites were significant predictors of ground-dwelling ant species richness. Canopy species richness was not correlated with any ecological variable measured. Subterranean species richness was negatively correlated with depth in the soil. When ant species were categorized using a functional group matrix based on diet, nest-site preference and foraging ecology, the greatest diversity was found in Omnivorous Canopy Nesters. Our study indicates ant species richness is exceptionally high at Tiputini. We project 647-736 ant species in this global hotspot of biodiversity. Considering the relatively small area surveyed, this region of western

  16. Expanding the Species and Chemical Diversity of Penicillium Section Cinnamopurpurea

    PubMed Central

    Peterson, Stephen W.; Jurjević, Željko; Frisvad, Jens C.

    2015-01-01

    A set of isolates very similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a BLAST search of ITS similarity among described (GenBank) and undescribed Penicillium isolates in our laboratories. DNA was amplified from six loci of the assembled isolates and sequenced. Two species in section Cinnamopurpurea are self-compatible sexual species, but the asexual species had polymorphic loci suggestive of sexual reproduction and variation in conidium size suggestive of ploidy level differences typical of heterothallism. Accordingly we use genealogical concordance analysis, a technique valid only in heterothallic organisms, for putatively asexual species. Seven new species were revealed in the analysis and are described here. Extrolite analysis showed that two of the new species, P. colei and P. monsserratidens produce the mycotoxin citreoviridin that has demonstrated pharmacological activity against human lung tumors. These isolates could provide leads in pharmaceutical research. PMID:25853891

  17. Cascade effects of crop species richness on the diversity of pest insects and their natural enemies.

    PubMed

    Shi, PeiJian; Hui, Cang; Men, XingYuan; Zhao, ZiHua; Ouyang, Fang; Ge, Feng; Jin, XianShi; Cao, HaiFeng; Li, B Larry

    2014-07-01

    Understanding how plant species richness influences the diversity of herbivorous and predatory/parasitic arthropods is central to community ecology. We explore the effects of crop species richness on the diversity of pest insects and their natural enemies. Using data from a four-year experiment with five levels of crop species richness, we found that crop species richness significantly affected the pest species richness, but there were no significant effects on richness of the pests' natural enemies. In contrast, the species richness of pest insects significantly affected their natural enemies. These findings suggest a cascade effect where trophic interactions are strong between adjacent trophic levels, while the interactions between connected but nonadjacent trophic levels are weakened by the intermediate trophic level. High crop species richness resulted in a more stable arthropod community compared with communities in monoculture crops. Our results highlight the complicated cross-trophic interactions and the crucial role of crop diversity in the food webs of agro-ecosystems.

  18. Evaluation of two monkey species (Macaca mulatta and Macaca fascicularis) as possible models for human Helicobacter pylori disease.

    PubMed Central

    Euler, A R; Zurenko, G E; Moe, J B; Ulrich, R G; Yagi, Y

    1990-01-01

    Endoscopic, histologic, and microbiologic evaluations of 21 cynomolgus and 34 rhesus monkeys for naturally occurring Helicobacter pylori infection were done. H. pylori was never isolated from any cynomolgus monkey, but was found in 12 rhesus monkeys. A general correlation existed between a positive culture and a gastric inflammatory response. Inoculation challenges were then undertaken. Four cynomolgus and five rhesus monkeys received two different H. pylori strains isolated from humans. Five rhesus monkeys received an isolate obtained from rhesus monkeys. Evaluation of the cynomolgus monkeys 7 and 14 days later revealed no H. pylori. Endoscopies of the rhesus monkeys were done 7, 14, 21, 28, and 56 days later. One rhesus monkey, which received the isolate from humans, became H. pylori positive at day 21 and remained positive through day 56. Restriction enzyme analysis of genomic DNA at day 56 revealed that the isolate was not identical to the challenge strain isolated from humans. All five rhesus monkeys that received the strain isolated from rhesus monkeys became H. pylori positive by day 14 and remained positive through day 56 Antral inflammation developed in all monkeys. Restriction enzyme analysis of genomic DNA on day 56 confirmed that four of five isolates were identical to the challenge strain isolated from rhesus monkeys. DNA hybridization documented homology between the challenge strains isolated from humans and rhesus monkeys plus those isolated at day 56. In this study, we showed that the rhesus monkey, if given a strain of H. pylori isolated from rhesus monkeys, develops a gastric infection with accompanying histological changes, making this model suitable for further development. Images PMID:2229353

  19. Hidden diversity in the Podarcis tauricus (Sauria, Lacertidae) species subgroup in the light of multilocus phylogeny and species delimitation.

    PubMed

    Psonis, Nikolaos; Antoniou, Aglaia; Kukushkin, Oleg; Jablonski, Daniel; Petrov, Boyan; Crnobrnja-Isailović, Jelka; Sotiropoulos, Konstantinos; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

    2017-01-01

    The monophyletic species subgroup of Podarcis tauricus is distributed in the western and southern parts of the Balkans, and includes four species with unresolved and unstudied inter- and intra-specific phylogenetic relationships. Using sequence data from two mitochondrial and three nuclear genes and applying several phylogenetic methods and species delimitation approaches to an extensive dataset, we have reconstructed the phylogeny of the Podarcis wall lizards in the Balkans, and re-investigated the taxonomic status of the P. tauricus species subgroup. Multilocus analyses revealed that the aforementioned subgroup consists of five major clades, with P. melisellensis as its most basal taxon. Monophyly of P. tauricus sensu stricto is not supported, with one of the subspecies (P. t. ionicus) displaying great genetic diversity (hidden diversity or cryptic species). It comprises five, geographically distinct, subclades with genetic distances on the species level. Species delimitation approaches revealed nine species within the P. tauricus species subgroup (P. melisellensis, P. gaigeae, P. milensis, and six in the P. tauricus complex), underlining the necessity of taxonomic re-evaluation. We thus synonymize some previously recognized subspecies in this subgroup, elevate P. t. tauricus and P. g. gaigeae to the species level and suggest a distinct Albanian-Greek clade, provisionally named as the P. ionicus species complex. The latter clade comprises five unconfirmed candidate species that call for comprehensive studies in the future.

  20. Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2

    PubMed Central

    Uchimura, Yasuhiro; Wyss, Madeleine; Brugiroux, Sandrine; Limenitakis, Julien P.; Stecher, Bärbel; McCoy, Kathy D.

    2016-01-01

    We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species. PMID:27634994

  1. Burning reveals cryptic diversity and promotes coexistence of native species in a restored California prairie

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grassland and prairie restoration projects in California often result in long-term establishment of only a few native plant species, even when they begin with a diverse palette of species. A likely explanation for the disappearance of certain native species over time is that they are outcompeted by ...

  2. Use of Neonatal Fostering To Remove Helicobacter spp. from Deer Mice (Peromyscus maniculatus)

    PubMed Central

    Pritchett-Corning, Kathleen R; Peery, Harry E; Crossland, Janet P; Wyatt, Heather M; Stuart, Marilyne; Mothersill, Carmel E

    2015-01-01

    Helicobacter species can be found in a wide variety of animals and remain common contaminants of laboratory rodents. Fostering of neonatal pups has been used to eliminate Helicobacter spp. from various laboratory rodents, including laboratory mice and gerbils. Deer mice (Peromyscus maniculatus) from a captive colony enzootic for at least one Helicobacter species were mated, and the pups produced were fostered on laboratory mice 24 h after birth. After 2 rounds of fostering, both foster dams and pups were free of Helicobacter spp. as determined by fecal PCR analysis. Removal of Helicobacter infection through neonatal fostering has not been described previously for Peromyscus maniculatus. PMID:26224445

  3. Links between tree species, symbiotic fungal diversity and ecosystem functioning in simplified tropical ecosystems.

    PubMed

    Lovelock, Catherine E; Ewel, John J

    2005-07-01

    We studied the relationships among plant and arbuscular mycorrhizal (AM) fungal diversity, and their effects on ecosystem function, in a series of replicate tropical forestry plots in the La Selva Biological Station, Costa Rica. Forestry plots were 12 yr old and were either monocultures of three tree species, or polycultures of the tree species with two additional understory species. Relationships among the AM fungal spore community, host species, plant community diversity and ecosystem phosphorus-use efficiency (PUE) and net primary productivity (NPP) were assessed. Analysis of the relative abundance of AM fungal spores found that host tree species had a significant effect on the AM fungal community, as did host plant community diversity (monocultures vs polycultures). The Shannon diversity index of the AM fungal spore community differed significantly among the three host tree species, but was not significantly different between monoculture and polyculture plots. Over all the plots, significant positive relationships were found between AM fungal diversity and ecosystem NPP, and between AM fungal community evenness and PUE. Relative abundance of two of the dominant AM fungal species also showed significant correlations with NPP and PUE. We conclude that the AM fungal community composition in tropical forests is sensitive to host species, and provide evidence supporting the hypothesis that the diversity of AM fungi in tropical forests and ecosystem NPP covaries.

  4. SSRs are useful to assess genetic diversity among Lagerstroemia species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The most recent and widely accepted taxonomic revision of Lagerstroemia occurred in 1969 and is based on morphological characters. As described, the genus is split into three sections and includes more than 50 species, several of which are grown for lumber in Asia and the Philippines. Three species,...

  5. Genetic diversity of wild European and Mediterranean pear species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many pear species are native to Europe, the Middle East, and Northern Africa. These seemingly distinct species readily hybridize resulting in nomenclatures that do not reflect their phylogenetic history. We have used microsatellite and chloroplast sequence markers as well as phenotypic traits to dif...

  6. DOES NITROGEN PARTITIONING PROMOTE SPECIES DIVERSITY IN ARCTIC TUSSOCK TUNDRA?

    EPA Science Inventory

    We used 15N soil-labeling techniques to examine how the dominant species in a N-limited, tussock tundra plant community partitioned soil N, and how such partitioning may contribute to community organization. The five most productive species were well differentiated with respect ...

  7. Unequal Contribution of Widespread and Narrow-Ranged Species to Botanical Diversity Patterns

    PubMed Central

    Raes, Niels; Wieringa, Jan J.; Sosef, Marc S. M.

    2016-01-01

    In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We

  8. Saturating effects of species diversity on life-history evolution in bacteria.

    PubMed

    Fiegna, Francesca; Scheuerl, Thomas; Moreno-Letelier, Alejandra; Bell, Thomas; Barraclough, Timothy G

    2015-09-22

    Species interactions can play a major role in shaping evolution in new environments. In theory, species interactions can either stimulate evolution by promoting coevolution or inhibit evolution by constraining ecological opportunity. The relative strength of these effects should vary as species richness increases, and yet there has been little evidence for evolution of component species in communities. We evolved bacterial microcosms containing between 1 and 12 species in three different environments. Growth rates and yields of isolates that evolved in communities were lower than those that evolved in monocultures, consistent with recent theory that competition constrains species to specialize on narrower sets of resources. This effect saturated or reversed at higher levels of richness, consistent with theory that directional effects of species interactions should weaken in more diverse communities. Species varied considerably, however, in their responses to both environment and richness levels. Mechanistic models and experiments are now needed to understand and predict joint evolutionary dynamics of species in diverse communities.

  9. The relationship between satellite-derived indices and species diversity across African savanna ecosystems

    NASA Astrophysics Data System (ADS)

    Mapfumo, Ratidzo B.; Murwira, Amon; Masocha, Mhosisi; Andriani, R.

    2016-10-01

    The ability to use remotely sensed diversity is important for the management of ecosystems at large spatial extents. However, to achieve this, there is still need to develop robust methods and approaches that enable large-scale mapping of species diversity. In this study, we tested the relationship between species diversity measured in situ with the Normalized Difference Vegetation Index (NDVI) and the Coefficient of Variation in the NDVI (CVNDVI) derived from high and medium spatial resolution satellite data at dry, wet and coastal savanna woodlands. We further tested the effect of logging on NDVI along the transects and between transects as disturbance may be a mechanism driving the patterns observed. Overall, the results of this study suggest that high tree species diversity is associated with low and high NDVI and at intermediate levels is associated with low tree species diversity and NDVI. High tree species diversity is associated with high CVNDVI and vice versa and at intermediate levels is associated with high tree species diversity and CVNDVI.

  10. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    PubMed

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity.

  11. A spider species complex revealed high cryptic diversity in South China caves.

    PubMed

    Zhang, Yuanyuan; Li, Shuqiang

    2014-10-01

    Cryptic species, which are an important component of biodiversity, have rarely been studied in South China karst. We investigated cryptic diversity in the cave species complex Telema cucurbitina, which has a narrow niche but widespread distribution among multiple caves. We sampled another 15 populations (caves) in addition to the population from the type locality. Phylogenetic results indicated that individuals from the same cave constituted well-supported clades. Species diversity within this species complex was assessed in a coalescent framework, first with a Bayesian extension of the general mixed Yule coalescent (bGMYC) model and a Bayesian species delimitation method (BPP). Both species delimitation methods identified each cave population as a separate species. We propose that each cave population within this species complex was a separate evolving lineage and therefore 16 OTUs were recovered based on our molecular data despite their high morphological similarities. We also propose that the unrecognized organism's diversity within South China caves might be extremely large considering our case. Furthermore, our work reveals that species discovery of cave organisms by morphological data has a high probability of underestimating hidden diversity. Our work also highlights the need for conservation strategies to protect this largely neglected diversity of cave organisms.

  12. Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

    PubMed

    Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

    2016-04-30

    Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures.

  13. Phylogenetic diversity of plants alters the effect of species richness on invertebrate herbivory.

    PubMed

    Dinnage, Russell

    2013-01-01

    Long-standing ecological theory proposes that diverse communities of plants should experience a decrease in herbivory. Yet previous empirical examinations of this hypothesis have revealed that plant species richness increases herbivory in just as many systems as it decreases it. In this study, I ask whether more insight into the role of plant diversity in promoting or suppressing herbivory can be gained by incorporating information about the evolutionary history of species in a community. In an old field system in southern Ontario, I surveyed communities of plants and measured levels of leaf damage on 27 species in 38 plots. I calculated a measure of phylogenetic diversity (PSE) that encapsulates information about the amount of evolutionary history represented in each of the plots and looked for a relationship between levels of herbivory and both species richness and phylogenetic diversity using a generalized linear mixed model (GLMM) that could account for variation in herbivory levels between species. I found that species richness was positively associated with herbivore damage at the plot-level, in keeping with the results from several other recent studies on this question. On the other hand, phylogenetic diversity was associated with decreased herbivory. Importantly, there was also an interaction between species richness and phylogenetic diversity, such that plots with the highest levels of herbivory were plots which had many species but only if those species tended to be closely related to one another. I propose that these results are the consequence of interactions with herbivores whose diets are phylogenetically specialized (for which I introduce the term cladophage), and how phylogenetic diversity may alter their realized host ranges. These results suggest that incorporating a phylogenetic perspective can add valuable additional insight into the role of plant diversity in explaining or predicting levels of herbivory at a whole-community scale.

  14. Historical factors shaped species diversity and composition of Salix in eastern Asia

    NASA Astrophysics Data System (ADS)

    Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

    2017-02-01

    Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species.

  15. Historical factors shaped species diversity and composition of Salix in eastern Asia.

    PubMed

    Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

    2017-02-08

    Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species.

  16. Historical factors shaped species diversity and composition of Salix in eastern Asia

    PubMed Central

    Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

    2017-01-01

    Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species. PMID:28176816

  17. Temporal latitudinal-gradient dynamics and tropical instability of deep-sea species diversity

    USGS Publications Warehouse

    Yasuhara, Moriaki; Hunt, G.; Cronin, T. M.; Okahashi, H.

    2009-01-01

    A benthic microfaunal record from the equatorial Atlantic Ocean over the past four glacial-interglacial cycles was investigated to understand temporal dynamics of deep-sea latitudinal species diversity gradients (LSDGs). The results demonstrate unexpected instability and high amplitude fluctuations of species diversity in the tropical deep ocean that are correlated with orbital-scale oscillations in global climate: Species diversity is low during glacial and high during interglacial periods. This implies that climate severely influences deep-sea diversity, even at tropical latitudes, and that deep-sea LSDGs, while generally present for the last 36 million years, were weakened or absent during glacial periods. Temporally dynamic LSDGs and unstable tropical diversity require reconsideration of current ecological hypotheses about the generation and maintenance of biodiversity as they apply to the deep sea, and underscore the potential vulnerability and conservation importance of tropical deep-sea ecosystems.

  18. Species-specific mercury bioaccumulation in a diverse fish community.

    PubMed

    Donald, David B; Wissel, Björn; Anas, M U Mohamed

    2015-12-01

    Mercury bioaccumulation models developed for fish provide insight into the sources and transfer of Hg within ecosystems. Mercury concentrations were assessed for 16 fish species of the western reach of Lake Diefenbaker, Saskatchewan, Canada. For top predators (northern pike, Esox Lucius; walleye, Sander vitreum), Hg concentrations were positively correlated to δ(15)N, and δ(15)N to fish age, suggesting that throughout life these fish fed on organisms with increasingly higher trophic values and Hg concentrations. However, fish mass and/or age were the principal parameters related to Hg concentrations for most species. For 9 common species combined, individual variation in Hg concentration was explained in declining order of importance by fish mass, trophic position (δ(15)N), and fish age. Delta (15)N value was not the leading variable related to Hg concentration for the assemblage, probably because of the longevity of lower--trophic-level species (3 species ≥ 20 yr), substantial overlap in Hg concentration and δ(15)N values for large-bodied fish up to 3000 g, and complex relationships between Hg concentration and δ(15)N among species. These results suggest that the quantity of food (and Hg) consumed each year and converted to fish mass, the quantity of Hg bioaccumulated over years and decades, and trophic position were significant determinants of Hg concentration in Lake Diefenbaker fish.

  19. Plot shape effects on plant species diversity measurements

    USGS Publications Warehouse

    Keeley, Jon E.; Fotheringham, C.J.

    2005-01-01

    Abstract. Question: Do rectangular sample plots record more plant species than square plots as suggested by both empirical and theoretical studies?Location: Grasslands, shrublands and forests in the Mediterranean-climate region of California, USA.Methods: We compared three 0.1-ha sampling designs that differed in the shape and dispersion of 1-m2 and 100-m2 nested subplots. We duplicated an earlier study that compared the Whittaker sample design, which had square clustered subplots, with the modified Whittaker design, which had dispersed rectangular subplots. To sort out effects of dispersion from shape we used a third design that overlaid square subplots on the modified Whittaker design. Also, using data from published studies we extracted species richness values for 400-m2 subplots that were either square or 1:4 rectangles partially overlaid on each other from desert scrub in high and low rainfall years, chaparral, sage scrub, oak savanna and coniferous forests with and without fire.Results: We found that earlier empirical reports of more than 30% greater richness with rectangles were due to the confusion of shape effects with spatial effects, coupled with the use of cumulative number of species as the metric for comparison. Average species richness was not significantly different between square and 1:4 rectangular sample plots at either 1- or 100-m2. Pairwise comparisons showed no significant difference between square and rectangular samples in all but one vegetation type, and that one exhibited significantly greater richness with squares. Our three intensive study sites appear to exhibit some level of self-similarity at the scale of 400 m2, but, contrary to theoretical expectations, we could not detect plot shape effects on species richness at this scale.Conclusions: At the 0.1-ha scale or lower there is no evidence that plot shape has predictable effects on number of species recorded from sample plots. We hypothesize that for the mediterranean

  20. Parametric scaling from species to growth-form diversity: an interesting analogy with multifractal functions.

    PubMed

    Ricotta, Carlo; Pacini, Alessandra; Avena, Giancarlo

    2002-01-01

    We propose a measure of divergence from species to life-form diversity aimed at summarizing the ecological similarity among different plant communities without losing information on traditional taxonomic diversity. First, species and life-form relative abundances within a given plant community are determined. Next, using Rényi's generalized entropy, the diversity profiles of the analyzed community are computed both from species and life-form relative abundances. Finally, the speed of decrease from species to life-form diversity is obtained by combining the outcome of both profiles. Interestingly, the proposed measure shows some formal analogies with multifractal functions developed in statistical physics for the analysis of spatial patterns. As an application for demonstration, a small data set from a plant community sampled in the archaeological site of Paestum (southern Italy) is used.

  1. [Species diversity of bryophytes in West Tianmu Mountain of Zhejiang Province].

    PubMed

    Li, Fenxia; Wang, Youfang; Liu, Li; Yang, Shuzhen

    2006-02-01

    In this paper, an investigation was made on the bryophytes at different altitudes of West Tianmu Mountain, with their species composition, similarity, and alpha- and beta-diversities. The results showed that at altitude 1100 m, the bryophytes under deciduous broad-leaved forest had the highest species number and richness, and the highest similarity with the bryophytes under deciduous broad-leaved shrub at 1300 m. The beta diversity index at altitude 800-1100 m was the largest, suggesting an obvious change and alternation of bryophyte species there. At altitude 1100 m, the species diversity of bryophytes was the highest, where should be the key area for bryophyte diversity conservation in West Tianmu Mountain.

  2. [Butterfly species diversity and its conservation in Wuyunjie National Nature Reserve, Hunan Province of China].

    PubMed

    Li, Mi; Zhou, Hong-Chun; Tan, Ji-Cai; Wang, Peng; Liu, Guo-Hua

    2011-06-01

    By using line-transect method, an investigation was conducted on the species diversity of butterfly in Wuyunjie National Nature Reserve, Changde City of Hunan Province from June 2008 to September 2010. Aiming at the main factors including plant species richness (D) , mean elevation (E) , average distance from stream/river (F), and human interference level (K) that affecting the species richness of butterfly in 31 segment-level transects in 4 line-transects, multiple regression analysis was made, and the diversity and similarity of the butterfly communities in the experimental zone, buffer zone, and core zone of the Reserve were compared. A total of 147 butterfly species were collected, belonging to 94 genera and 10 families, among which, 4 species was nationally conserved species. Multiple regression analysis showed that D, E, and K were the three most major factors affecting the distribution of butterfly. The species richness of butterfly had significant positive correlation with D (P < 0.01), and negative correlations with E and K (P < 0.05). The species diversity and evenness index of butterfly were higher in core zone than in experimental zone and buffer zone, dominance index was the highest in experimental zone, and a higher similarity index (0.526) was observed between buffer zone and core zone. To conserve the species diversity of butterfly in the Reserve, efforts should be made to protect the plant species richness, keep the natural forest succession, decrease the human interference properly, and tighten up the management of butterfly habitat.

  3. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages

    PubMed Central

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-01-01

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth (Lepidoptera: Geometridae) assemblages in the mature temperate forest on Changbai Mountain. A total of 9285 geometrid moths representing 131 species were collected, with many species displaying wide elevational distribution ranges. Moth α-diversity decreased monotonously, while the standardized effect size of mean pairwise phylogenetic distances (MPD) and phylogenetic diversity (PD) increased significantly with increasing elevation. At high elevations, the insect assemblages consisted largely of habitat generalists that were individually more phylogenetically distinct from co-occurring species than species in assemblages at lower altitudes. This could hint at higher speciation rates in more favourable low-elevation environments generating a species-rich geometrid assemblage, while exclusion of phylogenetically closely related species becomes increasingly important in shaping moth assemblages at higher elevations. Overall, it appears likely that high-elevation temperate moth assemblages are strongly resilient to environmental change, and that they contain a much larger proportion of the genetic diversity encountered at low-elevation assemblages in comparison to tropical geometrid communities. PMID:26979402

  4. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages

    NASA Astrophysics Data System (ADS)

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-03-01

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth (Lepidoptera: Geometridae) assemblages in the mature temperate forest on Changbai Mountain. A total of 9285 geometrid moths representing 131 species were collected, with many species displaying wide elevational distribution ranges. Moth α-diversity decreased monotonously, while the standardized effect size of mean pairwise phylogenetic distances (MPD) and phylogenetic diversity (PD) increased significantly with increasing elevation. At high elevations, the insect assemblages consisted largely of habitat generalists that were individually more phylogenetically distinct from co-occurring species than species in assemblages at lower altitudes. This could hint at higher speciation rates in more favourable low-elevation environments generating a species-rich geometrid assemblage, while exclusion of phylogenetically closely related species becomes increasingly important in shaping moth assemblages at higher elevations. Overall, it appears likely that high-elevation temperate moth assemblages are strongly resilient to environmental change, and that they contain a much larger proportion of the genetic diversity encountered at low-elevation assemblages in comparison to tropical geometrid communities.

  5. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages.

    PubMed

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-03-16

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth (Lepidoptera: Geometridae) assemblages in the mature temperate forest on Changbai Mountain. A total of 9285 geometrid moths representing 131 species were collected, with many species displaying wide elevational distribution ranges. Moth α-diversity decreased monotonously, while the standardized effect size of mean pairwise phylogenetic distances (MPD) and phylogenetic diversity (PD) increased significantly with increasing elevation. At high elevations, the insect assemblages consisted largely of habitat generalists that were individually more phylogenetically distinct from co-occurring species than species in assemblages at lower altitudes. This could hint at higher speciation rates in more favourable low-elevation environments generating a species-rich geometrid assemblage, while exclusion of phylogenetically closely related species becomes increasingly important in shaping moth assemblages at higher elevations. Overall, it appears likely that high-elevation temperate moth assemblages are strongly resilient to environmental change, and that they contain a much larger proportion of the genetic diversity encountered at low-elevation assemblages in comparison to tropical geometrid communities.

  6. Species diversity in the Antrodia crassa group (Polyporales, Basidiomycota).

    PubMed

    Spirin, Viacheslav; Runnel, Kadri; Vlasák, Josef; Miettinen, Otto; Põldmaa, Kadri

    2015-12-01

    Antrodia is a polyphyletic genus, comprising brown-rot polypores with annual or short-lived perennial resupinate, dimitic basidiocarps. Here we focus on species that are closely related to Antrodia crassa, and investigate their phylogeny and species delimitation using geographic, ecological, morphological and molecular data (ITS and LSU rDNA, tef1). Phylogenetic analyses distinguished four clades within the monophyletic group of eleven conifer-inhabiting species (five described herein): (1)A. crassa s. str. (boreal Eurasia), Antrodia cincta sp. nova (North America) and Antrodia cretacea sp. nova (holarctic), all three being characterized by inamyloid skeletal hyphae that dissolve quickly in KOH solution; (2) Antrodia ignobilis sp. nova, Antrodia sitchensis and Antrodia sordida from North America, and Antrodia piceata sp. nova (previously considered conspecific with A. sitchensis) from Eurasia, possessing amyloid skeletal hyphae; (3) Antrodia ladiana sp. nova from the southern part of the USA, Antrodia pinea from East Asia, and Antrodia ferox - so far known from subtropical North America, but here reported also from Eurasia. These three species have inamyloid hyphae and narrow basidiospores; (4) the North American Antrodia pini-cubensis, sharing similar morphological characters with A. pinea, forming a separate clade. The habitat data indicate that several species are threatened by intensive forestry.

  7. Diversity of small RNAs expressed in Pseudomonas species.

    PubMed

    Gómez-Lozano, María; Marvig, Rasmus L; Molina-Santiago, Carlos; Tribelli, Paula M; Ramos, Juan-Luis; Molin, Søren

    2015-04-01

    RNA sequencing (RNA-seq) has revealed several hundreds of previously undetected small RNAs (sRNAs) in all bacterial species investigated, including strains of Pseudomonas aeruginosa, Pseudomonas putida and Pseudomonas syringae. Nonetheless, only little is known about the extent of conservation of expressed sRNAs across strains and species. In this study, we have used RNA-seq to identify sRNAs in P. putida DOT-T1E and Pseudomonas extremaustralis 14-3b. This is the first strain of P. extremaustralis and the second strain of P. putida to have their transcriptomes analysed for sRNAs, and we identify the presence of around 150 novel sRNAs in each strain. Furthermore, we provide a comparison based on sequence conservation of all the sRNAs detected by RNA-seq in the Pseudomonas species investigated so far. Our results show that the extent of sRNA conservation across different species is very limited. In addition, when comparing the sRNAs expressed in different strains of the same species, we observe that numerous sRNAs exhibit a strain-specific expression pattern. These results support the idea that the evolution of most bacterial sRNAs is rapid, which limits the extent of both interspecies and intraspecies conservation.

  8. Diversity of Riparian Plants among and within Species Shapes River Communities

    PubMed Central

    Jackrel, Sara L.; Wootton, J. Timothy

    2015-01-01

    Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to

  9. Diversity of Riparian Plants among and within Species Shapes River Communities.

    PubMed

    Jackrel, Sara L; Wootton, J Timothy

    2015-01-01

    Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to

  10. Diversity and Distribution of Freshwater Amphipod Species in Switzerland (Crustacea: Amphipoda)

    PubMed Central

    Altermatt, Florian; Alther, Roman; Fišer, Cene; Jokela, Jukka; Konec, Marjeta; Küry, Daniel; Mächler, Elvira; Stucki, Pascal; Westram, Anja Marie

    2014-01-01

    Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems. PMID:25354099

  11. Diversity and distribution of freshwater amphipod species in Switzerland (Crustacea: Amphipoda).

    PubMed

    Altermatt, Florian; Alther, Roman; Fišer, Cene; Jokela, Jukka; Konec, Marjeta; Küry, Daniel; Mächler, Elvira; Stucki, Pascal; Westram, Anja Marie

    2014-01-01

    Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems.

  12. Evolving entities: towards a unified framework for understanding diversity at the species and higher levels

    PubMed Central

    Barraclough, Timothy G.

    2010-01-01

    Current approaches to studying the evolution of biodiversity differ in their treatment of species and higher level diversity patterns. Species are regarded as the fundamental evolutionarily significant units of biodiversity, both in theory and in practice, and extensive theory explains how they originate and evolve. However, most species are still delimited using qualitative methods that only relate indirectly to the underlying theory. In contrast, higher level patterns of diversity have been subjected to rigorous quantitative study (using phylogenetics), but theory that adequately explains the observed patterns has been lacking. Most evolutionary analyses of higher level diversity patterns have considered non-equilibrium explanations based on rates of diversification (i.e. exponentially growing clades), rather than equilibrium explanations normally used at the species level and below (i.e. constant population sizes). This paper argues that species level and higher level patterns of diversity can be considered within a common framework, based on equilibrium explanations. It shows how forces normally considered in the context of speciation, namely divergent selection and geographical isolation, can generate evolutionarily significant units of diversity above the level of reproductively isolated species. Prospects for the framework to answer some unresolved questions about higher level diversity patterns are discussed. PMID:20439282

  13. Diversity of Fusarium species and mycotoxins contaminating pineapple.

    PubMed

    Stępień, Łukasz; Koczyk, Grzegorz; Waśkiewicz, Agnieszka

    2013-08-01

    Pineapple (Ananas comosus var. comosus) is an important perennial crop in tropical and subtropical areas. It may be infected by various Fusarium species, contaminating the plant material with mycotoxins. The aim of this study was to evaluate Fusarium species variability among the genotypes isolated from pineapple fruits displaying fungal infection symptoms and to evaluate their mycotoxigenic abilities. Forty-four isolates of ten Fusarium species were obtained from pineapple fruit samples: F. ananatum, F. concentricum, F. fujikuroi, F. guttiforme, F. incarnatum, F. oxysporum, F. polyphialidicum, F. proliferatum, F. temperatum and F. verticillioides. Fumonisins B1-B3, beauvericin (BEA) and moniliformin (MON) contents were quantified by high-performance liquid chromatography (HPLC) in pineapple fruit tissue. Fumonisins are likely the most dangerous metabolites present in fruit samples (the maximum FB1 content was 250 μg g(-1) in pineapple skin and 20 μg ml(-1) in juice fraction). In both fractions, BEA and MON were of minor significance. FUM1 and FUM8 genes were identified in F. fujikuroi, F. proliferatum, F. temperatum and F. verticillioides. Cyclic peptide synthase gene (esyn1 homologue) from the BEA biosynthetic pathway was identified in 40 isolates of eight species. Based on the gene-specific polymerase chain reaction (PCR) assays, none of the isolates tested were found to be able to produce trichothecenes or zearalenone.

  14. Croatian mayflies (Insecta, Ephemeroptera): species diversity and distribution patterns

    PubMed Central

    Vilenica, Marina; Gattolliat, Jean-Luc; Mihaljević, Zlatko; Sartori, Michel

    2015-01-01

    Abstract Knowledge of the mayfly biodiversity in the Balkan Peninsula is still far from complete. Compared to the neighbouring countries, the mayfly fauna in Croatia is very poorly known. Situated at the crossroads of central and Mediterranean Europe and the Balkan Peninsula, Croatia is divided into two ecoregions: Dinaric western Balkan and Pannonian lowland. Mayflies were sampled between 2003 and 2013 at 171 sites, and a total of 66 species was recorded. Combined with the literature data, the Croatian mayfly fauna reached a total of 79 taxa. Of these, 29 species were recorded for the first time in Croatia while 15 species were not previously recorded in Dinaric western Balkan ecoregion. Based on the mayfly assemblage, sampling sites were first structured by ecoregion and then by habitat type. In comparison with the surrounding countries, the Croatian mayfly fauna is the most similar to the Hungarian and Bosnian fauna. Some morphologically interesting taxa such as Baetis cf. nubecularis Eaton, 1898 and Rhithrogena from the diaphana group were recorded. Ephemera cf. parnassiana Demoulin, 1958, the species previously recorded only from Greece, was also recorded. PMID:26478701

  15. Genetic diversity and conservation implications of four Cupressus species in China as revealed by microsatellite markers.

    PubMed

    Lu, Xu; Xu, Haiyan; Li, Zhonghu; Shang, Huiying; Adams, Robert P; Mao, Kangshan

    2014-04-01

    Understanding the extent and distribution of genetic diversity is crucial for the conservation and management of endangered species. Cupressus chengiana, C. duclouxiana, C. gigantea, and C. funebris are four ecologically and economically important species in China. We investigated their genetic diversity, population structure, and extant effective population size (35 populations, 484 individuals) employing six pairs of nuclear microsatellite markers (selected from 53). Their genetic diversity is moderate among conifers, and genetic differentiation among populations is much lower in C. gigantea than in the other three species; the estimated effective population size was largest for C. chengiana, at 1.70, 2.91, and 3.91 times the estimates for C. duclouxiana, C. funebris, and C. gigantea, respectively. According to Bayesian clustering analysis, the most plausible population subdivision scheme within species is two groups in C. chengiana, three groups in C. duclouxiana, and a single group for both C. funebris and C. gigantea. We propose a conservation strategy for these cypress species.

  16. Diversity and Activity of Lysobacter Species from Disease Suppressive Soils

    PubMed Central

    Gómez Expósito, Ruth; Postma, Joeke; Raaijmakers, Jos M.; De Bruijn, Irene

    2015-01-01

    The genus Lysobacter includes several species that produce a range of extracellular enzymes and other metabolites with activity against bacteria, fungi, oomycetes, and nematodes. Lysobacter species were found to be more abundant in soil suppressive against the fungal root pathogen Rhizoctonia solani, but their actual role in disease suppression is still unclear. Here, the antifungal and plant growth-promoting activities of 18 Lysobacter strains, including 11 strains from Rhizoctonia-suppressive soils, were studied both in vitro and in vivo. Based on 16S rRNA sequencing, the Lysobacter strains from the Rhizoctonia-suppressive soil belonged to the four species Lysobacter antibioticus, Lysobacter capsici, Lysobacter enzymogenes, and Lysobacter gummosus. Most strains showed strong in vitro activity against R. solani and several other pathogens, including Pythium ultimum, Aspergillus niger, Fusarium oxysporum, and Xanthomonas campestris. When the Lysobacter strains were introduced into soil, however, no significant and consistent suppression of R. solani damping-off disease of sugar beet and cauliflower was observed. Subsequent bioassays further revealed that none of the Lysobacter strains was able to promote growth of sugar beet, cauliflower, onion, and Arabidopsis thaliana, either directly or via volatile compounds. The lack of in vivo activity is most likely attributed to poor colonization of the rhizosphere by the introduced Lysobacter strains. In conclusion, our results demonstrated that Lysobacter species have strong antagonistic activities against a range of pathogens, making them an important source for putative new enzymes and antimicrobial compounds. However, their potential role in R. solani disease suppressive soil could not be confirmed. In-depth omics'–based analyses will be needed to shed more light on the potential contribution of Lysobacter species to the collective activities of microbial consortia in disease suppressive soils. PMID:26635735

  17. Species richness - Energy relationships and dung beetle diversity across an aridity and trophic resource gradient

    NASA Astrophysics Data System (ADS)

    Tshikae, B. Power; Davis, Adrian L. V.; Scholtz, Clarke H.

    2013-05-01

    Understanding factors that drive species richness and turnover across ecological gradients is important for insect conservation planning. To this end, we studied species richness - energy relationships and regional versus local factors that influence dung beetle diversity in game reserves along an aridity and trophic resource gradient in the Botswana Kalahari. Dung beetle species richness, alpha diversity, and abundance declined with increasing aridity from northeast to southwest and differed significantly between dung types (pig, elephant, cattle, sheep) and carrion (chicken livers). Patterns of between-study area species richness on ruminant dung (cattle, sheep) differed to other bait types. Patterns of species richness between bait types in two southwest study areas differed from those in four areas to the northeast. Regional species turnover between study areas was higher than local turnover between bait types. Patterns of southwest to northeast species loss showed greater consistency than northeast to southwest losses from larger assemblages. Towards the southwest, similarity to northeast assemblages declined steeply as beta diversity increased. High beta diversity and low similarity at gradsect extremes resulted from two groups of species assemblages showing either northeast or southwest biogeographical centres. The findings are consistent with the energy hypothesis that indicates insect species richness in lower latitudes is indirectly limited by declining water variables, which drive reduced food resources (lower energy availability) represented, here, by restriction of large mammals dropping large dung types to the northeast and dominance of pellet dropping mammals in the arid southwest Kalahari. The influence of theoretical causal mechanisms is discussed.

  18. Exploring species and site contributions to beta diversity in stream insect assemblages.

    PubMed

    Heino, Jani; Grönroos, Mira

    2017-01-01

    It was recently suggested that beta diversity can be partitioned into contributions of single sites to overall beta diversity (LCBD) or into contributions of individual species to overall beta diversity (SCBD). We explored the relationships of LCBD and SCBD to site and species characteristics, respectively, in stream insect assemblages. We found that LCBD was mostly explained by variation in species richness, with a negative relationship being detected. SCBD was strongly related to various species characteristics, such as occupancy, abundance, niche position and niche breadth, but was only weakly related to biological traits of species. In particular, occupancy and its quadratic terms showed a very strong unimodal relationship with SCBD, suggesting that intermediate species in terms of site occupancy contribute most to beta diversity. Our findings of unravelling the contributions of sites or species to overall beta diversity are of high importance to community ecology, conservation and bioassessment using stream insect assemblages, and may bear some overall generalities to be found in other organism groups.

  19. Legume Diversity Patterns in West Central Africa: Influence of Species Biology on Distribution Models

    PubMed Central

    de la Estrella, Manuel; Mateo, Rubén G.; Wieringa, Jan J.; Mackinder, Barbara; Muñoz, Jesús

    2012-01-01

    Objectives Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning. Methodology Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types. Results/Conclusions Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall

  20. Ranking Mammal Species for Conservation and the Loss of Both Phylogenetic and Trait Diversity

    PubMed Central

    Redding, David W.; Mooers, Arne O.

    2015-01-01

    The 'edge of existence' (EDGE) prioritisation scheme is a new approach to rank species for conservation attention that aims to identify species that are both isolated on the tree of life and at imminent risk of extinction as defined by the World Conservation Union (IUCN). The self-stated benefit of the EDGE system is that it effectively captures unusual 'unique' species, and doing so will preserve the total evolutionary history of a group into the future. Given the EDGE metric was not designed to capture total evolutionary history, we tested this claim. Our analyses show that the total evolutionary history of mammals preserved is indeed much higher if EDGE species are protected than if at-risk species are chosen randomly. More of the total tree is also protected by EDGE species than if solely threat status or solely evolutionary distinctiveness were used for prioritisation. When considering how much trait diversity is captured by IUCN and EDGE prioritisation rankings, interestingly, preserving the highest-ranked EDGE species, or indeed just the most threatened species, captures more total trait diversity compared to sets of randomly-selected at-risk species. These results suggest that, as advertised, EDGE mammal species contribute evolutionary history to the evolutionary tree of mammals non-randomly, and EDGE-style rankings among endangered species can also capture important trait diversity. If this pattern holds for other groups, the EDGE prioritisation scheme has greater potential to be an efficient method to allocate scarce conservation effort. PMID:26630179

  1. DRD4 dopamine receptor allelic diversity in various primate species

    SciTech Connect

    Adamson, M.; Higley, D.; O`Brien, S.

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  2. [On the Features of Embryonic Cleavage in Diverse Fish Species].

    PubMed

    Desnitskiy, A G

    2015-01-01

    Literature on the earliest steps of fish embryogenesis (including a number of "non-model" species) has been considered. The main attention has been paid to the loss of cleavage division synchrony and the first latitudinal cleavage furrow. In teleostean embryos, the features of their meroblastic cleavage are not rigidly associated with egg size. The midblastula transition (in a form clearly enough) occurs in some chondrostean and teleostean fishes, but it has not been detected in the representatives of sarcopterygian and chondrichthyan fishes.

  3. Detection of Helicobacter spp. in the saliva of dogs with gastritis.

    PubMed

    Jankowski, M; Spużak, J; Kubiak, K; Glińska-Suchocka, K; Biernat, M

    2016-01-01

    The aim of this study was to identify the species and determine the prevalence of gastric Helicobacter in the saliva of dogs with gastritis. The study was carried out on 30 dogs of different breeds, genders and ages, which were diagnosed with gastritis. The nested-PCR method was used to detect Helicobacter spp. in saliva. Helicobacter bacteria were found in the saliva samples of 23 (76.6%) dogs. Helicobacter heilmannii was the most commonly detected species of gastric Helicobacter spp. in canine saliva, and was found in 22 (73.3%) cases. The results indicate that gastric Helicobacter spp. occurs relatively frequently in dogs with gastritis. Moreover, the saliva of dogs with gastritis may be a source of Helicobacter spp. infection for humans and other animals. However, further studies are needed to confirm this finding as the PCR method does not distinguish active from inactive infections.

  4. Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A diversity reference set has been constructed for the Gossypium accessions in the U.S. National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers were used to study the alleli...

  5. Functional-diversity indices can be driven by methodological choices and species richness.

    PubMed

    Poos, Mark S; Walker, Steven C; Jackson, Donald A

    2009-02-01

    Functional diversity is an important concept in community ecology because it captures information on functional traits absent in measures of species diversity. One popular method of measuring functional diversity is the dendrogram-based method, FD. To calculate FD, a variety of methodological choices are required, and it has been debated about whether biological conclusions are sensitive to such choices. We studied the probability that conclusions regarding FD were sensitive, and that patterns in sensitivity were related to alpha and beta components of species richness. We developed a randomization procedure that iteratively calculated FD by assigning species into two assemblages and calculating the probability that the community with higher FD varied across methods. We found evidence of sensitivity in all five communities we examined, ranging from a probability of sensitivity of 0 (no sensitivity) to 0.976 (almost completely sensitive). Variations in these probabilities were driven by differences in alpha diversity between assemblages and not by beta diversity. Importantly, FD was most sensitive when it was most useful (i.e., when differences in alpha diversity were low). We demonstrate that trends in functional-diversity analyses can be largely driven by methodological choices or species richness, rather than functional trait information alone.

  6. Alterations of phytoplankton assemblages treated with chlorinated hydrocarbons: effects of dominant species sensitivity and initial diversity.

    PubMed

    Bácsi, István; Gonda, Sándor; B-Béres, Viktória; Novák, Zoltán; Nagy, Sándor Alex; Vasas, Gábor

    2015-05-01

    Changes in composition of phytoplankton assemblages due to short-chained chlorinated hydrocarbons (tetrachloroethane, tetrachloroethylene and trichloroethylene) were studied in microcosm experiments with different initial diversities. Diversity decreased further during treatments in the less diverse 2011 summer assemblages, dominated by the euglenid Trachelomonas volvocinopsis (its relative abundance was nearly 70 %). Diversity did not change significantly during treatments in the more diverse 2012 summer assemblages, dominated by cryptomonads (their relative abundance was 40 %). The dominant Trachelomonas volvocinopsis in 2011, due to its insensitivity to the treatment and presumably high competition skills, filled released habitats occurring when sensitive species were not detectable any more. In contrast, cryptomonads were extremely sensitive to the treatments, their abundance decreased under detection limit in the treated assemblages, regardless of diversity conditions. Our results showed that population dynamics of dominant species determine the response to the contamination of the entire community, if these species display high resistance or resilience. If the dominant species was highly sensitive and recovered slowly, compensatory growth of rare species maintained high levels of ecosystem performance.

  7. Effects of Fishing and Regional Species Pool on the Functional Diversity of Fish Communities

    PubMed Central

    Martins, Gustavo M.; Arenas, Francisco; Neto, Ana I.; Jenkins, Stuart R.

    2012-01-01

    The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities’ functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities’ functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning. PMID:22952950

  8. Effects of fishing and regional species pool on the functional diversity of fish communities.

    PubMed

    Martins, Gustavo M; Arenas, Francisco; Neto, Ana I; Jenkins, Stuart R

    2012-01-01

    The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities' functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities' functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning.

  9. Linking environmental drivers with amphibian species diversity in ponds from subtropical grasslands.

    PubMed

    Gonçalves, Darlene S; Crivellari, Lucas B; Conte, Carlos Eduardo

    2015-09-01

    Amphibian distribution patterns are known to be influenced by habitat diversity at breeding sites. Thus, breeding sites variability and how such variability influences anuran diversity is important. Here, we examine which characteristics at breeding sites are most influential on anuran diversity in grasslands associated with Araucaria forest, southern Brazil, especially in places at risk due to anthropic activities. We evaluate the associations between habitat heterogeneity and anuran species diversity in nine body of water from September 2008 to March 2010, in 12 field campaigns in which 16 species of anurans were found. Of the seven habitat descriptors we examined, water depth, pond surface area and distance to the nearest forest fragment explained 81% of total species diversity. Water depth, margin vegetation type, surface area and distance to the next body of water explained between 31-74% of the variance in abundance of nine of the 16 species. Thus, maintenance of body of water, of the vegetation along the water edge and natural forest fragments in the grasslands, along with fire control (used to renovation of pasture), are fundamentally important for the maintenance of anuran species diversity through the conservation of their breeding sites.

  10. Helicobacter pylori.

    PubMed Central

    Dunn, B E; Cohen, H; Blaser, M J

    1997-01-01

    Helicobacter pylori is a gram-negative bacterium which causes chronic gastritis and plays important roles in peptic ulcer disease, gastric carcinoma, and gastric lymphoma. H. pylori has been found in the stomachs of humans in all parts of the world. In developing countries, 70 to 90% of the population carries H. pylori. In developed countries, the prevalence of infection is lower. There appears to be no substantial reservoir of H. pylori aside from the human stomach. Transmission can occur by iatrogenic, fecal-oral, and oral-oral routes. H. pylori is able to colonize and persist in a unique biological niche within the gastric lumen. All fresh isolates of H. pylori express significant urease activity, which appears essential to the survival and pathogenesis of the bacterium. A variety of tests to diagnose H. pylori infection are now available. Histological examination of gastric tissue, culture, rapid urease testing, DNA probes, and PCR analysis, when used to test gastric tissue, all require endoscopy. In contrast, breath tests, serology, gastric juice PCR, and urinary excretion of [15N]ammonia are noninvasive tests that do not require endoscopy. In this review, we highlight advances in the detection of the presence of the organism and methods of differentiating among types of H. pylori, and we provide a background for appropriate chemotherapy of the infection. PMID:9336670

  11. Species diversity and environmental determinants of aquatic and terrestrial communities invaded by Alternanthera philoxeroides.

    PubMed

    Wu, Hao; Carrillo, Juli; Ding, Jianqing

    2017-03-01

    The impact of invasive species on native biodiversity varies across environments, with invasion effects of amphibious plant species across terrestrial and aquatic systems especially poorly understood. In this study, we established 29 terrestrial plots and 23 aquatic plots which were invaded by the alien plant alligator weed, Alternanthera philoxeroides in Southern China. We measured α-species diversity (Shannon-Wiener and Simpson index), species richness and evenness, species cover and the importance value (a comprehensive index of cover, height and abundance) of A. philoxeroides in invaded communities in both aquatic and terrestrial habitats. We recorded seven environmental factors (longitude, latitude, elevation above sea level, temperature, precipitation, ammonia and nitrate) across habitats. We then used Redundancy Analysis (RDA) to determine which factors best explain A. philoxeroides invasion in either environment type. We found that terrestrial habitats had greater species diversity (Shannon index) than aquatic habitats, and the biotic resistance of aquatic plant communities to the A. philoxeroides invasion was weaker than terrestrial plant communities. Accumulated ammonia improved some indices of species diversity (Shannon-Weiner, Simpson) and evenness, but decreased species cover of A. philoxeroides in both aquatic and terrestrial environments. Precipitation increased species richness in terrestrial habitats but decreased richness in aquatic habitats. Precipitation increased A. philoxeroides cover in both environment types, while elevated nitrate increased A. philoxeroides cover in terrestrial habitats only. In aquatic habitats, species richness increased but A. philoxeroides cover decreased with increasing longitude. Our study indicates that increased precipitation may accelerate A. philoxeroides spread across aquatic and terrestrial habitats, while reducing nitrate inputs could inhibit terrestrial A. philoxeroides invasion. Aquatic communities appear to

  12. Crop Species Diversity Changes in the United States: 1978–2012

    PubMed Central

    Aguilar, Jonathan; Gramig, Greta G.; Hendrickson, John R.; Archer, David W.; Forcella, Frank; Liebig, Mark A.

    2015-01-01

    Anecdotal accounts regarding reduced US cropping system diversity have raised concerns about negative impacts of increasingly homogeneous cropping systems. However, formal analyses to document such changes are lacking. Using US Agriculture Census data, which are collected every five years, we quantified crop species diversity from 1978 to 2012, for the contiguous US on a county level basis. We used Shannon diversity indices expressed as effective number of crop species (ENCS) to quantify crop diversity. We then evaluated changes in county-level crop diversity both nationally and for each of the eight Farm Resource Regions developed by the National Agriculture Statistics Service. During the 34 years we considered in our analyses, both national and regional ENCS changed. Nationally, crop diversity was lower in 2012 than in 1978. However, our analyses also revealed interesting trends between and within different Resource Regions. Overall, the Heartland Resource Region had the lowest crop diversity whereas the Fruitful Rim and Northern Crescent had the highest. In contrast to the other Resource Regions, the Mississippi Portal had significantly higher crop diversity in 2012 than in 1978. Also, within regions there were differences between counties in crop diversity. Spatial autocorrelation revealed clustering of low and high ENCS and this trend became stronger over time. These results show that, nationally counties have been clustering into areas of either low diversity or high diversity. Moreover, a significant trend of more counties shifting to lower rather than to higher crop diversity was detected. The clustering and shifting demonstrates a trend toward crop diversity loss and attendant homogenization of agricultural production systems, which could have far-reaching consequences for provision of ecosystem system services associated with agricultural systems as well as food system sustainability. PMID:26308552

  13. Plant Species Diversity and Distribution in Pastures of the Northeastern USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grazed pastures in the northeastern United contain far more than planted forage species. These species may contribute to forage production, but they may also detract from forage production or palatability. As the first step toward identifying the role of plant diversity in forage systems, we collect...

  14. Habitat Heterogeneity Affects Plant and Arthropod Species Diversity and Turnover in Traditional Cornfields.

    PubMed

    Martínez, Eliana; Rös, Matthias; Bonilla, María Argenis; Dirzo, Rodolfo

    2015-01-01

    The expansion of the agricultural frontier by the clearing of remnant forests has led to human-dominated landscape mosaics. Previous studies have evaluated the effect of these landscape mosaics on arthropod diversity at local spatial scales in temperate and tropical regions, but little is known about fragmentation effects in crop systems, such as the complex tropical traditional crop systems that maintain a high diversity of weeds and arthropods in low-Andean regions. To understand the factors that influence patterns of diversity in human-dominated landscapes, we investigate the effect of land use types on plant and arthropod diversity in traditionally managed cornfields, via surveys of plants and arthropods in twelve traditional cornfields in the Colombian Andes. We estimated alpha and beta diversity to analyze changes in diversity related to land uses within a radius of 100 m to 1 km around each cornfield. We observed that forests influenced alpha diversity of plants, but not of arthropods. Agricultural lands had a positive relationship with plants and herbivores, but a negative relationship with predators. Pastures positively influenced the diversity of plants and arthropods. In addition, forest cover seemed to influence changes in plant species composition and species turnover of herbivore communities among cornfields. The dominant plant species varied among fields, resulting in high differentiation of plant communities. Predator communities also exhibited high turnover among cornfields, but differences in composition arose mainly among rare species. The crop system evaluated in this study represents a widespread situation in the tropics, therefore, our results can be of broad significance. Our findings suggest that traditional agriculture may not homogenize biological communities, but instead could maintain the regional pool of species through high beta diversity.

  15. Habitat Heterogeneity Affects Plant and Arthropod Species Diversity and Turnover in Traditional Cornfields

    PubMed Central

    Martínez, Eliana; Rös, Matthias; Bonilla, María Argenis; Dirzo, Rodolfo

    2015-01-01

    The expansion of the agricultural frontier by the clearing of remnant forests has led to human-dominated landscape mosaics. Previous studies have evaluated the effect of these landscape mosaics on arthropod diversity at local spatial scales in temperate and tropical regions, but little is known about fragmentation effects in crop systems, such as the complex tropical traditional crop systems that maintain a high diversity of weeds and arthropods in low-Andean regions. To understand the factors that influence patterns of diversity in human-dominated landscapes, we investigate the effect of land use types on plant and arthropod diversity in traditionally managed cornfields, via surveys of plants and arthropods in twelve traditional cornfields in the Colombian Andes. We estimated alpha and beta diversity to analyze changes in diversity related to land uses within a radius of 100 m to 1 km around each cornfield. We observed that forests influenced alpha diversity of plants, but not of arthropods. Agricultural lands had a positive relationship with plants and herbivores, but a negative relationship with predators. Pastures positively influenced the diversity of plants and arthropods. In addition, forest cover seemed to influence changes in plant species composition and species turnover of herbivore communities among cornfields. The dominant plant species varied among fields, resulting in high differentiation of plant communities. Predator communities also exhibited high turnover among cornfields, but differences in composition arose mainly among rare species. The crop system evaluated in this study represents a widespread situation in the tropics, therefore, our results can be of broad significance. Our findings suggest that traditional agriculture may not homogenize biological communities, but instead could maintain the regional pool of species through high beta diversity. PMID:26197473

  16. Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy

    PubMed Central

    Baldeck, Claire A.; Asner, Gregory P.; Martin, Robin E.; Anderson, Christopher B.; Knapp, David E.; Kellner, James R.; Wright, S. Joseph

    2015-01-01

    Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods—binary support vector machine (SVM) and biased SVM—for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer’s accuracies of 94–97% for the three focal species, and field validation of the predicted crown objects indicated that these had user’s accuracies of 94–100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems. PMID:26153693

  17. Difficulties with estimating and interpreting species pools and the implcations for understanding patterns of diversity

    USGS Publications Warehouse

    Grace, J.B.

    2001-01-01

    Evidence has been accumulating that species pools play a major role in regulating variations in small-scale diversity. However, our ability to unambiguously estimate and interpret species pools remains a major impediment to understanding the processes that control patterns of diversity. Two main approaches have been employed to evaluate the relationships between species pools and species diversity. The direct approach has been to estimate the actual sizes of species pools by sampling discrete areas at larger spatial scales and then relating these estimates to samples taken at smaller scales. The indirect approach has been to search for correlations between abiotic environmental factors and patterns of diversity that are indicative of gradients in species pools. Both of these approaches have substantial predictive capability but also have limitations that impair our ability to draw unambiguous interpretations about causal factors. A primary difficulty for the direct approach is in deciding which species in the larger pool of potential species are actually capable of living in a sample. In this regard, the indirect approach requires fewer assumptions and has the ability to detect previously unsuspected gradients in species pools. As with the direct approach, assessing the causes for observed gradients in species pools remains a limitation for the indirect approach. Consideration of experimental studies of potential niches suggests that it may be valuable to distinguish between potential and observed species pools if the role of competitive exclusion is to be fully assessed. This paper concludes by arguing for (1) an increased use of multivariate studies that examine the effects of species pools indirectly and (2) further experimental studies designed to determine potential species pools.

  18. Soil fertility increases with plant species diversity in a long-term biodiversity experiment.

    PubMed

    Dybzinski, Ray; Fargione, Joseph E; Zak, Donald R; Fornara, Dario; Tilman, David

    2008-11-01

    Most explanations for the positive effect of plant species diversity on productivity have focused on the efficiency of resource use, implicitly assuming that resource supply is constant. To test this assumption, we grew seedlings of Echinacea purpurea in soil collected beneath 10-year-old, experimental plant communities containing one, two, four, eight, or 16 native grassland species. The results of this greenhouse bioassay challenge the assumption of constant resource supply; we found that bioassay seedlings grown in soil collected from experimental communities containing 16 plant species produced 70% more biomass than seedlings grown in soil collected beneath monocultures. This increase was likely attributable to greater soil N availability, which had increased in higher diversity communities over the 10-year-duration of the experiment. In a distinction akin to the selection/complementarity partition commonly made in studies of diversity and productivity, we further determined whether the additive effects of functional groups or the interactive effects of functional groups explained the increase in fertility with diversity. The increase in bioassay seedling biomass with diversity was largely explained by a concomitant increase in N-fixer, C4 grass, forb, and C3 grass biomass with diversity, suggesting that the additive effects of these four functional groups at higher diversity contributed to enhance N availability and retention. Nevertheless, diversity still explained a significant amount of the residual variation in bioassay seedling biomass after functional group biomass was included in a multiple regression, suggesting that interactions also increased fertility in diverse communities. Our results suggest a mechanism, the fertility effect, by which increased plant species diversity may increase community productivity over time by increasing the supply of nutrients via both greater inputs and greater retention.

  19. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota.

    PubMed

    Ellegaard, Kirsten M; Engel, Philipp

    2016-01-01

    Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.

  20. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

    PubMed Central

    Ellegaard, Kirsten M.; Engel, Philipp

    2016-01-01

    Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

  1. Vegetation in Bangalore's Slums: Composition, Species Distribution, Density, Diversity, and History

    NASA Astrophysics Data System (ADS)

    Gopal, Divya; Nagendra, Harini; Manthey, Michael

    2015-06-01

    There is widespread acknowledgement of the need for biodiversity and greening to be part of urban sustainability efforts. Yet we know little about greenery in the context of urban poverty, particularly in slums, which constitute a significant challenge for inclusive development in many rapidly growing cities. We assessed the composition, density, diversity, and species distribution of vegetation in 44 slums of Bangalore, India, comparing these to published studies on vegetation diversity in other land-use categories. Most trees were native to the region, as compared to other land-use categories such as parks and streets which are dominated by introduced species. Of the most frequently encountered tree species, Moringa oleifera and Cocos nucifera are important for food, while Ficus religiosa plays a critical cultural and religious role. Tree density and diversity were much lower in slums compared to richer residential neighborhoods. There are also differences in species preferences, with most plant (herb, shrub and vines) species in slums having economic, food, medicinal, or cultural use, while the species planted in richer residential areas are largely ornamental. Historic development has had an impact on species distribution, with older slums having larger sized tree species, while recent slums were dominated by smaller sized tree species with greater economic and food use. Extensive focus on planting trees and plant species with utility value is required in these congested neighborhoods, to provide livelihood support.

  2. Declining diversity in abandoned grasslands of the carpathian mountains: do dominant species matter?

    PubMed

    Csergő, Anna Mária; Demeter, László; Turkington, Roy

    2013-01-01

    Traditional haymaking has created exceptionally high levels of plant species diversity in semi-natural grasslands of the Carpathian Mountains (Romania), the maintenance of which is jeopardized by recent abandonment and subsequent vegetation succession. We tested the hypothesis that the different life history strategies of dominant grasses cause different patterns of diversity loss after abandonment of traditional haymaking in two types of meadow. Although diversity loss rate was not significantly different, the mechanism of loss depended on the life history of dominant species. In meadows co-dominated by competitive stress-tolerant ruderals, diversity loss occurred following the suppression of dominant grasses by tall forbs, whereas in meadows dominated by a stress-tolerant competitor, diversity loss resulted from increased abundance and biomass of the dominant grass. We conclude that management for species conservation in abandoned grasslands should manipulate the functional turnover in communities where the dominant species is a weaker competitor, and abundance and biomass of dominant species in communities where the dominant species is the stronger competitor.

  3. Reforestation of bottomland hardwoods and the issue of woody species diversity

    USGS Publications Warehouse

    Allen, J.A.

    1997-01-01

    Bottomland hardwood forests in the southcentral United States have been cleared extensively for agriculture, and many of the remaining forests are fragmented and degraded. During the last decade, however, approximately 75,000 ha of land-mainly agricultural fields-have been replanted or contracted for replanting, with many more acres likely to be reforested in the near future. The approach used in most reforestation projects to date has been to plant one to three overstory tree species, usually Quercus spp. (oaks), and to rely on natural dispersal for the establishment of other woody species. I critique this practice by two means. First, a brief literature review demonstrates that moderately high woody species diversity occurs in natural bottomland hardwood forests in the region. This review, which relates diversity to site characteristics, serves as a basis for comparison with stands established by means of current reforestation practices. Second, I reevaluate data on the invasion of woody species from an earlier study of 10 reforestation projects in Mississippi,with the goal of assessing the likelihood that stands with high woody species diversity will develop. I show that natural invasion cannot always be counted on to produce a diverse stand, particularly on sites more than about 60 m from an existing forest edge. I then make several recommendations for altering current reforestation pactices in order to establish stands with greater woody species diversity, a more natural appearance,and a more positive environmental impact at scales larger than individual sites.

  4. Species diversity of ectoparasitic chigger mites (Acari: Prostigmata) on small mammals in Yunnan Province, China.

    PubMed

    Peng, Pei-Ying; Guo, Xian-Guo; Ren, Tian-Guang; Song, Wen-Yu; Dong, Wen-Ge; Fan, Rong

    2016-09-01

    Chigger mites are a large group of arthropods and the larvae of mites are ectoparasites. Some species of ectoparasitic mites (larvae) can be the transmitting vectors of tsutsugamushi disease (scrub typhus). Yunnan Province is located in the southwest of China with complicated topographic landform and high biodiversity, where there are five zoogeographical subregions. Rodents and some other small mammals were trapped and examined for ectoparasitic chigger mites in 29 investigation sites in Yunnan during 2001-2013. From 13,760 individuals and 76 species of small mammal hosts, we collected 274 species of mites, which were identified as comprising 26 genera in two families. The species diversity of chigger mites (274 species) in the present study were not only much higher than that from other provinces of China but also largely exceeded that recorded from other regions and countries in the world. Of the five zoogeographical subregions, both the species diversity and Shannon-Weiner's diversity of mites were the highest in subregion II (southern subregion of Hengduan Mountains) with middle altitudes and middle latitude. Both the species diversity of mites and Shannon-Wiener diversity index showed a parabolic tendency from the low altitude (<500 m) to the high altitude (>3500 m) along the vertical gradients with the peak occurring in the middle-altitude regions (2000-2500 m). Of four dominant hosts, the species richness of mites was highest on Eothenomys miletus (S = 165) and Shannon-Wiener diversity index was highest on Rattus norvegicus (H = 3.13). Along latitude gradients, species richness of chigger mites increased first and then decreased, peaking at 25° to 26° N with 193 mite species. The geographical location, complex topography, and landscape with diverse small mammal hosts in Yunnan Province have contributed to the extremely high species diversity of mites in the province. The large sampling size of small mammal hosts in a wide geographical scope

  5. Does bird species diversity vary among forest types? A local-scale test in Southern Chile

    NASA Astrophysics Data System (ADS)

    Fontúrbel, Francisco E.; Jiménez, Jaime E.

    2014-10-01

    Birds are the most diverse vertebrate group in Chile, characterized by low species turnover at the country-size scale (high alpha but low beta diversities), resembling an island biota. We tested whether this low differentiation is valid at a local scale, among six forest habitat types. We detected 25 bird species; avifauna composition was significantly different among habitat types, with five species accounting for 60 % of the dissimilarity. We found a higher level of bird assemblage differentiation across habitats at the local scale than has been found at the country-size scale. Such differentiation might be attributed to structural differences among habitats.

  6. Removing the confounding effect of habitat specialization reveals the stabilizing contribution of diversity to species variability.

    PubMed Central

    Kolasa, Jurek; Li, Bai-Lian

    2003-01-01

    Earlier studies have found that diversity, S, stabilizes the relative variability of combined biomass or abundance of species making up a community. However, the effect of S on variability of constituent species has been elusive. We hypothesize that the proportion of specialists increases with S and, because specialists are more variable, this shift in composition will mask the stabilizing effect of S on populations of species making up a community. The test uses data on variability and ecological specialization of species in 49 natural rock pool invertebrate communities. Initial analyses produced inconclusive results similar to earlier studies. However, when variability owing to species' specialization was factored out, S reduced species' abundance variability, although not in all communities. Our study explains why the stabilizing effect of diversity on populations has not been found earlier. PMID:14667382

  7. Invasive plants have scale-dependent effects on diversity by altering species-area relationships.

    PubMed

    Powell, Kristin I; Chase, Jonathan M; Knight, Tiffany M

    2013-01-18

    Although invasive plant species often reduce diversity, they rarely cause plant extinctions. We surveyed paired invaded and uninvaded plant communities from three biomes. We reconcile the discrepancy in diversity loss from invaders by showing that invaded communities have lower local richness but steeper species accumulation with area than that of uninvaded communities, leading to proportionately fewer species loss at broader spatial scales. We show that invaders drive scale-dependent biodiversity loss through strong neutral sampling effects on the number of individuals in a community. We also show that nonneutral species extirpations are due to a proportionately larger effect of invaders on common species, suggesting that rare species are buffered against extinction. Our study provides a synthetic perspective on the threat of invasions to biodiversity loss across spatial scales.

  8. Diversity and enzyme activity of Penicillium species associated with macroalgae in Jeju Island.

    PubMed

    Park, Myung Soo; Lee, Seobihn; Oh, Seung-Yoon; Cho, Ga Youn; Lim, Young Woon

    2016-10-01

    A total of 28 strains of 19 Penicillium species were isolated in a survey of extracellular enzyme-producing fungi from macroalgae along the coast of Jeju Island of Korea. Penicillium species were identified based on morphological and β-tubulin sequence analyses. In addition, the halo-tolerance and enzyme activity of all strains were evaluated. The diversity of Penicillium strains isolated from brown algae was higher than the diversity of strains isolated from green and red algae. The commonly isolated species were Penicillium antarcticum, P. bialowiezense, P. brevicompactum, P. crustosum, P. oxalicum, P. rubens, P. sumatrense, and P. terrigenum. While many strains showed endoglucanase, β-glucosidase, and protease activity, no alginase activity was detected. There was a positive correlation between halo-tolerance and endoglucanase activity within Penicillium species. Among 19 Penicillium species, three species-P. kongii, P. olsonii, and P. viticola-have not been previously recorded in Korea.

  9. Genetic diversity and chemical polymorphism of some Thymus species.

    PubMed

    Rustaiee, Ali Reza; Yavari, Alireza; Nazeri, Vahideh; Shokrpour, Majid; Sefidkon, Fatemeh; Rasouli, Musa

    2013-06-01

    To ascertain whether there are chemical and genetic relationships among some Thymus species and also to determine correlation between these two sets of data, the essential-oil composition and genetic variability of six populations of Thymus including: T. daenensis ČELAK. (two populations), T. fallax FISCH. & C.A.MEY., T. fedtschenkoi RONNIGER, T. migricus KLOKOV & DES.-SHOST., and T. vulgaris L. were analyzed by GC and GC/MS, and also by randomly amplified polymorphic DNA (RAPD). Thus, 27 individuals were analyzed using 16 RAPD primers, which generated 264 polymorphic scorable bands and volatiles isolated by distillation extraction were subjected to GC and GC/MS analyses. The yields of oils ranged from 2.1 to 3.8% (v/w), and 34 components were identified, amounting to a total percentage of 97.8-99.9%. RAPD Markers allowed a perfect distinction between the different species based on their distinctive genetic background. However, they did not show identical clustering with the volatile-oil profiles.

  10. Diversity of Cercopithifilaria species in dogs from Portugal

    PubMed Central

    2014-01-01

    Background Filarioids belonging to the genus Cercopithifilaria (Spirurida: Onchocercidae) have been described in dogs in association with Rhipicephalus sanguineus group ticks, which act as their biological vectors. This study represents the first investigation on Cercopithifilaria spp. in dogs from Portugal. Findings Dogs (n = 102) from the Algarve region (south of Portugal) were sampled by skin snip collection and tissues were left to soak overnight in saline solution. Sediments were observed under a light microscope and the detected microfilariae identified according to their morphology. Twenty-four dogs (23.5%) were found infected with at least one species of Cercopithifilaria, namely C. bainae (9.8%), C. grassii (3.9%) and Cercopithifilaria sp. II sensu Otranto et al., 2013 (13.7%). Results were confirmed by molecular amplification of partial cytochrome c oxidase subunit I and 12S rRNA genes and sequence analysis. Co-infections with more than one Cercopithifilaria species were detected in 3.9% of the animals. Conclusions This is the first report of Cercopithifilaria spp. in dogs from Portugal. The estimated level of infection with C. bainae, C. grassii and Cercopithifilaria sp. II suggests that these filarioids are prevalent in the canine population of southern Portugal. PMID:24898125

  11. Endophytic Phomopsis species: host range and implications for diversity estimates.

    PubMed

    Murali, T S; Suryanarayanan, T S; Geeta, R

    2006-07-01

    Foliar endophyte assemblages of teak trees growing in dry deciduous and moist deciduous forests of Nilgiri Biosphere Reserve were compared. A species of Phomopsis dominated the endophyte assemblages of teak, irrespective of the location of the host trees. Internal transcribed spacer sequence analysis of 11 different Phomopsis isolates (ten from teak and one from Cassia fistula) showed that they fall into two groups, which are separated by a relatively long branch that is strongly supported. The results showed that this fungus is not host restricted and that it continues to survive as a saprotroph in teak leaf, possibly by exploiting senescent leaves as well as the litter. Although the endophyte assemblage of a teak tree growing about 500 km from the forests was also dominated by a Phomopsis sp., it separated into a different group based on internal transcribed spacer sequence analysis. Our results with an endophytic Phomopsis sp. reinforce the earlier conclusions reached by others for pathogenic Phomopsis sp., i.e., that this fungus is not host specific, and the species concept of Phomopsis needs to be redefined.

  12. Impact of resource availability on species composition and diversity in freshwater nematodes.

    PubMed

    Michiels, Iris C; Traunspurger, Walter

    2005-01-01

    This study investigates the long-term effects of resource availability in a freshwater nematode community. We carried out a mesocosm experiment where natural nematode communities were exposed to nutrient addition/depletion over 2 years. Compared to the nutrient-addition treatment, species richness and diversity were strongly reduced upon nutrient depletion. The functional group of bacterial feeders particularly suffered severely from nutrient depletion. The decrease in diversity of bacterial feeders was linked to reduced species richness and diversity of large omnivorous species, as predicted by trophic-dynamic models. Tilman's (1976) statement, that under low nutrient levels the best competitor dominates the system, was applicable in our system. Upon nutrient depletion, resource depletion led to a monoculture of 1 small bacterial feeder, but even after 2 years of resource depletion, up to 16 species still coexisted. Our results provide strong evidence that freshwater nematode systems can be regulated by nutrient competition.

  13. The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards.

    PubMed

    Russo, Laura; Park, Mia; Gibbs, Jason; Danforth, Bryan

    2015-09-01

    Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years. We used species rarefaction analyses to test for the completeness of sampling and the relationship between species richness and sampling effort, orchard size, and percent agriculture in the surrounding landscape. We performed more than 190 h of sampling, collecting 11,219 specimens representing 104 species. Despite the sampling intensity, we captured <75% of expected species richness at more than half of the sites. For most of these, the variation in bee community composition between years was greater than among sites. Species richness was influenced by percent agriculture, orchard size, and sampling effort, but we found no factors explaining the difference between observed and expected species richness. Competition between honeybees and wild bees did not appear to be a factor, as we found no correlation between honeybee and wild bee abundance. Our study shows that the pollinator fauna of agroecosystems can be diverse and challenging to thoroughly sample. We demonstrate that there is high temporal variation in community composition and that sites vary widely in the sampling effort required to fully describe their diversity. In order to maximize pollination services provided by wild bee species, we must first accurately estimate species richness. For researchers interested in providing this estimate, we recommend multiyear studies and rarefaction analyses to quantify the gap between observed and expected species richness.

  14. The diversity of antibacterial compounds of Terminalia species (Combretaceae).

    PubMed

    Shinde, S L; Junne, S B; Wadje, S S; Baig, M M V

    2009-11-15

    The antibacterial activity of acetone, hexane, dichloromethane leaf extract of five Terminalia species (Terminalia alata Heyne ex Roth., Terminalia arjuna (Roxb.) Wt. and Am., Terminalia bellerica (Gaertn.) Roxb., Terminalia catappa L. and Terminalia chebula Retz.) were tested by Agar-well-diffusion method against human pathogens E. coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus and Staphylococcus epidermidis. The Rf values and relative activities of separated compounds were tested. Hexane and dichloromethane extracts have shown more antibacterial components than the acetone extract indicating the non-polar character of the antibacterial compounds. The non-polar character of the antibacterial compounds was confirmed from the Rf values. It indicated that the antibacterial activity was not due to tannins. Terminalia catappa found to possess the compounds which are more antibacterial. Terminalia arjuna and T. catappa plants were found most promising for isolating antibacterial compounds.

  15. Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow.

    PubMed

    Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen

    2015-01-01

    Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao's index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production.

  16. Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow

    PubMed Central

    Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E.; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen

    2015-01-01

    Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao’s index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production. PMID:26295345

  17. Covariance in species diversity and facilitation among non-interactive parasite taxa: all against the host.

    PubMed

    Krasnov, B R; Mouillot, D; Khokhlova, I S; Shenbrot, G I; Poulin, R

    2005-10-01

    Different parasite taxa exploit different host resources and are often unlikely to interact directly. It is unclear, however, whether the diversity of any given parasite taxon is indirectly influenced by that of other parasite taxa on the same host. Some components of host immune defences may operate simultaneously against all kinds of parasites, whereas investment by the host in specific defences against one type of parasite may come at the expense of defence against other parasites. We investigated the relationships between the species diversity of 4 higher taxa of ectoparasites (fleas, sucking lice, mesostigmatid mites, and ixodid ticks), and between the species richness of ectoparasites and endoparasitic helminths, across different species of rodent hosts. Our analyses used 2 measures of species diversity, species richness and taxonomic distinctness, and controlled for the potentially confounding effects of sampling effort and phylogenetic relationships among host species. We found positive pairwise correlations between the species richness of fleas, mites and ticks; however, there was no association between species richness of any of these 3 groups and that of lice. We also found a strong positive relationship between the taxonomic distinctness of ecto- and endoparasite assemblages across host species. These results suggest the existence of a process of apparent facilitation among unrelated taxa in the organization of parasite communities. We propose explanations based on host immune responses, involving acquired cross-resistance to infection and interspecific variation in immunocompetence among hosts, to account for these patterns.

  18. Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia.

    PubMed

    Antonini, Yasmine; Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

    2017-01-01

    The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively.

  19. Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.

    PubMed

    Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

    2013-12-04

    The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation.

  20. Tree species diversity mitigates disturbance impacts on the forest carbon cycle.

    PubMed

    Pedro, Mariana Silva; Rammer, Werner; Seidl, Rupert

    2015-03-01

    Biodiversity fosters the functioning and stability of forest ecosystems and, consequently, the provision of crucial ecosystem services that support human well-being and quality of life. In particular, it has been suggested that tree species diversity buffers ecosystems against the impacts of disturbances, a relationship known as the "insurance hypothesis". Natural disturbances have increased across Europe in recent decades and climate change is expected to amplify the frequency and severity of disturbance events. In this context, mitigating disturbance impacts and increasing the resilience of forest ecosystems is of growing importance. We have tested how tree species diversity modulates the impact of disturbance on net primary production and the total carbon stored in living biomass for a temperate forest landscape in Central Europe. Using the simulation model iLand to study the effect of different disturbance regimes on landscapes with varying levels of tree species richness, we found that increasing diversity generally reduces the disturbance impact on carbon storage and uptake, but that this effect weakens or even reverses with successional development. Our simulations indicate a clear positive relationship between diversity and resilience, with more diverse systems experiencing lower disturbance-induced variability in their trajectories of ecosystem functioning. We found that positive effects of tree species diversity are mainly driven by an increase in functional diversity and a modulation of traits related to recolonization and resource usage. The results of our study suggest that increasing tree species diversity could mitigate the effects of intensifying disturbance regimes on ecosystem functioning and improve the robustness of forest carbon storage and the role of forests in climate change mitigation.

  1. Species diversity, selectivity, and habitat associations of small mammals from coastal California

    USGS Publications Warehouse

    Fellers, Gary M.

    1994-01-01

    Species diversity and habitat associations were documented for small mammals along 16 transects in a semiarid part of coastal California. Peromyscus were the most abundant, comprising 45.3% of all captures, followed by Dipodomys (21.2%), Neotoma (15.1%), and Perognathus (15.0%). Five additional genera made up the remaining captures (3.4%). Peromyscus truei and Perognathus californicus were both common and widespread, accounting for 42.1% of all captures. Both species were found on all but one transect. Neotoma lepida, the third most common species, was captured on rock transects 96% of the time. Dipodomys elephantinus was the fifth most common species, and was found exclusively in chamise chaparral. Species diversity (H') averaged 1.22 and ranged from 0.33 on a chamise chaparral transect to 1.74 on another chamise chaparral transect which crossed the edge of a burn. Nearly all transects demonstrated this same trend for diversity to vary widely both within and between habitats, indicating that local conditions were more of an influence on diversity than broad habitat types. Selectivity, averaged across the ten most common species, was only 0.06, indicating that habitat selectivity was quite low. The most geographically widespread species, Peromyscus maniculatus, was the least selective (0.03), whereas the two species with the smallest geographic ranges, D. venustus and D. elephantinus, showed the greatest habitat selectivity (0.11 and 0.20, respectively). These values are much lower than those reported from short-term studies and suggest that, like species diversity, brief studies may not accurately reflect community-level interactions.

  2. Large herbivores maintain termite-caused differences in herbaceous species diversity patterns.

    PubMed

    Okullo, Paul; Moe, Stein R

    2012-09-01

    Termites and large herbivores affect African savanna plant communities. Both functional groups are also important for nutrient redistribution across the landscape. We conducted an experiment to study how termites and large herbivores, alone and in combination, affect herbaceous species diversity patterns in an African savanna. Herbaceous vegetation on large vegetated Macrotermes mounds (with and without large herbivores) and on adjacent savanna areas (with and without large herbivores) was monitored over three years in Lake Mburo National Park, Uganda. We found substantial differences in species richness, alpha diversity, evenness, and stability between termite mound herbaceous vegetation and adjacent savanna vegetation. Within months of fencing, levels of species richness, evenness, and stability were no longer significantly different between savanna and mounds. However, fencing reduced the cumulative number of species, particularly for forbs, of which 48% of the species were lost. Fencing increased the beta diversity (dissimilarity among plots) on the resource-poor (in terms of both nutrients and soil moisture) savanna areas, while it did not significantly affect beta diversity on the resource-rich termite mounds. While termites cause substantial heterogeneity in savanna vegetation, large herbivores further amplify these differences by reducing beta diversity on the savanna areas. Large herbivores are, however, responsible for the maintenance of a large number of forbs at the landscape level. These findings suggest that the mechanisms underlying the effects of termites and large herbivores on savanna plant communities scale up to shape community structure and dynamics at a landscape level.

  3. Genetic diversity and structure of the threatened species Sinopodophyllum hexandrum (Royle) Ying.

    PubMed

    Liu, W; Wang, J; Yin, D X; Yang, M; Wang, P; Han, Q S; Ma, Q Q; Liu, J J; Wang, J X

    2016-06-10

    Sinopodophyllum hexandrum is an important medicinal plant that has been listed as an endangered species, making the conservation of its genetic diversity a priority. Therefore, the genetic diversity and population structure of S. hexandrum was investigated through inter-simple sequence repeat analysis of eight natural populations. Eleven selected primers generated 141 discernible fragments. The percentage of polymorphic bands was 37.59% at the species level, and 7.66-24.32% at the population level. Genetic diversity of S. hexandrum was low within populations (average HE = 0.0366), but higher at the species level (HE = 0.0963). Clear structure and high genetic differentiation were detected between populations using unweighted pair groups mean arithmetic and principle coordinate analysis. Clustering approaches clustered the eight sampled populations into three major groups, and AMOVA confirmed there to be significant variation between populations (63.27%). Genetic differentiation may have arisen through limited gene flow (Nm = 0.3317) in this species. Isolation by distance among populations was determined by comparing genetic distance versus geographical distance using the Mantel test. The results revealed no correlation between spatial pattern and geographic location. Given the low within-population genetic diversity, high differentiation among populations, and the increasing anthropogenic pressure on this species, in situ conservation measures, in addition to sampling and ex situ preservation, are recommended to preserve S. hexandrum populations and to retain their genetic diversity.

  4. Natural selection constrains neutral diversity across a wide range of species.

    PubMed

    Corbett-Detig, Russell B; Hartl, Daniel L; Sackton, Timothy B

    2015-04-01

    The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

  5. High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

    PubMed

    Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

    2015-09-01

    Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.

  6. Natural Selection Constrains Neutral Diversity across A Wide Range of Species

    PubMed Central

    Corbett-Detig, Russell B.; Hartl, Daniel L.; Sackton, Timothy B.

    2015-01-01

    The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics. PMID:25859758

  7. Regional diversity reverses the negative impacts of an alien predator on local species-poor communities.

    PubMed

    Loewen, Charlie J G; Vinebrooke, Rolf D

    2016-10-01

    Species diversity is often an implicit source of biological insurance for communities against the impacts of novel perturbations, such as the introduction of an invasive species. High environmental heterogeneity (e.g., a mountainous gradient) is expected to beget greater regional species diversity and variation in functional traits related to environmental tolerances. Thus, heterogeneous metacommunities are expected to provide more tolerant colonists that buffer stressed local communities in the absence of dispersal limitation. We tested the hypothesis that importation of a regional zooplankton pool assembled from a diverse array of lakes and ponds lessens the impacts of a novel predator on local species-poor alpine communities by increasing response diversity (i.e., diversity of tolerances to environmental change) as mediated by variation in functional traits related to predator evasion. We also tested whether impacts varied with temperature, as warming may modify (e.g., dampen or amplify) invasion effects. An eight-week factorial experiment ([fishless vs. introduced Oncorhynchus mykiss (rainbow trout)] × [ambient temperature vs. heated] × [local vs. local + regional species pool]) was conducted using 32 1,000-L mesocosms. Associations between experimental treatments and species functional traits were tested by R-mode linked to Q-mode (RLQ) and fourth-corner analyses. Although the introduced predator suppressed local species richness and community biomass, colonization by several montane zooplankters reversed these negative effects, resulting in increased species diversity and production. Invasion resistance was unaffected by higher temperatures, which failed to elicit any significance impacts on the community. We discovered that the smaller body sizes of imported species drove functional overcompensation (i.e., increased production) in invaded communities. The observed ecological surprise showed how regionally sourced biodiversity from a highly

  8. Glacial refugia and modern genetic diversity of 22 western North American tree species

    PubMed Central

    Roberts, David R.; Hamann, Andreas

    2015-01-01

    North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r2 = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711

  9. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

    PubMed

    Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

    2016-02-01

    Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

  10. Elevated CO2 and plant species diversity interact to slow root decomposition

    SciTech Connect

    De Graaff, Marie-Anne; Schadt, Christopher Warren; Rula, Kelly L; Six, Johan W U A; Schweitzer, Jennifer A; Classen, Aimee T

    2011-01-01

    Changes in plant species diversity can result in synergistic increases in decomposition rates, while elevated atmospheric CO2 can slow the decomposition rates; yet it remains unclear how diversity and changes in atmospheric CO2 may interact to alter root decomposition. To investigate how elevated CO2 interacts with changes in root-litter diversity to alter decomposition rates, we conducted a 120-day laboratory incubation. Roots from three species (Trifolium repens, Lespedeza cuneata, and Festuca pratense) grown under ambient or elevated CO2 were incubated individually or in combination in soils that were exposed to ambient or elevated CO2 for five years. Our experiment resulted in two main findings: (1) Roots from T. repens and L. cuneata, both nitrogen (N) fixers, grown under elevated CO2 treatments had significantly slower decomposition rates than similar roots grown under ambient CO2 treatments; but the decomposition rate of F. pratense roots (a non-N-fixing species) was similar regardless of CO2 treatment. (2) Roots of the three species grown under ambient CO2 and decomposed in combination with each other had faster decomposition rates than when they were decomposed as single species. However, roots of the three species grown under elevated CO2 had similar decomposition rates when they were incubated alone or in combination with other species. These data suggest that if elevated CO2 reduces the root decomposition rate of even a few species in the community, it may slow root decomposition of the entire plant community.

  11. Effects of Previous Land-Use on Plant Species Composition and Diversity in Mediterranean Forests.

    PubMed

    Kouba, Yacine; Martínez-García, Felipe; de Frutos, Ángel; Alados, Concepción L

    2015-01-01

    At some point in their history, most forests in the Mediterranean Basin have been subjected to intensive management or converted to agriculture land. Knowing how forest plant communities recovered after the abandonment of forest-management or agricultural practices (including livestock grazing) provides a basis for investigating how previous land management have affected plant species diversity and composition in forest ecosystems. Our study investigated the consequences of historical "land management" practices on present-day Mediterranean forests by comparing species assemblages and the diversity of (i) all plant species and (ii) each ecological group defined by species' habitat preferences and successional status (i.e., early-, mid-, and late-successional species). We compared forest stands that differed both in land-use history and in successional stage. In addition, we evaluated the value of those stands for biodiversity conservation. The study revealed significant compositional differentiation among stands that was due to among-stand variations in the diversity (namely, species richness and evenness) of early-, intermediate-, and late-successional species. Historical land management has led to an increase in compositional divergences among forest stands and the loss of late-successional forest species.

  12. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

    PubMed Central

    Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

    2016-01-01

    Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se. PMID:26172210

  13. Effects of species diversity on establishment and coexistence: a phylloplane fungal community model system.

    PubMed

    Stohr, S N; Dighton, J

    2004-10-01

    A model system was devised, evaluating the influence that species diversity (species richness) has on fungal establishment and coexistence. Seven members of the fungal phylloplane community of Vaccinium macrocarpon (American cranberry) were selected to assess how species diversity affected development and coexistence of another community member, Pestalotia vaccinii. Pestalotia was engaged in competitive interactions on 1% Malt Extract Agar (MEA) petri dishes with each of the seven individual saprotrophs (two-way interaction), in random combinations with three of the seven saprotrophs (four-way interaction), and in random combinations with five of the seven saprotrophs (six-way interaction). The saprotrophic fungi used in this study were Aspergillus sp., Alternaria alternata, Cladosporium cladosporoides, Curvularia lunata, Epicoccum purpuracens, Penicillium sp., and Pithomyces chartarum. We hypothesized that species diversity would have a significant impact on the establishment and coexistence of Pestalotia vaccinii in culture. In an effort to minimize density-dependent effects, the number of viable spores employed in the three types of interactions was kept constant. Target spore concentrations of 50 viable spores of P. vaccinii and 50 saprotroph spores were used, regardless of the number of species involved in the interaction. This proved to be a very important factor in the experiment. As our results show, species diversity had little or no effect on the establishment and coexistence of Pestalotia vaccinii; however, spore density played an extremely important role in the establishment and development of fungal propagules in our model.

  14. Diversity patterns in Iberian Calathus (Coleoptera, Carabidae: Harpalinae): species turnover shows a story overlooked by species richness.

    PubMed

    Gañán, Israel; Baselga, Andrés; Novoa, Francisco

    2008-12-01

    We assessed the relationships between diversity patterns of Iberian Calathus and current environmental gradients or broad-scale spatial constraints, using 50-km grid cells as sampling units. We assessed the completeness of the inventories using nonparametric estimators to avoid spurious results based on sampling biases. We modeled species richness and beta diversity, using spatial position, and 23 topographical, climatic, and geological variables as predictors in regression and constrained analysis of principal coordinates modeling. Geographical situation does not seem to affect Calathus species richness, because no spatial pattern was detected. The environmental variables only explained 23% of the variation in richness. Spatial and environmental predictors explained a large part of the variation in species composition (58%). The fraction shared by both groups of variables was relatively large, but the pure effect of each model was still important. Our results show that it is necessary to assess the completeness of inventories to avoid drawing false conclusions. Also, Iberian Calathus represent a clear example of the need for combined analyses of species richness and beta diversity patterns, because the lack of patterns in the former does not imply the invariance of biotic communities.

  15. Using species abundance distribution models and diversity indices for biogeographical analyses

    NASA Astrophysics Data System (ADS)

    Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

    2016-01-01

    We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for

  16. Functional diversity supports the physiological tolerance hypothesis for plant species richness along climatic gradients

    USGS Publications Warehouse

    Spasojevic, Marko J.; Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman

    2013-01-01

    1. The physiological tolerance hypothesis proposes that plant species richness is highest in warm and/or wet climates because a wider range of functional strategies can persist under such conditions. Functional diversity metrics, combined with statistical modeling, offer new ways to test whether diversity-environment relationships are consistent with this hypothesis. 2. In a classic study by R. H. Whittaker (1960), herb species richness declined from mesic (cool, moist, northerly) slopes to xeric (hot, dry, southerly) slopes. Building on this dataset, we measured four plant functional traits (plant height, specific leaf area, leaf water content and foliar C:N) and used them to calculate three functional diversity metrics (functional richness, evenness, and dispersion). We then used a structural equation model to ask if ‘functional diversity’ (modeled as the joint responses of richness, evenness, and dispersion) could explain the observed relationship of topographic climate gradients to species richness. We then repeated our model examining the functional diversity of each of the four traits individually. 3. Consistent with the physiological tolerance hypothesis, we found that functional diversity was higher in more favorable climatic conditions (mesic slopes), and that multivariate functional diversity mediated the relationship of the topographic climate gradient to plant species richness. We found similar patterns for models focusing on individual trait functional diversity of leaf water content and foliar C:N. 4. Synthesis. Our results provide trait-based support for the physiological tolerance hypothesis, suggesting that benign climates support more species because they allow for a wider range of functional strategies.

  17. Detection of Helicobacter in the digestive tract of an Atlantic spotted dolphin (Stenella frontalis).

    PubMed

    Suárez, Paula; Contreras, Monica; Fernández-Delgado, Milagro; Salazar, Victor; Peña, Ruth; Michelangeli, Fabian; García-Amado, M Alexandra

    2010-04-01

    Helicobacter spp. occur in the digestive system of a broad range of animal taxa, including marine mammals. Only one formally recognized species, Helicobacter cetorum, has been described in marine mammals. Helicobacter has not been reported in the Atlantic spotted dolphin (Stenella frontalis). The purpose of our study was to examine the digestive tract of a stranded spotted dolphin for Helicobacter. Tissue and content samples were collected at necropsy and examined by histopathology and molecular analyses using Helicobacter genus-specific 16S rDNA polymerase chain reaction (PCR) and DNA sequencing. Helicobacter was detected in all stomach divisions and the duodenal ampulla. A sequence type of the 16S rRNA gene shared a 98-99% identity to sequences from H. cetorum. This study reports for the first time Helicobacter in S. frontalis.

  18. Species diversity vs. morphological disparity in the light of evolutionary developmental biology

    PubMed Central

    Minelli, Alessandro

    2016-01-01

    Background Two indicators of a clade’s success are its diversity (number of included species) and its disparity (extent of morphospace occupied by its members). Many large genera show high diversity with low disparity, while others such as Euphorbia and Drosophila are highly diverse but also exhibit high disparity. The largest genera are often characterized by key innovations that often, but not necessarily, coincide with their diagnostic apomorphies. In terms of their contribution to speciation, apomorphies are either permissive (e.g. flightlessness) or generative (e.g. nectariferous spurs). Scope Except for Drosophila, virtually no genus among those with the highest diversity or disparity includes species currently studied as model species in developmental genetics or evolutionary developmental biology (evo-devo). An evo-devo approach is, however, potentially important to understand how diversity and disparity could rapidly increase in the largest genera currently accepted by taxonomists. The most promising directions for future research and a set of key questions to be addressed are presented in this review. Conclusions From an evo-devo perspective, the evolution of clades with high diversity and/or disparity can be addressed from three main perspectives: (1) evolvability, in terms of release from previous constraints and of the presence of genetic or developmental conditions favouring multiple parallel occurrences of a given evolutionary transition and its reversal; (2) phenotypic plasticity as a facilitator of speciation; and (3) modularity, heterochrony and a coupling between the complexity of the life cycle and the evolution of diversity and disparity in a clade. This simple preliminary analysis suggests a set of topics that deserve priority for scrutiny, including the possible role of saltational evolution in the origination of high diversity and/or disparity, the predictability of morphological evolution following release from a former constraint, and

  19. Functional Diversity of Boreal Bog Plant Species Decreases Seasonal Variation of Ecosystem Carbon Sink Function

    NASA Astrophysics Data System (ADS)

    Korrensalo, A.

    2015-12-01

    Species diversity has been found to decrease the temporal variance of productivity of a plant community, and diversity in species responses to environmental factors seems to make a plant community more stable in changing conditions. Boreal bogs are nutrient poor peatland ecosystems where the number of plant species is low but the species differ greatly in their growth form. In here we aim to assess the role of the variation in photosynthesis between species for the temporal variation in ecosystem carbon sink function. To quantify the photosynthetic properties and their seasonal variation for different bog plant species we measured photosynthetic parameters and stress-inducing chlorophyll fluorescence of vascular plant and Sphagnum moss species in a boreal bog over a growing season. We estimated monthly gross photosynthesis (PG) of the whole study site based on species level light response curves and leaf area development. The estimated PG was further compared with a gross primary production (GPP) estimate measured by eddy covariance (EC) technique. The sum of upscaled PG estimates agreed well with the GPP estimate measured by the EC technique. The contributions of the species and species groups to the ecosystem level PG changed over the growing season. The sharp mid-summer peak in sedge PG was balanced by more stable PG of evergreen shrubs and Sphagna. Species abundance rather than differences in photosynthetic properties between species and growth forms determined the most productive plants on the ecosystem scale. Sphagna had lower photosynthesis and clorophyll fluorescence than vascular plants but were more productive on the ecosystem scale throughout the growing season due to their high areal coverage. These results show that the diversity of growth forms stabilizes the seasonal variation of the ecosystem level PG in an ombrotrophic bog ecosystem. This may increase the resilience of the ecosystem to changing environmental conditions.

  20. Differential effects of plant diversity on functional trait variation of grass species

    PubMed Central

    Gubsch, Marlén; Buchmann, Nina; Schmid, Bernhard; Schulze, Ernst-Detlef; Lipowsky, Annett; Roscher, Christiane

    2011-01-01

    Background and Aims Functional trait differences and trait adjustment in response to influences of the biotic environment could reflect niche partitioning among species. In this study, we tested how variation in above-ground plant traits, chosen as indicators for light and nitrogen acquisition and use, differs among taxonomically closely related species (Poaceae) to assess their potential for niche segregation at increasing plant diversity. Methods Traits of 12 grass species were measured in experimental grasslands (Jena Experiment) of varying species richness (from 1 to 60) and presence of particular functional groups (grasses, legumes, tall herbs and small herbs). Key Results Grass species increased shoot and leaf length, investment into supporting tissue (stem mass fraction) and specific leaf area as well as reduced foliar δ13C values with increasing species richness, indicating higher efforts for light acquisition. These species-richness effects could in part be explained by a higher probability of legume presence in more diverse communities. Leaf nitrogen concentrations increased and biomas s : N ratios in shoots decreased when grasses grew with legumes, indicating an improved nitrogen nutrition. Foliar δ15N values of grasses decreased when growing with legumes suggesting the use of depleted legume-derived N, while decreasing δ15N values with increasing species richness indicated a shift in the uptake of different N sources. However, efforts to optimize light and nitrogen acquisition by plastic adjustment of traits in response to species richness and legume presence, varied significantly among grass species. It was possible to show further that trait adjustment of grass species increased niche segregation in more diverse plant communities but that complementarity through niche separation may differ between light and nutrient acquisition. Conclusions The results suggest that even among closely related species such as grasses different strategies are used to

  1. Measuring size and composition of species pools: a comparison of dark diversity estimates.

    PubMed

    de Bello, Francesco; Fibich, Pavel; Zelený, David; Kopecký, Martin; Mudrák, Ondřej; Chytrý, Milan; Pyšek, Petr; Wild, Jan; Michalcová, Dana; Sádlo, Jiří; Šmilauer, Petr; Lepš, Jan; Pärtel, Meelis

    2016-06-01

    Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat-specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so-called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co-occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co-occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods

  2. Forest species diversity reduces disease risk in a generalist plant pathogen invasion

    USGS Publications Warehouse

    Haas, Sarah E.; Hooten, Mevin B.; Rizzo, David M.; Meentemeyer, Ross K.

    2011-01-01

    Empirical evidence suggests that biodiversity loss can increase disease transmission, yet our understanding of the 'diversity-disease hypothesis' for generalist pathogens in natural ecosystems is limited. We used a landscape epidemiological approach to examine two scenarios regarding diversity effects on the emerging plant pathogen Phytophthora ramorum across a broad, heterogeneous ecoregion: (1) an amplification effect exists where disease risk is greater in areas with higher plant diversity due to the pathogen's wide host range, or (2) a dilution effect where risk is reduced with increasing diversity due to lower competency of alternative hosts. We found evidence for pathogen dilution, whereby disease risk was lower in sites with higher species diversity, after accounting for potentially confounding effects of host density and landscape heterogeneity. Our results suggest that although nearly all plants in the ecosystem are hosts, alternative hosts may dilute disease transmission by competent hosts, thereby buffering forest health from infectious disease.

  3. Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae) through DNA Barcoding

    PubMed Central

    Lee, Seunghwan; Park, In Gyun; Park, Haechul

    2016-01-01

    The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI) sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4%) was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5%) were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%–3.67%) suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU) identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having an

  4. Fine-scale urbanization affects Odonata species diversity in ponds of a megacity (Paris, France)

    NASA Astrophysics Data System (ADS)

    Jeanmougin, Martin; Leprieur, Fabien; Loïs, Grégoire; Clergeau, Philippe

    2014-08-01

    Current developments in urban ecology include very few studies focused on pond ecosystems, though ponds are recognized as biodiversity hotspots. Using Odonata as an indicator model, we explored changes in species composition in ponds localized along an urban gradient of a megacity (Paris, France). We then assessed the relative importance of local- and landscape-scale variables in shaping Odonata α-diversity patterns using a model-averaging approach. Analyses were performed for adult (A) and adult plus exuviae (AE) census data. At 26 ponds, we recorded 657 adults and 815 exuviae belonging to 17 Odonata species. The results showed that the Odonata species assemblage composition was not determined by pond localization along the urban gradient. Similarly, pond characteristics were found to be similar among urban, suburban and periurban ponds. The analyses of AE census data revealed that fine-scale urbanization (i.e., increased density of buildings surrounding ponds) negatively affects Odonata α-diversity. In contrast, pond localization along the urban gradient weakly explained the α-diversity patterns. Several local-scale variables, such as the coverage of submerged macrophytes, were found to be significant drivers of Odonata α-diversity. Together, these results show that the degree of urbanization around ponds must be considered instead of pond localization along the urban gradient when assessing the potential impacts of urbanization on Odonata species diversity. This work also indicates the importance of exuviae sampling in understanding the response of Odonata to urbanization.

  5. Generic and functional diversity in endophytic actinomycetes from wild Compositae plant species at South Sinai - Egypt.

    PubMed

    El-Shatoury, Sahar A; El-Kraly, Omnia A; Trujillo, Martha E; El-Kazzaz, Waleed M; El-Din, El-Sayeda Gamal; Dewedar, Ahmed

    2013-09-01

    The diversity of culturable endophytic actinomycetes associated with wild Compositae plants is scantily explored. In this study, one hundred and thirty one endophytic actinobacteria were isolated from ten Compositae plant species collected from South Sinai in Egypt. Microscopic and chemotaxonomic investigation of the isolates indicated fourteen genera. Rare genera, such as Microtetraspora, and Intrasporangium, which have never been previously reported to be endophytic, were identified. Each plant species accommodated between three to eight genera of actinobacteria and unidentified strains were recovered from seven plant species. The generic diversity analysis of endophytic assemblages grouped the plant species into three main clusters, representing high, moderate and low endophytic diversity. The endophytes showed high functional diversity, based on forty four catabolic and plant growth promotion traits; providing some evidence that such traits could represent key criteria for successful residence of endophytes in the endosphere. Stress-tolerance traits were more predictive measure of functional diversity differences between the endophyte assemblages (Shannon's index, p = 0.01). The results indicate a potential prominent role of endophytes for their hosts and emphasize the potency of plant endosphere as a habitat for actinobacteria with promising future applications.

  6. Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities

    PubMed Central

    Messika, Irit; Cohen, Carmit; Toh, Evelyn; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith; Hawlena, Hadas

    2014-01-01

    Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts. PMID:25343259

  7. Association of host and microbial species diversity across spatial scales in desert rodent communities.

    PubMed

    Gavish, Yoni; Kedem, Hadar; Messika, Irit; Cohen, Carmit; Toh, Evelyn; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith; Hawlena, Hadas

    2014-01-01

    Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.

  8. Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

    PubMed Central

    Chopra, Ratan; Burow, Gloria; Simpson, Charles E.; Chagoya, Jennifer; Mudge, Joann; Burow, Mark D.

    2016-01-01

    To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection. PMID:27729436

  9. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

    PubMed Central

    2013-01-01

    Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted

  10. Karyotype Diversity and Evolutionary Trends in Armored Catfish Species of the Genus Harttia (Siluriformes: Loricariidae).

    PubMed

    Blanco, Daniel Rodrigues; Vicari, Marcelo Ricardo; Lui, Roberto Laridondo; Traldi, Josiane Baccarin; Bueno, Vanessa; Martinez, Juliana de Fátima; Brandão, Heleno; Oyakawa, Osvaldo Takeshi; Moreira Filho, Orlando

    2017-04-01

    Most species of the genus Harttia inhabits the headwaters of small tributaries, but some species are restricted to the main channel of some rivers. This feature, combined with limited dispersal ability, leads to the formation of small isolated populations with reduced gene flow. Currently, there are 23 taxonomically defined and recognized species, and 17 of these are found in Brazil, distributed in several hydrographic basins. Despite this diversity, few chromosomal data for the species belonging to this genus are found in the literature. Thus, this study analyzed, by classical and molecular cytogenetics methodologies, the chromosomal diversity of this genus, to discuss the processes that are involved in the evolution and karyotype differentiation of the species of the group. Seven species of Harttia were analyzed: H. kronei, H. longipinna, H. gracilis, H. punctata, H. loricariformis, H. torrenticola, and H. carvalhoi. The chromosomal diversity found in these species includes different diploid and fundamental numbers, distinct distribution of several repetitive sequences, the presence of supernumerary chromosomes in H. longipinna and multiple sex chromosome systems of the type XX/XY1Y2 in H. carvalhoi and X1X1X2X2/X1X2Y in H. punctata. Lastly, our data highlight the genus Harttia as an excellent model for evolutionary studies.

  11. Large-scale patterns in morphological diversity and species assemblages in Neotropical Triatominae (Heteroptera: Reduviidae)

    PubMed Central

    Fergnani, Paula Nilda; Ruggiero, Adriana; Ceccarelli, Soledad; Menu, Frédéric; Rabinovich, Jorge

    2013-01-01

    We analysed the spatial variation in morphological diversity (MDiv) and species richness (SR) for 91 species of Neotropical Triatominae to determine the ecological relationships between SR and MDiv and to explore the roles that climate, productivity, environmental heterogeneity and the presence of biomes and rivers may play in the structuring of species assemblages. For each 110 km x 110 km-cell on a grid map of America, we determined the number of species (SR) and estimated the mean Gower index (MDiv) based on 12 morphological attributes. We performed bootstrapping analyses of species assemblages to identify whether those assemblages were more similar or dissimilar in their morphology than expected by chance. We applied a multi-model selection procedure and spatial explicit analyses to account for the association of diversity-environment relationships. MDiv and SR both showed a latitudinal gradient, although each peaked at different locations and were thus not strictly spatially congruent. SR decreased with temperature variability and MDiv increased with mean temperature, suggesting a predominant role for ambient energy in determining Triatominae diversity. Species that were more similar than expected by chance co-occurred near the limits of the Triatominae distribution in association with changes in environmental variables. Environmental filtering may underlie the structuring of species assemblages near their distributional limits. PMID:24402152

  12. Effects of Previous Land-Use on Plant Species Composition and Diversity in Mediterranean Forests

    PubMed Central

    Kouba, Yacine; Martínez-García, Felipe; de Frutos, Ángel; Alados, Concepción L.

    2015-01-01

    At some point in their history, most forests in the Mediterranean Basin have been subjected to intensive management or converted to agriculture land. Knowing how forest plant communities recovered after the abandonment of forest-management or agricultural practices (including livestock grazing) provides a basis for investigating how previous land management have affected plant species diversity and composition in forest ecosystems. Our study investigated the consequences of historical “land management” practices on present-day Mediterranean forests by comparing species assemblages and the diversity of (i) all plant species and (ii) each ecological group defined by species’ habitat preferences and successional status (i.e., early-, mid-, and late-successional species). We compared forest stands that differed both in land-use history and in successional stage. In addition, we evaluated the value of those stands for biodiversity conservation. The study revealed significant compositional differentiation among stands that was due to among-stand variations in the diversity (namely, species richness and evenness) of early-, intermediate-, and late-successional species. Historical land management has led to an increase in compositional divergences among forest stands and the loss of late-successional forest species. PMID:26397707

  13. Diversity and biogeography of a species-rich ant fauna of the Australian seasonal tropics.

    PubMed

    Andersen, Alan N; Hoffmann, Benjamin D; Oberprieler, Stefanie

    2016-09-15

    Although ants are an ecologically dominant and extensively studied faunal group throughout the tropics, there is a poor understanding of tropical ant diversity and distribution at large spatial scales. Here we use a collection developed from 3 decades of ant surveys to present the first analysis of ant diversity and biogeography of a large tropical region. Our objective was to document the species richness, composition, and biogeographic distributions of the ant fauna of the 400 000 km(2) "Top End" of Australia's Northern Territory. The known Top End ant fauna comprises 901 native species from 59 genera. The richest genera are Pheidole (90 species), Melophorus (83), Monomorium (83), Camponotus (71), Meranoplus (63), Polyrhachis (57), Rhytidoponera (50), Tetramorium (43), Cerapachys (32), and Iridomyrmex (31). The fauna is the center of diverse radiations within species-groups of genera such as Meranoplus, Rhytidoponera, and Leptogenys. It also includes IndoMalayan species that have likely bypassed the normal dispersal route into Australia through Cape York Peninsula in North Queensland. Faunistic similarity with other regions of far northern Australia is associated more with rainfall than with geographic proximity. Most (60%) of Top End ant species have not been recorded elsewhere, and, despite uncertainties relating to species delimitation and sampling intensity, this appears to be a credible estimate of the level of endemism. Such exceptionally high endemism can be attributed to the Top End's geographic isolation from other regions of northern Australia with comparably high rainfall.

  14. Large-scale patterns in morphological diversity and species assemblages in Neotropical Triatominae (Heteroptera: Reduviidae).

    PubMed

    Fergnani, Paula Nilda; Ruggiero, Adriana; Ceccarelli, Soledad; Menu, Frédéric; Rabinovich, Jorge

    2013-12-01

    We analysed the spatial variation in morphological diversity (MDiv) and species richness (SR) for 91 species of Neotropical Triatominae to determine the ecological relationships between SR and MDiv and to explore the roles that climate, productivity, environmental heterogeneity and the presence of biomes and rivers may play in the structuring of species assemblages. For each 110 km x 110 km-cell on a grid map of America, we determined the number of species (SR) and estimated the mean Gower index (MDiv) based on 12 morphological attributes. We performed bootstrapping analyses of species assemblages to identify whether those assemblages were more similar or dissimilar in their morphology than expected by chance. We applied a multi-model selection procedure and spatial explicit analyses to account for the association of diversity-environment relationships. MDiv and SR both showed a latitudinal gradient, although each peaked at different locations and were thus not strictly spatially congruent. SR decreased with temperature variability and MDiv increased with mean temperature, suggesting a predominant role for ambient energy in determining Triatominae diversity. Species that were more similar than expected by chance co-occurred near the limits of the Triatominae distribution in association with changes in environmental variables. Environmental filtering may underlie the structuring of species assemblages near their distributional limits.

  15. The Evolutionary History of the Arabidopsis arenosa Complex: Diverse Tetraploids Mask the Western Carpathian Center of Species and Genetic Diversity

    PubMed Central

    Schmickl, Roswitha; Paule, Juraj; Klein, Johannes; Marhold, Karol; Koch, Marcus A.

    2012-01-01

    The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNALeu and tRNAPhe, respectively]. We unravel the broad-scale cytogeographic and phylogeographic patterns of diploids and tetraploids. Diploid cytotypes were exclusively found on the Balkan Peninsula and in the Carpathians while tetraploid cytotypes were found throughout the remaining distribution range of the A. arenosa complex. Three centers of genetic diversity were identified: the Balkan Peninsula, the Carpathians, and the unglaciated Eastern and Southeastern Alps. All three could have served as long-term refugia during Pleistocene climate oscillations. We hypothesize that the Western Carpathians were and still are the cradle of speciation within the A. arenosa complex due to the high species number and genetic diversity and the concurrence of both cytotypes there. PMID:22880083

  16. Multiscale Mapping of Species Diversity under Changed Land-Use Using Imaging Spectroscopy.

    PubMed

    Paz-Kagan, Tarin; Caras, Tamir; Herrmann, Ittai; Shachak, Moshe; Karnieli, Arnon

    2017-03-28

    Land-use changes are one of the most important factors causing environmental transformations and species diversity alterations. The aim of the current study was to develop a geoinformatics-based framework to quantify alpha and beta diversity indices in two sites in Israel with different land-uses, i.e., an agricultural system of fruit orchards, an afforestation system of planted groves, and an unmanaged system of groves. The framework comprises four scaling steps: (1) classification of a tree species distribution (SD) map using imaging spectroscopy (IS) at a pixel size of 1 m; (2) estimation of local species richness by calculating the alpha diversity index for 30-m grid cells; (3) calculation of beta diversity for different land-use categories and sub-categories at different sizes; and (4) calculation of the beta diversity difference between the two sites. The SD was classified based on a hyperspectral image with 448 bands within the 380-2500 nm spectral range and a spatial resolution of 1 m. Twenty-three tree species were classified with high overall accuracy values of 82.57 and 86.93% for the two sites. Significantly high values of the alpha index characterize the unmanaged land-use, and the lowest values were calculated for the agricultural land-use. In addition, high values of alpha indices were found at the borders between the polygons related to the "edge-effect" phenomenon, whereas low alpha indices were found in areas with high invasion species rates. The beta index value, calculated for 58 polygons, was significantly lower in the agricultural land-use. The suggested framework of this study succeeded in quantifying land-use effects on tree species distribution, evenness, and richness. IS and spatial statistics techniques offer an opportunity to study woody plant species variation with a multiscale approach that is useful for managing land-use, especially under increasing environmental changes. This article is protected by copyright. All rights reserved.

  17. Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment.

    PubMed

    Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

    2016-01-01

    Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2%) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates.

  18. Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis.

    PubMed

    Dikshit, Harsh Kumar; Singh, Akanksha; Singh, Dharmendra; Aski, Muraleedhar Sidaram; Prakash, Prapti; Jain, Neelu; Meena, Suresh; Kumar, Shiv; Sarker, Ashutosh

    2015-01-01

    Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei's genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard's structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations.

  19. Amphibian Diversity and Threatened Species in a Severely Transformed Neotropical Region in Mexico

    PubMed Central

    Meza-Parral, Yocoyani; Pineda, Eduardo

    2015-01-01

    Many regions around the world concentrate a large number of highly endangered species that have very restricted distributions. The mountainous region of central Veracruz, Mexico, is considered a priority area for amphibian conservation because of its high level of endemism and the number of threatened species. The original tropical montane cloud forest in the region has been dramatically reduced and fragmented and is now mainly confined to ravines and hillsides. We evaluated the current situation of amphibian diversity in the cloud forest fragments of this region by analyzing species richness and abundance, comparing assemblage structure and species composition, examining the distribution and abundance of threatened species, and identifying the local and landscape variables associated with the observed amphibian diversity. From June to October 2012 we sampled ten forest fragments, investing 944 person-hours of sampling effort. A total of 895 amphibians belonging to 16 species were recorded. Notable differences in species richness, abundance, and assemblage structure between forest fragments were observed. Species composition between pairs of fragments differed by an average of 53%, with the majority (58%) resulting from species replacement and the rest (42%) explained by differences in species richness. Half of the species detected are under threat of extinction according to the International Union for Conservation of Nature, and although their distribution and abundance varied markedly, there were also ubiquitous and abundant species, along with rare species of restricted distribution. The evident heterogeneity of the ten study sites indicates that to conserve amphibians in a mountainous region such as this one it is necessary to protect groups of fragments which represent the variability of the system. Both individually and together cloud forest fragments are very important to conservation because each remnant is inhabited by several threatened species, some of

  20. Amphibian diversity and threatened species in a severely transformed neotropical region in Mexico.

    PubMed

    Meza-Parral, Yocoyani; Pineda, Eduardo

    2015-01-01

    Many regions around the world concentrate a large number of highly endangered species that have very restricted distributions. The mountainous region of central Veracruz, Mexico, is considered a priority area for amphibian conservation because of its high level of endemism and the number of threatened species. The original tropical montane cloud forest in the region has been dramatically reduced and fragmented and is now mainly confined to ravines and hillsides. We evaluated the current situation of amphibian diversity in the cloud forest fragments of this region by analyzing species richness and abundance, comparing assemblage structure and species composition, examining the distribution and abundance of threatened species, and identifying the local and landscape variables associated with the observed amphibian diversity. From June to October 2012 we sampled ten forest fragments, investing 944 person-hours of sampling effort. A total of 895 amphibians belonging to 16 species were recorded. Notable differences in species richness, abundance, and assemblage structure between forest fragments were observed. Species composition between pairs of fragments differed by an average of 53%, with the majority (58%) resulting from species replacement and the rest (42%) explained by differences in species richness. Half of the species detected are under threat of extinction according to the International Union for Conservation of Nature, and although their distribution and abundance varied markedly, there were also ubiquitous and abundant species, along with rare species of restricted distribution. The evident heterogeneity of the ten study sites indicates that to conserve amphibians in a mountainous region such as this one it is necessary to protect groups of fragments which represent the variability of the system. Both individually and together cloud forest fragments are very important to conservation because each remnant is inhabited by several threatened species, some of

  1. Rapid Diversity Loss of Competing Animal Species in Well-Connected Landscapes

    PubMed Central

    Schippers, Peter; Hemerik, Lia; Baveco, Johannes M.; Verboom, Jana

    2015-01-01

    Population viability of a single species, when evaluated with metapopulation based landscape evaluation tools, always increases when the connectivity of the landscape increases. However, when interactions between species are taken into account, results can differ. We explore this issue using a stochastic spatially explicit meta-community model with 21 competing species in five different competitive settings: (1) weak, coexisting competition, (2) neutral competition, (3) strong, excluding competition, (4) hierarchical competition and (5) random species competition. The species compete in randomly generated landscapes with various fragmentation levels. With this model we study species loss over time. Simulation results show that overall diversity, the species richness in the entire landscape, decreases slowly in fragmented landscapes whereas in well-connected landscapes rapid species losses occur. These results are robust with respect to changing competitive settings, species parameters and spatial configurations. They indicate that optimal landscape configuration for species conservation differs between metapopulation approaches, modelling species separately and meta-community approaches allowing species interactions. The mechanism behind this is that species in well-connected landscapes rapidly outcompete each other. Species that become abundant, by chance or by their completive strength, send out large amounts of dispersers that colonize and take over other patches that are occupied by species that are less abundant. This mechanism causes rapid species loss. In fragmented landscapes the colonization rate is lower, and it is difficult for a new species to establish in an already occupied patch. So, here dominant species cannot easily take over patches occupied by other species and higher diversity is maintained for a longer time. These results suggest that fragmented landscapes have benefits for species conservation previously unrecognized by the landscape ecology

  2. Co-infection of the Siberian hamster (Phodopus sungorus) with a novel Helicobacter sp. and Campylobacter sp.

    PubMed

    Nagamine, Claude M; Shen, Zeli; Luong, Richard H; McKeon, Gabriel P; Ruby, Norman F; Fox, James G

    2015-05-01

    We report the isolation of a novel helicobacter isolated from the caecum of the Siberian hamster (Phodopus sungorus). Sequence analysis showed 97% sequence similarity to Helicobacter ganmani. In addition, we report the co-infection of these Siberian hamsters with a Campylobacter sp. and a second Helicobacter sp. with 99% sequence similarity to Helicobacter sp. flexispira taxon 8 (Helicobacter bilis), a species isolated previously from patients with bacteraemia. Gross necropsy and histopathology did not reveal any overt pathological lesions of the liver and gastrointestinal tract that could be attributed to the Helicobacter or Campylobacter spp. infections. This is the first helicobacter to be identified in the Siberian hamster and the first report of co-infection of Helicobacter spp. and Campylobacter sp. in asymptomatic Siberian hamsters.

  3. Co-infection of the Siberian hamster (Phodopus sungorus) with a novel Helicobacter sp. and Campylobacter sp.

    PubMed Central

    Shen, Zeli; Luong, Richard H.; McKeon, Gabriel P.; Ruby, Norman F.; Fox, James G.

    2015-01-01

    We report the isolation of a novel helicobacter isolated from the caecum of the Siberian hamster (Phodopus sungorus). Sequence analysis showed 97 % sequence similarity to Helicobacter ganmani. In addition, we report the co-infection of these Siberian hamsters with a Campylobacter sp. and a second Helicobacter sp. with 99 % sequence similarity to Helicobacter sp. flexispira taxon 8 (Helicobacter bilis), a species isolated previously from patients with bacteraemia. Gross necropsy and histopathology did not reveal any overt pathological lesions of the liver and gastrointestinal tract that could be attributed to the Helicobacter or Campylobacter spp. infections. This is the first helicobacter to be identified in the Siberian hamster and the first report of co-infection of Helicobacter spp. and Campylobacter sp. in asymptomatic Siberian hamsters. PMID:25752854

  4. RESTORING SPECIES RICHNESS AND DIVERSITY IN A RUSSIAN KNAPWEED (ACROPTILON REPENS)-INFESTED RIPARIAN PLANT COMMUNITY USING HERBICIDES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species richness and diversity are important indicators of ecosystem function and may be related to plant community resistance to invasion by non-indigenous species. Knowledge about the influence of various strategies on species richness and diversity is central to making wise invasive plant manage...

  5. Temperature dependence, spatial scale, and tree species diversity in eastern Asia and North America

    PubMed Central

    Wang, Zhiheng; Brown, James H.; Tang, Zhiyao; Fang, Jingyun

    2009-01-01

    The increase of biodiversity from poles to equator is one of the most pervasive features of nature. For 2 centuries since von Humboldt, Wallace, and Darwin, biogeographers and ecologists have investigated the environmental and historical factors that determine the latitudinal gradient of species diversity, but the underlying mechanisms remain poorly understood. The recently proposed metabolic theory of ecology (MTE) aims to explain ecological patterns and processes, including geographical patterns of species richness, in terms of the effects of temperature and body size on the metabolism of organisms. Here we use 2 comparable databases of tree distributions in eastern Asia and North America to investigate the roles of environmental temperature and spatial scale in shaping geographical patterns of species diversity. We find that number of species increases exponentially with environmental temperature as predicted by the MTE, and so does the rate of spatial turnover in species composition (slope of the species-area relationship). The magnitude of temperature dependence of species richness increases with spatial scale. Moreover, the relationship between species richness and temperature is much steeper in eastern Asia than in North America: in cold climates at high latitudes there are more tree species in North America, but the reverse is true in warmer climates at lower latitudes. These patterns provide evidence that the kinetics of ecological and evolutionary processes play a major role in the latitudinal pattern of biodiversity. PMID:19628692

  6. Genetic Diversity of Neotropical Myotis (Chiroptera: Vespertilionidae) with an Emphasis on South American Species

    PubMed Central

    Larsen, Roxanne J.; Genoways, Hugh H.; Khan, Faisal Ali Anwarali; Larsen, Peter A.; Wilson, Don E.; Baker, Robert J.

    2012-01-01

    Background Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America. Methodology and Principal Findings Cytochrome-b sequences were generated and phylogenetically analyzed from 215 specimens, providing DNA sequence data for the most species of New World Myotis to date. Based on genetic data in our sample, and on comparisons with available DNA sequence data from GenBank, we estimate the number of species-level genetic lineages in South America alone to be at least 18, rather than the 15 species currently recognized. Conclusions Our findings provide evidence that the perception of lower species richness in South American Myotis is largely due to a combination of cryptic morphological variation and insufficient sampling coverage in genetic-based systematic studies. A more accurate assessment of the level of diversity and species richness in New World Myotis is not only helpful for delimiting species boundaries, but also for understanding evolutionary processes within this globally distributed bat genus. PMID:23056352

  7. The contribution of seed dispersers to tree species diversity in tropical rainforests

    PubMed Central

    Kakishima, Satoshi; Morita, Satoru; Yoshida, Katsuhiko; Ishida, Atsushi; Hayashi, Saki; Asami, Takahiro; Ito, Hiromu; Miller, Donald G.; Uehara, Takashi; Mori, Shigeta; Hasegawa, Eisuke; Matsuura, Kenji; Kasuya, Eiiti; Yoshimura, Jin

    2015-01-01

    Tropical rainforests are known for their extreme biodiversity, posing a challenging problem in tropical ecology. Many hypotheses have been proposed to explain the diversity of tree species, yet our understanding of this phenomenon remains incomplete. Here, we consider the contribution of animal seed dispersers to the species diversity of trees. We built a multi-layer lattice model of trees whose animal seed dispersers are allowed to move only in restricted areas to disperse the tree seeds. We incorporated the effects of seed dispersers in the traditional theory of allopatric speciation on a geological time scale. We modified the lattice model to explicitly examine the coexistence of new tree species and the resulting high biodiversity. The results indicate that both the coexistence and diversified evolution of tree species can be explained by the introduction of animal seed dispersers. PMID:26587246

  8. Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

    PubMed Central

    Saunders, Nigel J; Boonmee, Prawit; Peden, John F; Jarvis, Stephen A

    2005-01-01

    Background Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. Results This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. Conclusion New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation. PMID:15676066

  9. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron

    PubMed Central

    Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang

    2015-01-01

    Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction. PMID:25477251

  10. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron.

    PubMed

    Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang

    2014-12-04

    Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction.

  11. Diversity and utilization of tree species in Meitei homegardens of Barak Valley, Assam.

    PubMed

    Devi, N Linthoingambi; Das, Ashesh Kumar

    2013-03-01

    An inventory of tree diversity in traditional homegardens of Meitei community was conducted in a Bontarapur village in Cachar district of Barak Valley, Assam. Meitei homegarden locally called Ingkhol exhibits a wide diversity in size, shape, location and composition. Seventy one tree species were enumerated from 50 homegardens belonging to 60 genus and 35 families. Among the families encountered, Rutaceae was the dominant family (4 genus and 7 species) followed by Meliaceae (5 genus and 5 species), Arecaceae (4 genus and 4 species) and Moraceae (3 genus and 5 species). Total 7946 tree individuals were recorded, with the density of 831 No ha(-1) of and total basal area of 9.54 m2 ha(-1). Areco catechu was the dominant species with the maximum number of individuals. Other dominant trees include Mangifera indica, Artocarpus heterophyllus, Citrus grandis, Parkia timoriana, Syzygium cumini and Psidium guajava. Being a cash crop, the intensification of betel nut has been preferred in many homegardens. Homegardens form an important component of land use of Meitei community which fulfills the socio-cultural and economic needs of the family and helps in conserving plant diversity through utilization.

  12. DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera)

    PubMed Central

    2016-01-01

    Species of the genus Moina Baird (Cladocera: Moinidae) often dominate freshwater crustacean communities in temporary water bodies. Several species of Moina are used as food for fish larvae in aquaculture, as bioindicators in toxicological studies, and as common subjects for physiological studies. The aim of this paper is to estimate biodiversity of Moina in northern Eurasia using the standard DNA barcoding approach based on the cytochrome c oxidase subunit I (COI) gene. We analysed 160 newly obtained and 157 existing COI sequences, and found evidence for 21 phylogroups of Moina, some of which were detected here for the first time. Our study confirmed the opinion that the actual species diversity of cladocerans is several times higher than is presently accepted. Our results also indicated that Moina has the second richest species diversity among the cladoceran genera (with only Daphnia O. F. Mueller having a greater diversity of species). Our study strongly supports division of Moina into two faunistic groups: European-Western Siberian and Eastern Siberian-Far Eastern, with a transitional zone at the Yenisey River basin (Eastern Siberia). Here, we refrain from taxonomic descriptions of new species, as this requires a thorough morphological and taxonomic study for each putative taxon. PMID:27556403

  13. Progress Towards an Interdisciplinary Science of Plant Phenology: Building Predictions Across Space, Time and Species Diversity

    NASA Technical Reports Server (NTRS)

    Wolkovich, Elizabeth M.; Cook, Benjamin I.; Davies, T. Jonathan

    2013-01-01

    Climate change has brought renewed interest in the study of plant phenology - the timing of life history events. Data on shifting phenologies with warming have accumulated rapidly, yet research has been comparatively slow to explain the diversity of phenological responses observed across latitudes, growing seasons and species. Here, we outline recent efforts to synthesize perspectives on plant phenology across the fields of ecology, climate science and evolution. We highlight three major axes that vary among these disciplines: relative focus on abiotic versus biotic drivers of phenology, on plastic versus genetic drivers of intraspecific variation, and on cross-species versus autecological approaches. Recent interdisciplinary efforts, building on data covering diverse species and climate space, have found a greater role of temperature in controlling phenology at higher latitudes and for early-flowering species in temperate systems. These efforts have also made progress in understanding the tremendous diversity of responses across species by incorporating evolutionary relatedness, and linking phenological flexibility to invasions and plant performance. Future research with a focus on data collection in areas outside the temperate mid-latitudes and across species' ranges, alongside better integration of how risk and investment shape plant phenology, offers promise for further progress.

  14. Species Diversity and Phylogeographical Affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada

    PubMed Central

    Jeffery, Nicholas W.; Elías-Gutiérrez, Manuel; Adamowicz, Sarah J.

    2011-01-01

    The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale. PMID:21610864

  15. Limits to randomness in paleobiologic models: the case of Phanerozoic species diversity

    NASA Technical Reports Server (NTRS)

    Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

    1994-01-01

    The question of how random, or unconstrained, paleobiologic models should be is examined with a case study: Signor's (1982, 1985) inverse calculation of levels of marine species diversity through the Phanerozoic. His calculation involved an ingenious model that estimated species numbers and species abundances in the world oceans of the past by correcting known numbers of fossil species for variations in sedimentary rocks available for sampling and in effort paleontologists might devote to sampling. The model proves robust to changes in possible shapes of species-abundance distributions, but it is sensitive to alterations in the assumption that paleontologists collect fossils at random. If it is assumed that ease of collecting varies with age of sediment (with the Cenozoic offering easy sampling) or that paleontologists tend to seek out rarer fossils, results of the inverse calculation change. In particular, the magnitude of the calculated Cenozoic diversity increase always declines from the factor of about seven as originally reported to something considerably smaller. This leaves open the problem of the magnitude of Cenozoic increase in marine species diversity, awaiting better empirical data and, perhaps, more exacting models, random or otherwise.

  16. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea.

    PubMed

    Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

    2011-04-01

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.

  17. Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada.

    PubMed

    Jeffery, Nicholas W; Elías-Gutiérrez, Manuel; Adamowicz, Sarah J

    2011-01-01

    The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.

  18. New Records of Lake Baikal Leech Fauna: Species Diversity and Spatial Distribution in Chivyrkuy Gulf

    PubMed Central

    Kaygorodova, Irina A.; Pronin, Nikolay M.

    2013-01-01

    The study of several Lake Baikal leech collections offered us the possibility to determine species diversity in the Chivyrkuy Gulf, the biggest one in the lake. As a result, the first information on the Chivyrkuy Hirudinea fauna (Annelida, Clitellata) has been revealed. There are two orders and four families of leeches in the Chivyrkuy Gulf: order Rhynchobdellida (families Glossiphoniidae and Piscicolidae) and order Arhynchobdellida (families Erpobdellidae and Haemopidae). In total, 22 leech species and 2 subspecies belonging to 11 genera were identified. Of these, 4 taxa belong to the family Glossiphoniidae (G. concolor, A. hyalina, A. heteroclita f. papillosa, and A. heteroclita f. striata) recorded in Baikal for the first time. Representatives of 8 unidentified species (Glossophinia sp., Baicaloclepsis sp., Baicalobdella sp., Piscicola sp. 1, Piscicola sp. 2, Erpobdella sp. 1, Erpobdella sp. 2, and Erpobdella sp. 3) have been also recorded. The checklist gives a contemporary overview of the species composition of leech parasites, their hosts, and distribution within the Chivyrkuy Gulf. The analysis of spatial distribution has shown that the leech species diversity is correlated with the biological productivity of the bay. The most diverse community of leech species is detected in the eutrophic zone of the lake. PMID:23844382

  19. Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong).

    PubMed

    Chen, Weitao; Shen, Yanjun; Gan, Xiaoni; Wang, Xuzhen; He, Shunping

    2016-09-01

    The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai-Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re-examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.

  20. Progress towards an interdisciplinary science of plant phenology: building predictions across space, time and species diversity.

    PubMed

    Wolkovich, Elizabeth M; Cook, Benjamin I; Davies, T Jonathan

    2014-03-01

    Climate change has brought renewed interest in the study of plant phenology - the timing of life history events. Data on shifting phenologies with warming have accumulated rapidly, yet research has been comparatively slow to explain the diversity of phenological responses observed across latitudes, growing seasons and species. Here, we outline recent efforts to synthesize perspectives on plant phenology across the fields of ecology, climate science and evolution. We highlight three major axes that vary among these disciplines: relative focus on abiotic versus biotic drivers of phenology, on plastic versus genetic drivers of intraspecific variation, and on cross-species versus autecological approaches. Recent interdisciplinary efforts, building on data covering diverse species and climate space, have found a greater role of temperature in controlling phenology at higher latitudes and for early-flowering species in temperate systems. These efforts have also made progress in understanding the tremendous diversity of responses across species by incorporating evolutionary relatedness, and linking phenological flexibility to invasions and plant performance. Future research with a focus on data collection in areas outside the temperate mid-latitudes and across species' ranges, alongside better integration of how risk and investment shape plant phenology, offers promise for further progress.

  1. Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa

    USGS Publications Warehouse

    Champagne, Juilette; Paine, C. E. Timothy; Schoolmaster, Donald; Stejskal, Robert; Volařík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

    2016-01-01

    Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory.

  2. Effects of native species diversity and resource additions on invader impact.

    PubMed

    Maron, John L; Marler, Marilyn

    2008-07-01

    Theory and empirical work have demonstrated that diverse communities can inhibit invasion. Yet, it is unclear how diversity influences invader impact, how impact varies among exotics, and what the relative importance of diversity is versus extrinsic factors that themselves can influence invasion. To address these issues, we established plant assemblages that varied in native species and functional richness and crossed this gradient in diversity with resource (water) addition. Identical assemblages were either uninvaded or invaded with one of three exotic forbs: spotted knapweed (Centaurea maculosa), dalmatian toadflax (Linaria dalmatica), or sulfur cinquefoil (Potentilla recta). To determine impacts, we measured the effects of exotics on native biomass and, for spotted knapweed, on soil moisture and nitrogen levels. Assemblages with high species richness were less invaded and less impacted than less diverse assemblages. Impact scaled with exotic biomass; spotted knapweed had the largest impact on native biomass compared with the other exotics. Although invasion depressed native biomass, the net result was to increase total community yield. Water addition increased invasibility (for knapweed only) but had no effect on invader impact. Together, these results suggest that diversity inhibits invasion and reduces impact more than resource additions facilitate invasion or impact.

  3. Correlating Species and Spectral Diversity using Remote Sensing in Successional Fields in Virginia

    NASA Astrophysics Data System (ADS)

    Aneece, I.; Epstein, H. E.

    2015-12-01

    Conserving biodiversity can help preserve ecosystem properties and function. As the increasing prevalence of invasive plant species threatens biodiversity, advances in remote sensing technology can help monitor invasive species and their effects on ecosystems and plant communities. To assess whether we could study the effects of invasive species on biodiversity using remote sensing, we asked whether species diversity was positively correlated with spectral diversity, and whether correlations differed among spectral regions along the visible and near-infrared range. To answer these questions, we established community plots in secondary successional fields at the Blandy Experimental Farm in northern Virginia and collected vegetation surveys and ground-level hyperspectral data from 350 to 1025 nm wavelengths. Pearson correlation analysis revealed a positive correlation between spectral diversity and species diversity in the visible ranges of 350-499 nm (Pearson correlation=0.69, p=0.01), 500-589 nm (Pearson=0.64, p=0.03), and 590-674 nm (Pearson=0.70, p=0.01), slight positive correlation in the red edge range of 675-754 nm (Pearson=0.56, p=0.06), and no correlation in the near-infrared ranges of 755-924 nm (Pearson=-0.06, p=0.85) and 925-1025 nm (Pearson=0.30, p=0.34). These differences in correlations across spectral regions may be due to the elements that contribute to signatures in those regions and spectral data transformation methods. To investigate the role of pigment variability in these correlations, we estimated chlorophyll, carotenoid, and anthocyanin concentrations of five dominant species in the plots using vegetation indices. Although interspecific variability in pigment levels exceeded intraspecific variability, chlorophyll (F value=118) was more varied within species than carotenoids (F=322) and anthocyanins (F=126), perhaps contributing to the lack of correlation between species diversity and spectral diversity in the red edge region. Interspecific

  4. The importance of rare species: a trait-based assessment of rare species contributions to functional diversity and possible ecosystem function in tall-grass prairies

    PubMed Central

    Jain, Meha; Flynn, Dan FB; Prager, Case M; Hart, Georgia M; DeVan, Caroline M; Ahrestani, Farshid S; Palmer, Matthew I; Bunker, Daniel E; Knops, Johannes MH; Jouseau, Claire F; Naeem, Shahid

    2014-01-01

    The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait-based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species are functionally redundant when rarity is defined by mean abundance. Furthermore, when using abundance-weighted analyses, we find that rare species typically contribute significantly less to functional diversity than common species due to their low abundances. These results suggest that rare species have the potential to play an important role in ecosystem functioning, either by offering novel contributions to functional diversity or via functional redundancy depending on how rare species are defined. Yet, these contributions are likely to be greatest if the abundance of rare species increases due to environmental change. We argue that given the paucity of data on rare species, understanding the contribution of rare species to community functional diversity is an important first step to understanding the potential role of rare species in ecosystem functioning. PMID:24455165

  5. The importance of rare species: a trait-based assessment of rare species contributions to functional diversity and possible ecosystem function in tall-grass prairies.

    PubMed

    Jain, Meha; Flynn, Dan Fb; Prager, Case M; Hart, Georgia M; Devan, Caroline M; Ahrestani, Farshid S; Palmer, Matthew I; Bunker, Daniel E; Knops, Johannes Mh; Jouseau, Claire F; Naeem, Shahid

    2014-01-01

    The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait-based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species are functionally redundant when rarity is defined by mean abundance. Furthermore, when using abundance-weighted analyses, we find that rare species typically contribute significantly less to functional diversity than common species due to their low abundances. These results suggest that rare species have the potential to play an important role in ecosystem functioning, either by offering novel contributions to functional diversity or via functional redundancy depending on how rare species are defined. Yet, these contributions are likely to be greatest if the abundance of rare species increases due to environmental change. We argue that given the paucity of data on rare species, understanding the contribution of rare species to community functional diversity is an important first step to understanding the potential role of rare species in ecosystem functioning.

  6. Native fish diversity alters the effects of an invasive species on food webs.

    PubMed

    Carey, Michael P; Wahl, David H

    2010-10-01

    Aquatic communities have been altered by invasive species, with impacts on native biodiversity and ecosystem function. At the same time, native biodiversity may mitigate the effects of an invader. Common carp (Cyprinus carpio) is a ubiquitous, invasive fish species that strongly influences community and ecosystem processes. We used common carp to test whether the potential effects of an invasive species are altered across a range of species diversity in native communities. In mesocosms, treatments of zero, one, three, and six native fish species were used to represent the nested subset patterns observed in fish communities of lakes in Illinois, USA. The effect of the invader was tested across fish richness treatments by adding common carp to the native community and substituting native biomass with common carp. Native species and intraspecific effects reduced invader growth. The invader reduced native fish growth; however, the negative effect was minimized with increasing native richness. The zooplankton grazer community was modified by a top-down effect from the invader that increased the amount of phytoplankton. Neither the invader nor richness treatments influenced total phosphorus or community metabolism. Overall, the invader reduced resources for native species; and the effect scaled with how the invader was incorporated into the community. Higher native diversity mitigated the impact of the invader, confirming the need to consider biodiversity when predicting the impacts of invasive species.

  7. Brood Parasitism Is Linked to Egg Pattern Diversity within and among Species of Australian Passerines.

    PubMed

    Medina, Iliana; Troscianko, Jolyon; Stevens, Martin; Langmore, Naomi E

    2016-03-01

    Bird eggs show striking diversity in color and pattern. One explanation for this is that interactions between avian brood parasites and their hosts drive egg phenotype evolution. Brood parasites lay their eggs in the nests of other species, their hosts. Many hosts defend their nests against parasitism by rejecting foreign eggs, which selects for parasite eggs that mimic those of the host. In theory, this may in turn select for changes in host egg phenotypes over time to facilitate discrimination of parasite eggs. Here, we test for the first time whether parasitism by brood parasites has led to increased divergence in egg phenotype among host species. Using Australian host and nonhost species and objective measures of egg color and pattern, we show that (i) hosts of brood parasites have higher within-species variation in egg pattern than nonhosts, supporting previous findings in other systems, and (ii) host species have diverged more in their egg patterns than nonhost species after controlling for divergence time. Overall, our results suggest that brood parasitism has played a significant role in the evolution of egg diversity and that these effects are evident, not only within species, but also among species.

  8. Predicting coral species richness: the effect of input variables, diversity and scale.

    PubMed

    Richards, Zoe T; Hobbs, Jean-Paul A

    2014-01-01

    Coral reefs are facing a biodiversity crisis due to increasing human impacts, consequently, one third of reef-building corals have an elevated risk of extinction. Logistic challenges prevent broad-scale species-level monitoring of hard corals; hence it has become critical that effective proxy indicators of species richness are established. This study tests how accurately three potential proxy indicators (generic richness on belt transects, generic richness on point-intercept transects and percent live hard coral cover on point-intercept transects) predict coral species richness at three different locations and two analytical scales. Generic richness (measured on a belt transect) was found to be the most effective predictor variable, with significant positive linear relationships across locations and scales. Percent live hard coral cover consistently performed poorly as an indicator of coral species richness. This study advances the practical framework for optimizing coral reef monitoring programs and empirically demonstrates that generic richness offers an effective way to predict coral species richness with a moderate level of precision. While the accuracy of species richness estimates will decrease in communities dominated by species-rich genera (e.g. Acropora), generic richness provides a useful measure of phylogenetic diversity and incorporating this metric into monitoring programs will increase the likelihood that changes in coral species diversity can be detected.

  9. Relationship between species diversity and reef growth in the Holocene at Ishigaki Island, Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Hongo, Chuki; Kayanne, Hajime

    2010-01-01

    Coral reefs are influenced by global and local factors, and living corals are currently faced with a potential loss of species diversity. Knowledge of the relationship between species diversity and reef growth during the Holocene is important in terms of accurately reconstructing natural conditions prior to recent disturbances (e.g., human impact, pollution, and over-harvesting) and in predicting future scenarios (e.g., abrupt sea-level rise, coastal change, and economic services). This study seeks to characterize the Holocene and present-day reef at Ishigaki Island in the Ryukyu Islands, focusing on spatial and temporal variations in the relationship between species diversity and reef growth. The analysis is based on a drilling core obtained for the Holocene reefs and quantitative species-diversity data (Shannon and Weaver's diversity index, H') obtained for the present-day reef. H' was calculated for four coral communities surveyed at the Ibaruma and Fukido reefs. The Holocene sequence was dominated by the corymbose coral community (e.g., Acropora digitifera, A. hyacinthus, Goniastrea retiformis, and Platygyra ryukyuensis), yielding an H' value of 1.6. The encrusting coral community (e.g., Echinopora lamellose and Pachyseris rugosa) showed the highest diversity at the reef ( H' = 2.2); however, this community was not one of the main reef builders during the Holocene. The massive coral community (e.g., Porites lutea and Favites chinensis) showed the lowest diversity ( H' = 0.6). It also made a minor contribution to reef building; this community appeared in a shallow lagoon once sea level had stabilized. The arborescent coral community (e.g., A. formosa and A. nobilis) was one of the main reef builders, although yielding an H' value of much less than 1.0. Species diversity is not a prerequisite in terms of Holocene reef growth. Thus, a few species (e.g., A. digitifera, A. hyacinthus, A. formosa, A. nobilis, G. retiformis, and P. ryukyuensis) from two main reef

  10. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    USGS Publications Warehouse

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  11. Genetic Diversity of Grasspea and Its Relative Species Revealed by SSR Markers

    PubMed Central

    Wang, Fang; Yang, Tao; Burlyaeva, Marina; Li, Ling; Jiang, Junye; Fang, Li; Redden, Robert; Zong, Xuxiao

    2015-01-01

    The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives. PMID:25793712

  12. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake.

    PubMed

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, Jana; Knudsen, Rune; Kuhn, Jesper A; Henriksen, Eirik H; Siwertsson, Anna; Shaw, Jenny C; Kuris, Armand M; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D; Kostadinova, Aneta

    2017-03-14

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  13. Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

    PubMed Central

    Leffler, Ellen M.; Andolfatto, Peter; Przeworski, Molly

    2012-01-01

    Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it. PMID:22984349

  14. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    NASA Astrophysics Data System (ADS)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

  15. White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity.

    PubMed

    Begley-Miller, Danielle R; Hipp, Andrew L; Brown, Bethany H; Hahn, Marlene; Rooney, Thomas P

    2014-06-09

    Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H'), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H' and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly.

  16. Evolutionary history determines how plant productivity responds to phylogenetic diversity and species richness.

    PubMed

    Genung, Mark A; Schweitzer, Jennifer A; Bailey, Joseph K

    2014-01-01

    The relationship between biodiversity and ecosystem function has received a great deal of attention in ecological research and recent results, from re-analyses, suggest that ecosystem function improves with increases in phylogenetic diversity. However, many of these results have been generalized across a range of different species and clades, and plants with different evolutionary histories could display different relationships between biodiversity and ecosystem function. To experimentally test this hypothesis, we manipulated species richness and phylogenetic diversity using 26 species from two subgenera of the genus Eucalyptus (subgenus Eucalyptus and subgenus Symphyomyrtus). We found that plant biomass (a measurement of ecosystem function) sometimes, but not always, responded to increases in species richness and phylogenetic diversity. Specifically, Symphyomyrtus plants showed a positive response while no comparable effect was observed for Eucalyptus plants, showing that responses to biodiversity can vary across different phylogenetic groups. Our results show that the impacts of evolutionary history may complicate the relationship between the diversity of plant communities and plant biomass.

  17. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems.

    PubMed

    Maslov, Sergei; Sneppen, Kim

    2017-01-04

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

  18. White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity

    PubMed Central

    Begley-Miller, Danielle R.; Hipp, Andrew L.; Brown, Bethany H.; Hahn, Marlene; Rooney, Thomas P.

    2014-01-01

    Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H′), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H′ and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly. PMID:24916059

  19. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    PubMed Central

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  20. Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis.

    PubMed

    Gill, B A; Kondratieff, B C; Casner, K L; Encalada, A C; Flecker, A S; Gannon, D G; Ghalambor, C K; Guayasamin, J M; Poff, N L; Simmons, M P; Thomas, S A; Zamudio, K R; Funk, W C

    2016-06-15

    The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns.

  1. San Francisco Bay Area Endangered Species Litigation - Center for Biological Diversity v. EPA

    EPA Pesticide Factsheets

    EPA and the Center for Biological Diversity have agreed to a revised settlement agreement that amends a 2010 court order for effects determinations on 11 endangered or threatened (listed) species in the San Francisco Bay area. Find out about the new order.

  2. Genetic diversity of grasspea and its relative species revealed by SSR markers.

    PubMed

    Wang, Fang; Yang, Tao; Burlyaeva, Marina; Li, Ling; Jiang, Junye; Fang, Li; Redden, Robert; Zong, Xuxiao

    2015-01-01

    The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives.

  3. Conservation of avian diversity in the Sierra Nevada: moving beyond a single-species management focus

    USGS Publications Warehouse

    White, Angela M.; Zipkin, Elise F.; Manley, Patricia N.; Schlesinger, Matthew D.

    2013-01-01

    Background: As a result of past practices, many of the dry coniferous forests of the western United States contain dense, even-aged stands with uncharacteristically high levels of litter and downed woody debris. These changes to the forest have received considerable attention as they elevate concerns regarding the outcome of wildland fire. However, attempts to reduce biomass through fuel reduction (i.e., thinning of trees) are often opposed by public interest groups whose objectives include maintaining habitat for species of concern such as the spotted owl, Strix occidentalis, the northern goshawk, Accipiter gentilis, and the Pacific fisher, Martes pennanti. Whether protection of these upper-trophic level species confers adequate conservation of avian forest diversity is unknown. Methodology and Principal Findings: We use a multi-species occurrence model to estimate the habitat associations of 47 avian species detected at 742 sampling locations within an 880-km2 area in the Sierra Nevada. Our approach, which accounts for variations in detectability of species, estimates occurrence probabilities of all species in a community by linking species occurrence models into one hierarchical community model, thus improving inferences on all species, especially those that are rare or observed infrequently. We address how the avian community is influenced by covariates related to canopy cover, tree size and shrub cover while accounting for the impacts of abiotic variables known to affect species distributions. Conclusions and Significance: Environmental parameters estimated through our approach emphasize the importance of within and between stand-level heterogeneity in meeting biodiversity objectives and suggests that many avian species would increase under more open canopy habitat conditions than those favored by umbrella species of high conservation concern. Our results suggest that a more integrated approach that emphasizes maintaining a diversity of habitats across

  4. Conservation of Avian Diversity in the Sierra Nevada: Moving beyond a Single-Species Management Focus

    PubMed Central

    White, Angela M.; Zipkin, Elise F.; Manley, Patricia N.; Schlesinger, Matthew D.

    2013-01-01

    Background As a result of past practices, many of the dry coniferous forests of the western United States contain dense, even-aged stands with uncharacteristically high levels of litter and downed woody debris. These changes to the forest have received considerable attention as they elevate concerns regarding the outcome of wildland fire. However, attempts to reduce biomass through fuel reduction (i.e., thinning of trees) are often opposed by public interest groups whose objectives include maintaining habitat for species of concern such as the spotted owl, Strix occidentalis, the northern goshawk, Accipiter gentilis, and the Pacific fisher, Martes pennanti. Whether protection of these upper-trophic level species confers adequate conservation of avian forest diversity is unknown. Methodology and Principal Findings We use a multi-species occurrence model to estimate the habitat associations of 47 avian species detected at 742 sampling locations within an 880-km2 area in the Sierra Nevada. Our approach, which accounts for variations in detectability of species, estimates occurrence probabilities of all species in a community by linking species occurrence models into one hierarchical community model, thus improving inferences on all species, especially those that are rare or observed infrequently. We address how the avian community is influenced by covariates related to canopy cover, tree size and shrub cover while accounting for the impacts of abiotic variables known to affect species distributions. Conclusions and Significance Environmental parameters estimated through our approach emphasize the importance of within and between stand-level heterogeneity in meeting biodiversity objectives and suggests that many avian species would increase under more open canopy habitat conditions than those favored by umbrella species of high conservation concern. Our results suggest that a more integrated approach that emphasizes maintaining a diversity of habitats across

  5. Spatial scale and species identity influence the indigenous-alien diversity relationship in springtails.

    PubMed

    Terauds, Aleks; Chown, Steven L; Bergstrom, Dana M

    2011-07-01

    Although theory underlying the invasion paradox, or the change in the relationship between the richness of alien and indigenous species from negative to positive with increasing spatial scale, is well developed and much empirical work on the subject has been undertaken, most of the latter has concerned plants and to a lesser extent marine invertebrates. Here we therefore examine the extent to which the relationships between indigenous and alien species richness change from the local metacommunity to the interaction neighborhood scales, and the influences of abundance, species identity, and environmental favorability thereon, in springtails, a significant component of the soil fauna. Using a suite of modeling techniques, including generalized least squares and geographically weighted regressions to account for spatial autocorrelation or nonstationarity of the data, we show that the abundance and species richness of both indigenous and alien species at the metacommunity scale respond strongly to declining environmental favorability, represented here by altitude. Consequently, alien and indigenous diversity covary positively at this scale. By contrast, relationships are more complex at the interaction neighborhood scale, with the relationship among alien species richness and/or density and the density of indigenous species varying between habitats, being negative in some, but positive in others. Additional analyses demonstrated a strong influence of species identity, with negative relationships identified at the interaction neighborhood scale involving alien hypogastrurid springtails, a group known from elsewhere to have negative effects on indigenous species in areas where they have been introduced. By contrast, diversity relationships were positive with the other alien species. These results are consistent with both theory and previous empirical findings for other taxa, that interactions among indigenous and alien species change substantially with spatial scale and

  6. Widespread density-dependent seedling mortality promotes species coexistence in a highly diverse Amazonian rain forest.

    PubMed

    Metz, Margaret R; Sousa, Wayne P; Valencia, Renato

    2010-12-01

    Negative density-dependent mortality can promote species coexistence through a spacing mechanism that prevents species from becoming too locally abundant. Negative density-dependent seedling mortality can be caused by interactions among seedlings or between seedlings and neighboring adults if the density of neighbors affects the strength of competition or facilitates the attack of natural enemies. We investigated the effects of seedling and adult neighborhoods on the survival of newly recruited seedlings for multiple cohorts of known age from 163 species in Yasuni National Park, Ecuador, an ever-wet, hyper-diverse lowland Amazonian rain forest. At local scales, we found a strong negative impact on first-year survival of conspecific seedling densities and adult abundance in multiple neighborhood sizes and a beneficial effect of a local tree neighborhood that is distantly related to the focal seedling. Once seedlings have survived their first year, they also benefit from a more phylogenetically dispersed seedling neighborhood. Across species, we did not find evidence that rare species have an advantage relative to more common species, or a community compensatory trend. These results suggest that the local biotic neighborhood is a strong influence on early seedling survival for species that range widely in their abundance and life history. These patterns in seedling survival demonstrate the role of density-dependent seedling dynamics in promoting and maintaining diversity in understory seedling assemblages. The assemblage-wide impacts of species abundance distributions may multiply with repeated cycles of recruitment and density-dependent seedling mortality and impact forest diversity or the abundance of individual species over longer time scales.

  7. Plant species richness drives the density and diversity of Collembola in temperate grassland

    NASA Astrophysics Data System (ADS)

    Sabais, Alexander C. W.; Scheu, Stefan; Eisenhauer, Nico

    2011-05-01

    Declining biodiversity is one of the most important aspects of anthropogenic global change phenomena, but the implications of plant species loss for soil decomposers are little understood. We used the experimental grassland community of the Jena Experiment to assess the response of density and diversity of Collembola to varying plant species richness, plant functional group richness and plant functional group identity. We sampled the experimental plots in spring and autumn four years after establishment of the experimental plant communities. Collembola density and diversity significantly increased with plant species and plant functional group richness highlighting the importance of the singular hypothesis for soil invertebrates. Generally, grasses and legumes beneficially affected Collembola density and diversity, whereas effects of small herbs usually were detrimental. These impacts were largely consistent in spring and autumn. By contrast, in the presence of small herbs the density of hemiedaphic Collembola and the diversity of Isotomidae increased in spring whereas they decreased in autumn. Beneficial impacts of plant diversity as well as those of grasses and legumes were likely due to increased root and microbial biomass, and elevated quantity and quality of plant residues serving as food resources for Collembola. By contrast, beneficial impacts of small herbs in spring probably reflect differences in microclimatic conditions, and detrimental effects in autumn likely were due to low quantity and quality of resources. The results point to an intimate relationship between plants and the diversity of belowground biota, even at small spatial scales, contrasting the findings of previous studies. The pronounced response of soil animals in the present study was presumably due to the fact that plant communities had established over several years. As decomposer invertebrates significantly impact plant performance, changes in soil biota density and diversity are likely

  8. Cryptic diversity revealed by DNA barcoding in Colombian illegally traded bird species.

    PubMed

    Mendoza, Ángela María; Torres, María Fernanda; Paz, Andrea; Trujillo-Arias, Natalia; López-Alvarez, Diana; Sierra, Socorro; Forero, Fernando; Gonzalez, Mailyn A

    2016-07-01

    Colombia is the country with the largest number of bird species worldwide, yet its avifauna is seriously threatened by habitat degradation and poaching. We built a DNA barcode library of nearly half of the bird species listed in the CITES appendices for Colombia, thereby constructing a species identification reference that will help in global efforts for controlling illegal species trade. We obtained the COI barcode sequence of 151 species based on 281 samples, representing 46% of CITES bird species registered for Colombia. The species analysed belong to nine families, where Trochilidae and Psittacidae are the most abundant ones. We sequenced for the first time the DNA barcode of 47 species, mainly hummingbirds endemic of the Northern Andes region. We found a correct match between morphological and genetic identification for 86-92% of the species analysed, depending on the cluster analysis performed (BIN, ABGD and TaxonDNA). Additionally, we identified eleven cases of high intraspecific divergence based on K2P genetic distances (up to 14.61%) that could reflect cryptic diversity. In these cases, the specimens were collected in geographically distant sites such as different mountain systems, opposite flanks of the mountain or different elevations. Likewise, we found two cases of possible hybridization and incomplete lineage sorting. This survey constitutes the first attempt to build the DNA barcode library of endangered bird species in Colombia establishing as a reference for management programs of illegal species trade, and providing major insights of phylogeographic structure that can guide future taxonomic research.

  9. Herbivory and nutrient limitation protect warming tundra from lowland species' invasion and diversity loss.

    PubMed

    Eskelinen, Anu; Kaarlejärvi, Elina; Olofsson, Johan

    2017-01-01

    Herbivory and nutrient limitation can increase the resistance of temperature-limited systems to invasions under climate warming. We imported seeds of lowland species to tundra under factorial treatments of warming, fertilization, herbivore exclusion and biomass removal. We show that warming alone had little impact on lowland species, while exclusion of native herbivores and relaxation of nutrient limitation greatly benefitted them. In contrast, warming alone benefitted resident tundra species and increased species richness; however, these were canceled by negative effects of herbivore exclusion and fertilization. Dominance of lowland species was associated with low cover of tundra species and resulted in decreased species richness. Our results highlight the critical role of biotic and abiotic filters unrelated to temperature in protecting tundra under warmer climate. While scarcity of soil nutrients and native herbivores act as important agents of resistance to invasions by lowland species, they concurrently promote overall species coexistence. However, when these biotic and abiotic resistances are relaxed, invasion of lowland species can lead to decreased abundance of resident tundra species and diminished diversity.

  10. Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity

    PubMed Central

    Giam, Xingli; Scheffers, Brett R.; Sodhi, Navjot S.; Wilcove, David S.; Ceballos, Gerardo; Ehrlich, Paul R.

    2012-01-01

    In the last few decades, there has been a remarkable discovery of new species of plants, invertebrates and vertebrates, in what have been called the new age of discovery. However, owing to anthropogenic impacts such as habitat conversion, many of the still unknown species may go extinct before being scientifically documented (i.e. ‘crypto-extinctions’). Here, by applying a mathematical model of species descriptions which accounts for taxonomic effort, we show that even after 250 years of taxonomic classification, about 3050 amphibians and at least 160 land mammal species remain to be discovered and described. These values represent, respectively, 33 and 3 per cent of the current species total for amphibians and land mammals. We found that tropical moist forests of the Neotropics, Afrotropics and Indomalaya probably harbour the greatest numbers of undescribed species. Tropical forests with minimal anthropogenic disturbance are predicted to have larger proportions of undescribed species. However, the protected area coverage is low in many of these key biomes. Moreover, undescribed species are likely to be at a greater risk of extinction compared with known species because of small geographical ranges among other factors. By highlighting the key areas of undescribed species diversity, our study provides a starting template to rapidly document these species and protect them through better habitat management. PMID:21593037

  11. The roles of community biomass and species pools in the regulation of plant diversity

    USGS Publications Warehouse

    Grace, J.B.

    2001-01-01

    Considerable debate has developed over the importance of community biomass and species pools in the regulation of community diversity. Attempts to explain patterns of plant diversity as a function of community biomass or productivity have been only partially successful and in general, have explained only a fraction of the observed variation in diversity. At the same time studies that have focused on the importance of species pools have led some to conclude that diversity is primarily regulated in the short term by the size of the species pool rather than by biotic interactions. In this paper, I explore how community biomass and species pools may work in combination to regulate diversity in herbaceous plant communities. To address this problem, I employ a simple model in which the dynamics of species richness are a function of aboveground community biomass and environmentally controlled gradients in species pools. Model results lead to two main predictions about the role of biomass regulation: (1) Seasonal dynamics of richness will tend to follow a regular oscillation, with richness rising to peak values during the early to middle portion of the growing season and then declining during the latter part of the season. (2.) Seasonal dieback of aboveground tissues facilitates the long-term maintenance of high levels of richness in the community. The persistence of aboveground tissues and accumulation of litter are especially important in limiting the number of species through the suppression of recruitment. Model results also lead to two main predictions about the role of species pools: (1) The height and position of peak richness relative to community biomass will be influenced by the rate at which the species pool increases as available soil resources increase. (2) Variations in nonresource environmental factors (e.g. soil pH or soil salinity) have the potential to regulate species pools in a way that is uncorrelated with aboveground biomass. Under extreme conditions

  12. Genetic diversity and species pattern of Trichoderma and Hypocrea in Manipur using in silico analysis.

    PubMed

    Kamala, Thongram; Devi, Sarangthem Indira; Thingnam, Gourshyam; Somkuwar, Bharat Gopalrao

    2013-01-01

    We investigated the occurrence and genetic diversity of Trichoderma and Hypocrea in Manipur which lies in the Indo-Burma biodiversity hot spot region. 65 Trichoderma isolates were identified at species level by morphological as well as sequence based analysis of the internal transcribed spacer region 1 and 4. Altogether 22 different species of Trichoderma and Hypocrea were found, of which Trichoderma harzianum represent the dominant species. Phylogenetic analysis reveals a clear cut distinction of strains isolated from various collection sites which further hints the need for detail study of Trichoderma on molecular level.

  13. Landscape corridors can increase invasion by an exotic species and reduce diversity of native species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although corridors have become commonplace in conservation to mitigate negative effects of habitat fragmentation, concerns persist that they may facilitate spread of invasive species. In a large-scale experiment, we measured effects of corridors on invasive fire ants, Solenopsis invicta, and on comm...

  14. Cryptic Diversity in the Ubiquist Species Parisotoma notabilis (Collembola, Isotomidae): A Long-Used Chimeric Species?

    PubMed Central

    Porco, David; Potapov, Mikhail; Bedos, Anne; Busmachiu, Galina; Weiner, Wanda M.; Hamra-Kroua, Salah; Deharveng, Louis

    2012-01-01

    Parisotoma notabilis is the most common species of Collembola in Europe and is currently designated as ubiquist. This species has been extensively used in numerous studies and is considered as well characterized on a morphological ground. Despite the homogeneity of its morphology, the sequencing of the barcoding fragment (5′ end of COI) for several populations throughout Europe and North America revealed four distinct genetic lineages. The divergence found between these lineages was similar to the genetic distance among other species of the genus Parisotoma included in the analysis. All four lineages have been confirmed by the nuclear gene 28S. This congruence between mitochondrial and nuclear signals, as well as the geographical distribution pattern of lineages observed in Europe, supports the potential specific status of these lineages. Based on specimens from the type locality (Hamburg), the species name was successfully assigned to one of these lineages. This finding raises several problems as Parisotoma notabilis has been widely used in many ecological studies. Accumulation of new data for the different lineages detected, especially ecological information and life history traits, is needed to help resolve this situation. PMID:23049931

  15. Predator diversity and density affect levels of predation upon strongly interactive species in temperate rocky reefs.

    PubMed

    Guidetti, Paolo

    2007-12-01

    Indirect effects of predators in the classic trophic cascade theory involve the effects of basal species (e.g. primary producers) mediated by predation upon strongly interactive consumers (e.g. grazers). The diversity and density of predators, and the way in which they interact, determine whether and how the effects of different predators on prey combine. Intraguild predation, for instance, was observed to dampen the effects of predators on prey in many ecosystems. In marine systems, species at high trophic levels are particularly susceptible to extinction (at least functionally). The loss of such species, which is mainly attributed to human activities (mostly fishing), is presently decreasing the diversity of marine predators in many areas of the world. Experimental studies that manipulate predator diversity and investigate the effects of this on strongly interactive consumers (i.e. those potentially capable of causing community-wide effects) in marine systems are scant, especially in the rocky sublittoral. I established an experiment that utilised cage enclosures to test whether the diversity and density of fish predators (two sea breams and two wrasses) would affect predation upon juvenile and adult sea urchins, the most important grazers in Mediterranean sublittoral rocky reefs. Changes in species identity (with sea breams producing major effects) and density of predators affected predation upon sea urchins more than changes in species richness per se. Predation upon adult sea urchins decreased in the presence of multiple predators, probably due to interference competition between sea breams and wrasses. This study suggests that factors that influence both fish predator diversity and density in Mediterranean rocky reefs (e.g. fishing and climate change) may have the potential to affect the predators' ability to control sea urchin population density, with possible repercussions for the whole benthic community structure.

  16. The relation between productivity and species diversity in temperate-Arctic marine ecosystems.

    PubMed

    Witman, Jon D; Cusson, Mathieu; Archambault, Philippe; Pershing, Andrew J; Mieszkowska, Nova

    2008-11-01

    Energy variables, such as evapotranspiration, temperature, and productivity explain significant variation in the diversity of many groups of terrestrial plants and animals at local to global scales. Although the ocean represents the largest continuous habitat on earth with a vast spectrum of primary productivity and species richness, little is known about how productivity influences species diversity in marine systems. To search for general relationships between productivity and species richness in the ocean, we analyzed data from three different benthic marine ecosystems (epifaunal communities on subtidal rock walls, on navigation buoys in the Gulf of St. Lawrence, and Canadian Arctic macrobenthos) across local to continental spatial scales (<20 to >1000 km) using a standardized proxy for productivity, satellite-derived chlorophyll a. Theoretically, the form of the function between productivity and species richness is either monotonically increasing or decreasing, or curvilinear (hump- or U-shaped). We found three negative linear and three hump-shaped relationships between chlorophyll a and species richness out of 10 independent comparisons. Scale dependence was suggested by more prevalent diversity-productivity relationships at smaller (local, landscape) than larger (regional, continental) spatial scales. Differences in the form of the functions were more closely allied with community type than with scale, as negative linear functions were restricted to sessile epifauna while hump-shaped functions occurred in Arctic macrobenthos (mixed epifauna, infauna). In two of the data sets, (St. Lawrence epifauna and Arctic macrobenthos) significant effects of chlorophyll a co-varied with the effects of salinity, suggesting that environmental stress as well as productivity influences diversity in these marine systems. The co-varying effect of salinity may commonly arise in broad-scale studies of productivity and diversity in marine ecosystems when attempting to sample the

  17. Enterococcus species diversity in fecal samples of wild marine species as determined by real-time PCR.

    PubMed

    Medeiros, Aline Weber; Blaese Amorim, Derek; Tavares, Maurício; de Moura, Tiane Martin; Franco, Ana Claudia; d'Azevedo, Pedro Alves; Frazzon, Jeverson; Frazzon, Ana Paula Guedes

    2017-02-01

    Analyses using culture-independent molecular techniques have improved our understanding of microbial composition. The aim of this work was to identify and quantify enterococci in fecal samples of wild marine species using real-time quantitative PCR. Seven Enterococcus species were examined in fecal DNA of South American fur seals (Arctocephalus australis), Subantarctic fur seals (Arctocephalus tropicalis), green turtles (Chelonia mydas), Magellanic penguins (Spheniscus magellanicus), snowy-crowned tern (Sterna trudeaui), white-backed stilt (Himantopus melanurus), white-chinned petrels (Procellaria aequinoctialis), red knot (Calidris canutus), and black-browed albatross (Thalassarche melanophris). All Enterococcus species evaluated were detected in all fecal samples of wild marine species, with a concentration ranging between 10(6) and 10(12) copies/ng of total DNA. Differences in the enterococci distribution were observed. Enterococcus faecalis and Enterococcus mundtii were most abundant in marine mammals. Enterococcus faecalis was frequent in green turtle, Magellanic penguin, snowy-crowned tern, red knot, and black-browed albatross. Enterococcus hirae and Enterococcus gallinarum showed elevated occurrence in white-backed stilt, and Enterococcus faecium in white-chinned petrel. This study showed highest diversity of enterococci in feces of wild marine species than currently available data, and reinforced the use of culture-independent analysis to help us to enhance our understanding of enterococci in gastrointestinal tracts of wild marine species.

  18. Comparative Genomics Revealed Genetic Diversity and Species/Strain-Level Differences in Carbohydrate Metabolism of Three Probiotic Bifidobacterial Species

    PubMed Central

    Odamaki, Toshitaka; Horigome, Ayako; Sugahara, Hirosuke; Hashikura, Nanami; Minami, Junichi; Xiao, Jin-zhong; Abe, Fumiaki

    2015-01-01

    Strains of Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium animalis are widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains of B. breve and B. longum, whereas there were nine common clusters between strains of B. animalis and B. longum and four common clusters between strains of B. animalis and B. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. As B. longum and B. breve are human-residential bifidobacteria (HRB), whereas B. animalis is a non-HRB species, several of the differences in these species' gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics. PMID:26236711

  19. Vietnam, a Hotspot for Chromosomal Diversity and Cryptic Species in Black Flies (Diptera: Simuliidae).

    PubMed

    Adler, Peter H; Takaoka, Hiroyuki; Sofian-Azirun, Mohd; Low, Van Lun; Ya'cob, Zubaidah; Chen, Chee Dhang; Lau, Koon Weng; Pham, Xuan Da

    2016-01-01

    The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country's status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam.

  20. Vietnam, a Hotspot for Chromosomal Diversity and Cryptic Species in Black Flies (Diptera: Simuliidae)

    PubMed Central

    Takaoka, Hiroyuki; Sofian-Azirun, Mohd; Low, Van Lun; Ya’cob, Zubaidah; Chen, Chee Dhang; Lau, Koon Weng; Pham, Xuan Da

    2016-01-01

    The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country’s status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam. PMID:27695048

  1. Acceptable symbiont cell size differs among cnidarian species and may limit symbiont diversity.

    PubMed

    Biquand, Elise; Okubo, Nami; Aihara, Yusuke; Rolland, Vivien; Hayward, David C; Hatta, Masayuki; Minagawa, Jun; Maruyama, Tadashi; Takahashi, Shunichi

    2017-03-21

    Reef-building corals form symbiotic relationships with dinoflagellates of the genus Symbiodinium. Symbiodinium are genetically and physiologically diverse, and corals may be able to adapt to different environments by altering their dominant Symbiodinium phylotype. Notably, each coral species associates only with specific Symbiodinium phylotypes, and consequently the diversity of symbionts available to the host is limited by the species specificity. Currently, it is widely presumed that species specificity is determined by the combination of cell-surface molecules on the host and symbiont. Here we show experimental evidence supporting a new model to explain at least part of the specificity in coral-Symbiodinium symbiosis. Using the laboratory model Aiptasia-Symbiodinium system, we found that symbiont infectivity is related to cell size; larger Symbiodinium phylotypes are less likely to establish a symbiotic relationship with the host Aiptasia. This size dependency is further supported by experiments where symbionts were replaced by artificial fluorescent microspheres. Finally, experiments using two different coral species demonstrate that our size-dependent-infection model can be expanded to coral-Symbiodinium symbiosis, with the acceptability of large-sized Symbiodinium phylotypes differing between two coral species. Thus the selectivity of the host for symbiont cell size can affect the diversity of symbionts in corals.The ISME Journal advance online publication, 21 March 2017; doi:10.1038/ismej.2017.17.

  2. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands.

    PubMed

    Pailles, Yveline; Ho, Shwen; Pires, Inês S; Tester, Mark; Negrão, Sónia; Schmöckel, Sandra M

    2017-01-01

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  3. Polyphenolic diversity and characterization in the red-purple berries of East Asian wild Vitis species.

    PubMed

    Koyama, Kazuya; Kamigakiuchi, Hiroshi; Iwashita, Kazuhiro; Mochioka, Ryosuke; Goto-Yamamoto, Nami

    2017-02-01

    Grapes (Vitis spp.) produce diverse polyphenolic compounds, which are phytochemicals that contribute to human health. In this study, the polyphenolic profiles of the red-purple berries of two wild grape species native to Japan, Vitis ficifolia and V. coignetiae, and their interspecific hybrid cultivars were investigated and compared with the profiles of V. vinifera and V. × labruscana cultivars. Proanthocyanidins (PAs) were present at lower concentrations in both skins and seeds of wild grape species and their hybrid cultivars than those in V. vinifera cultivars. They also differed in their composition, consisting mainly of epicatechin in wild grape species, but containing considerable amounts of both epigallocatechin in the skins and epicatechin gallate in the seeds of V. vinifera. In contrast, V. ficifolia varieties and their hybrid cultivars accumulated high concentrations of diverse anthocyanins, and whose compositions of anthocyanins and flavonols differed between species in their degree of modification by glucosylation, acylation, methylation and B-ring hydroxylation. Principal component analysis (PCA) indicated that the polyphenolic constituents clearly separate V. vinifera and V. × labruscana cultivars from the wild grape species as well as between wild grape species, V. coignetiae and V. ficifolia. Intermediate compositions were also observed in the hybrid cultivars between these wild grape species and V. vinifera.

  4. A comparative study of AMF diversity in annual and perennial plant species from semiarid gypsum soils.

    NASA Astrophysics Data System (ADS)

    Alguacil, M. M.; Torrecillas, E.; Roldán, A.; Díaz, G.; Torres, P.

    2012-04-01

    The arbuscular mycorrhizal fungi (AMF) communities composition regulate plant interactions and determine the structure of plant communities. In this study we analysed the diversity of AMF in the roots of two perennial gypsophyte plant species, Herniaria fruticosa and Senecio auricula, and an annual herbaceous species, Bromus rubens, growing in a gypsum soil from a semiarid area. The objective was to determine whether perennial and annual host plants support different AMF communities in their roots and whether there are AMF species that might be indicators of specific functional plant roles in these ecosystems. The roots were analysed by nested PCR, cloning, sequencing of the ribosomal DNA small subunit region and phylogenetic analysis. Twenty AMF sequence types, belonging to the Glomus group A, Glomus group B, Diversisporaceae, Acaulosporaceae, Archaeosporaceae and Paraglomeraceae, were identified. Both gypsophyte perennial species had differing compositions of the AMF community and higher diversity when compared with the annual species, showing preferential selection by specific AMF sequences types. B. rubens did not show host specificity, sharing the full composition of its AMF community with both perennial plant species. Seasonal variations in the competitiveness of AM fungi could explain the observed differences in AMF community composition, but this is still a working hypothesis that requires the analysis of further data obtained from a higher number of both annual and perennial plant species in order to be fully tested.

  5. Comparison of small mammal species diversity near wastewater outfalls, natural streams, and dry canyons

    SciTech Connect

    Raymer, D.F.; Biggs, J.R.

    1994-03-01

    A wide range of plant and wildlife species utilizes water discharged from facilities at Los Alamos National Laboratory (LANL). The purpose of this study was to compare nocturnal small mammal communities at wet areas created by wastewater outfalls with communities in naturally created wet and dry areas. Thirteen locations within LANL boundaries were selected for small mammal mark-recapture trapping. Three of these locations lacked surface water sources and were classified as {open_quotes}dry,{close_quotes} while seven sites were associated with wastewater outfalls ({open_quotes}outfall{close_quotes} sites), and three were located near natural sources of surface water ({open_quotes}natural{close_quotes} sites). Data was collected on site type (dry, outfall or natural), location, species trapped, and the tag number of each individual captured. This data was used to calculate mean number of species, percent capture rate, and species diversity at each type of site. When data from each type of site was pooled, there were no significant differences in these variables between dry, outfall, and natural types. However, when data from individual sites was compared, tests revealed significant differences. All sites in natural areas were significantly higher than dry areas in daily mean number of species, percent capture rate, and species diversity. Most outfall sites were significantly higher than dry areas in all three variables tested. When volume of water from each outfall site was considered, these data indicated that the number of species, percent capture rate, and species diversity of nocturnal small mammals were directly related to the volume of water at a given outfall.

  6. Ground Layer Plant Species Turnover and Beta Diversity in Southern-European Old-Growth Forests

    PubMed Central

    Sabatini, Francesco Maria; Burrascano, Sabina; Tuomisto, Hanna; Blasi, Carlo

    2014-01-01

    Different assembly processes may simultaneously affect local-scale variation of species composition in temperate old-growth forests. Ground layer species diversity reflects chance colonization and persistence of low-dispersal species, as well as fine-scale environmental heterogeneity. The latter depends on both purely abiotic factors, such as soil properties and topography, and factors primarily determined by overstorey structure, such as light availability. Understanding the degree to which plant diversity in old-growth forests is associated with structural heterogeneity and/or to dispersal limitation will help assessing the effectiveness of silvicultural practices that recreate old-growth patterns and structures for the conservation or restoration of plant diversity. We used a nested sampling design to assess fine-scale species turnover, i.e. the proportion of species composition that changes among sampling units, across 11 beech-dominated old-growth forests in Southern Europe. For each stand, we also measured a wide range of environmental and structural variables that might explain ground layer species turnover. Our aim was to quantify the relative importance of dispersal limitation in comparison to that of stand structural heterogeneity while controlling for other sources of environmental heterogeneity. For this purpose, we used multiple regression on distance matrices at the within-stand extent, and mixed effect models at the extent of the whole dataset. Species turnover was best predicted by structural and environmental heterogeneity, especially by differences in light availability and in topsoil nutrient concentration and texture. Spatial distances were significant only in four out of eleven stands with a relatively low explanatory power. This suggests that structural heterogeneity is a more important driver of local-scale ground layer species turnover than dispersal limitation in southern European old-growth beech forests. PMID:24748155

  7. Ground layer plant species turnover and beta diversity in southern-European old-growth forests.

    PubMed

    Sabatini, Francesco Maria; Burrascano, Sabina; Tuomisto, Hanna; Blasi, Carlo

    2014-01-01

    Different assembly processes may simultaneously affect local-scale variation of species composition in temperate old-growth forests. Ground layer species diversity reflects chance colonization and persistence of low-dispersal species, as well as fine-scale environmental heterogeneity. The latter depends on both purely abiotic factors, such as soil properties and topography, and factors primarily determined by overstorey structure, such as light availability. Understanding the degree to which plant diversity in old-growth forests is associated with structural heterogeneity and/or to dispersal limitation will help assessing the effectiveness of silvicultural practices that recreate old-growth patterns and structures for the conservation or restoration of plant diversity. We used a nested sampling design to assess fine-scale species turnover, i.e. the proportion of species composition that changes among sampling units, across 11 beech-dominated old-growth forests in Southern Europe. For each stand, we also measured a wide range of environmental and structural variables that might explain ground layer species turnover. Our aim was to quantify the relative importance of dispersal limitation in comparison to that of stand structural heterogeneity while controlling for other sources of environmental heterogeneity. For this purpose, we used multiple regression on distance matrices at the within-stand extent, and mixed effect models at the extent of the whole dataset. Species turnover was best predicted by structural and environmental heterogeneity, especially by differences in light availability and in topsoil nutrient concentration and texture. Spatial distances were significant only in four out of eleven stands with a relatively low explanatory power. This suggests that structural heterogeneity is a more important driver of local-scale ground layer species turnover than dispersal limitation in southern European old-growth beech forests.

  8. Rich and rare—First insights into species diversity and abundance of Antarctic abyssal Gastropoda (Mollusca)

    NASA Astrophysics Data System (ADS)

    Schwabe, Enrico; Michael Bohn, Jens; Engl, Winfried; Linse, Katrin; Schrödl, Michael

    2007-08-01

    The abyssal depths of the polar oceans are thought to be low in diversity compared with the shallower polar shelves and temperate and tropical deep-sea basins. Our recent study on the gastropod fauna of the deep Southern Ocean gives evidence of the existence of a rich gastropod assemblage at abyssal depths. During the ANDEEP I and II expeditions to the southern Drake Passage, Northwestern Weddell Sea, and South Sandwich Trench, gastropods were collected by bottom and Agassiz trawls, epibenthic sledge, and multicorer, at 40 stations in depths between 127 and 5194 m. On the whole, 473 specimens, corresponding to 93 species of 36 families, were obtained. Of those, 414 specimens were caught below 750 m depth and refer to 84 (90%) benthic species of 32 (89%) families. Most families were represented by a single species only. The numerically dominant families were Skeneidae and Buccinidae (with 10 and 11 species, respectively), Eulimidae and Trochidae (with 9 species each), and Turridae (6 species). Thirty-Seven benthic deep-sea species (44%) were represented by a single specimen, and another 20 species (24%) were found at a single station, suggesting that more than two thirds of Antarctic deep-sea gastropod species are very rare or have a very scattered distribution. Of the 27 species occurring at two or more deep-sea stations, 14 were collected with different gear. Approximately half of the deep-water species are new to science or have been recently described. The present investigation increases the total number of recorded benthic Antarctic deep-sea gastropods (below 750 m) from 115 to 177. The previously known depth ranges have been extended, often considerably, for 31 species. The collected deep-sea gastropods comprise both eurybathic shelf species (29%) and apparently true deep-sea species (58%); some of the latter may belong to a so far unknown Antarctic abyssal fauna. Geographical ranges of the collected Antarctic benthic deep-sea gastropod species appear limited

  9. Unrecognized diversity in New Guinean crayfish species (Decapoda, Parastacidae): The evidence from molecular data.

    PubMed

    Bláha, Martin; Patoka, Jiří; Kozák, Pavel; Kouba, Antonín

    2016-11-01

    The phylogenetic relationships among imported ornamental crayfish belonging to the genus Cherax were inferred from a combined dataset of 3 mitochondrial genes (COI, 16S and 12S) and by comparison with available GenBank sequences of 14 Cherax species. Furthermore, the concordance of previously described species obtained from a wholesaler (Cherax boesemani, C. holthuisi and C. peknyi) with available GenBank sequences was verified based on COI with special respect to comparison with sequences assigned as Cherax species. Recently described species C. gherardiae, C. pulcher and C. subterigneus belong to the northern group of Cherax species. Comparison and analysis with other GenBank COI sequences show previously unreported diversity of New Guinean species, suggesting 5 putative new species. Surprisingly, species assigned to the subgenus Astaconephrops do not form a monophyletic clade; this subgenus should be reappraised relative to the purported typical morphological characteristic of the uncalcified patch on male chelae. Increasing importation of crayfish underscores the importance of accurate species identification. Use of basic molecular methods is a necessary requisite for documenting occurrence, abundance and population trends of target species. Consequently, it helps to support eventual conservation decision-making by stakeholders.

  10. From one to six: unrecognized species diversity in the genus Acantholichen (lichenized Basidiomycota: Hygrophoraceae).

    PubMed

    Dal-Forno, Manuela; Lücking, Robert; Bungartz, Frank; Yánez-Ayabaca, Alba; Marcelli, Marcelo P; Spielmann, Adriano A; Coca, Luis Fernando; Chaves, José Luis; Aptroot, Andre; Sipman, Harrie J M; Sikaroodi, Masoumeh; Gillevet, Patrick; Lawrey, James D

    2016-01-01

    We present a taxonomic revision of the lichenized basidiomycete genus Acantholichen, species of which produce a characteristic blue-gray, microsquamulose thallus with spiny apical hyphal cells known as acanthohyphidia. Since its discovery, the genus was thought to be monospecific, only including the generic type, A. pannarioides. However, a detailed morphological and anatomical study of recently collected specimens from the Galápagos, Costa Rica, Brazil and Colombia, combined with a molecular phylogenetic analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and 28S of the nuc rDNA and RPB2 sequences, revealed a much more diverse and widespread species assemblage. Based on the results of these analyses, we describe five new species in the genus: A. albomarginatus, A. campestris, A. galapagoensis, A. sorediatus and A. variabilis. We also provide an identification key to all species, anatomical and morphological descriptions, photographs and a table comparing main characters of each species.

  11. Effects of plant species identity, diversity and soil fertility on biodegradation of phenanthrene in soil.

    PubMed

    Oyelami, Ayodeji O; Okere, Uchechukwu V; Orwin, Kate H; De Deyn, Gerlinde B; Jones, Kevin C; Semple, Kirk T

    2013-02-01

    The work presented in this paper investigated the effects of plant species composition, species diversity and soil fertility on biodegradation of (14)C-phenanthrene in soil. The two soils used were of contrasting fertility, taken from long term unfertilised and fertilised grassland, showing differences in total nitrogen content (%N). Plant communities consisted of six different plant species: two grasses, two forbs, and two legume species, and ranged in species richness from 1 to 6. The degradation of (14)C-phenanthrene was evaluated by measuring indigenous catabolic activity following the addition of the contaminant to soil using respirometry. Soil fertility was a driving factor in all aspects of (14)C-phenanthrene degradation; lag phase, maximum rates and total extents of (14)C-phenanthrene mineralisation were higher in improved soils compared to unimproved soils. Plant identity had a significant effect on the lag phase and extents of mineralisation. Soil fertility was the major influence also on abundance of microbial communities.

  12. Epidemiological study on feline gastric Helicobacter spp. in Japan.

    PubMed

    Kubota-Aizawa, Sanae; Ohno, Koichi; Kanemoto, Hideyuki; Nakashima, Ko; Fukushima, Kenjiro; Uchida, Kazuyuki; Chambers, James K; Goto-Koshino, Yuko; Mimuro, Hitomi; Watanabe, Takayasu; Sekizaki, Tsutomu; Tsujimoto, Hajime

    2017-03-26

    Epidemiological and pathological studies on Helicobacter spp. in feline stomachs in Japan were conducted using genus- and species-specific (H. felis, H. bizzozeronii, H. heilmannii sensu stricto[s.s.] and H. pylori) polymerase chain reactions (PCRs), ureAB gene sequencing and histopathology. PCR results showed that 28 of 56 cats were infected with Helicobacter spp., and H. heilmannii s.s. was the most prevalent species by both PCR (28/28) and ureAB gene sequencing (26/28). Some of the sequences showed high similarities with those from human patients with gastric diseases (99%). There were no significant differences between Helicobacter spp.-positive and -negative cats in the severity of chronic gastritis (P=0.69). This is the first extensive epidemiological study on feline gastric Helicobacter spp. in Japan.

  13. Gastric Helicobacter Spp. Infection in Captive Neotropical Brazilian Feline

    PubMed Central

    Luiz de Camargo, Pedro; Akemi Uenaka, Simone; Bette Motta, Maitê; Harumi Adania, Cristina; Yamasaki, Letícia; Alfieri, Amauri A.; Bracarense, Ana Paula F. R. L.

    2011-01-01

    Ten captive neotropical Brazilian feline were submitted to gastroscopic examination and samples of gastric mucosa from fundus, corpus and pyloric antrum were evaluated for the presence of Helicobacter species. Warthin-Starry (WS) staining and PCR assay with species-specific primers and enzymatic cleavage were applied for bacterial detection and identification. Histological lesions were evaluated by haematoxylin and eosin staining. All animals showed normal gross aspect of gastric mucosa. Helicobacter heilmannii was confirmed in 100% of the samples by WS and PCR assay. Mild lymphocytic infiltrate in the lamina propria was observed in eight animals, mainly in the fundus region. Small lymphoid follicles were seen in three animals. No significant association between Helicobacter infection and histological findings was verified. These observations suggest that gastric Helicobacter spp. could be a commensal or a eventual pathogen to captive neotropical feline, and that procedures, way life, and stress level on the shelter apparently had no negative repercussion over the integrity of the stomach. PMID:24031634

  14. Population structure and genetic diversity of a medicinal plant species Retama raetam in southern Tunisia.

    PubMed

    Abdellaoui, Raoudha; Yahyaoui, Faouzia; Neffati, Mohamed

    2014-01-15

    Retama raetam is a stem-assimilating, C3, evergreen, medicinal plant species, desert legume common to arid ecosystems around the Mediterranean basin. This study addresses the genetic diversity and relationship among and within three populations collected from different habitats in southern Tunisia by Random Amplified Polymorphic DNA (RAPD). Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were determined. Results showed that population from the Island Djerba has the lowest Nei's gene diversity; this also was for Shannon diversity index. An analysis of molecular variance indicated that the majority of variation existed within populations (68%) and that there was significant differentiation among populations (phiPT = 0.316, p < 0.001). Genetic distance (phiPT based values) between pairwise populations ranged from 0.098 to 0.505 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the coefficient of gene differentiation (Gst), gene flow (Nm) was estimated and was found to vary from 0.490 to 4.609 between pair-wise populations and 1.42 among populations. The results of UPGMA cluster analysis and PCoA analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of R. raetam in southern Tunisia and will be useful for conservation managers to work out an effective strategy to protect this important species.

  15. Species Diversity and Population Dynamics of Entomopathogenic Fungal Species in the Genus Metarhizium-a Spatiotemporal Study.

    PubMed

    Hernández-Domínguez, Carmela; Guzmán-Franco, Ariel W

    2017-01-26

    We studied the species diversity and population genetic structure of isolates of fungi from the entomopathogenic genus Metarhizium that had been isolated from sugarcane crops and surrounding grass. Soil and leaf samples were taken on four sampling occasions over 13 months (October 2014-October 2015). Isolations were made using the Galleria mellonella baiting method and selective media. Phylogenetic placement of isolates was done by sequencing a fragment of the 5' of the elongation factor 1-α gene (EF1-α). Population genetic structure was determined by analysing this sequence information using AMOVA and Haplotype network analyses. Genotypic diversity was studied using microsatellite genotyping. The most abundant species was M. anisopliae s.s. (80 isolates), then M. pingshaense (three isolates), and M. guizhouense (one isolate). More than 50% of the genetic variation was explained by the time the samples were collected regardless of plant host association. Some haplotypes were found on the first sampling date and then not found on subsequent sampling dates, while other haplotypes were found initially, disappeared, but then found again on the last sampling date. To the best of our knowledge, this is the first report of the population genetic structure of M. anisopliae species in time and space. The effect of abiotic factors is discussed.

  16. Temporal dynamics of deep-sea latitudinal species diversity gradient based on paleoceanographic/micropaleontologic data

    NASA Astrophysics Data System (ADS)

    Yasuhara, M.; Hunt, G.; Okahashi, H.

    2009-12-01

    Macroecology investigates large-scale ecological phenomena, such as regional-global trends in ecosystem properties and biodiversity, and is used to better understand recent human-induced ecosystem degradation. Paleoceanography investigates physical/chemical parameters, biogeochemical cycles, ocean circulation, and ocean-atmosphere interaction, but rarely includes ecosystem-scale biological processes. Here we adopt a macroecological approach to paleoceanography and present sediment core records of the temporal dynamics of deep-sea species diversity gradients using ostracodes from the equatorial Atlantic Ocean for the past four glacial-interglacial cycles. Results show unexpected instability and high amplitude fluctuations in species diversity in the tropical deep ocean. The results imply that the modern deep-sea latitudinal species diversity gradient is unexpectedly dynamic over short time intervals and collapsed during glacial periods. Unstable tropical diversity requires reconsideration of current ecological hypotheses about the generation and maintenance of biodiversity as they apply to the deep sea, and underscores the potential vulnerability and conservation importance of tropical deep-sea ecosystems.

  17. Spectral distance decay: Assessing species beta-diversity by quantile regression

    USGS Publications Warehouse

    Rocchinl, D.; Nagendra, H.; Ghate, R.; Cade, B.S.

    2009-01-01

    Remotely sensed data represents key information for characterizing and estimating biodiversity. Spectral distance among sites has proven to be a powerful approach for detecting species composition variability. Regression analysis of species similarity versus spectral distance may allow us to quantitatively estimate how beta-diversity in species changes with respect to spectral and ecological variability. In classical regression analysis, the residual sum of squares is minimized for the mean of the dependent variable distribution. However, many ecological datasets are characterized by a high number of zeroes that can add noise to the regression model. Quantile regression can be used to evaluate trend in the upper quantiles rather than a mean trend across the whole distribution of the dependent variable. In this paper, we used ordinary least square (ols) and quantile regression to estimate the decay of species similarity versus spectral distance. The achieved decay rates were statistically nonzero (p < 0.05) considering both ols and quantile regression. Nonetheless, ols regression estimate of mean decay rate was only half the decay rate indicated by the upper quantiles. Moreover, the intercept value, representing the similarity reached when spectral distance approaches zero, was very low compared with the intercepts of upper quantiles, which detected high species similarity when habitats are more similar. In this paper we demonstrated the power of using quantile regressions applied to spectral distance decay in order to reveal species diversity patterns otherwise lost or underestimated by ordinary least square regression. ?? 2009 American Society for Photogrammetry and Remote Sensing.

  18. Tree species diversity affects decomposition through modified micro-environmental conditions across European forests.

    PubMed

    Joly, François-Xavier; Milcu, Alexandru; Scherer-Lorenzen, Michael; Jean, Loreline-Katia; Bussotti, Filippo; Dawud, Seid Muhie; Müller, Sandra; Pollastrini, Martina; Raulund-Rasmussen, Karsten; Vesterdal, Lars; Hättenschwiler, Stephan

    2017-02-09

    Different tree species influence litter decomposition directly through species-specific litter traits, and indirectly through distinct modifications of the local decomposition environment. Whether these indirect effects on decomposition are influenced by tree species diversity is presently not clear. We addressed this question by studying the decomposition of two common substrates, cellulose paper and wood sticks, in a total of 209 forest stands of varying tree species diversity across six major forest types at the scale of Europe. Tree species richness showed a weak but positive correlation with the decomposition of cellulose but not with that of wood. Surprisingly, macroclimate had only a minor effect on cellulose decomposition and no effect on wood decomposition despite the wide range in climatic conditions among sites from Mediterranean to boreal forests. Instead, forest canopy density and stand-specific litter traits affected the decomposition of both substrates, with a particularly clear negative effect of the proportion of evergreen tree litter. Our study suggests that species richness and composition of tree canopies modify decomposition indirectly through changes in microenvironmental conditions. These canopy-induced differences in the local decomposition environment control decomposition to a greater extent than continental-scale differences in macroclimatic conditions.

  19. Vertical differences in species turnover and diversity of amphipod assemblages associated with coralline mats

    NASA Astrophysics Data System (ADS)

    Bueno, M.; Tanaka, M. O.; Flores, A. A. V.; Leite, F. P. P.

    2016-11-01

    Environmental gradients are common in rocky shore habitats and may determine species spatial distributions at different scales. In this study, we tested whether environmental filtering affects amphipod assemblages inhabiting coralline algal mats at different vertical heights in southeastern Brazil. Samples obtained from the upper and lower zones of the infralittoral fringe were used to estimate mat descriptors (algal mass, sediment retention, organic matter contents, grain size and sediment sorting) and describe amphipod assemblages (abundance, species richness and diversity indices). Coralline algal mats and amphipod assemblages were similar between intertidal zones in several aspects. However, a more variable retention of sediment (positively related to algal mass), together with the accumulation of larger grains lower on the shore, likely provide higher habitat heterogeneity that hosts generally more diverse (both α- and β-diversity, as well as higher species turnover) amphipod assemblages in the lower intertidal zone. Poorer assemblages in the upper intertidal zone are dominated by omnivores, while carnivorous species are more often found in richer assemblages in the lower intertidal zone, as predicted by traditional niche theory.

  20. Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning.

    PubMed

    Huang, Jihong; Huang, Jianhua; Lu, Xinghui; Ma, Keping

    2016-09-23

    Endemism is an important concept in biogeography and biodiversity conservation. China is one of the richest countries in biodiversity, with very high levels of plant endemism. In this study, we analysed the distribution patterns of diversity, the degree of differentiation, and the endemicity of Chinese endemic seed plants using the floristic unit as a basic spatial analysis unit and 11 indices. The analysis was based on distribution data of 24,951 native seed plant species (excluding subspecies and varieties) and 12,980 Chinese endemic seed plant species, which were sourced from both specimen records and published references. The distribution patterns of Chinese endemic flora were generally consistent but disproportionate across China for diversity, degree of differentiation and endemicity. The South Hengduan Mountains Subregion had the highest values for all indices. At the regional level, both the Hengduan Mountains and the Central China regions were highest in diversity and degrees of differentiation. However, both the rate of local endemic to native species and the rate of local to Chinese endemic species were highest in the Taiwan Region and the South Taiwan Region. The Hengduan Mountains Region and the Central China Region are two key conservation priority areas for Chinese endemic seed plants.

  1. Connecting ground water influxes with fish species diversity in an urbanized watershed

    USGS Publications Warehouse

    Steffy, L.Y.; McGinty, A.L.; Welty, C.; Kilham, S.S.

    2004-01-01

    Valley Creek watershed is a small stream system that feeds the Schuylkill River near Philadelphia, Pennsylvania. The watershed is highly urbanized, including over 17 percent impervious surface cover (ISC) by area. Imperviousness in a watershed has been linked to fish community structure and integrity. Generally, above 10 to 12 percent ISC there is marked decline in fish assemblages with fish being absent above 25 percent ISC. This study quantifies the importance of ground water in maintaining fish species diversity in subbasins with over 30 percent ISC. Valley Creek contains an atypical fish assemblage in that the majority of the fish are warm-water species, and the stream supports naturally reproducing brown trout, which were introduced and stocked from the early 1900s to 1985. Fish communities were quantified at 13 stations throughout the watershed, and Simpson's species diversity index was calculated. One hundred and nine springs were located, and their flow rates measured. A cross covariance analysis between Simpson's species diversity index and spring flow rates upstream of fish stations was performed to quantify the spatial correlation between these two variables. The correlation was found to be highest at lag distances up to about 400 m and drop off significantly beyond lag distances of about 800 m.

  2. Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning

    PubMed Central

    Huang, Jihong; Huang, Jianhua; Lu, Xinghui; Ma, Keping

    2016-01-01

    Endemism is an important concept in biogeography and biodiversity conservation. China is one of the richest countries in biodiversity, with very high levels of plant endemism. In this study, we analysed the distribution patterns of diversity, the degree of differentiation, and the endemicity of Chinese endemic seed plants using the floristic unit as a basic spatial analysis unit and 11 indices. The analysis was based on distribution data of 24,951 native seed plant species (excluding subspecies and varieties) and 12,980 Chinese endemic seed plant species, which were sourced from both specimen records and published references. The distribution patterns of Chinese endemic flora were generally consistent but disproportionate across China for diversity, degree of differentiation and endemicity. The South Hengduan Mountains Subregion had the highest values for all indices. At the regional level, both the Hengduan Mountains and the Central China regions were highest in diversity and degrees of differentiation. However, both the rate of local endemic to native species and the rate of local to Chinese endemic species were highest in the Taiwan Region and the South Taiwan Region. The Hengduan Mountains Region and the Central China Region are two key conservation priority areas for Chinese endemic seed plants. PMID:27658845

  3. Vector species richness increases haemorrhagic disease prevalence through functional diversity modulating the duration of seasonal transmission.

    PubMed

    Park, Andrew W; Cleveland, Christopher A; Dallas, Tad A; Corn, Joseph L

    2016-06-01

    Although many parasites are transmitted between hosts by a suite of arthropod vectors, the impact of vector biodiversity on parasite transmission is poorly understood. Positive relationships between host infection prevalence and vector species richness (SR) may operate through multiple mechanisms, including (i) increased vector abundance, (ii) a sampling effect in which species of high vectorial capacity are more likely to occur in species-rich communities, and (iii) functional diversity whereby communities comprised species with distinct phenologies may extend the duration of seasonal transmission. Teasing such mechanisms apart is impeded by a lack of appropriate data, yet could highlight a neglected role for functional diversity in parasite transmission. We used statistical modelling of extensive host, vector and microparasite data to test the hypothesis that functional diversity leading to longer seasonal transmission explained variable levels of disease in a wildlife population. We additionally developed a simple transmission model to guide our expectation of how an increased transmission season translates to infection prevalence. Our study demonstrates that vector SR is associated with increased levels of disease reporting, but not via increases in vector abundance or via a sampling effect. Rather, the relationship operates by extending the length of seasonal transmission, in line with theoretical predictions.

  4. Effect of host diversity and species assemblage composition on bovine tuberculosis (bTB) risk in Ethiopian cattle.

    PubMed

    Sintayehu, Dejene W; Heitkönig, Ignas M A; Prins, Herbert H T; Tessema, Zewdu K; DE Boer, Willem F

    2017-01-30

    Current theories on diversity-disease relationships describe host species diversity and species identity as important factors influencing disease risk, either diluting or amplifying disease prevalence in a community. Whereas the simple term 'diversity' embodies a set of animal community characteristics, it is not clear how different measures of species diversity are correlated with disease risk. We therefore tested the effects of species richness, Pielou's evenness and Shannon's diversity on bovine tuberculosis (bTB) risk in cattle in the Afar Region and Awash National Park between November 2013 and April 2015. We also analysed the identity effect of a particular species and the effect of host habitat use overlap on bTB risk. We used the comparative intradermal tuberculin test to assess the number of bTB-infected cattle. Our results suggested a dilution effect through species evenness. We found that the identity effect of greater kudu - a maintenance host - confounded the dilution effect of species diversity on bTB risk. bTB infection was positively correlated with habitat use overlap between greater kudu and cattle. Different diversity indices have to be considered together for assessing diversity-disease relationships, for understanding the underlying causal mechanisms. We posit that unpacking diversity metrics is also relevant for formulating disease control strategies to manage cattle in ecosystems characterized by seasonally limited resources and intense wildlife-livestock interactions.

  5. Mycorrhizal Fungal Diversity and Community Composition in Two Closely Related Platanthera (Orchidaceae) Species.

    PubMed

    Esposito, Fabiana; Jacquemyn, Hans; Waud, Michael; Tyteca, Daniel

    2016-01-01

    While it is generally acknowledged that orchid species rely on mycorrhizal fungi for completion of their life cycle, little is yet known about how mycorrhizal fungal diversity and community composition vary within and between closely related orchid taxa. In this study, we used 454 amplicon pyrosequencing to investigate variation in mycorrhizal communities between pure (allopatric) and mixed (sympatric) populations of two closely related Platanthera species (Platanthera bifolia and P. chlorantha) and putative hybrids. Consistent with previous research, the two species primarily associated primarily with members of the Ceratobasidiaceae and, to a lesser extent, with members of the Sebacinales and Tulasnellaceae. In addition, a large number of ectomycorrhizal fungi belonging to various families were observed. Although a considerable number of mycorrhizal fungi were common to both species, the fungal communities were significantly different between the two species. Individuals with intermediate morphology showed communities similar to P. bifolia, confirming previous results based on the genetic architecture and fragrance composition that putative hybrids essentially belonged to one of the parental species (P. bifolia). Differences in mycorrhizal communities between species were smaller in mixed populations than between pure populations, suggesting that variation in mycorrhizal communities was largely controlled by local environmental conditions. The small differences in mycorrhizal communities in mixed populations suggests that mycorrhizal fungi are most likely not directly involved in maintaining species boundaries between the two Platanthera species. However, seed germination experiments are needed to unambiguously assess the contribution of mycorrhizal divergence to reproductive isolation.

  6. [Species diversity and colony characteristics of bumblebees in the Hebei region of North China].

    PubMed

    An, Jian-Dong; Huang, Jia-Xing; Williams, Paul H; Wu, Jie; Zhou, Bing-Feng

    2010-06-01

    Based on the 1893 specimens collected from Hebei Province, Beijing City, and Tianjin City in 2005-2009, and the specimens deposited in the Institute of Zoology, Chinese Academy of Sciences, this paper analyzed the species diversity and colony characteristics of bumblebees in the Hebei region of North China. A total of 32 species belonging to 8 subgenera of Bombus were recorded, with 32 species in Hebei Province, 18 species in Beijing, and 5 species in Tianjin. The bumblebee in Taihang Mountains, Yanshan Mountains, and Bashang Plateau had the highest richness and abundance, and its food-plant included 80 species of 21 families, among which, Compositae, Leguminosae, and Labiatae were most important. Five bumblebee species, i. e., Bombus hypocrita, B. ignitus, B. patagiatus, B. pyrosoma, and B. picipes, had the largest colony, with more than 110 workers, 160 drones, and 30 young queens produced per colony. The success in rearing colonies of each of the 5 species by queens was > 50%, demonstrating that these 5 species had the potential to be mass-reared, with important applied value for crop pollination.

  7. Mycorrhizal Fungal Diversity and Community Composition in Two Closely Related Platanthera (Orchidaceae) Species

    PubMed Central

    Esposito, Fabiana; Jacquemyn, Hans; Waud, Michael; Tyteca, Daniel

    2016-01-01

    While it is generally acknowledged that orchid species rely on mycorrhizal fungi for completion of their life cycle, little is yet known about how mycorrhizal fungal diversity and community composition vary within and between closely related orchid taxa. In this study, we used 454 amplicon pyrosequencing to investigate variation in mycorrhizal communities between pure (allopatric) and mixed (sympatric) populations of two closely related Platanthera species (Platanthera bifolia and P. chlorantha) and putative hybrids. Consistent with previous research, the two species primarily associated primarily with members of the Ceratobasidiaceae and, to a lesser extent, with members of the Sebacinales and Tulasnellaceae. In addition, a large number of ectomycorrhizal fungi belonging to various families were observed. Although a considerable number of mycorrhizal fungi were common to both species, the fungal communities were significantly different between the two species. Individuals with intermediate morphology showed communities similar to P. bifolia, confirming previous results based on the genetic architecture and fragrance composition that putative hybrids essentially belonged to one of the parental species (P. bifolia). Differences in mycorrhizal communities between species were smaller in mixed populations than between pure populations, suggesting that variation in mycorrhizal communities was largely controlled by local environmental conditions. The small differences in mycorrhizal communities in mixed populations suggests that mycorrhizal fungi are most likely not directly involved in maintaining species boundaries between the two Platanthera species. However, seed germination experiments are needed to unambiguously assess the contribution of mycorrhizal divergence to reproductive isolation. PMID:27695108

  8. Species Delimitation and Phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): Cryptic Diversity in North American Tarantulas

    PubMed Central

    Hamilton, Chris A.; Formanowicz, Daniel R.; Bond, Jason E.

    2011-01-01

    Background The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal “barcoding gene”. An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame. Methods and Findings A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a “barcode gap” using percent of pairwise sequence divergence (uncorrected p-distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups. Conclusions The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an

  9. When does diversity matter? Species functional diversity and ecosystem functioning across habitats and seasons in a field experiment.

    PubMed

    Frainer, André; McKie, Brendan G; Malmqvist, Björn

    2014-03-01

    Despite ample experimental evidence indicating that biodiversity might be an important driver of ecosystem processes, its role in the functioning of real ecosystems remains unclear. In particular, the understanding of which aspects of biodiversity are most important for ecosystem functioning, their importance relative to other biotic and abiotic drivers, and the circumstances under which biodiversity is most likely to influence functioning in nature, is limited. We conducted a field study that focussed on a guild of insect detritivores in streams, in which we quantified variation in the process of leaf decomposition across two habitats (riffles and pools) and two seasons (autumn and spring). The study was conducted in six streams, and the same locations were sampled in the two seasons. With the aid of structural equations modelling, we assessed spatiotemporal variation in the roles of three key biotic drivers in this process: functional diversity, quantified based on a species trait matrix, consumer density and biomass. Our models also accounted for variability related to different litter resources, and other sources of biotic and abiotic variability among streams. All three of our focal biotic drivers influenced leaf decomposition, but none was important in all habitats and seasons. Functional diversity had contrasting effects on decomposition between habitats and seasons. A positive relationship was observed in pool habitats in spring, associated with high trait dispersion, whereas a negative relationship was observed in riffle habitats during autumn. Our results demonstrate that functional biodiversity can be as significant for functioning in natural ecosystems as other important biotic drivers. In particular, variation in the role of functional diversity between seasons highlights the importance of fluctuations in the relative abundances of traits for ecosystem process rates in real ecosystems.

  10. Genetic diversity of functional food species Spinacia oleracea L. by protein markers.

    PubMed

    Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A

    2014-01-01

    Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers.

  11. Remote Sensing of Vegetation Species Diversity: The Utility of Integrated Airborne Hyperspectral and Lidar Data

    NASA Astrophysics Data System (ADS)

    Krause, Keith Stuart

    The change, reduction, or extinction of species is a major issue currently facing the Earth. Efforts are underway to measure, monitor, and protect habitats that contain high species diversity. Remote sensing technology shows extreme value for monitoring species diversity by mapping ecosystems and using those land cover maps or other derived data as proxies to species number and distribution. The National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) consists of remote sensing instruments such as an imaging spectrometer, a full-waveform lidar, and a high-resolution color camera. AOP collected data over the Ordway-Swisher Biological Station (OSBS) in May 2014. A majority of the OSBS site is covered by the Sandhill ecosystem, which contains a very high diversity of vegetation species and is a native habitat for several threatened fauna species. The research presented here investigates ways to analyze the AOP data to map ecosystems at the OSBS site. The research attempts to leverage the high spatial resolution data and study the variability of the data within a ground plot scale along with integrating data from the different sensors. Mathematical features are derived from the data and brought into a decision tree classification algorithm (rpart), in order to create an ecosystem map for the site. The hyperspectral and lidar features serve as proxies for chemical, functional, and structural differences in the vegetation types for each of the ecosystems. K-folds cross validation shows a training accuracy of 91%, a validation accuracy of 78%, and a 66% accuracy using independent ground validation. The results presented here represent an important contribution to utilizing integrated hyperspectral and lidar remote sensing data for ecosystem mapping, by relating the spatial variability of the data within a ground plot scale to a collection of vegetation types that make up a given ecosystem.

  12. Species-Specific Traits Rather Than Resource Partitioning Mediate Diversity Effects on Resource Use

    PubMed Central

    Godbold, Jasmin A.; Rosenberg, Rutger; Solan, Martin

    2009-01-01

    Background The link between biodiversity and ecosystem processes has firmly been established, but the mechanisms underpinning this relationship are poorly documented. Most studies have focused on terrestrial plant systems where resource use can be difficult to quantify as species rely on a limited number of common resources. Investigating resource use at the bulk level may not always be of sufficient resolution to detect subtle differences in resource use, as species-specific nutritional niches at the biochemical level may also moderate diversity effects on resource use. Methodology/Principal Findings Here we use three co-occurring marine benthic echinoderms (Brissopsis lyrifera, Mesothuria intestinalis, Parastichopus tremulus) that feed on the same phytodetrital food source, to determine whether resource partitioning is the principal mechanism underpinning diversity effects on resource use. Specifically we investigate the use of phytodetrital pigments (chlorophylls and carotenoids) because many of these are essential for biological functions, including reproduction. Pigments were identified and quantified using reverse-phase high performance liquid Chromatography (HPLC) and data were analysed using a combination of extended linear regression with generalised least squares (GLS) estimation and standard multivariate techniques. Our analyses reveal no species-specific selectivity for particular algal pigments, confirming that these three species do not partition food resources at the biochemical level. Nevertheless, we demonstrate increased total resource use in diverse treatments as a result of selection effects and the dominance of one species (B. lyrifera). Conclusion Overall, we found no evidence for resource partitioning at the biochemical level, as pigment composition was similar between individuals, which is likely due to plentiful food availability. Reduced intra-specific competition in the species mixture combined with greater adsorption efficiency and

  13. Ecosystem engineering effects on species diversity across ecosystems: a meta-analysis.

    PubMed

    Romero, Gustavo Q; Gonçalves-Souza, Thiago; Vieira, Camila; Koricheva, Julia

    2015-08-01

    Ecosystem engineering is increasingly recognized as a relevant ecological driver of diversity and community composition. Although engineering impacts on the biota can vary from negative to positive, and from trivial to enormous, patterns and causes of variation in the magnitude of engineering effects across ecosystems and engineer types remain largely unknown. To elucidate the above patterns, we conducted a meta-analysis of 122 studies which explored effects of animal ecosystem engineers on species richness of other organisms in the community. The analysis revealed that the overall effect of ecosystem engineers on diversity is positive and corresponds to a 25% increase in species richness, indicating that ecosystem engineering is a facilitative process globally. Engineering effects were stronger in the tropics than at higher latitudes, likely because new or modified habitats provided by engineers in the tropics may help minimize competition and predation pressures on resident species. Within aquatic environments, engineering impacts were stronger in marine ecosystems (rocky shores) than in streams. In terrestrial ecosystems, engineers displayed stronger positive effects in arid environments (e.g. deserts). Ecosystem engineers that create new habitats or microhabitats had stronger effects than those that modify habitats or cause bioturbation. Invertebrate engineers and those with lower engineering persistence (<1 year) affected species richness more than vertebrate engineers which persisted for >1 year. Invertebrate species richness was particularly responsive to engineering impacts. This study is the first attempt to build an integrative framework of engineering effects on species diversity; it highlights the importance of considering latitude, habitat, engineering functional group, taxon and persistence of their effects in future theoretical and empirical studies.

  14. Genetic diversity of Chilean and Brazilian alstroemeria species assessed by AFLP analysis.

    PubMed

    Han, T H; de Jeu, M; van Eck, H; Jacobsen, E

    2000-05-01

    One to three accessions of 22 Alstroemeria species, an interspecific hybrid (A. aurea x A. inodora), and single accessions of Bomarea salsilla and Leontochir ovallei were evaluated using the AFLP-marker technique to estimate the genetic diversity within the genus Alstroemeria. Three primer combinations generated 716 markers and discriminated all Alstroemeria species. The dendrogram inferred from the AFLP fingerprints supported the conjecture of the generic separation of the Chilean and Brazilian Alstroemeria species. The principal co-ordinate plot showed the separate allocation of the A. ligtu group and the allocation of A. aurea, which has a wide range of geographical distribution and genetic variation, in the middle of other Alstroemeria species. The genetic distances, based on AFLP markers, determined the genomic contribution of the parents to the interspecific hybrid.

  15. Characterization of Serum Phospholipase A2 Activity in Three Diverse Species of West African Crocodiles

    PubMed Central

    Merchant, Mark; Juneau, Kate; Gemillion, Jared; Falconi, Rodolfo; Doucet, Aaron; Shirley, Matthew H.

    2011-01-01

    Secretory phospholipase A2, an enzyme that exhibits substantial immunological activity, was measured in the serum of three species of diverse West African crocodiles. Incubation of different volumes of crocodile serum with bacteria labeled with a fluorescent fatty acid in the sn-2 position of membrane lipids resulted in a volume-dependent liberation of fluorescent probe. Serum from the Nile crocodile (Crocodylus niloticus) exhibited slightly higher activity than that of the slender-snouted crocodile (Mecistops cataphractus) and the African dwarf crocodile (Osteolaemus tetraspis). Product formation was inhibited by BPB, a specific PLA2 inhibitor, confirming that the activity was a direct result of the presence of serum PLA2. Kinetic analysis showed that C. niloticus serum produced product more rapidly than M. cataphractus or O. tetraspis. Serum from all three species exhibited temperature-dependent PLA2 activities but with slightly different thermal profiles. All three crocodilian species showed high levels of activity against eight different species of bacteria. PMID:22110960

  16. Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia.

    PubMed

    Wolde-Meskel, Endalkachew; Terefework, Zewdu; Frostegård, Asa; Lindström, Kristina

    2005-07-01

    The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR-RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500-1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR-RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100% similar to those of previously described species and 34 were novel sequences with 94-99% similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

  17. Habitat and species identity, not diversity, predict the extent of refuse consumption by urban arthropods.

    PubMed

    Youngsteadt, Elsa; Henderson, Ryanna C; Savage, Amy M; Ernst, Andrew F; Dunn, Robert R; Frank, Steven D

    2015-03-01

    Urban green spaces provide ecosystem services to city residents, but their management is hindered by a poor understanding of their ecology. We examined a novel ecosystem service relevant to urban public health and esthetics: the consumption of littered food waste by arthropods. Theory and data from natural systems suggest that the magnitude and resilience of this service should increase with biological diversity. We measured food removal by presenting known quantities of cookies, potato chips, and hot dogs in street medians (24 sites) and parks (21 sites) in New York City, USA. At the same sites, we assessed ground-arthropod diversity and abiotic conditions, including history of flooding during Hurricane Sandy 7 months prior to the study. Arthropod diversity was greater in parks (on average 11 hexapod families and 4.7 ant species per site), than in medians (nine hexapod families and 2.7 ant species per site). However, counter to our diversity-based prediction, arthropods in medians removed 2-3 times more food per day than did those in parks. We detected no effect of flooding (at 19 sites) on this service. Instead, greater food removal was associated with the presence of the introduced pavement ant (Tetramorium sp. E) and with hotter, drier conditions that may have increased arthropod metabolism. When vertebrates also had access to food, more was removed, indicating that arthropods and vertebrates compete for littered food. We estimate that arthropods alone could remove 4-6.5 kg of food per year in a single street median, reducing its availability to less desirable fauna such as rats. Our results suggest that species identity and habitat may be more relevant than diversity for predicting urban ecosystem services. Even small green spaces such as street medians provide ecosystem services that may complement those of larger habitat patches across the urban landscape.

  18. Resolving the roles of body size and species identity in driving functional diversity

    PubMed Central

    Rudolf, Volker H. W.; Rasmussen, Nick L.; Dibble, Christopher J.; Van Allen, Benjamin G.

    2014-01-01

    Efforts to characterize food webs have generated two influential approaches that reduce the complexity of natural communities. The traditional approach groups individuals based on their species identity, while recently developed approaches group individuals based on their body size. While each approach has provided important insights, they have largely been used in parallel in different systems. Consequently, it remains unclear how body size and species identity interact, hampering our ability to develop a more holistic framework that integrates both approaches. We address this conceptual gap by developing a framework which describes how both approaches are related to each other, revealing that both approaches share common but untested assumptions about how variation across size classes or species influences differences in ecological interactions among consumers. Using freshwater mesocosms with dragonfly larvae as predators, we then experimentally demonstrate that while body size strongly determined how predators affected communities, these size effects were species specific and frequently nonlinear, violating a key assumption underlying both size- and species-based approaches. Consequently, neither purely species- nor size-based approaches were adequate to predict functional differences among predators. Instead, functional differences emerged from the synergistic effects of body size and species identity. This clearly demonstrates the need to integrate size- and species-based approaches to predict functional diversity within communities. PMID:24598423

  19. Diverse Colletotrichum species cause anthracnose of tea plants (Camellia sinensis (L.) O. Kuntze) in China

    PubMed Central

    Wang, Yu-Chun; Hao, Xin-Yuan; Wang, Lu; Bin Xiao; Wang, Xin-Chao; Yang, Ya-Jun

    2016-01-01

    Anthracnose caused by Colletotrichum is one of the most severe diseases that can afflict Camellia sinensis. However, research on the diversity and geographical distribution of Colletotrichum in China remain limited. In this study, 106 Colletotrichum isolates were collected from diseased leaves of Ca. sinensis cultivated in the 15 main tea production provinces in China. Multi-locus phylogenetic analysis coupled with morphological identification showed that the collected isolates belonged to 11 species, including 6 known species (C. camelliae, C. cliviae, C. fioriniae, C. fructicola, C. karstii, and C. siamense), 3 new record species (C. aenigma, C. endophytica, and C. truncatum), 1 novel species (C. wuxiense), and 1 indistinguishable strain, herein described as Colletotrichum sp. Of these species, C. camelliae and C. fructicola were the dominant species causing anthracnose in Ca. sinensis. In addition, our study provided further evidence that phylogenetic analysis using a combination of ApMat and GS sequences can be used to effectively resolve the taxonomic relationships within the C. gloeosporioides species complex. Finally, pathogenicity tests suggested that C. camelliae, C. aenigma, and C. endophytica are more invasive than other species after the inoculation of the leaves of Ca. sinensis. PMID:27782129

  20. Testing species boundaries in the Antrodiaetus unicolor complex (Araneae: Mygalomorphae: Antrodiaetidae): "paraphyly" and cryptic diversity.

    PubMed

    Hendrixson, Brent E; Bond, Jason E

    2005-08-01

    The inability to correctly identify species has far reaching implications in nearly all areas of biology, yet few studies investigate methods for delineating species boundaries. Moreover, once these boundaries have been hypothesized, little thought has been given to how these constructs can be further evaluated. We employ a molecular phylogenetic approach using nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I genes to test the general efficacy of species boundaries in the Antrodiaetus unicolor spider species complex. Our analyses provide evidence that An. unicolor is "paraphyletic" with respect to An. microunicolor, indicating that morphological criteria used to delineate species boundaries undersplits actual species-level diversity in this group of spiders. These analyses also demonstrate that individuals from geographically proximate populations sometimes exhibit considerable molecular divergence, strongly suggesting that An. unicolor is a cryptic species complex. Finally, this molecular approach has provided the phylogenetic framework that is necessary to begin interpreting the vast amount of morphological variation observed in these spiders based upon findings from previous studies. Our approach using multiple genes appears to be a rigorous method to critically examine species boundaries originally based on traditional morphological approaches to spider taxonomy.

  1. Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures.

    PubMed

    Vázquez-Nion, D; Rodríguez-Castro, J; López-Rodríguez, M C; Fernández-Silva, I; Prieto, B

    2016-07-01

    Microbial communities of natural subaerial biofilms developed on granitic historic buildings of a World Heritage Site (Santiago de Compostela, NW Spain) were characterized and cultured in liquid BG11 medium. Environmental barcoding through next-generation sequencing (Pacific Biosciences) revealed that the biofilms were mainly composed of species of Chlorophyta (green algae) and Ascomycota (fungi) commonly associated with rock substrata. Richness and diversity were higher for the fungal than for the algal assemblages and fungi showed higher heterogeneity among samples. Cultures derived from natural biofilms showed the establishment of stable microbial communities mainly composed of Chlorophyta and Cyanobacteria. Although most taxa found in these cultures were not common in the original biofilms, they are likely common pioneer colonizers of building stone surfaces, including granite. Stable phototrophic multi-species cultures of known microbial diversity were thus obtained and their reliability to emulate natural colonization on granite should be confirmed in further experiments.

  2. Deep-sea ostracode species diversity: Response to late Quaternary climate change

    USGS Publications Warehouse

    Cronin, T. M.; DeMartino, D.M.; Dwyer, G.S.; Rodriguez-Lazaro, J.

    1999-01-01

    Late Quaternary ostracode assemblages from the North Atlantic Ocean were studied to establish the effect of climatic changes of the past 210,000 yr (marine oxygen isotope stages 7-1) on deep-sea benthic biodiversity and faunal composition. Two-hundred and twenty five samples from the Chain 82-24 Core 4PC (41??43'N, 32??51'W, 3427 m water depth) on the western Mid-Atlantic Ridge revealed high amplitude fluctuations in ostracode abundance and diversity coincident with orbital and suborbital scale climate oscillations measured by several paleoceanographic proxy records. During the past 210,000 yr, ostracode biodiversity as measured by species number (S) and the Shannon-Weaver index, H(S), oscillated from H(S) = 0.4 during glacial periods (marine isotope stages 6, 5d, 5b, 4, and 2) to H(S) = 1.1 during interglacial and interstadial periods (stages 7, 5e, 5c, 5a, 3 and 1). A total of 23 diversity peaks could be recognized. Eleven of these signify major periods of high diversity [H(S) > 0.8, S = 10-21] occurring every 15-20 ka. Twelve were minor peaks which may represent millennial-scale diversity oscillations. The composition of ostracode assemblages varies with Krithe-dominated assemblages characterizing glacial intervals, and Argilloecia-Cytheropteron characterizing deglacials, and trachyleberid genera (Poseidonamicus, Echinocythereis, Henryhowella, Oxycythereis) abundant during interglacials. Diversity and faunal composition changes can be matched to independent deep-sea paleoceanographic tracers such as benthic foraminiferal carbon isotopes, Krithe trace elements (Mg/Ca ratios), and to North Atlantic region climate records such as Greenland ice cores. When interpreted in light of ostracode species' ecology, these faunal and diversity patterns provide evidence that deep-sea benthic ecosystems experience significant reorganization in response to climate changes over orbital to millennial timescales.

  3. Commercial Plant Production and Consumption Still Follow the Latitudinal Gradient in Species Diversity despite Economic Globalization.

    PubMed

    Nelson, Erik J; Helmus, Matthew R; Cavender-Bares, Jeannine; Polasky, Stephen; Lasky, Jesse R; Zanne, Amy E; Pearse, William D; Kraft, Nathan J B; Miteva, Daniela A; Fagan, William F

    2016-01-01

    Increasing trade between countries and gains in income have given consumers around the world access to a richer and more diverse set of commercial plant products (i.e., foods and fibers produced by farmers). According to the economic theory of comparative advantage, countries open to trade will be able to consume more-in terms of volume and diversity-if they concentrate production on commodities that they can most cost-effectively produce, while importing goods that are expensive to produce, relative to other countries. Here, we perform a global analysis of traded commercial plant products and find little evidence that increasing globalization has incentivized agricultural specialization. Instead, a country's plant production and consumption patterns are still largely determined by local evolutionary legacies of plant diversification. Because tropical countries harbor a greater diversity of lineages across the tree of life than temperate countries, tropical countries produce and consume a greater diversity of plant products than do temperate countries. In contrast, the richer and more economically advanced temperate countries have the capacity to produce and consume more plant species than the generally poorer tropical countries, yet this collection of plant species is drawn from fewer branches on the tree of life. Why have countries not increasingly specialized in plant production despite the theoretical financial incentive to do so? Potential explanations include the persistence of domestic agricultural subsidies that distort production decisions, cultural preferences for diverse local food production, and that diverse food production protects rural households in developing countries from food price shocks. Less specialized production patterns will make crop systems more resilient to zonal climatic and social perturbations, but this may come at the expense of global crop production efficiency, an important step in making the transition to a hotter and more

  4. Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach

    PubMed Central

    Nanjappa, Deepak; Audic, Stephane; Romac, Sarah; Kooistra, Wiebe H. C. F.; Zingone, Adriana

    2014-01-01

    Background Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by

  5. Species diversity and seasonal abundance of Culicoides biting midges in northwestern Argentina.

    PubMed

    Aybar, C A Veggiani; Juri, M J Dantur; De Grosso, M S Lizarralde; Spinelli, G R

    2010-03-01

    The species diversity and seasonal abundance of biting midges of the genus Culicoides (Diptera: Ceratopogonidae) were studied in northwestern Argentina during the period 2003-2005. A total of 5437 Culicoides specimens were collected using CDC light traps in three areas of the mountainous rainforest area. The most common species were Culicoides paraensis (Goeldi) and C. insignis Lutz, Culicoides lahillei (Iches), C. venezuelensis Ortiz & Mirsa, C. debilipalpis Lutz and C. crescentis Wirth & Blanton were also collected. Culicoides paraensis was abundant during the summer, and C. insignis and C. lahillei during late summer and early fall. Accumulated rainfall was the climatic variable most related to fluctuation in abundance of C. paraensis.

  6. Woody plant phylogenetic diversity mediates bottom-up control of arthropod biomass in species-rich forests.

    PubMed

    Schuldt, Andreas; Baruffol, Martin; Bruelheide, Helge; Chen, Simon; Chi, Xiulian; Wall, Marcus; Assmann, Thorsten

    2014-09-01

    Global change is predicted to cause non-random species loss in plant communities, with consequences for ecosystem functioning. However, beyond the simple effects of plant species richness, little is known about how plant diversity and its loss influence higher trophic levels, which are crucial to the functioning of many species-rich ecosystems. We analyzed to what extent woody plant phylogenetic diversity and species richness contribute to explaining the biomass and abundance of herbivorous and predatory arthropods in a species-rich forest in subtropical China. The biomass and abundance of leaf-chewing herbivores, and the biomass dispersion of herbivores within plots, increased with woody plant phylogenetic diversity. Woody plant species richness had much weaker effects on arthropods, but interacted with plant phylogenetic diversity to negatively affect the ratio of predator to herbivore biomass. Overall, our results point to a strong bottom-up control of functionally important herbivores mediated particularly by plant phylogenetic diversity, but do not support the general expectation that top-down predator effects increase with plant diversity. The observed effects appear to be driven primarily by increasing resource diversity rather than diversity-dependent primary productivity, as the latter did not affect arthropods. The strong effects of plant phylogenetic diversity and the overall weaker effects of plant species richness show that the diversity-dependence of ecosystem processes and interactions across trophic levels can depend fundamentally on non-random species associations. This has important implications for the regulation of ecosystem functions via trophic interaction pathways and for the way species loss may impact these pathways in species-rich forests.

  7. Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America.

    PubMed

    Narum, Shawn R; Gallardo, Pablo; Correa, Cristian; Matala, Amanda; Hasselman, Daniel; Sutherland, Ben J G; Bernatchez, Louis

    2017-04-01

    Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in North America. Estimates of genetic diversity were not significantly different between introduced and source populations for either species, indicative of propagule pressure that has been shown to maintain diversity in founding populations relative to their native range. Introduced populations also demonstrated higher connectivity and gene flow than those in their native range. Evidence for candidate loci under divergent selection was observed, but was limited to specific introduced populations and was not widely evident. Patterns of genomic variation were consistent with general dispersal potential of each species and therefore also the notion that life history variation may contribute to both invasion success and subsequent genetic structure of these two salmonids in Patagonia.

  8. Tree species composition, diversity and biomass of Bukit Panchor State Park, Pulau Pinang, Malaysia

    NASA Astrophysics Data System (ADS)

    Norazlinda, M.; Nizam, M. S.; Latiff, A.; Fitri, Z. Ahmad; Sani, M.

    2016-11-01

    A study on species composition, diversity and biomass of tree communities at Bukit Panchor State Park, Pulau Pinang, Malaysia was conducted. A total of 20 ecological plots of 25 m × 20 m that covered a total area of 1.0 ha were established. All trees with diameter at breast height (dbh) of 5.0 cm and above were tagged, measured and collected for voucher specimens. The floristic composition of Bukit Panchor State Park consists of 1,039 individuals represented by 46 families, 124 genera and 224 species. The most abundant family recorde