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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. Diversity of zoonotic enterohepatic Helicobacter species and detection of a putative novel gastric Helicobacter species in wild and wild-born captive chimpanzees and western lowland gorillas.

    PubMed

    Flahou, Bram; Modrý, David; Pomajbíková, Kateřina; Petrželková, Klára J; Smet, Annemieke; Ducatelle, Richard; Pasmans, Frank; Sá, Rui M; Todd, Angelique; Hashimoto, Chie; Mulama, Martin; Kiang, John; Rossi, Mirko; Haesebrouck, Freddy

    2014-11-01

    A number of Helicobacter species cause gastrointestinal or hepatic disease in humans, including H. pylori, gastric non-H. pylori helicobacters from animal origin and enterohepatic Helicobacter species. Little is known on the presence of Helicobacter species in great apes, our closest living relatives and potential reservoirs of microorganisms that might emerge in humans. The aim of the present study was to investigate the presence of gastric and enterohepatic Helicobacter species in African chimpanzees and gorillas. Fresh fecal samples were collected from wild endangered chimpanzees and critically endangered western lowland gorillas from different African National Parks, as well as wild-born captive animals from primate sanctuaries. Intact Helicobacter bacteria were demonstrated in feces by fluorescence in situ hybridization. Screening using a Helicobacter genus-specific PCR revealed the presence of Helicobacter DNA in the majority of animals in all groups. Cloning and sequencing of 16S rRNA gene fragments revealed a high homology to sequences from various zoonotic enterohepatic Helicobacter species, including H. cinaedi and H. canadensis. A number of gorillas and chimpanzees also tested positive using PCR assays designed to amplify part of the ureAB gene cluster and the hsp60 gene of gastric helicobacters. Phylogenetic analysis revealed the presence of a putative novel zoonotic gastric Helicobacter taxon/species. For this species, we propose the name 'Candidatus Helicobacter homininae', pending isolation and further genetic characterization. The presence of several Helicobacter species not only implies a possible health threat for these endangered great apes, but also a possible zoonotic transmission of gastric and enterohepatic helicobacters from these primate reservoirs to humans. PMID:25248691

  3. Intestinal microbiota and species diversity of Campylobacter and Helicobacter spp. in migrating shorebirds in Delaware Bay.

    PubMed

    Ryu, Hodon; Grond, Kirsten; Verheijen, Bram; Elk, Michael; Buehler, Deborah M; Santo Domingo, Jorge W

    2014-03-01

    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

  4. 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

  5. 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 ...

  6. 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.

  7. Helicobacter pylori Diversity and Gastric Cancer Risk

    PubMed Central

    2016-01-01

    ABSTRACT Gastric cancer is a leading cause of cancer-related death worldwide. Helicobacter pylori infection is the strongest known risk factor for this malignancy. An important goal is to identify H. pylori-infected persons at high risk for gastric cancer, so that these individuals can be targeted for therapeutic intervention. H. pylori exhibits a high level of intraspecies genetic diversity, and over the past two decades, many studies have endeavored to identify strain-specific features of H. pylori that are linked to development of gastric cancer. One of the most prominent differences among H. pylori strains is the presence or absence of a 40-kb chromosomal region known as the cag pathogenicity island (PAI). Current evidence suggests that the risk of gastric cancer is very low among persons harboring H. pylori strains that lack the cag PAI. Among persons harboring strains that contain the cag PAI, the risk of gastric cancer is shaped by a complex interplay among multiple strain-specific bacterial factors as well as host factors. This review discusses the strain-specific properties of H. pylori that correlate with increased gastric cancer risk, focusing in particular on secreted proteins and surface-exposed proteins, and describes evidence from cell culture and animal models linking these factors to gastric cancer pathogenesis. Strain-specific features of H. pylori that may account for geographic variation in gastric cancer incidence are also discussed. PMID:26814181

  8. Helicobacter marmotae and novel Helicobacter and Campylobacter species isolated from the livers and intestines of prairie dogs.

    PubMed

    Beisele, Maike; Shen, Zeli; Parry, Nicola; Mobley, Melissa; Taylor, Nancy S; Buckley, Ellen; Abedin, Mohammad Z; Dewhirst, Floyd E; Fox, James G

    2011-09-01

    Prairie dogs (Cynomys ludovicianus) are used to study the aetiology and prevention of gallstones because of the similarities of prairie dog and human bile gallstone composition. Epidemiological and experimental studies have suggested a connection between infection with Helicobacter species and cholesterol cholelithiasis, cholecystis and gallbladder cancer. Ten of the 34 prairie dogs in this study had positive Helicobacter species identified by PCR using Helicobacter genus-specific primers. Ten of 34 prairie dogs had positive Campylobacter species identified in the intestine by PCR with Campylobacter genus-specific primers. Six Helicobacter sp. isolates and three Campylobacter sp. isolates were identified taxonomically by 16S rRNA gene analysis. The prairie dog helicobacters fell into three clusters adjacent to Helicobacter marmotae. On the basis of 16S rRNA gene sequence analysis, three strains in two adjacent clusters were included in the species H. marmotae. Three strains were only 97.1 % similar to the sequence of H. marmotae and can be considered a novel species with the provisional designation Helicobacter sp. Prairie Dog 3. The prairie dog campylobacters formed a single novel cluster and represent a novel Campylobacter sp. with the provisional designation Campylobacter sp. Prairie Dog. They branched with Campylobacter cuniculorum at 96.3 % similarity and had the greatest sequence similarity to Campylobacter helveticus at 97.1 % similarity. Whether H. marmotae or the novel Helicobacter sp. and Campylobacter sp. identified in prairie dogs play a role in cholesterol gallstones or hepatobiliary disease requires further studies. PMID:21546560

  9. Helicobacter apodemus sp. nov., a new Helicobacter species identified from the gastrointestinal tract of striped field mice in Korea

    PubMed Central

    Jeon, Woo Jin; Dong, Hee-Jin; Shin, Jae Hoon; Kim, Il Yong; Ho, Hungwui; Oh, Seung Hyun; Yoon, Young Min; Choi, Yang-Kyu; Suh, Jun Gyo; Nam, Ki-Hoan; Kim, Hyoung-Chin

    2015-01-01

    A novel Helicobacter species was identified from the gastrointestinal tract of the Korean striped field mouse (Apodemus agrarius). Biochemical testing, ultrastructure characterization, and 16S rRNA gene sequence analysis suggested that this bacterium represents a distinct taxon. The bacterium was positive for urease activity, susceptible to cephalothin and nalidixic acid, and weakly positive for oxidase and catalase activity. Electron microscopy revealed that the bacterium has spirally curved rod morphology with singular bipolar nonsheathed flagella. Genotypically, the isolated bacterial strains (YMRC 000215, YMRC 000216, and YMRC 000419) were most closely related to a reference strain of Helicobacter mesocricetorum (97.25%, 97.32%, and 97.03% 16S rRNA sequence similarities, respectively). The 16S rRNA sequences of these strains were deposited into GenBank under accession numbers AF284754, AY009129, and AY009130, respectively. We propose the name Helicobacter apodemus for this novel species. PMID:25797297

  10. Comparison of four diagnostic methods for detection of Helicobacter species in laboratory mice.

    PubMed

    Mähler, M; Bedigian, H G; Burgett, B L; Bates, R J; Hogan, M E; Sundberg, J P

    1998-02-01

    Four species of Helicobacter--H. muridarum, "H. rappini," H. hepaticus, and H. bilis--have been identified in the gastrointestinal tract of rodents. The association of Helicobacter species with chronic gastrointestinal diseases in mice has raised concern about their impact on research results. In this study, different methods for detection of Helicobacter species in the mouse intestinal tract were compared: polymerase chain reaction (PCR) amplification of 16S rRNA gene sequences, bacterial culture, electron microscopy, and histologic examination (Steiner stain). The PCR method was more sensitive in detecting murine Helicobacter species than was culture, electron microscopy, or histologic examination. Of the cecal specimens identified as Helicobacter species-positive by PCR, approximately 60% were identified as positive by each of the other methods. An 87.5% concordance was obtained by PCR screening of DNA from fecal and cecal specimens. Differentiation among murine Helicobacter species by colony morphologic or histologic features was not possible. Scanning electron microscopy and histologic examination indicated greater numbers of helical microorganisms, specifically H. hepaticus, in the cecum than in the colon. These results indicate that the PCR assays used can be performed on feces as a noninvasive means for rapidly screening large numbers of colony mice for murine Helicobacter species. PMID:9517897

  11. An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives.

    PubMed

    Puri, Ayush; Rai, Arshiya; Dhanaraj, P S; Lal, Rup; Patel, Dev Dutt; Kaicker, Anju; Verma, Mansi

    2016-09-01

    Helicobacter is an economically important genus within the phylum Proteobacteria and include many species which cause many diseases in humans. With the conventional methods, it is difficult to identify them easily due to the high genetic similarity among its species. In the present study, 361 16S rRNA (rrs) gene sequences belonging to 45 species of genus Helicobacter were analyzed. Out of these, 264 sequences of 10 clinically relevant species (including Helicobacter pylori) were used. rrs gene sequences were analyzed to obtain a phylogenetic framework tree, in silico restriction enzyme analysis and species-specific conserved motifs. Protein sequences of another housekeeping gene, hsp60 were also subjected to phylogenetic analysis to supplement the data obtained using rrs sequences. Using these approaches, six out of ten species (including H. pylori) were easily segregated, whereas four species namely H. bilis, H. cinaedi, H. felis and Candidatus H. heilmannii were found to be heterogeneous. The above approaches have also helped in segregating unclassified sequences, thus proving them as an easy diagnostic method for identifying members of genus Helicobacter up to species level. PMID:27407291

  12. 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...

  13. 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

  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. The Carcinogenic Liver Fluke Opisthorchis viverrini is a Reservoir for Species of Helicobacter

    PubMed Central

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

    2016-01-01

    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 and

  17. Distinct diversity of the cag pathogenicity island among Helicobacter pylori strains in Japan.

    PubMed

    Azuma, Takeshi; Yamakawa, Akiyo; Yamazaki, Shiho; Ohtani, Masahiro; Ito, Yoshiyuki; Muramatsu, Atsushi; Suto, Hiroyuki; Yamazaki, Yukinao; Keida, Yoshihide; Higashi, Hideaki; Hatakeyama, Masanori

    2004-06-01

    The severity of Helicobacter pylori-related disease is correlated with the presence of a cag pathogenicity island (PAI). Genetic diversity within the cag PAI may have a modifying effect on the pathogenic potential of the infecting strain. We analyzed the complete cag PAI sequences of 11 representative Japanese strains according to their vacA genotypes and clinical effects and examined the relationship between the diversity of the cag PAI and clinical features. The cag PAI genes were divided into two major groups, a Western and a Japanese group, by phylogenetic analysis based on the entire cag PAI sequences. The predominant Japanese strains formed a Japanese cluster which was different from the cluster formed by Western strains. The diversity of the cag PAI was associated with the vacA and cagA genotypes. All strains with the s1c vacA genotype were in the Japanese cluster. In addition, all strains with the East Asian-type cagA genotype were also in the Japanese cluster. Patients infected with the Japanese-cluster strain had high-grade gastric mucosal atrophy. These results suggest that a distinct diversity of the cag PAI of H. pylori is present among Japanese strains and that this diversity may be involved in the development of atrophic gastritis and may increase the risk for gastric cancer. PMID:15184428

  18. Distinct Diversity of the cag Pathogenicity Island among Helicobacter pylori Strains in Japan

    PubMed Central

    Azuma, Takeshi; Yamakawa, Akiyo; Yamazaki, Shiho; Ohtani, Masahiro; Ito, Yoshiyuki; Muramatsu, Atsushi; Suto, Hiroyuki; Yamazaki, Yukinao; Keida, Yoshihide; Higashi, Hideaki; Hatakeyama, Masanori

    2004-01-01

    The severity of Helicobacter pylori-related disease is correlated with the presence of a cag pathogenicity island (PAI). Genetic diversity within the cag PAI may have a modifying effect on the pathogenic potential of the infecting strain. We analyzed the complete cag PAI sequences of 11 representative Japanese strains according to their vacA genotypes and clinical effects and examined the relationship between the diversity of the cag PAI and clinical features. The cag PAI genes were divided into two major groups, a Western and a Japanese group, by phylogenetic analysis based on the entire cag PAI sequences. The predominant Japanese strains formed a Japanese cluster which was different from the cluster formed by Western strains. The diversity of the cag PAI was associated with the vacA and cagA genotypes. All strains with the s1c vacA genotype were in the Japanese cluster. In addition, all strains with the East Asian-type cagA genotype were also in the Japanese cluster. Patients infected with the Japanese-cluster strain had high-grade gastric mucosal atrophy. These results suggest that a distinct diversity of the cag PAI of H. pylori is present among Japanese strains and that this diversity may be involved in the development of atrophic gastritis and may increase the risk for gastric cancer. PMID:15184428

  19. Detecting diversity: emerging methods to estimate species diversity.

    PubMed

    Iknayan, Kelly J; Tingley, Morgan W; Furnas, Brett J; Beissinger, Steven R

    2014-02-01

    Estimates of species richness and diversity are central to community and macroecology and are frequently used in conservation planning. Commonly used diversity metrics account for undetected species primarily by controlling for sampling effort. Yet the probability of detecting an individual can vary among species, observers, survey methods, and sites. We review emerging methods to estimate alpha, beta, gamma, and metacommunity diversity through hierarchical multispecies occupancy models (MSOMs) and multispecies abundance models (MSAMs) that explicitly incorporate observation error in the detection process for species or individuals. We examine advantages, limitations, and assumptions of these detection-based hierarchical models for estimating species diversity. Accounting for imperfect detection using these approaches has influenced conclusions of comparative community studies and creates new opportunities for testing theory. PMID:24315534

  20. 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...

  1. 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. PMID:23910524

  2. Novel Helicobacter species isolated from rhesus monkeys with chronic idiopathic colitis.

    PubMed

    Fox, J G; Handt, L; Xu, S; Shen, Z; Dewhirst, F E; Paster, B J; Dangler, C A; Lodge, K; Motzel, S; Klein, H

    2001-05-01

    Chronic, idiopathic diffuse colitis is a well recognised clinical and pathological entity in captive rhesus monkeys. Six rhesus monkeys were diagnosed with clinically debilitating, chronic diarrhoea. Histologically, colonic tissues were characterised as chronic, moderate to severe colitis and typhlitis, with diffuse mononuclear inflammation of lamina propria, reactive lymphoid hyperplasia and multifocal micro-abscesses. Colonic tissues were cultured for Salmonella spp. and Shigella spp.; all results were negative. Samples were negative for Clostridium difficile A and B toxins, and special stains of colonic tissue for acid-fast bacteria were also negative. The six diarrhoeic monkeys tested gave negative results for serum IgG antibodies to herpes B virus, STLV, SRV and SIV. Colonic tissue from the six diarrhoeic and two clinically normal monkeys with histologically confirmed colitis from the same colony were also subjected to micro-aerobic culture. Micro-aerobic cultures from all eight monkeys incubated at 37 degrees C and 42 degrees C revealed pinpoint or spreading colonies on antibiotic-containing media. Bacteria were identified as gram-negative, oxidase positive and urease negative. Of the nine strains characterised biochemically, two separate biotypes (corresponding to different species by 16S rRNA analysis) were identified. One biotype (type 1), from non-diarrhoeic monkeys and the second biotype (type 2) from diarrhoeic animals with subclinical chronic colonic inflammation, differed by catalase activity, ability to reduce nitrate to nitrite and sensitivity to cephalothin. Complete 16S rRNA analysis of five of the nine strains characterised biochemically indicated that the organisms isolated were two novel Helicobacter spp. By electron microscopy, these novel helicobacters had spiral morphology with bipolar sheathed flagella. This is the first report describing the isolation of novel Helicobacter spp. from inflamed colons of rhesus monkeys. Studies are needed to

  3. Region effects influence local tree species diversity

    PubMed Central

    Ricklefs, Robert E.; He, Fangliang

    2016-01-01

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  4. Region effects influence local tree species diversity.

    PubMed

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  5. 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

  6. Species Diversity of Hypogeous Ascomycetes in Israel

    PubMed Central

    Wasser, Solomon P.

    2010-01-01

    We conducted a species diversity study of the hypogeous Ascomycetes of Israel. The hypogeous Ascomycetes in Israel include members of the families Pyronemataceae, Pezizaceae, and Tuberaceae, which are represented by seven species: Hydnocystis piligera, Terfezia arenaria, T. claveryi, T. oligosperma, Tirmania africana, Tuber asa, and T. nitidum; only T. asa is new to Israeli mycobiota. Synonymy, locations, collection data, general distribution, distribution in Israel, descriptions, a key to identification, illustrations, and taxonomic remarks are provided. PMID:23956647

  7. Helicobacter pylori CagL Hypervariable Motif: A Global Analysis of Geographical Diversity and Association With Gastric Cancer.

    PubMed

    Gorrell, Rebecca J; Zwickel, Nicolas; Reynolds, John; Bulach, Dieter; Kwok, Terry

    2016-06-15

    Previous studies suggest overrepresentation of particular polymorphisms within the Helicobacter pylori CagL hypervariable motif (CagLHM) in gastric cancer-associated isolates. However, these disease correlations were geographically variable and ambiguous. We compared the disease correlation of several hundred geographically diverse CagL sequences and identified 33 CagLHM sequence combinations with disparate geographical distribution, revealing substantial worldwide CagLHM diversity, particularly within Asian countries. Notably, polymorphisms E59 and I60 were significantly overrepresented, whereas D58 and E62 were underrepresented, in gastric cancer-associated H. pylori isolates worldwide. Thus, CagLHM regional diversity may contribute to the varied prevalence of H. pylori-related gastric cancer observed in diverse populations. PMID:26908724

  8. The Other Helicobacters.

    PubMed

    Flahou, Bram; Rimbara, Emiko; Mori, Shigetarou; Haesebrouck, Freddy; Shibayama, Keigo

    2015-09-01

    In the past year, a substantial number of (putative) novel Helicobacter species have been described, including Helicobacter himalayensis colonizing the Himalayan marmot and Helicobacter apodemus, colonizing the Korean striped field mouse. In addition, a putative novel gastric Helicobacter species was identified in wild gorillas and chimpanzees, for which the name "Candidatus H. homininae" was proposed. A high incidence of gastric non-H. pylori Helicobacter infection was described in China and multiple case reports have described the involvement of enterohepatic Helicobacter species, especially Helicobacter cinaedi, in a wide range of diseases. Several studies in rodent models further elucidated the mechanisms underlying the development of gastric mucosa-associated lymphoid tissue lymphoma during infection with gastric non-H. pylori Helicobacters. The effects of infection with gastric Helicobacters on the development of neuroinflammation were investigated and several enterohepatic Helicobacter species were shown to affect the composition of the gut microbiota, to influence vaccine efficiency as well as the progression of cancer in distant sites of the body. PMID:26372827

  9. Diverse CLE peptides from cyst nematode species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant CLAVATA3/ESR (CLE)-like peptides play diverse roles in plant growth and development including maintenance of the stem cell population in the root meristem. Small secreted peptides sharing similarity to plant CLE signaling peptides have been isolated from several cyst nematode species including...

  10. 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. PMID:26374788

  11. 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

  12. Dominant species constrain effects of species diversity on 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...

  13. 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

  14. 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.

  15. Species diversity: Benthonic Foraminifera in Western North Atlantic

    USGS Publications Warehouse

    Buzas, M.A.; Gibson, T.G.

    1969-01-01

    Maximum species diversity occurs at abyssal depths of greater than 2500 meters. Other diversity peaks occur at depths of 35 to 45 meters and 100 to 200 meters. The peak at 35 to 45 meters is due to species equitability, whereas the other two peaks correspond to an increase in the number of species.

  16. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

    PubMed Central

    2011-01-01

    Background The genome of Helicobacter pylori, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains. Results A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean) from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including oipA, hopMN, babABC, sabAB and vacA-2) through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia) and the European (hpEurope) genomes in proteins in host interaction, specifically virulence factors (tipα), outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry) enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (miaA, tilS), a DNA recombinase/exonuclease that recognizes genome identity (addA), and DNA/RNA hybrid nucleases (rnhAB). Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of cagA, vacA, homC (outer membrane protein), sotB (sugar transport), and a translation fidelity factor (miaA). Large divergence was seen in genes related to antibiotics: frxA (metronidazole resistance), def (peptide deformylase, drug target), and ftsA (actin-like, drug target

  17. Genomic patterns of species diversity and divergence in Eucalyptus.

    PubMed

    Hudson, Corey J; Freeman, Jules S; Myburg, Alexander A; Potts, Brad M; Vaillancourt, René E

    2015-06-01

    We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. PMID:25678438

  18. Revisiting the relation between species diversity and information theory.

    PubMed

    Camargo, Julio A

    2008-12-01

    The Shannon information function (H) has been extensively used in ecology as a statistic of species diversity. Yet, the use of Shannon diversity index has also been criticized, mainly because of its ambiguous ecological interpretation and because of its relatively great sensitivity to the relative abundances of species in the community. In my opinion, the major shortcoming of the traditional perspective (on the possible relation of species diversity with information theory) is that species need for an external receiver (the scientist or ecologist) to exist and transmit information. Because organisms are self-catalized replicating structures that can transmit genotypic information to offspring, it should be evident that any single species has two possible states or alternatives: to be or not to be. In other words, species have no need for an external receiver since they are their own receivers. Therefore, the amount of biological information (at the species scale) in a community with one only species would be log2(2)1 = 1 species, and not log2(1) = 0 bits as in the traditional perspective. Moreover, species diversity appears to be a monotonic increasing function of log2(2)S (or S) when all species are equally probable (S being species richness), and not a function of log2 S as in the traditional perspective. To avoid the noted shortcoming, we could use 2(H) (instead of H) for calculating species diversity and species evenness (= 2(H)/S). However, owing to the relatively great sensitivity of H to the relative abundances of species in the community, the value of species dominance (= 1 - 2(H)/S) is unreasonably high when differences between dominant and subordinate species are considerable, thereby lowering the value of species evenness and diversity. This unsatisfactory behaviour is even more evident for Simpson index and related algorithms. I propose the use of other statistics for a better analysis of community structure, their relationship being: species evenness

  19. Diversity, Pathogenicity And Control of Verticillium Species.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Verticillium is a cosmopolitan group of ascomycetous fungi, encompassing phytopathogenic species that cause vascular wilts of plants. Two of these species, V. dahliae and V. albo-atrum, cause billions of dollars in annual crop losses worldwide. The soil habitat of these species, the exte...

  20. 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. PMID:23006492

  1. Theory predicts the uneven distribution of genetic diversity within species.

    PubMed

    Rauch, Erik M; Bar-Yam, Yaneer

    2004-09-23

    Global efforts to conserve species have been strongly influenced by the heterogeneous distribution of species diversity across the Earth. This is manifest in conservation efforts focused on diversity hotspots. The conservation of genetic diversity within an individual species is an important factor in its survival in the face of environmental changes and disease. Here we show that diversity within species is also distributed unevenly. Using simple genealogical models, we show that genetic distinctiveness has a scale-free power law distribution. This property implies that a disproportionate fraction of the diversity is concentrated in small sub-populations, even when the population is well-mixed. Small groups are of such importance to overall population diversity that even without extrinsic perturbations, there are large fluctuations in diversity owing to extinctions of these small groups. We also show that diversity can be geographically non-uniform--potentially including sharp boundaries between distantly related organisms--without extrinsic causes such as barriers to gene flow or past migration events. We obtained these results by studying the fundamental scaling properties of genealogical trees. Our theoretical results agree with field data from global samples of Pseudomonas bacteria. Contrary to previous studies, our results imply that diversity loss owing to severe extinction events is high, and focusing conservation efforts on highly distinctive groups can save much of the diversity. PMID:15386012

  2. Detection of gastric Helicobacter spp. in stool samples 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 determine the prevalence and identify the species of gastric Helicobacter in the stool of dogs with gastritis. The study was carried out on thirty dogs of different breeds, of both genders and of various ages, diagnosed with gastritis. Helicobacter spp. was detected in stool samples using the nested-PCR method. Helicobacter bacteria were identified in stool samples from seven (23.3%) dogs. Helicobacter heilmannii was found to be the most common species of gastric Helicobacter. Helicobacter salomonis was identified much less frequently, while Helicobacter felis, Helicobacter pylori and Helicobacter bizzozeronii were not detected in any of the samples. PMID:27487496

  3. Species richness and morphological diversity of passerine birds

    PubMed Central

    Ricklefs, Robert E.

    2012-01-01

    The relationship between species richness and the occupation of niche space can provide insight into the processes that shape patterns of biodiversity. For example, if species interactions constrained coexistence, one might expect tendencies toward even spacing within niche space and positive relationships between diversity and total niche volume. I use morphological diversity of passerine birds as a proxy for diet, foraging maneuvers, and foraging substrates and examine the morphological space occupied by regional and local passerine avifaunas. Although independently diversified regional faunas exhibit convergent morphology, species are clustered rather than evenly distributed, the volume of the morphological space is weakly related to number of species per taxonomic family, and morphological volume is unrelated to number of species within both regional avifaunas and local assemblages. These results seemingly contradict patterns expected when species interactions constrain regional or local diversity, and they suggest a larger role for diversification, extinction, and dispersal limitation in shaping species richness. PMID:22908271

  4. High levels of cryptic species diversity uncovered in Amazonian frogs

    PubMed Central

    Funk, W. Chris; Caminer, Marcel; Ron, Santiago R.

    2012-01-01

    One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador (Engystomops: 252 individuals from 36 localities; Hypsiboas: 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops, the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas, two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought. PMID:22130600

  5. Species Divergence and the Measurement of Microbial Diversity

    PubMed Central

    Lozupone, Catherine A.; Knight, Rob

    2008-01-01

    Diversity measurement is important for understanding community structure and dynamics, but has been particularly challenging for microbes. Microbial community characterization using small subunit ribosomal RNA (SSU rRNA) gene sequences has revealed an extensive, previously unsuspected diversity that we are only now beginning to understand, especially now that advanced sequencing technologies are producing data sets containing hundreds of thousands of sequences from hundreds of samples. Efforts to quantify microbial diversity often use taxon-based methods that ignore the fact that not all species are equally related, which can therefore obscure important patterns in the data. For example, α diversity (diversity within communities) is often estimated as the number of species in a community (species richness), and β diversity (partitioning of diversity among communities) is often based on the number of shared species. Methods for measuring α diversity and β diversity that account for different levels of divergence between individuals have recently been more widely applied. These methods are more powerful than taxon-based methods because microbes in a community differ dramatically in sequence similarity, which also often correlates with phenotypic similarity in key features such as metabolic capabilities. Consequently, divergence-based methods are providing new insights into microbial community structure and function. PMID:18435746

  6. Across species-pool aggregation alters grassland productivity and diversity.

    PubMed

    McKenna, Thomas P; Yurkonis, Kathryn A

    2016-08-01

    Plant performance is determined by the balance of intra- and interspecific neighbors within an individual's zone of influence. If individuals interact over smaller scales than the scales at which communities are measured, then altering neighborhood interactions may fundamentally affect community responses. These interactions can be altered by changing the number (species richness), abundances (species evenness), and positions (species pattern) of the resident plant species, and we aimed to test whether aggregating species at planting would alter effects of species richness and evenness on biomass production at a common scale of observation in grasslands. We varied plant species richness (2, 4, or 8 species and monocultures), evenness (0.64, 0.8, or 1.0), and pattern (planted randomly or aggregated in groups of four individuals) within 1 × 1 m plots established with transplants from a pool of 16 tallgrass prairie species and assessed plot-scale biomass production and diversity over the first three growing seasons. As expected, more species-rich plots produced more biomass by the end of the third growing season, an effect associated with a shift from selection to complementarity effects over time. Aggregating conspecifics at a 0.25-m scale marginally reduced biomass production across all treatments and increased diversity in the most even plots, but did not alter biodiversity effects or richness-productivity relationships. Results support the hypothesis that fine-scale species aggregation affects diversity by promoting species coexistence in this system. However, results indicate that inherent changes in species neighborhood relationships along grassland diversity gradients may only minimally affect community (meter) - scale responses among similarly designed biodiversity-ecosystem function studies. Given that species varied in their responses to local aggregation, it may be possible to use such species-specific results to spatially design larger-scale grassland

  7. Do stacked species distribution models reflect altitudinal diversity patterns?

    PubMed

    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

  8. [Species diversity and managed ecosystem stability].

    PubMed

    Feng, Yaozong

    2003-06-01

    Based on partial experimental data of the studies on managed communities over 40 years, various managed communities in terms of ecological structures, e.g., rubber or tea plantation in one species with one community layer, rubber-tea and rubber-coffee of two species with two community layers, rubber-luofumu-qiannianjian of three species with three community layers, and artificial rain forest with multiple species and layers (hundred species with five layers) were discussed. The differences in systematic functions among three structures of the community were discussed, mainly from the followint spects: Biomass, productivity, and economical productivity; capability of protection and improvement of community environment (microclimate, soil etc.); capability of resistant to natural disaster (chilling and storm). The biomass and productivity in the system were significantly increased, as there were more species and vertical layers in the community. As the community structure became complicated, the microclimatic factors inside the system were marked changed: relative humidity was higher, maximum temperature was lower, minimum temperature was higher, wind slowdown velocity was slowed down, soil erosion reduced, and the resistance to chilling and storm become stronger. It is concluded that the stability of the system could be greatly affected by an artificial ecosystem. PMID:12973982

  9. Diversity in Protein Glycosylation among Insect Species

    PubMed Central

    Vandenborre, Gianni; Smagghe, Guy; Ghesquière, Bart; Menschaert, Gerben; Nagender Rao, Rameshwaram; Gevaert, Kris; Van Damme, Els J. M.

    2011-01-01

    Background A very common protein modification in multicellular organisms is protein glycosylation or the addition of carbohydrate structures to the peptide backbone. Although the Class of the Insecta is the largest animal taxon on Earth, almost all information concerning glycosylation in insects is derived from studies with only one species, namely the fruit fly Drosophila melanogaster. Methodology/Principal Findings In this report, the differences in glycoproteomes between insects belonging to several economically important insect orders were studied. Using GNA (Galanthus nivalis agglutinin) affinity chromatography, different sets of glycoproteins with mannosyl-containing glycan structures were purified from the flour beetle (Tribolium castaneum), the silkworm (Bombyx mori), the honeybee (Apis mellifera), the fruit fly (D. melanogaster) and the pea aphid (Acyrthosiphon pisum). To identify and characterize the purified glycoproteins, LC-MS/MS analysis was performed. For all insect species, it was demonstrated that glycoproteins were related to a broad range of biological processes and molecular functions. Moreover, the majority of glycoproteins retained on the GNA column were unique to one particular insect species and only a few glycoproteins were present in the five different glycoprotein sets. Furthermore, these data support the hypothesis that insect glycoproteins can be decorated with mannosylated O-glycans. Conclusions/Significance The results presented here demonstrate that oligomannose N-glycosylation events are highly specific depending on the insect species. In addition, we also demonstrated that protein O-mannosylation in insect species may occur more frequently than currently believed. PMID:21373189

  10. 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. PMID:20383613

  11. Genetic Diversity Estimates for Dichroa Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Dichroa consists of 12 species of flowering plants in the family Hydrangeaceae, native to eastern and southeastern Asia. They are deciduous shrubs growing 1 to 3 meters tall in full sun or light shade and may exhibit evergreen growth habit in warmer climes. Flowers are hermaphroditic and s...

  12. Soil Nematode Diversity: Species Coexistence and Ecosystem Function

    PubMed Central

    Ettema, Christien H.

    1998-01-01

    Soil nematode species diversity is often high, both at ecosystem and single soil-core scales. First, how can so many species coexist? There is evidence of niche partitioning, notably of physical space, but vast interspecific overlaps and trait plasticity seem equally common. It appears that coexistence of species with similar resource needs is made possible by small-scale disturbance and predation, which likely reduce local population sizes and interspecific competition. Regional processes such as dispersal, large-scale disturbance, and aggregation, which govern ecosystem level diversity, may also affect local species interactions and soil-core scale diversity. Second, what is the significance of having so many species, with so few trophic functions, for ecosystem processes? Focusing on bacterivore diversity, it is clear that species contributions to decomposition, likely to differ as a function of individual biologies, are concealed by the trophic group approach. However, considerable functional redundancy probably exists, which may explain why decomposition processes are maintained in highly disturbed soils despite the extinction of many species. Thus, soil nematode diversity is important for the long-term stability of soil functioning, and merits protection and further study. PMID:19274206

  13. Effect of Landscape Structure on Species Diversity

    PubMed Central

    Campos, Paulo R. A.; Rosas, Alexandre; de Oliveira, Viviane M.; Gomes, Marcelo A. F.

    2013-01-01

    The effects of habitat fragmentation and their implications for biodiversity is a central issue in conservation biology which still lacks an overall comprehension. There is not yet a clear consensus on how to quantify fragmentation even though it is quite common to couple the effects of habitat loss with habitat fragmentation on biodiversity. Here we address the spatial patterns of species distribution in fragmented landscapes, assuming a neutral community model. To build up the fragmented landscapes, we employ the fractional Brownian motion approach, which in turn permits us to tune the amount of habitat loss and degree of clumping of the landscape independently. The coupling between the neutral community model, here simulated by means of the coalescent method, and fractal neutral landscape models enables us to address how the species–area relationship changes as the spatial patterns of a landscape is varied. The species–area relationship is one of the most fundamental laws in ecology, considered as a central tool in conservation biology, and is used to predict species loss following habitat disturbances. Our simulation results indicate that the level of clumping has a major role in shaping the species–area relationship. For instance, more compact landscapes are more sensitive to the effects of habitat loss and speciation rate. Besides, the level of clumping determines the existence and extension of the power-law regime which is expected to hold at intermediate scales. The distributions of species abundance are strongly influenced by the degree of fragmentation. We also show that the first and second commonest species have approximately self-similar spatial distributions across scales, with the fractal dimensions of the support of the first and second commonest species being very robust to changes in the spatial patterns of the landscape. PMID:23840490

  14. 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

    2010-06-01

    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

  15. Standardizing germination protocols for diverse raspberry and blackberry species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most Rubus species exhibit delayed or poor germination because of a deep double dormancy. The objective of this study was to improve Rubus seed germination protocols by defining the seed characteristics of diverse Rubus species and determining scarification and germination requirements. Seeds of fie...

  16. 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

  17. High-order species interactions shape ecosystem diversity.

    PubMed

    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

  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. 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

  20. Bacterial Community Diversity Harboured by Interacting Species.

    PubMed

    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

  1. 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

  2. Rare Species Support Vulnerable Functions in High-Diversity Ecosystems

    PubMed Central

    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

  3. 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.

  4. Patterns of species diversity in the deep sea as a function of sediment particle size diversity

    NASA Astrophysics Data System (ADS)

    Etter, Ron J.; Grassle, J. Frederick

    1992-12-01

    UNDERSTANDING the processes that generate and maintain patterns of species diversity is a major focus of contemporary ecological and evolutionary research. In the deep sea, species diversity varies geographically and bathymetrically1-3, and may attain levels that rival tropical communities4. Many hypotheses have been proposed concerning the forces that shape patterns of species diversity in the deep sea5, but so far it has not been possible to relate these patterns to potential causes in a direct quantitative way. The nature of sediments should be important in structuring deep-sea communities because deposit feeders rely on the sediments for nutrition and comprise most of the organisms in the deep sea6. The composition of soft sediment communities is influenced by sediment particle size7,8. Shallow-water deposit feeders selectively ingest particular size fractions of the sediments9,10 and there are interspecific differences in particle size preference11-13. Partitioning of sediments with respect to size may be more likely in the deep sea if there is strong selection for macrophagy as a result of reduced food supply and digestive constraints imposed by feeding on deposits14; macrophagy would permit species to ingest selectively the more labile components of the sediments. If deposit feeders in the deep sea partition the sediments with respect to size, species diversity may in part be a function of sediment particle size diversity. Also, sediment particle size diversity may reflect habitat complexity because the organisms live on or within the sediments15-21. Here we show that species diversity is a significant positive function of sediment particle size diversity. The relationship seems to be scale-invariant, accounting for a similar proportion of the variance at inter-regional, regional and local scales. Bathymetric patterns of species diversity also appear to be largely attributable to changes in sediment characteristics with depth. These results suggest that

  5. 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

  6. 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. PMID:26774060

  7. 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. PMID:24575218

  8. 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

  9. 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

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

    PubMed

    Joosten, Myrthe; Lindén, Sara; Rossi, Mirko; Tay, Alfred Chin Yen; 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; Smet, Annemieke

    2016-01-01

    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

  11. 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

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

    PubMed

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

    2016-01-01

    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

  13. 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

  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

    Chung, Tae-Ho; Kim, Hee-Dong; Lee, Young-Sun; Hwang, Cheol-Yong

    2014-01-01

    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. 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.

  16. Comparison of Helicobacter spp. genetic sequences in wild and captive seals, and gulls.

    PubMed

    Oxley, Andrew P A; McKay, David B

    2005-06-01

    Helicobacter species are widely distributed in the gastrointestinal system of humans and many animal taxa. Investigations of natural infections are essential to elucidating their role within the host. The feces of fur seals Arctocephalus pusillus doriferus and sea lions Neophoca cinerea from 3 separate captive populations, as well as a wild colony from Kangaroo Island, Australia, were examined for the occurrence of Helicobacter spp. The feces from several wild silver gulls Larus novahollandiae were also investigated. As detected by PCR, 18 of 21 samples from captive and 12 of 16 samples from wild seals were positive for Helicobacter spp. Three species were identified in these animals. Whilst one possibly novel type was identified from wild fur seals, the majority of wild and captive individuals had the same species. This species also occurred in more than 1 seal type and in silver gulls, and shared a 98.1 to 100% identity to other Helicobacter spp. from harp seals and sea otters. A similar sequence type to species identified from cetaceans was also detected in several captive seals. This study reports for the first time the presence of Helicobacter spp. in wild and captive seals and demonstrates the diversity and broad-host range of these organisms in the marine host. PMID:16060262

  17. 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. PMID:25996858

  18. Synthetic riboswitches that induce gene expression in diverse bacterial species.

    PubMed

    Topp, Shana; Reynoso, Colleen M K; Seeliger, Jessica C; Goldlust, Ian S; Desai, Shawn K; Murat, Dorothée; Shen, Aimee; Puri, Aaron W; Komeili, Arash; Bertozzi, Carolyn R; Scott, June R; Gallivan, Justin P

    2010-12-01

    We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria. PMID:20935124

  19. Nutritive value in relation to plant species diversity of pastures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Planting forage mixtures may benefit pasture herbage production; however, changes in botanical composition could cause unstable nutritive value. Data from two grazing studies and a farm survey were used to examine how plant species diversity influenced herbage nutritive value. In one grazing study,...

  20. Conservation tillage affects species composition but not species diversity: a comparative study in Northern Italy.

    PubMed

    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. PMID:25392019

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Phylogenetic and biological species diversity within the Neurospora tetrasperma complex.

    PubMed

    Menkis, A; Bastiaans, E; Jacobson, D J; Johannesson, H

    2009-09-01

    The objective of this study was to explore the evolutionary history of the morphologically recognized filamentous ascomycete Neurospora tetrasperma, and to reveal the genetic and reproductive relationships among its individuals and populations. We applied both phylogenetic and biological species recognition to a collection of strains representing the geographic and genetic diversity of N. tetrasperma. First, we were able to confirm a monophyletic origin of N. tetrasperma. Furthermore, we found nine phylogenetic species within the morphospecies. When using the traditional broad biological species recognition all investigated strains of N. tetrasperma constituted a single biological species. In contrast, when using a quantitative measurement of the reproductive success, incorporating characters such as viability and fertility of offspring, we found a high congruence between the phylogenetic and biological species recognition. Taken together, phylogenetically and biologically defined groups of individuals exist in N. tetrasperma, and these should be taken into account in future studies of its life history traits. PMID:19682307

  7. Analyzing fractal property of species abundance distribution and diversity indexes.

    PubMed

    Su, Qiang

    2016-03-01

    Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf-Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the "dominance" of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity. PMID:26746388

  8. Neotropical Bats: Estimating Species Diversity with DNA Barcodes

    PubMed Central

    Clare, Elizabeth L.; Lim, Burton K.; Fenton, M. Brock; Hebert, Paul D. N.

    2011-01-01

    DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0–11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats. PMID:21818359

  9. 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. PMID:26017448

  10. 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

  11. An exactly solvable coarse-grained model for species diversity

    NASA Astrophysics Data System (ADS)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  12. 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

  13. 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. PMID:26241962

  14. Sequence Diversity, Reproductive Isolation and Species Concepts in Saccharomyces

    PubMed Central

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

    2006-01-01

    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. PMID:16951060

  15. 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

  16. 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.

  17. Mining diverse small RNA species in the deep transcriptome.

    PubMed

    Vickers, Kasey C; Roteta, Leslie A; Hucheson-Dilks, Holli; Han, Leng; Guo, Yan

    2015-01-01

    Transcriptomes of many species are proving to be exquisitely diverse, and many investigators are now using high-throughput sequencing to quantify non-protein-coding RNAs, namely small RNAs (sRNA). Unfortunately, most studies are focused solely on microRNA changes, and many investigators are not analyzing the full compendium of sRNA species present in their large datasets. We provide here a rationale to include all types of sRNAs in sRNA sequencing analyses, which will aid in the discovery of their biological functions and physiological relevance. PMID:25435401

  18. 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

  19. 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...

  20. 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...

  1. 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

  2. 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

    2016-01-01

    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

  3. 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

  4. Unexpected Variation in Neuroanatomy among Diverse Nematode Species

    PubMed Central

    Han, Ziduan; Boas, Stephanie; Schroeder, Nathan E.

    2016-01-01

    Nematodes are considered excellent models for understanding fundamental aspects of neuron function. However, nematodes are less frequently used as models for examining the evolution of nervous systems. While the habitats and behaviors of nematodes are diverse, the neuroanatomy of nematodes is often considered highly conserved. A small number of nematode species greatly influences our understanding of nematode neurobiology. The free-living species Caenorhabditis elegans and, to a lesser extent, the mammalian gastrointestinal parasite Ascaris suum are, historically, the primary sources of knowledge regarding nematode neurobiology. Despite differences in size and habitat, C. elegans and A. suum share a surprisingly similar neuroanatomy. Here, we examined species across several clades in the phylum Nematoda and show that there is a surprising degree of neuroanatomical variation both within and among nematode clades when compared to C. elegans and Ascaris. We found variation in the numbers of neurons in the ventral nerve cord and dye-filling pattern of sensory neurons. For example, we found that Pristionchus pacificus, a bacterial feeding species used for comparative developmental research had 20% fewer ventral cord neurons compared to C. elegans. Steinernema carpocapsae, an insect-parasitic nematode capable of jumping behavior, had 40% more ventral cord neurons than C. elegans. Interestingly, the non-jumping congeneric nematode, S. glaseri showed an identical number of ventral cord neurons as S. carpocapsae. There was also variability in the timing of neurodevelopment of the ventral cord with two of five species that hatch as second-stage juveniles showing delayed neurodevelopment. We also found unexpected variation in the dye-filling of sensory neurons among examined species. Again, sensory neuron dye-filling pattern did not strictly correlate with phylogeny. Our results demonstrate that variation in nematode neuroanatomy is more prevalent than previously assumed and

  5. Unexpected Variation in Neuroanatomy among Diverse Nematode Species.

    PubMed

    Han, Ziduan; Boas, Stephanie; Schroeder, Nathan E

    2015-01-01

    Nematodes are considered excellent models for understanding fundamental aspects of neuron function. However, nematodes are less frequently used as models for examining the evolution of nervous systems. While the habitats and behaviors of nematodes are diverse, the neuroanatomy of nematodes is often considered highly conserved. A small number of nematode species greatly influences our understanding of nematode neurobiology. The free-living species Caenorhabditis elegans and, to a lesser extent, the mammalian gastrointestinal parasite Ascaris suum are, historically, the primary sources of knowledge regarding nematode neurobiology. Despite differences in size and habitat, C. elegans and A. suum share a surprisingly similar neuroanatomy. Here, we examined species across several clades in the phylum Nematoda and show that there is a surprising degree of neuroanatomical variation both within and among nematode clades when compared to C. elegans and Ascaris. We found variation in the numbers of neurons in the ventral nerve cord and dye-filling pattern of sensory neurons. For example, we found that Pristionchus pacificus, a bacterial feeding species used for comparative developmental research had 20% fewer ventral cord neurons compared to C. elegans. Steinernema carpocapsae, an insect-parasitic nematode capable of jumping behavior, had 40% more ventral cord neurons than C. elegans. Interestingly, the non-jumping congeneric nematode, S. glaseri showed an identical number of ventral cord neurons as S. carpocapsae. There was also variability in the timing of neurodevelopment of the ventral cord with two of five species that hatch as second-stage juveniles showing delayed neurodevelopment. We also found unexpected variation in the dye-filling of sensory neurons among examined species. Again, sensory neuron dye-filling pattern did not strictly correlate with phylogeny. Our results demonstrate that variation in nematode neuroanatomy is more prevalent than previously assumed and

  6. 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

  7. Soft coral Sarcophyton (Cnidaria: Anthozoa: Octocorallia) species diversity and chemotypes.

    PubMed

    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

  8. Size and species diversity of zooplankton communities in fluctuating Mediterranean salt marshes

    NASA Astrophysics Data System (ADS)

    Brucet, Sandra; Boix, Dani; López-Flores, Rocío; Badosa, Anna; Quintana, Xavier D.

    2006-04-01

    Differences in size and species diversity were analysed in a zooplankton community of a Mediterranean salt marsh (Empordà wetlands, NE Iberian Peninsula), where the dominance of a single species was frequent. In the permanent salt marsh, species diversity and size diversity had similar patterns along zooplankton succession. In the temporary salt marsh species diversity was high after flooding and diminished once water inputs ceased. As species diversity declined size diversity increased. Eventually, one species of calanoid dominated the zooplankton community. The high size diversity in situations of calanoid dominance was possibly due to the co-occurrence of different developmental stages, each of which have different diets. Size diversity would thus indicate trophic niche segregation among different sizes. The combined use of species and size diversity values allows the identification of the successional phases.

  9. SSRs transferability and genetic diversity of three allogamous ryegrass species.

    PubMed

    Guo, Zhi-Hui; Fu, Kai-Xin; Zhang, Xin-Quan; Zhang, Cheng-Lin; Sun, Ming; Huang, Ting; Peng, Yan; Huang, Lin-Kai; Yan, Yan-Hong; Ma, Xiao

    2016-02-01

    Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, and high repeatability. However, microsatellites are not always available for the species to be studied and their isolation could be time- and cost-consuming. To investigate transferability in cross-species applications, 102 primer pairs previously developed in ryegrass and tall fescue were amplified across three allogamous ryegrass species including Lolium rigidum, Lolium perenne and Lolium multiflorum. Their highly transferability (100%) were evidenced. While, most of these markers were multiple loci, only 17 loci were selected for a robust, single-locus pattern, which may be due to the recentness of the genome duplication or duplicated genomic regions, as well as speciation. A total of 87 alleles were generated with an average of 5.1 per locus. The mean polymorphism information content (PIC) and observed heterozygosity (Ho) values at genus was 0.5532 and 0.5423, respectively. Besides, analysis of molecular variance (AMOVA) revealed that all three levels contributed significantly to the overall genetic variation, with the species level contributing the least (P<0.001). Also, the unweighted pair group method with arithmetic averaging dendrogram (UPGMA), Bayesian model-based STRUCTURE analysis and the principal coordinate analysis (PCoA) showed that accessions within species always tended to the same cluster firstly and then to related species. The results showed that these markers developed in related species are transferable efficiently across species, and likely to be useful in analyzing genetic diversity. PMID:26874459

  10. 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

  11. Integrons in Xanthomonas: A source of species genome diversity

    PubMed Central

    Gillings, Michael R.; Holley, Marita P.; Stokes, H. W.; Holmes, Andrew J.

    2005-01-01

    Integrons are best known for assembling antibiotic resistance genes in clinical bacteria. They capture genes by using integrase-mediated site-specific recombination of mobile gene cassettes. Integrons also occur in the chromosomes of many bacteria, notably β- and γ-Proteobacteria. In a survey of Xanthomonas, integrons were found in all 32 strains representing 12 pathovars of two species. Their chromosomal location was downstream from the acid dehydratase gene, ilvD, suggesting that an integron was present at this site in the ancestral xanthomonad. There was considerable sequence and structural diversity among the extant integrons. The majority of integrase genes were predicted to be inactivated by frameshifts, stop codons, or large deletions, suggesting that the associated gene cassettes can no longer be mobilized. In support, groups of strains with the same deletions or stop codons/frameshifts in their integrase gene usually contained identical arrays of gene cassettes. In general, strains within individual pathovars had identical cassettes, and these exhibited no similarity to cassettes detected in other pathovars. The variety and characteristics of contemporary gene cassettes suggests that the ancestral integron had access to a diverse pool of these mobile elements, and that their genes originated outside the Xanthomonas genome. Subsequent inactivation of the integrase gene in particular lineages has largely fixed the gene cassette arrays in particular pathovars during their differentiation and specialization into ecological niches. The acquisition of diverse gene cassettes by different lineages within Xanthomonas has contributed to the species-genome diversity of the genus. The role of gene cassettes in survival on plant surfaces is currently unknown. PMID:15755815

  12. 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. PMID:24025243

  13. Species diversity and predation strategies in a multiple species predator-prey model

    NASA Astrophysics Data System (ADS)

    Mullan, Rory; Glass, David H.; McCartney, Mark

    2015-08-01

    A single predator, single prey ecological model, in which the behaviour of the populations relies upon two control parameters has been expanded to allow for multiple predators and prey to occupy the ecosystem. The diversity of the ecosystem that develops as the model runs is analysed by assessing how many predator or prey species survive. Predation strategies that dictate how the predators distribute their efforts across the prey are introduced in this multiple species model. The paper analyses various predation strategies and highlights their effect on the survival of the predators and prey species.

  14. Recurrent habitat disturbance and species diversity in a multiple-competitive species system.

    PubMed

    Ohsawa, Kyoko; Kawasaki, Kohkichi; Takasu, Fugo; Shigesada, Nanako

    2002-05-21

    To address how species interactions, dispersal and environmental disturbances interplay to affect the spatial distribution and diversity of species, we present a compartment model in which multiple species undergo competitive interaction of Lotka-Volterra type in a patchy environment arranged in a square lattice. Dispersal of species occurs between adjacent patches. Disturbances are periodically imposed on a central part of the environment in a belt-like block or an island-like block of various sizes where each species is killed for a certain time interval and then allowed to recover for the rest of a disturbance cycle. We deal with a case in which the local population dynamics within each patch is analytically determinable and has multiple locally stable equilibrium states in the absence of environmental disturbance. We further assume a trade-off between the reproductive rate of species and its dispersal ability. With these settings, we numerically examine how the spatio-temporal distributions of species are affected by changes in the pattern, size and duration of disturbances. The results demonstrate that: (1) in the undisturbed area, environmental disturbances could generate spatially segregated distributions of species; (2) in the disturbed area, species with higher dispersal abilities quickly invade and preferentially recover their population during the post-disturbance period, being temporarily relieved of competition from other species. These mechanisms collectively lead to increased species diversity in the whole habitat, functioning best when both the size and duration of disturbances are intermediate. In particular, the belt-like disturbance is more effective than the island-like disturbance in sustaining spatial heterogeneity for a wider range of duration of disturbance. PMID:12079366

  15. Diversity of endophytic bacteria in medicinally important Nepenthes species

    PubMed Central

    Bhore, Subhash J.; Komathi, Vijayan; Kandasamy, Kodi I.

    2013-01-01

    Background: Nepenthes species are used in traditional medicines to treat various health ailments. However, we do not know which types of endophytic bacteria (EB) are associated with Nepenthes spp. Objective: The objective of this study was to isolate and to identify EB associated with Nepenthes spp. Materials and Methods: Surface-sterilized leaf and stem tissues from nine Nepenthes spp. collected from Peninsular Malaysia were used to isolate EB. Isolates were identified using the polymerase chain reaction-amplified 16S ribosomal DNA (rDNA) sequence similarity based method. Results: Cultivable, 96 isolates were analyzed; and the 16S rDNA sequences analysis suggest that diverse bacterial species are associated with Nepenthes spp. Majority (55.2%) of the isolates were from Bacillus genus, and Bacillus cereus was the most dominant (14.6%) among isolates. Conclusion: Nepenthes spp. do harbor a wide array of cultivable endophytic bacteria. PMID:24082746

  16. 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

  17. Evolution of Invasion in a Diverse Set of Fusobacterium Species

    PubMed Central

    Manson McGuire, Abigail; Cochrane, Kyla; Griggs, Allison D.; Haas, Brian J.; Abeel, Thomas; Zeng, Qiandong; Nice, Justin B.; MacDonald, Hanlon; Birren, Bruce W.; Berger, Bryan W.; Allen-Vercoe, Emma

    2014-01-01

    ABSTRACT The diverse Fusobacterium genus contains species implicated in multiple clinical pathologies, including periodontal disease, preterm birth, and colorectal cancer. The lack of genetic tools for manipulating these organisms leaves us with little understanding of the genes responsible for adherence to and invasion of host cells. Actively invading Fusobacterium species can enter host cells independently, whereas passively invading species need additional factors, such as compromise of mucosal integrity or coinfection with other microbes. We applied whole-genome sequencing and comparative analysis to study the evolution of active and passive invasion strategies and to infer factors associated with active forms of host cell invasion. The evolution of active invasion appears to have followed an adaptive radiation in which two of the three fusobacterial lineages acquired new genes and underwent expansions of ancestral genes that enable active forms of host cell invasion. Compared to passive invaders, active invaders have much larger genomes, encode FadA-related adhesins, and possess twice as many genes encoding membrane-related proteins, including a large expansion of surface-associated proteins containing the MORN2 domain of unknown function. We predict a role for proteins containing MORN2 domains in adhesion and active invasion. In the largest and most comprehensive comparison of sequenced Fusobacterium species to date, we have generated a testable model for the molecular pathogenesis of Fusobacterium infection and illuminate new therapeutic or diagnostic strategies. PMID:25370491

  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. 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. PMID:18494171

  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. PMID:25327842

  1. A novel theory to explain species diversity in landscapes: positive frequency dependence and habitat suitability.

    PubMed Central

    Molofsky, Jane; Bever, James D

    2002-01-01

    Theories to explain the diversity of species have required that individual species occupy unique niches and/or vary in their response to environmental factors. Positive interactions within a species, although common in communities, have not been thought to maintain species diversity because in non-spatial models the more abundant species always outcompetes the rarer species. Here, we show, using a stochastic spatial model, that positive intraspecific interactions such as those caused by positive frequency dependence and/or priority effects, can maintain species diversity if interactions between individuals are primarily local and the habitat contains areas that cannot be colonized by any species, such as boulders or other physical obstructions. When intraspecific interactions are primarily neutral, species diversity will eventually erode to a single species. When the landscape is homogeneous (i.e. does not contain areas that cannot be colonized by any species), the presence of strong intraspecific interactions will not maintain diversity. PMID:12495479

  2. Diversity of Listeria Species in Urban and Natural Environments

    PubMed Central

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

    2012-01-01

    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. PMID:22504820

  3. 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

  4. 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

  5. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    PubMed Central

    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/. PMID:26578696

  6. 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

  7. Caspar Controls Resistance to Plasmodium falciparum in Diverse Anopheline Species

    PubMed Central

    Garver, Lindsey S.; Dong, Yuemei; Dimopoulos, George

    2009-01-01

    Immune responses mounted by the malaria vector Anopheles gambiae are largely regulated by the Toll and Imd (immune deficiency) pathways via the NF-kappaB transcription factors Rel1 and Rel2, which are controlled by the negative regulators Cactus and Caspar, respectively. Rel1- and Rel2-dependent transcription in A. gambiae has been shown to be particularly critical to the mosquito's ability to manage infection with the rodent malaria parasite Plasmodium berghei. Using RNA interference to deplete the negative regulators of these pathways, we found that Rel2 controls resistance of A. gambiae to the human malaria parasite Plasmodium falciparum, whereas Rel 1 activation reduced infection levels. The universal relevance of this defense system across Anopheles species was established by showing that caspar silencing also prevents the development of P. falciparum in the major malaria vectors of Asia and South America, A. stephensi and A. albimanus, respectively. Parallel studies suggest that while Imd pathway activation is most effective against P. falciparum, the Toll pathway is most efficient against P. berghei, highlighting a significant discrepancy between the human pathogen and its rodent model. High throughput gene expression analyses identified a plethora of genes regulated by the activation of the two Rel factors and revealed that the Toll pathway played a more diverse role in mosquito biology than the Imd pathway, which was more immunity-specific. Further analyses of key anti-Plasmodium factors suggest they may be responsible for the Imd pathway–mediated resistance phenotype. Additionally, we found that the fitness cost caused by Rel2 activation through caspar gene silencing was undetectable in sugar-fed, blood-fed, and P. falciparum-infected female A. gambiae, while activation of the Toll pathway's Rel1 had a major impact. This study describes for the first time a single gene that influences an immune mechanism that is able to abort development of P

  8. Enterohepatic Helicobacter other than Helicobacter pylori.

    PubMed

    Mateos-Muñoz, Beatriz; Pérez-de-la-Serna, Julio; Ruiz-de-León, Antonio; Serrano-Falcón, Blanca; Casabona-Francés, Sergio; Velasco-Cerrudo, Aurelio; Rey-Díaz-Rubio, Enrique

    2013-09-01

    The Helicobacter genus includes Gram negative bacteria which were originally considered to belong to the Campylobacter genus. They have been classified in a separate genus since 1989 because they have different biochemical characteristics, with more than 24 species having been identified and more still being studied.H. pylori is the best known. It has an important etiopathogenic role in peptic ulcer disease and gastric cancer. Enterohepatic Helicobacters (EHH) other than H. pylori colonize the bowel, biliary tree and liver of animals and human beings with pathogenic potential. The difficulties existing to correctly isolate these microorganisms limit the description of their true prevalence and of the diseases they cause. Many studies have tried to discover the different clinical implications of EHH. Diseases like chronic liver disease, autoimmune hepatitis, hepatocarcinoma, autoimmune hepatobiliary disease, biliary lithiasis, cholangiocarcinoma and gallbladder cancer, Meckel´s diverticulum, acute appendicitis and inflammatory bowel disease have been related with different EHH species with different results, although their prevalence is greater than in healthy subjects. However, these data are currently not sufficient to draw definitive conclusions. Finally, the best known role of EHH in bowel disease is production of acute and chronic diarrhea pictures initially referred to as Campylobacter. H. pullorum has been identified in patients with acute gastroenteritis. The correct identification of EHH as producers of infectious gastroenteritis is found in its antibiotic susceptibility. It is generally macrolide-susceptible and quinolone-resistant. PMID:24274445

  9. Metabolism of sugars by genetically diverse species of oral Leptotrichia

    PubMed Central

    Thompson, John; Pikis, Andreas

    2011-01-01

    SUMMARY Leptotrichia buccalis ATCC 14201 is a Gram-negative, anaerobic rod-shaped bacterium resident in oral biofilm at the tooth surface. The sequenced genome of this organism reveals three contiguous genes at loci: Lebu_1525,1526 and 1527. The translation products of these genes exhibit significant homology with phospho-α-glucosidase (Pagl), a regulatory protein (GntR) and a phosphoenol pyruvate-dependent sugar transport protein (EIICB), respectively. In non-oral bacterial species, these genes comprise the sim operon that facilitates sucrose isomer metabolism. Growth studies showed that L. buccalis fermented a wide variety of carbohydrates, including four of the five isomers of sucrose. Growth on the isomeric disaccharides elicited expression of a 50kDa polypeptide comparable in size to that encoded by Lebu_1525. The latter gene was cloned, and the expressed protein was purified to homogeneity from Escherichia coli TOP 10 cells. In the presence of two cofactors, NAD+ and Mn2+ ion, the enzyme readily hydrolyzed p-nitrophenyl-α-glucopyranoside 6-phosphate (pNPαG6P), a chromogenic analog of the phosphorylated isomers of sucrose. By comparative sequence alignment, immuno-reactivity and signature motifs, the enzyme can be assigned to the phospho-α-glucosidase (Pagl) clade of Family 4 of the glycosyl hydrolase super family. We suggest that the products of Lebu_1527 and 1525, catalyze the phosphorylative translocation and hydrolysis of sucrose isomers in L. buccalis, respectively. Four genetically diverse, but 16S rDNA related species of Leptotrichia have recently been described: L. goodfellowii, L. hofstadii, L. shahii and L. wadei. The phenotypic traits of these new species, with respect to carbohydrate utilization, have also been determined. PMID:22230464

  10. Genista anglica (Fabaceae): One very diverse species or one species complex?

    PubMed

    Fernández Prieto, José A; Sanna, Mauro; Bueno, Álvaro; Pérez, Marta

    2016-05-01

    Genista anglica represents a widely distributed group of shrubs in the Iberian Peninsula, as well as in the North of the Moroccan Mountains, the South of Italy and in most oceanic territories of Western Europe, with its northern limit in Sweden. Up to five different species within the group have been described in these territories: Genista ancistrocarpa, G. acutifolia, G. brutia and G. silana, as well as G. anglica sensu stricto. The diversity of Genista anglica sensu lato as well as the phylogenetic patterns that have generated this diversity have been analyzed through the use of nuclear (ITS, ETS) and chloroplastic (trnL, trnL-F, rbcL, matK) DNA sequences. Our results show that the group probably originated in the West of the Iberian Peninsula and subsequently spread to the rest of the European oceanic territories. Additionally, the results support the idea that the presence of a group of plants in the South of Italy, where G. brutia and G. silana were previously described, has been the consequence of the introduction of seeds collected in the Northwest of the Iberian Peninsula. Our results also indicate that, in contrast to some authors, the populations from the West of the Iberian Peninsula are not isolated and, consequently, they should be grouped into one species with high diversity, therefore differentiation into different taxa is no longer adequate. PMID:26879932

  11. 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

  12. 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. PMID:25545860

  13. Woody Species Diversity in Forest Plantations in a Mountainous Region of Beijing, China: Effects of Sampling Scale and Species Selection

    PubMed Central

    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. PMID:25545860

  14. Soil type and species diversity influence selection on physiology in Panicum virgatum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species diversity influences the productivity and stability of plant communities, but its effect on the evolution of species within those communities is poorly understood. In this study, we tested whether species diversity and soil type influence selection on physiology in switchgrass (Panicum virga...

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Diverse characteristics of the CagA gene of Helicobacter pylori strains collected from patients from southern vietnam with gastric cancer and peptic ulcer.

    PubMed

    Truong, Bui Xuan; Mai, Vo Thi Chi; Tanaka, Hiroshi; Ly, Le Thanh; Thong, Tran Minh; Hai, Hoang Hoa; Van Long, Dao; Furumatsu, Keisuke; Yoshida, Masaru; Kutsumi, Hiromu; Azuma, Takeshi

    2009-12-01

    The pathogenesis of gastroduodenal diseases is related to the diversity of Helicobacter pylori strains. CagA-positive strains are more likely to cause gastric cancer than CagA-negative strains. Based on EPIYA (Glu-Pro-Ile-Tyr-Ala) motifs at the carboxyl terminus corresponding to phosphorylation sites, H. pylori CagA is divided into East Asian CagA and Western CagA. The former type prevails in East Asia and is more closely associated with gastric cancer. The present study used full sequences of the cagA gene and CagA protein of 22 H. pylori strains in gastric cancer and peptic ulcer patients from Southern Vietnam to make a comparison of genetic homology among Vietnamese strains and between them and other strains in East Asia. A phylogenetic tree was constructed based on full amino acid sequences of 22 Vietnamese strains in accordance with 54 references from around the world. The cagA gene was found in all Vietnamese H. pylori strains. Twenty-one of 22 (95.5%) strains belonged to the East Asian type and had similar characteristics of amino acid sequence at the carboxyl terminus to other strains from the East Asian region. From evidence of East Asian CagA and epidemiologic cancerous lesions in Vietnam, H. pylori-infected Vietnamese can be classified into a high-risk group for gastric cancer, but further studies on the interaction among environmental and virulence factors should be done. Finally, phylogenetic data support that there is a Japanese subtype in the Western CagA type. PMID:19846630

  20. Diverse Characteristics of the cagA Gene of Helicobacter pylori Strains Collected from Patients from Southern Vietnam with Gastric Cancer and Peptic Ulcer▿

    PubMed Central

    Truong, Bui Xuan; Mai, Vo Thi Chi; Tanaka, Hiroshi; Ly, Le Thanh; Thong, Tran Minh; Hai, Hoang Hoa; Van Long, Dao; Furumatsu, Keisuke; Yoshida, Masaru; Kutsumi, Hiromu; Azuma, Takeshi

    2009-01-01

    The pathogenesis of gastroduodenal diseases is related to the diversity of Helicobacter pylori strains. CagA-positive strains are more likely to cause gastric cancer than CagA-negative strains. Based on EPIYA (Glu-Pro-Ile-Tyr-Ala) motifs at the carboxyl terminus corresponding to phosphorylation sites, H. pylori CagA is divided into East Asian CagA and Western CagA. The former type prevails in East Asia and is more closely associated with gastric cancer. The present study used full sequences of the cagA gene and CagA protein of 22 H. pylori strains in gastric cancer and peptic ulcer patients from Southern Vietnam to make a comparison of genetic homology among Vietnamese strains and between them and other strains in East Asia. A phylogenetic tree was constructed based on full amino acid sequences of 22 Vietnamese strains in accordance with 54 references from around the world. The cagA gene was found in all Vietnamese H. pylori strains. Twenty-one of 22 (95.5%) strains belonged to the East Asian type and had similar characteristics of amino acid sequence at the carboxyl terminus to other strains from the East Asian region. From evidence of East Asian CagA and epidemiologic cancerous lesions in Vietnam, H. pylori-infected Vietnamese can be classified into a high-risk group for gastric cancer, but further studies on the interaction among environmental and virulence factors should be done. Finally, phylogenetic data support that there is a Japanese subtype in the Western CagA type. PMID:19846630

  1. Testing the mechanisms of diversity-dependent overyielding in a grass species.

    PubMed

    Atwater, Daniel Z; Callaway, Ragan M

    2015-12-01

    Plant diversity enhances many ecosystem processes, including productivity, but these effects have been studied almost exclusively at the taxonomic scale of species. We explore the effect of intraspecific diversity on the productivity of a widespread and dominant grassland species using accessions collected from populations throughout its range. We found that increasing population/ecotype diversity of Pseudoroegneria spicata increased productivity to a similar degree as that reported for species diversity. However, we did not find evidence that overyielding was related to either resource depletion or to pathogenic soil fungi, two causes of overyielding in species-diverse communities. Instead, larger accessions overyielded at low diversity at the expense of smaller accessions, and small accessions overyielded through complementarity at all levels of diversity. Furthermore, overyielding was stronger for accessions from mesic environments, suggesting that local adaptation might predictably influence how plants respond to increases in diversity. This suggests that mass-based competition or other cryptic accession-specific processes had complex but important effects on overyielding. Our results indicate that the effects of diversity within a species can be substantial but that overyielding by intraspecifically diverse populations may not be through the same processes thought to cause overyielding in species diverse communities. PMID:26909438

  2. Abundance, diversity, and resource use in an assemblage of Conus species in Enewetak lagoon

    SciTech Connect

    Kohn, A.J.

    1980-10-01

    Eight species of the gastropod genus Conus co-occur in sand substrate and an adjacent meadow of Halimeda stuposa in Enewetak lagoon, an unusually diverse assemblage for this type of habitat. Population density is high, and large species predominate; they represent all major feeding groups in the genus: predators on polychaetes, enteropneusts, gastropods, and fishes. Although the two most common Conus species eat primarily the same prey species, they mainly take prey of different sizes in different microhabitats. The results suggest that sufficient microhabitat heterogeneity and prey diversity exist to permit spatial segregation and specialization on different prey resources by the different Conus species present. Between-species dissimilarity in resource use thus agrees with previous observations on more diverse Conus assemblages of subtidal coral reef platforms. Prey species diversity is inversely related to body size, confirming and extending a previously identified pattern among Conus species that prey on sedentary polychaetes.

  3. 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...

  4. 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

  5. Patterns of tree species diversity in relation to climatic factors on the Sierra Madre Occidental, Mexico.

    PubMed

    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

  6. Recombination and DNA Repair in Helicobacter pylori

    PubMed Central

    Dorer, Marion S.; Sessler, Tate H.; Salama, Nina R.

    2013-01-01

    All organisms have pathways that repair the genome, ensuring their survival and that of their progeny. But these pathways also serve to diversify the genome, causing changes on the level of nucleotide, whole gene, and genome structure. Sequencing of bacteria has revealed wide allelic diversity and differences in gene content within the same species, highlighting the importance of understanding pathways of recombination and DNA repair. The human stomach pathogen Helicobacter pylori is an excellent model system for studying these pathways. H. pylori harbors major recombination and repair pathways and is naturally competent, facilitating its ability to diversify its genome. Elucidation of DNA recombination, repair, and diversification programs in this pathogen will reveal connections between these pathways and their importance to infection. PMID:21682641

  7. Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

    PubMed

    Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

    2013-07-01

    Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems. PMID:23229391

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

    PubMed

    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

  9. 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 Individual…

  10. Temporal stability in forest productivity increases with tree diversity due to asynchrony in species dynamics.

    PubMed

    Morin, Xavier; Fahse, Lorenz; de Mazancourt, Claire; Scherer-Lorenzen, Michael; Bugmann, Harald

    2014-12-01

    Theory predicts a positive relationship between biodiversity and stability in ecosystem properties, while diversity is expected to have a negative impact on stability at the species level. We used virtual experiments based on a dynamic simulation model to test for the diversity-stability relationship and its underlying mechanisms in Central European forests. First our results show that variability in productivity between stands differing in species composition decreases as species richness and functional diversity increase. Second we show temporal stability increases with increasing diversity due to compensatory dynamics across species, supporting the biodiversity insurance hypothesis. We demonstrate that this pattern is mainly driven by the asynchrony of species responses to small disturbances rather than to environmental fluctuations, and is only weakly affected by the net biodiversity effect on productivity. Furthermore, our results suggest that compensatory dynamics between species may enhance ecosystem stability through an optimisation of canopy occupancy by coexisting species. PMID:25212251

  11. Global-scale latitudinal patterns of species diversity in the deep-sea benthos

    NASA Astrophysics Data System (ADS)

    Rex, Michael A.; Stuart, Carol T.; Hessler, Robert R.; Allen, John A.; Sanders, Howard L.; Wilson, George D. F.

    1993-10-01

    LATITUDINAL gradients of species diversity are ubiquitous features of terrestrial and coastal marine biotas, and they have inspired the development of theoretical ecology1-3. Since the discovery of high species diversity in the deep-sea benthos4, much has been learned about local5,6and regional7-9patterns of diversity. Variation in diversity on larger scales remains poorly described. Latitudinal gradients of diversity were unexpected because it was assumed that the environmental gradients that cause large-scale patterns in surface environments could not affect communities living at great depths10. Here we report that deep-sea bivalves, gastropods and isopods show clear latitudinal diversity gradients in the North Atlantic, and strong interregional variation in the South Atlantic. Many seemingly incompatible mechanisms have been proposed to explain deep-sea species diversity11. The existence of regular global patterns suggests that these mechanisms operate at different spatial and temporal scales.

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

    PubMed Central

    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. PMID:26691919

  13. 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 ...

  14. Evaluating β Diversity as a Surrogate for Species Representation at Fine Scale.

    PubMed

    Beier, Paul; Albuquerque, Fábio

    2016-01-01

    Species turnover or β diversity is a conceptually attractive surrogate for conservation planning. However, there has been only 1 attempt to determine how well sites selected to maximize β diversity represent species, and that test was done at a scale too coarse (2,500 km2 sites) to inform most conservation decisions. We used 8 plant datasets, 3 bird datasets, and 1 mammal dataset to evaluate whether sites selected to span β diversity will efficiently represent species at finer scale (sites sizes < 1 ha to 625 km2). We used ordinations to characterize dissimilarity in species assemblages (β diversity) among plots (inventory data) or among grid cells (atlas data). We then selected sites to maximize β diversity and used the Species Accumulation Index, SAI, to evaluate how efficiently the surrogate (selecting sites for maximum β diversity) represented species in the same taxon. Across all 12 datasets, sites selected for maximum β diversity represented species with a median efficiency of 24% (i.e., the surrogate was 24% more effective than random selection of sites), and an interquartile range of 4% to 41% efficiency. β diversity was a better surrogate for bird datasets than for plant datasets, and for atlas datasets with 10-km to 14-km grid cells than for atlas datasets with 25-km grid cells. We conclude that β diversity is more than a mere descriptor of how species are distributed on the landscape; in particular β diversity might be useful to maximize the complementarity of a set of sites. Because we tested only within-taxon surrogacy, our results do not prove that β diversity is useful for conservation planning. But our results do justify further investigation to identify the circumstances in which β diversity performs well, and to evaluate it as a cross-taxon surrogate. PMID:26943170

  15. Evaluating β Diversity as a Surrogate for Species Representation at Fine Scale

    PubMed Central

    Beier, Paul; Albuquerque, Fábio

    2016-01-01

    Species turnover or β diversity is a conceptually attractive surrogate for conservation planning. However, there has been only 1 attempt to determine how well sites selected to maximize β diversity represent species, and that test was done at a scale too coarse (2,500 km2 sites) to inform most conservation decisions. We used 8 plant datasets, 3 bird datasets, and 1 mammal dataset to evaluate whether sites selected to span β diversity will efficiently represent species at finer scale (sites sizes < 1 ha to 625 km2). We used ordinations to characterize dissimilarity in species assemblages (β diversity) among plots (inventory data) or among grid cells (atlas data). We then selected sites to maximize β diversity and used the Species Accumulation Index, SAI, to evaluate how efficiently the surrogate (selecting sites for maximum β diversity) represented species in the same taxon. Across all 12 datasets, sites selected for maximum β diversity represented species with a median efficiency of 24% (i.e., the surrogate was 24% more effective than random selection of sites), and an interquartile range of 4% to 41% efficiency. β diversity was a better surrogate for bird datasets than for plant datasets, and for atlas datasets with 10-km to 14-km grid cells than for atlas datasets with 25-km grid cells. We conclude that β diversity is more than a mere descriptor of how species are distributed on the landscape; in particular β diversity might be useful to maximize the complementarity of a set of sites. Because we tested only within-taxon surrogacy, our results do not prove that β diversity is useful for conservation planning. But our results do justify further investigation to identify the circumstances in which β diversity performs well, and to evaluate it as a cross-taxon surrogate. PMID:26943170

  16. 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

  17. Hybrid origin of a cichlid population in Lake Malawi: implications for genetic variation and species diversity.

    PubMed

    Smith, Peter F; Konings, Ad; Kornfield, Irv

    2003-09-01

    The importance of species recognition to taxonomic diversity among Lake Malawi cichlids has been frequently discussed. Hybridization - the apparent breakdown of species recognition - has been observed sporadically among cichlids and has been viewed as both a constructive and a destructive force with respect to species diversity. Here we provide genetic evidence of a natural hybrid cichlid population with a unique colour phenotype and elevated levels of genetic variation. We discuss the potential evolutionary consequences of interspecific hybridization in Lake Malawi cichlids and propose that the role of hybridization in generating both genetic variability and species diversity of Lake Malawi cichlids warrants further consideration. PMID:12919487

  18. 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

  19. 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...

  20. Strong density- and diversity-related effects help to maintain tree species diversity in a neotropical forest

    PubMed Central

    Wills, Christopher; Condit, Richard; Foster, Robin B.; Hubbell, Stephen P.

    1997-01-01

    Intraspecific density-dependent effects in the Barro Colorado Island (Panama) study area are far stronger, and involve far more species, than previously had been suspected. Significant effects on recruitment, many extremely strong, are seen for 67 out of the 84 most common species in the plot, including the 10 most common. Significant effects on the intrinsic rate of increase are seen in 54 of the 84 species. These effects are far more common than interspecific effects, and are predominantly of the type that should maintain tree diversity. As a result, the more diverse an area in the forest is, the higher is the overall rate of increase of the trees in that area, although sheer crowding has by itself a negative effect. These findings are consistent with, but do not prove, an important role for host–pathogen interactions (defined broadly) in the maintenance of diversity. Ways are suggested by which to test host–pathogen models and competing models. PMID:11038601

  1. Diversity of Woodland Communities and Plant Species along an Altitudinal Gradient in the Guancen Mountains, China

    PubMed Central

    Meng, Dongping; Zhang, Jin-Tun; Li, Min

    2012-01-01

    Study on plant diversity is the base of woodland conservation. The Guancen Mountains are the northern end of Luliang mountain range in North China. Fifty-three quadrats of 10 m × 20 m of woodland communities were randomly established along an altitudinal gradient. Data for species composition and environmental variables were measured and recorded in each quadrat. To investigate the variation of woodland communities, a Two-Way Indicator Species Analysis (TWINSPAN) and a Canonical Correspondence Analysis (CCA) were conducted, while species diversity indices were used to analyse the relationships between species diversity and environmental variables in this study. The results showed that there were eight communities of woodland vegetation; each of them had their own characteristics in composition, structure, and environment. The variation of woodland communities was significantly related to elevation and also related to slope, slope aspect, and litter thickness. The cumulative percentage variance of species-environment relation for the first three CCA axes was 93.5%. Elevation was revealed as the factor which most influenced community distribution and species diversity. Species diversity was negatively correlated with elevation, slope aspect, and litter thickness, but positively with slope. Species richness and heterogeneity increased first and then decreased but evenness decreased significantly with increasing elevation. Species diversity was correlated with slope, slope aspect, and litter thickness. PMID:22566768

  2. 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. PMID:17002952

  3. Effect of resveratrol on Helicobacter pylori-induced interleukin-8 secretion, reactive oxygen species generation and morphological changes in human gastric epithelial cells.

    PubMed

    Zaidi, Syed Faisal Haider; Ahmed, Kanwal; Yamamoto, Takeshi; Kondo, Takashi; Usmanghani, Khan; Kadowaki, Makoto; Sugiyama, Toshiro

    2009-11-01

    Inflammatory cytokine interleukin-8 (IL-8) and reactive oxygen species (ROS) overexpressed in the gastric mucosa when exposed to Helicobacter pylori, defined as a class I carcinogen. Moreover, infection with H. pylori leads to morphological changes in co-cultured cells known as hummingbird phenomenon along with increased motility. Resveratrol, a highly abundant polyphenol in red grapes, has shown anti-inflammatory, anti-cancer, cardioprotective and neuroprotective activities. However, the effect of resveratrol in H. pylori-infected cells has not been investigated. The present study was, therefore, aimed to evaluate the effect of resveratrol on the induction of IL-8, ROS and hummingbird morphology in H. pylori-infected gastric epithelial cells. The non-toxic concentration of resveratrol for both H. pylori and epithelial cells was determined by brucella broth dilution method and DNA fragmentation assay. The non-toxic resveratrol (< or =100 microM) treatment did not demonstrate any inhibitory effect against H. pylori adhesion to gastric epithelial cells. However, preincubation of the cells with 75 and 100 muM of resveratrol significantly (p<0.05 and p<0.01 respectively) inhibited the secretion of IL-8 from H. pylori-infected cells. In addition, resveratrol pretreatment at 1-100 muM suppressed H. pylori-induced ROS generation in a concentration dependent manner. Moreover, H. pylori-initiated morphological changes were markedly blocked by resveratrol. Hence, resveratrol can be considered as a potential candidate against various H. pylori related gastric pathogenic processes. PMID:19881312

  4. Species and genetic diversity in the genus Drosophila inhabiting the Indian subcontinent.

    PubMed

    Singh, Bashisth N

    2015-06-01

    Biodiversity is the sum total of all living things on the earth with particular reference to the profound variety in structure,function and genetic constitution. It includes both number and frequency of species or genes in a given assemblage and the variety of resulting ecosystems in a region. It is usually considered at three different levels: genetic, species and ecological diversities. Genus Drosophila belongs to the family Drosophilidae (class Insecta, order Diptera), characterized by rich species diversity at global level and also in India, which is a megadiverse country. At global level, more than 1500 species have been described and several thousands estimated. Hawaiian Islands are particularly rich in species diversity with more than 500 species which provides a unique opportunity to study evolution in genus Drosophila. About 150 species of Drosophila have been reported from India. Certain species of Drosophila found in India have been investigated for genetic diversity within the species. In this regard, Drosophila ananassae is noteworthy. It is a cosmopolitan and domestic species with common occurrence in India and is endowed with many genetic peculiarities. Population genetics and evolutionary studies in this species have revealed as to how genetic diversity within a species play an important role in adaptation of populations to varying environments. In addition, the work carried on D. melanogaster, D. nasuta, D. bipectinata and certain other species in India has shown that these species vary in degree and pattern of genetic diversity, and have evolved different mechanisms for adjusting to their environments. The ecological adaptations to various kinds of stress studied in certain species of Drosophila inhabiting the Indian subcontinent are also discussed. PMID:26174688

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

    PubMed

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

    2010-01-01

    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

  6. Species Diversity and Distribution Patterns of the Ants of Amazonian Ecuador

    PubMed Central

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

    2010-01-01

    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

  7. 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

  8. Application of species richness estimators for the assessment of fungal diversity.

    PubMed

    Unterseher, Martin; Schnittler, Martin; Dormann, Carsten; Sickert, Andreas

    2008-05-01

    Species richness and distribution patterns of wood-inhabiting fungi and mycetozoans (slime moulds) were investigated in the canopy of a Central European temperate mixed deciduous forest. Species richness was described with diversity indices and species-accumulation curves. Nonmetrical multidimensional scaling was used to assess fungal species composition on different tree species. Different species richness estimators were used to extrapolate species richness beyond our own data. The reliability of the abundance-based coverage estimator, Chao, Jackknife and other estimators of species richness was evaluated for mycological surveys. While the species-accumulation curve of mycetozoans came close to saturation, that of wood-inhabiting fungi was continuously rising. The Chao 2 richness estimator was considered most appropriate to predict the number of species at the investigation site if sampling were continued. Gray's predictor of species richness should be used if statements of the number of species in larger areas are required. Multivariate analysis revealed the importance of different tree species for the conservation and maintenance of fungal diversity within forests, because each tree species possessed a characteristic fungal community. The described mathematical approaches of estimating species richness possess great potential to address fungal diversity on a regional, national, and global scale. PMID:18355274

  9. 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

  10. 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 ...

  11. 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,...

  12. Diversity is maintained by seasonal variation in species abundance

    PubMed Central

    2013-01-01

    Background Some of the most marked temporal fluctuations in species abundances are linked to seasons. In theory, multispecies assemblages can persist if species use shared resources at different times, thereby minimizing interspecific competition. However, there is scant empirical evidence supporting these predictions and, to the best of our knowledge, seasonal variation has never been explored in the context of fluctuation-mediated coexistence. Results Using an exceptionally well-documented estuarine fish assemblage, sampled monthly for over 30 years, we show that temporal shifts in species abundances underpin species coexistence. Species fall into distinct seasonal groups, within which spatial resource use is more heterogeneous than would be expected by chance at those times when competition for food is most intense. We also detect seasonal variation in the richness and evenness of the community, again linked to shifts in resource availability. Conclusions These results reveal that spatiotemporal shifts in community composition minimize competitive interactions and help stabilize total abundance. PMID:24007204

  13. PLANT SPECIES DIVERSITY, ECOSYSTEM FUNCTION, AND PASTURE MANAGEMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grassland farmers face new challenges in pasture management including improving sustainability, reducing inputs of fertilizers and pesticides, and protecting soil resources. Managing plant diversity within and among pastures may be one tool to aid producers in meeting these new challenges. Pasture e...

  14. 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. PMID:24994029

  15. Global diversity and biogeography of Skeletonema species (bacillariophyta).

    PubMed

    Kooistra, Wiebe H C F; Sarno, Diana; Balzano, Sergio; Gu, Haifeng; Andersen, Robert A; Zingone, Adriana

    2008-04-01

    Recent studies have shown that the cosmopolitan diatom Skeletonema costatum sensu lato is composed of several morphologically and genetically distinct species. To assess whether the separate species have a cosmopolitan distribution, we analysed 184 strains from marine and estuarine sites worldwide. We identified the strains using light and electron microscopy, and we sequenced the hyper-variable region of nuclear LSU rDNA. All recently described species were genetically distinct, and all but two were morphologically distinct. Variability was found for the only ultrastructural character used to distinguish Skeletonema dohrnii and S. marinoi, which cannot be identified based on morphology alone. Furthermore, multiple genetically distinct taxa, which may represent cryptic species, were found within the S. menzelii and S. tropicum clades. We found that all currently recognized species of Skeletonema are widespread, however, gaps seem to occur in their geographical ranges. For example, some species are found in both the northern and southern temperate latitudes whereas other species appear to have only subtropical to tropical ranges. Skeletonema pseudocostatum and S. grethae seem to have more restricted geographical ranges because the former was not found along American coasts and the latter was encountered only in US waters. A taxonomic update is provided for Skeletonema strains currently available in several culture collections, which could aid reinterpretation of results obtained in comparative studies using these strains. PMID:18042429

  16. 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. PMID:26656801

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

    PubMed Central

    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. PMID:23825795

  18. 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.

  19. Relating species and functional diversity using stable isotope probing

    NASA Astrophysics Data System (ADS)

    Prosser, J. I.; Rangel-Castro, J. I.; Mahmood, S.; Nicol, G.; Meharg, A. A.; Killham, K. S.

    2004-12-01

    Microbial communities play an essential role in biogeochemical cycles and analysis of laboratory cultures has provided much information on biochemical processes and physiological characteristics of functional groups of microorganisms responsible for these processes. However, the majority of microorganisms cannot be grown readily in laboratory culture and cultivation-independent molecular techniques are required for analysis of community structure and diversity. These techniques have demonstrated considerable microbial diversity in natural communities and have revealed the existence of abundant microorganisms belonging to novel, previously unsuspected microbial groups. Molecular analysis of natural communities typically provides little information on links between specific microorganisms and the biogeochemical processes that they carry out. We are therefore ignorant of the significance of microbial diversity for ecosystem processes and of the ecosystem function of uncultivated, but abundant microbial groups. Stable isotope probing enables identification of which members of a community are involved in the utilisation of specific substrates, particularly carbon substrates. It involves amendment of environmental samples, or field application with 13C-labelled carbon substrates and, after a period of exposure, extraction of nucleic acids and separation of 13C-labelled (heavy) and 12C-labelled (light) nucleic acid pools by density gradient centrifugation. The heavy nucleic acid pool will be derived only from organisms assimilating the labelled substrate.Molecular analysis of this pool provides information on identity and relative abundance of active members of the community. The technique therefore enables in situ functional analysis of microbial groups without the requirement for laboratory cultivation. Stable isotope probing has been used to determine which organisms are involved in the degradation of specific organic substrates, including recalcitrant compounds, and

  20. Plot shape effects on plant species diversity measurements

    USGS Publications Warehouse

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

    2005-01-01

    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-climate vegetation types

  1. [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. PMID:21941763

  2. 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

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

    PubMed

    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. Influence of secondary compound complementarity and species diversity on consumption of Mediterranean shrubs by sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Generalist herbivores foraging in chemically diverse grazing ecosystems like the Mediterranean maquis increase intake on mixed diets, suggesting they are more able to meet nutritional needs and avoid toxicosis. Thus, our objectives were to determine how shrub species diversity and complementary inte...

  5. Are herbage yield and yield stability affected by plant species diversity in sown pasture mixtures?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A tenet of plant biodiversity theory in grasslands is that increased diversity contributes to the stability of ecosystems. In managed grasslands, such as pastures, greater stability of herbage production as a result of increased plant species diversity would be beneficial. In this study, I combined ...

  6. 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

  7. 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

  8. 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

  9. 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. PMID:26615751

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

    PubMed

    Barraclough, Timothy G

    2010-06-12

    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

  11. 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

  12. 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. PMID:24096740

  13. Resource pulses, species interactions, and diversity maintenance in arid and semi-arid environments.

    PubMed

    Chesson, Peter; Gebauer, Renate L E; Schwinning, Susan; Huntly, Nancy; Wiegand, Kerstin; Ernest, Morgan S K; Sher, Anna; Novoplansky, Ariel; Weltzin, Jake F

    2004-10-01

    Arid environments are characterized by limited and variable rainfall that supplies resources in pulses. Resource pulsing is a special form of environmental variation, and the general theory of coexistence in variable environments suggests specific mechanisms by which rainfall variability might contribute to the maintenance of high species diversity in arid ecosystems. In this review, we discuss physiological, morphological, and life-history traits that facilitate plant survival and growth in strongly water-limited variable environments, outlining how species differences in these traits may promote diversity. Our analysis emphasizes that the variability of pulsed environments does not reduce the importance of species interactions in structuring communities, but instead provides axes of ecological differentiation between species that facilitate their coexistence. Pulses of rainfall also influence higher trophic levels and entire food webs. Better understanding of how rainfall affects the diversity, species composition, and dynamics of arid environments can contribute to solving environmental problems stemming from land use and global climate change. PMID:15069635

  14. Digenean species diversity in teleost fishes from the Gulf of Gabes, Tunisia (Western Mediterranean)

    PubMed Central

    Derbel, H.; Châari, M.; Neifar, L.

    2012-01-01

    This study is the first attempt to survey the diversity of fish digeneans in the Gulf of Gabes (southern coast of Tunisia). A total of 779 fishes belonging to 32 species were sampled. 53 species of Digenea belonging to 15 families were recorded. Among these species, 24 are reported for the first time from the coast of Tunisia. We report one new host record, Lecithochirium sp. from Sardinella aurita. The Hemiuridae is the dominant family. A host-parasite list is presented with the information on the prevalence, abundance and mean intensity of each species collected. The diversity of Digenea is compared with other localities in the Mediterranean Sea and the northern east of Tunisia. The Gulf of Gabes shows the lowest diversity linked to the anthropogenic activities and impact of exotic species. The use of Digenea as indicators of the state of the ecosystem is discussed. PMID:22550623

  15. The Influences of Canopy Species and Topographic Variables on Understory Species Diversity and Composition in Coniferous Forests

    PubMed Central

    Huo, Hong; Feng, Qi; Su, Yong-hong

    2014-01-01

    Understanding the factors that influence the distribution of understory vegetation is important for biological conservation and forest management. We compared understory species composition by multi-response permutation procedure and indicator species analysis between plots dominated by Qinghai spruce (Picea crassifolia Kom.) and Qilian juniper (Sabina przewalskii Kom.) in coniferous forests of the Qilian Mountains, northwestern China. Understory species composition differed markedly between the forest types. Many heliophilous species were significantly associated with juniper forest, while only one species was indicative of spruce forest. Using constrained ordination and the variation partitioning model, we quantitatively assessed the relative effects of two sets of explanatory variables on understory species composition. The results showed that topographic variables had higher explanatory power than did site conditions for understory plant distributions. However, a large amount of the variation in understory species composition remained unexplained. Forward selection revealed that understory species distributions were primarily affected by elevation and aspect. Juniper forest had higher species richness and α-diversity and lower β-diversity in the herb layer of the understory plant community than spruce forest, suggesting that the former may be more important in maintaining understory biodiversity and community stability in alpine coniferous forest ecosystems. PMID:25097871

  16. 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.

  17. Genetic Diversity In Abiotic Stress Tolerances Among Wheat Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Landraces and close related species of hexaploid wheat (Triticum aestivum L.) offer a vast reservoir of genetic resources for wheat improvement to production on abiotic stressed soils. In order to utilize the wheat landrace and close relative gene pools, the evaluation of wheat landrace and close r...

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

    PubMed

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

    2015-01-01

    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

  19. Genetic Diversity of Japanese Strawberry Species Based on Microsatellite Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The strawberry collection at the United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, consists of 1769 accessions from 17 species and 37 countries. Molecular techniques which include DNA-Based methods...

  20. REVEGETATING RUSSIAN KNAPWEED INFESTATIONS USING MORPHOLOGICALLLY DIVERSE SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Highly degraded pastures and rangeland dominated by Russian knapweed (Acroptilon repens [L.] DC) are often devoid of desirable plants. Control efforts may be ephemeral because propagules of desirable species are not available to reoccupy niches made available by control procedures. Establishing desi...

  1. 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

  2. Variation in species losses from islands: artifacts, extirpation rates, or pre-fragmentation diversity?

    PubMed

    Gurd, D Brent

    2006-02-01

    Species are being lost from isolated reserves as predicted by ecological theory, prompting calls for larger reserves with higher species immigration rates. However, some large islands have lost a large proportion of their species, whereas some small islands have not lost any. Conservation efforts would be more efficient if the cause of such variation in the relationships among number of species lost, island size, and immigration rate were known. Observed species losses could be affected by the time since islands were isolated, species immigration rates, species extirpation rates, the pre-fragmentation diversity of the region relative to steady state, or overestimation of the pre-fragmentation diversity of islands. To test the last three hypotheses, I compared the intersection points of the island, intraprovincial, and interprovincial species-area relationships of terrestrial mammals from nine archipelagos of land-bridge islands and terrestrial habitat isolates. Species losses from three archipelagos were greater than expected due to reduced immigration rates alone, although I could not resolve if this was due to increased extirpation rates or overestimation of the pre-fragmentation diversity of the islands. Analysis of six archipelagos indicates that the diversity of mammals in two regions of North America is currently below steady state, probably due to the extinction of mammals and glacial retreat during the late Pleistocene. These results have direct implications for reserve planning. When provincial diversity is below steady state, some combinations of reserve size and species immigration rate will allow reserves to maintain their pre-isolation diversity. However, the diversity of provinces relative to steady state is likely to vary, so conservation of a given proportion of a province may not always conserve the same proportion of its species. I present a new species-area relationship for islands formed by fragmentation that replaces the parameter c (fitted

  3. 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

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

    PubMed

    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

  5. 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

  6. Species, trophic, and functional diversity in marine protected and non-protected areas

    NASA Astrophysics Data System (ADS)

    Villamor, Adriana; Becerro, Mikel A.

    2012-10-01

    The number of Marine Protected Areas (MPAs) has grown exponentially in the last decades as marine environments steadily deteriorate. The success of MPAs stems from the overall positive benefits attributed to the "reserve effect," the totality of the consequences of protecting marine systems. The reserve effect includes but is beyond the goal of protecting particular species or areas with economical or cultural value. However, most data on the effects of MPAs focus on target species and there is limited evidence for the consequences of protection at larger levels of organization. Quantitative information on the reserve effect remains elusive partly because of its complex nature. Data on biodiversity can be used to quantify the reserve effect if not restricted to specific taxonomic groups. In our study, we quantified species diversity, trophic diversity, and an approach to functional diversity in five MPAs and adjacent non-protected areas along the Mediterranean coast of Spain. Our three measures of diversity were based on the abundance of algae, fish, sessile and mobile invertebrates in shallow water rocky communities and could be used to estimate the reserve effect based on species, trophic levels, or functional roles. We tested the hypothesis that species, trophic, and functional diversity were higher in protected areas than in adjacent non-protected areas. Species diversity varied with geographic area but not with protection status. However, we found higher functional diversity inside MPAs. Also, the effect of protection on functional diversity varied as a function of the geographic area. Our results support the uniqueness of MPAs at a species level and the universality of the reserve effect at the level of the trophic groups' composition. This type of comprehensive ecological approach may broaden our understanding of MPAs and their efficiency as management tools.

  7. The Phytophthora species assemblage and diversity in riparian alder ecosystems of western Oregon, USA.

    PubMed

    Sims, Laura Lee; Sutton, Wendy; Reeser, Paul; Hansen, Everett M

    2015-01-01

    Phytophthora species were systematically sampled, isolated, identified and compared for presence in streams, soil and roots of alder (Alnus species) dominated riparian ecosystems in western Oregon. We describe the species assemblage and evaluate Phytophthora diversity associated with alder. We recovered 1250 isolates of 20 Phytophthora species. Only three species were recovered from all substrates (streams, soil, alder roots): P. gonapodyides, the informally described "P. taxon Pgchlamydo", and P. siskiyouensis. P. alni ssp. uniformis along with five other species not previously recovered in Oregon forests are included in the assemblage: P.citricola s.l., P. gregata, P. gallica, P. nicotianae and P. parsiana. Phytophthora species diversity was greatest in downstream riparian locations. There was no significant difference in species diversity comparing soil and unwashed roots (the rhizosphere) to stream water. There was a difference between the predominating species from the rhizosphere compared to stream water. The most numerous species was the informally described "P. taxon Oaksoil", which was mainly recovered from, and most predominant in, stream water. The most common species from riparian forest soils and alder root systems was P. gonapodyides. PMID:26240311

  8. 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

  9. 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. PMID:27096797

  10. Drosophila Embryogenesis Scales Uniformly across Temperature in Developmentally Diverse Species

    PubMed Central

    Kuntz, Steven G.; Eisen, Michael B.

    2014-01-01

    Temperature affects both the timing and outcome of animal development, but the detailed effects of temperature on the progress of early development have been poorly characterized. To determine the impact of temperature on the order and timing of events during Drosophila melanogaster embryogenesis, we used time-lapse imaging to track the progress of embryos from shortly after egg laying through hatching at seven precisely maintained temperatures between 17.5°C and 32.5°C. We employed a combination of automated and manual annotation to determine when 36 milestones occurred in each embryo. D. melanogaster embryogenesis takes 33 hours at 17.5°C, and accelerates with increasing temperature to a low of 16 hours at 27.5°C, above which embryogenesis slows slightly. Remarkably, while the total time of embryogenesis varies over two fold, the relative timing of events from cellularization through hatching is constant across temperatures. To further explore the relationship between temperature and embryogenesis, we expanded our analysis to cover ten additional Drosophila species of varying climatic origins. Six of these species, like D. melanogaster, are of tropical origin, and embryogenesis time at different temperatures was similar for them all. D. mojavensis, a sub-tropical fly, develops slower than the tropical species at lower temperatures, while D. virilis, a temperate fly, exhibits slower development at all temperatures. The alpine sister species D. persimilis and D. pseudoobscura develop as rapidly as tropical flies at cooler temperatures, but exhibit diminished acceleration above 22.5°C and have drastically slowed development by 30°C. Despite ranging from 13 hours for D. erecta at 30°C to 46 hours for D. virilis at 17.5°C, the relative timing of events from cellularization through hatching is constant across all species and temperatures examined here, suggesting the existence of a previously unrecognized timer controlling the progress of embryogenesis that has

  11. 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

  12. 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.

  13. 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

  14. 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. PMID:26421457

  15. 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. PMID:22952950

  16. 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...

  17. Volatile chemicals released by Tephritid flies as a tool to understanding species diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is clear that the Tephritids are a wonderfully diverse group of flies. However, as is evident from the current Coordinated Research Project many times clear species identifications are next to impossible using common systematic methods. Excellent examples of cryptic species are documented amon...

  18. 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...

  19. 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.

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

    PubMed

    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

  1. 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

  2. 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

  3. Crop Species Diversity Changes in the United States: 1978-2012.

    PubMed

    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

  4. 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. PMID:26197473

  5. 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

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

    PubMed

    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. PMID:25840697

  7. 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.

  8. 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. PMID:18690478

  9. Butterfly Species Richness and Diversity in the Trishna Wildlife Sanctuary in South Asia

    PubMed Central

    Majumder, Joydeb; Lodh, Rahul; Agarwala, B. K.

    2013-01-01

    Several wildlife sanctuaries in the world are home to the surviving populations of many endemic species. Trishna wildlife sanctuary in northeast India is protected by law, and is home to the last surviving populations of Asian bison (Bos gorus Smith), spectacle monkey (Trachypithecus phayrie Blyth), capped langur (Trachypithecus pileatus Blyth), slow loris (Nycticebus coucang Boddaert), wild cat (Felis chaus Schreber), and wild boars (Sus scrofa L.), among many other animals and plants. The sanctuary was explored for species richness and diversity of butterflies. A six-month-long study revealed the occurrence of 59 butterfly species that included 21 unique species and 9 species listed in the threatened category. The mixed moist deciduous mature forest of the sanctuary harbored greater species richness and species diversity (39 species under 31 genera) than other parts of the sanctuary, which is comprised of regenerated secondary mixed deciduous forest (37 species under 32 genera), degraded forests (32 species under 28 genera), and open grassland with patches of plantations and artificial lakes (24 species under 17 genera). The majority of these species showed a distribution range throughout the Indo-Malayan region and Australasia tropics, and eight species were distributed in the eastern parts of South Asia, including one species, Labadea martha (F.), which is distributed in the eastern Himalayas alone. Estimator Chao 2 provided the best-predicted value of species richness. The steep slope of the species accumulation curve suggested the occurrence of a large number of rare species, and a prolonged gentle slope suggested a higher species richness at a higher sample abundance. The species composition of vegetation-rich habitats showed high similarity in comparison to vegetation-poor habitats. PMID:24219624

  10. 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.

  11. Declining Diversity in Abandoned Grasslands of the Carpathian Mountains: Do Dominant Species Matter?

    PubMed Central

    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. PMID:24014148

  12. 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

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

    PubMed

    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. PMID:25113741

  14. 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.

  15. [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. PMID:26859966

  16. 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. PMID:15365809

  17. 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. PMID:26380684

  18. Sequence Divergence and Conservation in Genomes of Helicobacter cetorum Strains from a Dolphin and a Whale

    PubMed Central

    Kersulyte, Dangeruta; Rossi, Mirko; Berg, Douglas E.

    2013-01-01

    Background and Objectives Strains of Helicobacter cetorum have been cultured from several marine mammals and have been found to be closely related in 16 S rDNA sequence to the human gastric pathogen H. pylori, but their genomes were not characterized further. Methods The genomes of H. cetorum strains from a dolphin and a whale were sequenced completely using 454 technology and PCR and capillary sequencing. Results These genomes are 1.8 and 1.95 mb in size, some 7–26% larger than H. pylori genomes, and differ markedly from one another in gene content, and sequences and arrangements of shared genes. However, each strain is more related overall to H. pylori and its descendant H. acinonychis than to other known species. These H. cetorum strains lack cag pathogenicity islands, but contain novel alleles of the virulence-associated vacuolating cytotoxin (vacA) gene. Of particular note are (i) an extra triplet of vacA genes with ≤50% protein-level identity to each other in the 5′ two-thirds of the gene needed for host factor interaction; (ii) divergent sets of outer membrane protein genes; (iii) several metabolic genes distinct from those of H. pylori; (iv) genes for an iron-cofactored urease related to those of Helicobacter species from terrestrial carnivores, in addition to genes for a nickel co-factored urease; and (v) members of the slr multigene family, some of which modulate host responses to infection and improve Helicobacter growth with mammalian cells. Conclusions Our genome sequence data provide a glimpse into the novelty and great genetic diversity of marine helicobacters. These data should aid further analyses of microbial genome diversity and evolution and infection and disease mechanisms in vast and often fragile ocean ecosystems. PMID:24358262

  19. 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. PMID:16917524

  20. 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. PMID:23776024

  1. Diverse novel mesorhizobia nodulate New Zealand native Sophora species.

    PubMed

    Tan, Heng Wee; Heenan, Peter B; De Meyer, Sofie E; Willems, Anne; Andrews, Mitchell

    2015-03-01

    Forty eight rhizobial isolates from New Zealand (NZ) native Sophora spp. growing in natural ecosystems were characterised. Thirty eight isolates across five groups showed greatest similarity to Mesorhizobium ciceri LMG 14989(T) with respect to their 16S rRNA and concatenated recA, glnll and rpoB sequences. Seven isolates had a 16S rRNA sequence identical to M. amorphae ATCC 19665(T) but showed greatest similarity to M. septentrionale LMG 23930(T) on their concatenated recA, glnll and rpoB sequences. All isolates grouped closely together for their nifH, nodA and nodC sequences, clearly separate from all other rhizobia in the GenBank database. None of the type strains closest to the Sophora isolates based on 16S rRNA sequence similarity nodulated Sophora microphylla but they all nodulated their original host. Twenty one Sophora isolates selected from the different 16S rRNA groupings produced N2-fixing nodules on three Sophora spp. but none nodulated any host of the type strains for the related species. DNA hybridisations indicated that these isolates belong to novel Mesorhizobium spp. that nodulate NZ native Sophora species. PMID:25498849

  2. Declines in both redundant and trace species characterize the latitudinal diversity gradient in tintinnid ciliates.

    PubMed

    Dolan, John R; Yang, Eun Jin; Kang, Sung-Ho; Rhee, Tae Siek

    2016-09-01

    The latitudinal diversity gradient is a well-known biogeographic pattern. However, rarely considered is how a cline in species richness may be reflected in the characteristics of species assemblages. Fewer species may equal fewer distinct ecological types, or declines in redundancy (species functionally similar to one another) or fewer trace species, those occurring in very low concentrations. We focused on tintinnid ciliates of the microzooplankton in which the ciliate cell is housed inside a species-specific lorica or shell. The size of lorica oral aperture, the lorica oral diameter (LOD), is correlated with a preferred prey size and maximum growth rate. Consequently, species of a distinct LOD are distinct in key ecologic characteristics, whereas those of a similar LOD are functionally similar or redundant species. We sampled from East Sea/Sea of Japan to the High Arctic Sea. We determined abundance distributions of biological species and also ecological types by grouping species in LOD size-classes, sets of ecologically similar species. In lower latitudes there are more trace species, more size-classes and the dominant species are accompanied by many apparently ecologically similar species, presumably able to replace the dominant species, at least with regard to the size of prey exploited. Such redundancy appears to decline markedly with latitude in assemblages of tintinnid ciliates. Furthermore, the relatively small species pools of the northern high latitude assemblages suggest a low capacity to adapt to changing conditions. PMID:26990873

  3. 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

    2013-01-01

    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. PMID:24338421

  4. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding.

    PubMed

    Evans, Nathan T; Olds, Brett P; Renshaw, Mark A; Turner, Cameron R; Li, Yiyuan; Jerde, Christopher L; Mahon, Andrew R; Pfrender, Michael E; Lamberti, Gary A; Lodge, David M

    2016-01-01

    Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206-L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina-sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance. PMID:26032773

  5. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae).

    PubMed

    Niemiller, Matthew L; Near, Thomas J; Fitzpatrick, Benjamin M

    2012-03-01

    A major challenge facing biodiversity conservation and management is that a significant portion of species diversity remains undiscovered or undescribed. This is particularly evident in subterranean animals in which species delimitation based on morphology is difficult because differentiation is often obscured by phenotypic convergence. Multilocus genetic data constitute a valuable source of information for species delimitation in such organisms, but until recently, few methods were available to objectively test species delimitation hypotheses using genetic data. Here, we use recently developed methods for discovering and testing species boundaries and relationships using a multilocus dataset in a widely distributed subterranean teleost fish, Typhlichthys subterraneus, endemic to Eastern North America. We provide evidence that species diversity in T. subterraneus is currently underestimated and that the picture of a single, widely distributed species is not supported. Rather, several morphologically cryptic lineages comprise the diversity in this clade, including support for the recognition of T. eigenmanni. The high number of cryptic species in Typhlichthys highlights the utility of multilocus genetic data in delimiting species, particularly in lineages that exhibit slight morphological disparity, such as subterranean organisms. However, results depend on sampling of individuals and loci; this issue needs further study. PMID:22380444

  6. 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

  7. 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. PMID:20180323

  8. Fast estimation of solvation free energies for diverse chemical species.

    PubMed

    Boyer, Robert D; Bryan, Richard L

    2012-03-29

    The free energy of solvation can play an important or even dominant role in the accurate prediction of binding affinities and various other molecular-scale interaction phenomena critical to the study of biochemical processes. Many research applications for solvation modeling, such as fragment-based drug design, require algorithms that are both accurate and computationally inexpensive. We have developed a calculation of solvation free energy which runs fast enough for interactive applications, functions for a wide range of chemical species relevant to simulating molecules for biological and pharmaceutical applications, and is readily extended when data for new species becomes available. We have also demonstrated that the incorporation of ab initio data provides necessary access to sufficient reference data for a broad range of chemical features. Our empirical model, including an electrostatic term and a different set of atom types, demonstrates improvements over a previous, solvent-accessible surface area-only model by Wang et al. when fit to identical training sets (mean absolute error of 0.513 kcal/mol versus the 0.538 kcal/mol reported by Wang). The incorporation of ab initio solvation free energies provides a significant increase in the breadth of chemical features for which the model can be applied by introducing classes of compounds for which little or no experimental data is available. The increased breadth and the speed of this solvation model allow for conformational minimization, conformational search, and ligand binding free energy calculations that economically account for the complex interplay of bonded, nonbonded, and solvation free energies as conformations with varying solvent-accessible surfaces are sampled. PMID:22339050

  9. 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. PMID:25526843

  10. 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

    2016-01-01

    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. PMID:27323174

  11. Genetic diversity of Aquilegia (Ranunculaceae) species and cultivars assessed by AFLPs.

    PubMed

    Zhu, R R; Gao, Y K; Xu, L J; Zhang, Q X

    2011-01-01

    Species of the genus Aquilegia are exceptionally diverse in their floral morphology and color, commonly known as columbine. They are widely planted ornamentals and are highly attractive for hummingbirds. However, little is known about their genetic diversity. We examined the genetic diversity of the species and cultivars using amplified fragment length polymorphism (AFLP) markers. Sixteen EcoRI/MseI AFLP primer combinations produced 327 informative polymorphic bands, with a mean of 20.4 bands scored per primer. Jaccard's coefficient of similarity varied from 0.61 to 0.93, indicative of high levels of genetic variation. Cluster analysis using the unweighted pair group method with arithmetic mean algorithm placed the 64 accessions into two main clusters, each divided into two sub-clusters. The AFLP variability was significantly associated with the geographic origins, as the Asian species and the North American species grouped into two distinct clusters. The genetic diversity found among Aquilegia demonstrated the potential value of Chinese germplasm for cultivar improvement and for widening the genetic basis of breeding programs and breeding material selection. We concluded that AFLPs are informative and can provide significant insights for genetic diversity research in columbine species. PMID:21574138

  12. 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

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

    PubMed

    Roberts, David R; Hamann, Andreas

    2015-04-01

    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 (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711

  14. 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

  15. Species and size diversity in protective services offered by coral guard-crabs.

    PubMed

    McKeon, C Seabird; Moore, Jenna M

    2014-01-01

    Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo'orea, French Polynesia showed the Trapezia-coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species. PMID:25289176

  16. 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.

  17. 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. PMID:26172210

  18. Species and size diversity in protective services offered by coral guard-crabs

    PubMed Central

    Moore, Jenna M.

    2014-01-01

    Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo’orea, French Polynesia showed the Trapezia—coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species. PMID:25289176

  19. 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. PMID:26397707

  20. 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. PMID:15692863

  1. 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

  2. Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

    NASA Astrophysics Data System (ADS)

    Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

    2012-12-01

    Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

  3. 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.

  4. Nitrogen and phosphorus additions negatively affect tree species diversity in tropical forest regrowth trajectories.

    PubMed

    Siddique, Ilyas; Vieira, Ima Célia Guimarães; Schmidt, Susanne; Lamb, David; Carvalho, Cláudio José Reis; Figueiredo, Ricardo de Oliveira; Blomberg, Simon; Davidson, Eric A

    2010-07-01

    Nutrient enrichment is increasingly affecting many tropical ecosystems, but there is no information on how this affects tree biodiversity. To examine dynamics in vegetation structure and tree species biomass and diversity, we annually remeasured tree species before and for six years after repeated additions of nitrogen (N) and phosphorus (P) in permanent plots of abandoned pasture in Amazonia. Nitrogen and, to a lesser extent, phosphorus addition shifted growth among woody species. Nitrogen stimulated growth of two common pioneer tree species and one common tree species adaptable to both high- and low-light environments, while P stimulated growth only of the dominant pioneer tree Rollinia exsucca (Annonaceae). Overall, N or P addition reduced tree assemblage evenness and delayed tree species accrual over time, likely due to competitive monopolization of other resources by the few tree species responding to nutrient enrichment with enhanced establishment and/or growth rates. Absolute tree growth rates were elevated for two years after nutrient addition. However, nutrient-induced shifts in relative tree species growth and reduced assemblage evenness persisted for more than three years after nutrient addition, favoring two nutrient-responsive pioneers and one early-secondary tree species. Surprisingly, N + P effects on tree biomass and species diversity were consistently weaker than N-only and P-only effects, because grass biomass increased dramatically in response to N + P addition. The resulting intensified competition probably prevented an expected positive N + P synergy in the tree assemblage. Thus, N or P enrichment may favor unknown tree functional response types, reduce the diversity of coexisting species, and delay species accrual during structurally and functionally complex tropical rainforest secondary succession. PMID:20715634

  5. 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

  6. 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.

  7. The crystal structure of Helicobacter pylori HP1029 highlights the functional diversity of the sialic acid-related DUF386 family.

    PubMed

    Vallese, Francesca; Percudani, Riccardo; Fischer, Wolfgang; Zanotti, Giuseppe

    2015-09-01

    The proteins of the YhcH/YjgK/YiaL (DUF386) family have been implicated in the bacterial metabolism of host-derived sialic acids and biofilm formation, although their precise biochemical function remains enigmatic. We present here the crystal structure of protein HP1029 from Helicobacter pylori. The protein is a homodimer, in which each monomer comprises a molecular core formed by 12 antiparallel β-strands arranged in two β-sheets flanked by helices. The sandwich formed by the sheets assumes the shape of a funnel opened at one end, with a zinc ion present at the bottom of the funnel. The crystal structure unequivocally shows that HP1029 belongs to the DUF386 family. Although no bioinformatics evidence has been found for sialic acid catabolism in H. pylori, the genomic context of HP1029 in Helicobacter and related organisms suggests a possible role in the metabolism of bacterial surface saccharides, such as pseudaminic acid and its derivatives. PMID:26096900

  8. 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

  9. Life history influences how fire affects genetic diversity in two lizard species.

    PubMed

    Smith, Annabel L; Bull, C Michael; Gardner, Michael G; Driscoll, Don A

    2014-05-01

    'Fire mosaics' are often maintained in landscapes to promote successional diversity in vegetation with little understanding of how this will affect ecological processes in animal populations such as dispersal, social organization and re-establishment. To investigate these processes, we conducted a replicated, spatiotemporal landscape genetics study of two Australian woodland lizard species [Amphibolurus norrisi (Agamidae) and Ctenotus atlas (Scincidae)]. Agamids have a more complex social and territory structure than skinks, so fire might have a greater impact on their population structure and thus genetic diversity. Genetic diversity increased with time since fire in C. atlas and decreased with time since fire in A. norrisi. For C. atlas, this might reflect its increasing population size after fire, but we could not detect increased gene flow that would reduce the loss of genetic diversity through genetic drift. Using landscape resistance analyses, we found no evidence that postfire habitat succession or topography affected gene flow in either species and we were unable to distinguish between survival and immigration as modes of postfire re-establishment. In A. norrisi, we detected female-biased dispersal, likely reflecting its territorial social structure and polygynous mating system. The increased genetic diversity in A. norrisi in recently burnt habitat might reflect a temporary disruption of its territoriality and increased male dispersal, a hypothesis that was supported with a simulation experiment. Our results suggest that the effects of disturbance on genetic diversity will be stronger for species with territorial social organization. PMID:24750427

  10. 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.

  11. Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

    PubMed Central

    Crawford, Andrew J.; Lips, Karen R.; Bermingham, Eldredge

    2010-01-01

    Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity. PMID:20643927

  12. Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama.

    PubMed

    Crawford, Andrew J; Lips, Karen R; Bermingham, Eldredge

    2010-08-01

    Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity. PMID:20643927

  13. 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.

  14. 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

  15. 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. PMID:25343259

  16. Is lipophosphoglycan a virulence factor? A surprising diversity between Leishmania species.

    PubMed

    Turco, S J; Späth, G F; Beverley, S M

    2001-05-01

    Lipophosphoglycan is a prominent member of the phosphoglycan-containing surface glycoconjugates of Leishmania. Genetic tests enable confirmation of its role in parasite virulence and permit discrimination between the roles of lipophosphoglycan and related glycoconjugates. When two different lipophosphoglycan biosynthetic genes from Leishmania major were knocked out, there was a clear loss of virulence in several steps of the infectious cycle but, with Leishmania mexicana, no effect on virulence was found. This points to an unexpected diversity in the reliance of Leishmania species on virulence factors, a finding underscored by recent studies showing great diversity in the host response to Leishmania species. PMID:11323305

  17. 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

  18. 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

  19. 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

  20. 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. PMID:25752854

  1. 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

  2. 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

  3. 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

  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. 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. PMID:26381889

  6. Species and endosymbiont diversity of Bemisia tabaci (Homoptera: Aleyrodidae) on vegetable crops in Senegal.

    PubMed

    Hélène, Delatte; Rémy, Baudin; Nathalie, Becker; Anne-Laure, Girard; Traoré, Ramatoulaye Sidebe; Jean-Michel, Lett; Bernard, Reynaud

    2015-03-01

    Bemisia tabaci-transmitted geminiviruses are one of the major threats on cassava and vegetable crops in Africa. However, to date, few studies are available on the diversity of B. tabaci and their associated endosymbionts in Africa. More than 28 species have been described in the complex of B. tabaci cryptic species; among them, 2 are invasive pests worldwide: MED and MEAM1. In order to assess the species diversity of B. tabaci in vegetable crops in Senegal, several samplings in different localities, hosts and seasons were collected and analyzed with nuclear (microsatellite) and mitochondrial (COI) markers. The bacterial endosymbiont community was also studied for each sample. Two species were detected: MED Q1 and MEAM1 B. Patterns of MED Q1 (dominance on most of the samples and sites, highest nuclear and mitochondrial diversity and broader secondary endosymbiont community: Hamiltonella, Cardinium, Wolbachia and Rickettsia), point toward a predominant resident begomovirus vector group for MED Q1 on market gardening crops. Furthermore, the lower prevalence of the second species MEAM1 B, its lower nuclear and mitochondrial diversity and a narrower secondary endosymbiont community (Hamiltonella/Rickettsia), indicate that this genetic group is exotic and results from a recent invasion in this area. PMID:24789572

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

    PubMed Central

    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. PMID:26381889

  8. Species concepts, diversity, and evolution in primates: lessons to be learned from mouse lemurs.

    PubMed

    Zimmermann, Elke; Radespiel, Ute

    2014-01-01

    Humans primarily rely on vision when categorizing the world. If you just look at the same-sized but strikingly differently colored Neotropical poison-dart frogs such as strawberry frogs (Fig. ), you would be convinced that they must belong to different species. However, this is an excellent example of a polymorphic species, meaning that although these frogs look quite different, mating decisions are made based on their conspicuous and species-specific advertisements calls, which are not primarily linked to specific color pattern. The situation is quite different among nocturnal primates living in dense forest environments, such as the tiny nocturnal Malagasy mouse lemurs. In this case, even geographically isolated, well-accepted species look superficially quite similar and are therefore often termed cryptic species (Fig. ). Some morphs are a bit larger than others or show minor phenotypic differences, but morph-specific differences are difficult to detect in living subjects. This phenomenon explains why, until the end of the last century, species diversity in mouse lemurs was assumed to be low, with only two morphologically distinct species. Over the last two decades, several international working groups, including our own, undertook a massive island-wide sampling effort, including DNA sequencing and phylogenetic analyses of mouse lemurs. These revealed a 10-fold higher species diversity, with 21 currently described species. Are these new species, mostly defined based on the phylogenetic species concept (sensu Cracraft), or independent evolutionary lineages or, perhaps, only artifacts of taxonomic inflation? What is a species? How can we identify primate species? How and why do species emerge during evolution? PMID:24591134

  9. Active colonization dynamics and diversity patterns are influenced by dendritic network connectivity and species interactions

    PubMed Central

    Seymour, Mathew; Altermatt, Florian

    2014-01-01

    Habitat network connectivity influences colonization dynamics, species invasions, and biodiversity patterns. Recent theoretical work suggests dendritic networks, such as those found in rivers, alter expectations regarding colonization and dispersal dynamics compared with other network types. As many native and non-native species are spreading along river networks, this may have important ecological implications. However, experimental studies testing the effects of network structure on colonization and diversity patterns are scarce. Up to now, experimental studies have only considered networks where sites are connected with small corridors, or dispersal was experimentally controlled, which eliminates possible effects of species interactions on colonization dynamics. Here, we tested the effect of network connectivity and species interactions on colonization dynamics using continuous linear and dendritic (i.e., river-like) networks, which allow for active dispersal. We used a set of six protist species and one rotifer species in linear and dendritic microcosm networks. At the start of the experiment, we introduced species, either singularly or as a community within the networks. Species subsequently actively colonized the networks. We periodically measured densities of species throughout the networks over 2 weeks to track community dynamics, colonization, and diversity patterns. We found that colonization of dendritic networks was faster compared with colonization of linear networks, which resulted in higher local mean species richness in dendritic networks. Initially, community similarity was also greater in dendritic networks compared with linear networks, but this effect vanished over time. The presence of species interactions increased community evenness over time, compared with extrapolations from single-species setups. Our experimental findings confirm previous theoretical work and show that network connectivity, species-specific dispersal ability, and species

  10. 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

  11. Local and regional species diversity of benthic Isopoda (Crustacea) in the deep Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Wilson, George D. F.

    2008-12-01

    Recent studies of deep-sea faunas considered the influence of mid-domain models in the distribution of species diversity and richness with depth. In this paper, I show that separating local diversity from regional species richness in benthic isopods clarifies mid-domain effects in the distribution of isopods in the Gulf of Mexico. Deviations from the randomised implied species ranges can be informative to understanding general patterns within the Gulf of Mexico. The isopods from the GoMB study contained 135 species, with a total of 156 species including those from an earlier study. More than 60 species may be new to science. Most families of deep-sea isopods (suborder Asellota) were present, although some were extremely rare. The isopod family Desmosomatidae dominated the samples, and one species of Macrostylis (Macrostylidae) was found in many samples. Species richness for samples pooled within sites ranged from 1 to 52 species. Because species in pooled samples were highly correlated with individuals, species diversity was compared across sites using the expected species estimator ( n=15 individuals, ES 15). Six depth transects had idiosyncratic patterns of ES 15, and transects with the greatest short-range variation in topography, such as basins and canyons, had the greatest short-range disparity. Basins on the deep slope did not have a consistent influence (i.e., relatively higher or lower than surrounding areas) on the comparative species diversity. ES 15 of all transects together showed a weak mid-domain effect, peaking around 1200-1500 m, with low values at the shallowest and deepest samples (Sigsbee Abyssal Plain); no longitudinal (east-west) pattern was found. The regional species pool was analyzed by summing the implied ranges of all species. The species ranges in aggregate did not have significant patterns across longitudes, and many species had broad depth ranges, suggesting that the isopod fauna of the Gulf of Mexico is well dispersed. The summed

  12. 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

  13. Morphological and Phytochemical Diversity among Hypericum Species of the Mediterranean Basin

    PubMed Central

    Nürk, Nicolai M.; Crockett, Sara L.

    2012-01-01

    The genus Hypericum L. (St. John’s wort, Hypericaceae) includes more than 450 species that occur in temperature or tropical mountain regions of the world. Monographic work on the genus has resulted in the recognition and description of 36 taxonomic sections, delineated by specific combinations of morphological characteristics and biogeographic distribution. The Mediterranean Basin has been recognized as a hot spot of diversity for the genus Hypericum, and as such is a region in which many endemic species occur. Species belonging to sections distributed in this area of the world display considerable morphological and phytochemical diversity. Results of a cladistic analysis, based on 89 morphological characters that were considered phylogenetically informative, are given here. In addition, a brief overview of morphological characteristics and the distribution of pharmaceutically relevant secondary metabolites for species native to this region of the world are presented. PMID:22662020

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

    PubMed

    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

    2015-10-01

    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

  15. 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

  16. Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography.

    PubMed

    Scordato, Elizabeth S C; Kardish, Melissa R

    2014-11-01

    Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species and the geographical scale of comparisons. In this study, we asked whether these factors also predict diversity and turnover in parasite communities. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked whether parasite prevalence and community structure varied with host population, host phylogeography or geographical distance. We used PCR to screen birds for infections and then used Bayesian methods to determine phylogenetic relationships among malaria strains. Metrics of both community and phylogenetic beta diversity were used to examine patterns of malaria strain turnover between host populations, and partial Mantel tests were used determine the correlation between malaria beta diversity and geographical distance. Finally, we developed microsatellite markers to describe the genetic structure of host populations and assess the relationship between host phylogeography and parasite beta diversity. We found that different genera of malaria parasites infect the two hosts at different rates. Within hosts, parasite communities in one population were phylogenetically clustered, but there was otherwise no correlation between metrics of parasite beta diversity and geographical or genetic distance between host populations. Patterns of parasite turnover among host populations are consistent with malaria transmission occurring in the winter rather than on the breeding grounds. Our results indicate greater turnover in parasite communities between different hosts than between different study sites. Differences in host species, as well as transmission location and vector ecology, seem to be more important in structuring malaria communities than the distance-decay relationships frequently found in macroorganisms. Determining the factors

  17. Hierarchical controls on patterns of habitat and species diversity in river networks

    NASA Astrophysics Data System (ADS)

    Beechie, T.; Pess, G.

    2007-12-01

    Patterns of habitat heterogeneity and species diversity in river networks are constrained by a nested hierarchy of physical controls. Large-scale, long-term controls set bounds for habitat and biological expression, whereas short-term and smaller-scale processes determine conditions at a point in time. At the river basin scale, geologic and topographic controls constrain reach attributes such as channel slope and channel confinement, which in turn constrains finer scale habitat structure. Overlain on this geologic template are down-valley trends in relative sediment supply that cause a systematic shift in channel-floodplain dynamics. At the reach-scale, channel slope is a primary control on habitat types (e.g., pools, riffles, ponds) in single thread channels, but local bed load and wood supply influence local habitat diversity. In floodplain reaches, diversity of habitat types is controlled mainly by the rate of lateral channel movement and floodplain turnover, which decrease down-valley with decreasing bed load supply. These controls drive two important aspects of environmental complexity, which in turn drive biological diversity in river networks: diversity of patch ages, and diversity of patch types. Ecological theory suggests that floodplain forest communities will be most diverse in floodplain reaches with intermediate rates of floodplain turnover, and reach-level aquatic communities will be most diverse in mid-network where habitat heterogeneity is highest.

  18. 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.

  19. 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. PMID:24620581

  20. 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

  1. 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.

  2. 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.

  3. DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera).

    PubMed

    Bekker, Eugeniya I; Karabanov, Dmitry P; Galimov, Yan R; Kotov, Alexey A

    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

  4. 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

  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 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

  6. 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. PMID:24455165

  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. PMID:26913947

  8. 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

  9. Enterohepatic Helicobacter in Ulcerative Colitis: Potential Pathogenic Entities?

    PubMed Central

    Thomson, John M.; Hansen, Richard; Berry, Susan H.; Hope, Mairi E.; Murray, Graeme I.; Mukhopadhya, Indrani; McLean, Mairi H.; Shen, Zeli; Fox, James G.; El-Omar, Emad; Hold, Georgina L.

    2011-01-01

    Background Changes in bacterial populations termed “dysbiosis” are thought central to ulcerative colitis (UC) pathogenesis. In particular, the possibility that novel Helicobacter organisms play a role in human UC has been debated but not comprehensively investigated. The aim of this study was to develop a molecular approach to investigate the presence of Helicobacter organisms in adults with and without UC. Methodology/Principal Findings A dual molecular approach to detect Helicobacter was developed. Oligonucleotide probes against the genus Helicobacter were designed and optimised alongside a validation of published H. pylori probes. A comprehensive evaluation of Helicobacter genus and H. pylori PCR primers was also undertaken. The combined approach was then assessed in a range of gastrointestinal samples prior to assessment of a UC cohort. Archival colonic samples were available from 106 individuals for FISH analysis (57 with UC and 49 non-IBD controls). A further 118 individuals were collected prospectively for dual FISH and PCR analysis (86 UC and 32 non-IBD controls). An additional 27 non-IBD controls were available for PCR analysis. All Helicobacter PCR-positive samples were sequenced. The association between Helicobacter and each study group was statistically analysed using the Pearson Chi Squared 2 tailed test. Helicobacter genus PCR positivity was significantly higher in UC than controls (32 of 77 versus 11 of 59, p = 0.004). Sequence analysis indicated enterohepatic Helicobacter species prevalence was significantly higher in the UC group compared to the control group (30 of 77 versus 2 of 59, p<0.0001). PCR and FISH results were concordant in 74 (67.9%) of subjects. The majority of discordant results were attributable to a higher positivity rate with FISH than PCR. Conclusions/Significance Helicobacter organisms warrant consideration as potential pathogenic entities in UC. Isolation of these organisms from colonic tissue is needed to enable

  10. Effects of colonization processes on genetic diversity: differences between annual plants and tree species.

    PubMed Central

    Austerlitz, F; Mariette, S; Machon, N; Gouyon, P H; Godelle, B

    2000-01-01

    Tree species are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than trees. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for trees. This explanation is problematic because it relies on equilibrium hypotheses. Because trees have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest trees, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of trees are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in trees and annual species by much less diversity and much more differentiation than nuclear genes. PMID:10757772

  11. Tick species (Acari: Ixodida) in Antalya City, Turkey: species diversity and seasonal activity.

    PubMed

    Koc, Samed; Aydın, Levent; Cetin, Huseyin

    2015-07-01

    Ticks (Acari: Ixodida) are an important group of ectoparasites of vertebrates. Most species are known vectors of diseases including Lyme disease, Q fever, and Crimean-Congo hemorrhagic fever. A 3-year research was conducted in Antalya, Turkey, to determine tick species composition, seasonal abundance, and spatial distribution. The study was carried out in five districts (Aksu, Dosemealtı, Kepez, Konyaaltı, and Muratpasa) of Antalya Metropolitan Municipality area in Turkey, between May 2010 and May 2013, where 1393 tick specimens were collected from domestic and wild animals (cattle, goats, sheep, hedgehogs, tortoises, dogs, cats, chickens) and from the environment. The collected ticks were preserved in 70 % alcohol and then were identified. Five genus and eight hard and soft tick species were identified, including Argas persicus, Rhipicephalus annulatus, R. sanguineus, R. turanicus, Hyalomma aegyptium, H. marginatum, Haemaphysalis parva, and Dermacentor niveus. Rhipicephalus sanguineus, R. turanicus, and H. aegyptium were the most common tick species in Antalya city. Rhipicephalus turanicus and R. sanguineus were the most abundant tick species infesting dogs in the city. The hosts of H. aegyptium are primarily tortoises in Antalya. The results of this research will contribute to establishing appropriate measures to control tick infestations on animals and humans and their environment in the city of Antalya. PMID:25869959

  12. Species diversity, pathogenicity and toxigenicity of Fusarium associated with rice seeds in Brazil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusarium is commonly reported in association with rice seeds in Brazil, but knowledge on the species diversity and toxigenic potential is lacking. Such information is critical because maximum limits for Fusarium mycotoxins were set for Brazilian rice in 2011. Ninety-eight rice seed samples from the ...

  13. 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

  14. 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

  15. 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. PMID:27306051

  16. Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

    PubMed Central

    Chisholm, Ryan A.; Pacala, Stephen W.

    2010-01-01

    A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function. PMID:20733073

  17. Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Malus sieversii (Lebed.)M. Roem. is a wild progenitor species of the domesticated apple. It is found across a mountainous region of central Asia and has been the focus of several collection expeditions by the USDA. This study used SSR variation at seven loci to estimate diversity and differentiat...

  18. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advances in next-generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restri...

  19. Genetic diversity and phylogenetic relationships among sugarcane and related species determined from microsatellite DNA data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and phylogenetic relationships were assessed among 105 clones of commercial sugarcane hybrids and related Saccharum species using 22 microsatellite (SSR) DNA markers. These included 17 sugarcane cultivars from the U.S. mainland, 23 S. officinarum clones, 16 S. robustum clones, 15 ...

  20. Genetic diversity assessment of Saccharum species and elite cultivars from China using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity amongst 52 sugarcane clones including Saccharum species and cultivars (used for breeding and commercial production since the beginning of 20th century) has been assessed using 21 Simple Sequence Repeat (SSR) markers and capillary electrophoresis (CE) technique. Use of 21 SSR primer...

  1. 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

  2. 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

  3. 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

  4. 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. PMID:26929271

  5. Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity.

    PubMed

    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

  6. 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

  7. 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

  8. 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

  9. 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...

  10. 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

  11. Diversity of Diaporthe species associated with wood cankers of fruit and nut crops in northern California.

    PubMed

    Lawrence, Daniel P; Travadon, Renaud; Baumgartner, Kendra

    2015-01-01

    Diaporthe ampelina, causal agent of Phomopsis cane and leaf spot of grapevine (Vitis vinifera L.) is isolated frequently from grapevine wood cankers, causing Phomopsis dieback. The latter disease is associated with four other Diaporthe species, three of which also are reported from hosts other than grape. To better understand the role of this Diaporthe community in Phomopsis dieback of grapevine and the potential for infection routes among alternate hosts, 76 Diaporthe isolates were recovered from wood cankers of cultivated grape, pear, apricot, almond and the wild host willow in four California counties. Isolates were characterized morphologically and assigned to species based on multigene sequence analyses. This study identified eight Diaporthe species from grapevine and one novel taxon from willow, D. benedicti. We report the first findings of D. australafricana and D. novem in North America. Our findings also expand the host ranges of D. ambigua to apricot and willow, D. australafricana to almond and willow, D. chamaeropis to grapevine and willow, D. foeniculina to willow and D. novem to almond. The generalists D. ambigua and D. eres were the most genetically diverse species, based on high nucleotide and haplotypic diversity, followed by the grapevine specialist D. ampelina. Analyses based on multilocus linkage disequilibrium could not reject the hypothesis of random mating for D. ambigua, which is further supported by relatively high haplotypic diversity, reports of both mating types and reports of successful matings in vitro. Pathogenicity assays revealed that D. ampelina was the most pathogenic species to grapevine wood. PMID:26240309

  12. 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.

  13. Culture of a gastric non-Helicobacter pylori Helicobacter from the stomach of a 14-year-old girl.

    PubMed

    Wüppenhorst, Nicole; von Loewenich, Friederike; Hobmaier, Beate; Vetter-Knoll, Marianne; Mohadjer, Sona; Kist, Manfred

    2013-02-01

    Helicobacter felis belongs to the fastidious gastric non-Helicobacter pylori helicobacter species that are typically found in the stomach of cats and dogs. These bacteria have the potential to colonize the human stomach and are then associated with gastritis, gastroduodenal ulcers, and MALT lymphoma. Strains cultured from the human stomach are rare. Here, we present the first isolation of H. felis from a gastric biopsy specimen of a 14-year-old girl who presented with persistent epigastric pain. The strain was cultured using our routine protocol for H. pylori and identified by phylogenetic analyses of partial urease AB and gyrB gene sequences. PMID:23067246

  14. 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.

  15. Effects of species diversity on community biomass production change over the course of succession.

    PubMed

    Weis, Jerome J; Cardinale, Bradley J; Forshay, Kenneth J; Ives, Anthony R

    2007-04-01

    Over the past decade an increasing number of studies have experimentally manipulated the number of species in a community and examined how this alters the aggregate production of species biomass. Many of these studies have shown that the effects of richness on biomass change through time, but we have limited understanding of the mechanisms that produce these dynamic trends. Here we report the results of an experiment in which we manipulated the richness of freshwater algae in laboratory microcosms. We used two experimental designs (additive and substitutive) that make different assumptions about how patches are initially colonized, and then tracked the development of community biomass from the point of initial colonization through a period of 6-12 generations of the focal species. We found that the effect of initial species richness on biomass production qualitatively shifted twice over the course of the experiment. The first shift occurred as species transitioned from density-independent to dependent phases of population growth. At this time, intraspecific competition caused monocultures to approach their respective carrying capacities more slowly than polycultures. As a consequence, species tended to over-yield for a brief time, generating a positive, but transient effect of diversity on community biomass. The second shift occurred as communities approached carrying capacity. At this time, strong interspecific interactions caused biomass to be dominated by the competitively superior species in polycultures. As this species had the lowest carrying capacity, a negative effect of diversity on biomass resulted in late succession. Although these two shifts produced dynamics that appeared complex, we show that the patterns can be fit to a simple Lotka-Volterra model of competition. Our results suggest that the effects of algal diversity on primary production change in a predictable sequence through successional time. PMID:17536709

  16. 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

  17. 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

  18. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota).

    PubMed

    Alors, David; Lumbsch, H Thorsten; Divakar, Pradeep K; Leavitt, Steven D; Crespo, Ana

    2016-01-01

    High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species. PMID:26863231

  19. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota)

    PubMed Central

    Alors, David; Lumbsch, H. Thorsten; Divakar, Pradeep K.; Leavitt, Steven D.; Crespo, Ana

    2016-01-01

    High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species. PMID:26863231

  20. Uncovering cryptic species diversity of a termite community in a West African savanna.

    PubMed

    Hausberger, Barbara; Kimpel, Dorothea; van Neer, Abbo; Korb, Judith

    2011-12-01

    To uncover the termite species diversity of a natural African savanna ecosystem, we combined morphological analyses and sequencing of three gene fragments (cytochrome oxidase I, cytochrome oxidase II and 28SrDNA, total length about 2450 bp) to infer putative species from phylogenetic trees. We identified 18 putative species clusters with high support values and which we retrieved consistently. Samples from two genera (Ancistrotermes and Microcerotermes) were excluded from the mitochondrial phylogenetic analyses as they might represent nuclear mitochondrial sequences (NUMTs). In total, our data suggest a species richness of at least 20 species, all but one belonging to the Termitidae (higher termites), and among them the fungus-growing Macrotermitinae were most prevalent with at least nine putative species. Within the fungus-growers the most species-rich genus was Microtermes and its four putative species were all cryptic species. Their abundance in the samples suggests that they play an important ecological role which is completely unstudied also due to the lack of reliable identification means. Our study shows that morphological traits are unreliable means of species identification for several termite taxa. Yet reliable and consistent identification is necessary for studying the functional role of termites in ecosystem and global processes. PMID:21896335

  1. 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. PMID:26577612

  2. Discriminating plant species across California's diverse ecosystems using airborne VSWIR and TIR imagery

    NASA Astrophysics Data System (ADS)

    Meerdink, S.; Roberts, D. A.; Roth, K. L.

    2015-12-01

    Accurate knowledge of the spatial distribution of plant species is required for many research and management agendas that track ecosystem health. Because of this, there is continuous development of research focused on remotely-sensed species classifications for many diverse ecosystems. While plant species have been mapped using airborne imaging spectroscopy, the geographic extent has been limited due to data availability and spectrally similar species continue to be difficult to separate. The proposed Hyperspectral Infrared Imager (HyspIRI) space-borne mission, which includes a visible near infrared/shortwave infrared (VSWIR) imaging spectrometer and thermal infrared (TIR) multi-spectral imager, would present an opportunity to improve species discrimination over a much broader scale. Here we evaluate: 1) the capability of VSWIR and/or TIR spectra to discriminate plant species; 2) the accuracy of species classifications within an ecosystem; and 3) the potential for discriminating among species across a range of ecosystems. Simulated HyspIRI imagery was acquired in spring/summer of 2013 spanning from Santa Barbara to Bakersfield, CA with the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and the MODIS/ASTER Airborne Simulator (MASTER) instruments. Three spectral libraries were created from these images: AVIRIS (224 bands from 0.4 - 2.5 µm), MASTER (8 bands from 7.5 - 12 µm), and AVIRIS + MASTER. We used canonical discriminant analysis (CDA) as a dimension reduction technique and then classified plant species using linear discriminant analysis (LDA). Our results show the inclusion of TIR spectra improved species discrimination, but only for plant species with emissivities departing from that of a gray body. Ecosystems with species that have high spectral contrast had higher classification accuracies. Mapping plant species across all ecosystems resulted in a classification with lower accuracies than a single ecosystem due to the complex nature of

  3. Environmental factors influence both abundance and genetic diversity in a widespread bird species

    PubMed Central

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

  4. Diversity, molecular phylogeny and fingerprint profiles of airborne Aspergillus species using random amplified polymorphic DNA.

    PubMed

    Kermani, Firoozeh; Shams-Ghahfarokhi, Masoomeh; Gholami-Shabani, Mohammadhassan; Razzaghi-Abyaneh, Mehdi

    2016-06-01

    In the present study, diversity and phylogenetic relationship of Aspergillus species isolated from Tehran air was studied using random amplified polymorphic DNA (RAPD)-polymerase chain reaction (RAPD-PCR). Thirty-eight Aspergillus isolates belonging to 12 species i.e. A. niger (28.94 %, 11 isolates), A. flavus (18.42 %, 7 isolates), A. tubingensis (13.15 %, 5 isolates), A. japonicus (10.52 %, 4 isolates), A. ochraceus (10.52 %, 4 isolates), and 2.63 %, 1 isolate from each A. nidulans, A. amstelodami, A. oryzae, A. terreus, A. versicolor, A. flavipes and A. fumigatus were obtained by settle plate method which they were distributed in 18 out of 22 sampling sites examined. Fungal DNA was extracted from cultured mycelia of all Aspergillus isolates on Sabouraud Dextrose Agar and used for amplification of gene fragments in RAPD-PCR using 11 primers. RAPD-PCR data was analyzed using UPGMA software. Resulting dendrogram of combined selected primers including PM1, OPW-04, OPW-05, P160, P54, P10 and OPA14 indicated the distribution of 12 Aspergillus species in 8 major clusters. The similarity coefficient of all 38 Aspergillus isolates ranged from 0.02 to 0.40 indicating a wide degree of similarities and differences within and between species. Taken together, our results showed that various Aspergillus species including some important human pathogenic ones exist in the outdoor air of Tehran by different extents in distribution and diversity and suggested inter- and intra-species genetic diversity among Aspergillus species by RAPD-PCR as a rapid, sensitive and reproducible method. PMID:27116962

  5. 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.

  6. Remote tree species identification in a diverse tropical forest using airborne imaging spectroscopy

    NASA Astrophysics Data System (ADS)

    Baldeck, C.; Asner, G. P.; Kellner, J. R.; Martin, R.; Anderson, C.; Knapp, D. E.

    2013-12-01

    Plant species identification and mapping based on remotely-sensed spectral signatures is a challenging task with the potential to contribute enormously to ecological studies. This task is especially difficult in highly diverse ecosystems such as tropical forests, and for these ecosystems it may be more strategic to direct efforts to identifying crowns of a focal species. We used imaging spectrometer data collected by the Carnegie Airborne Observatory over Barro Colorado Island, Panama, to develop classification models for the identification of tree crowns belonging to selected focal species. We explored alternative methods for detecting crowns of focal species, which included binary, one-class, and biased support vector machines (SVM). Best performance was given by binary and biased SVM, with poor performance observed for one-class SVM. Binary and biased SVM were able to identify crowns of focal species with classification sensitivity and specificity of 87-91% and 89-94%, respectively. The main tradeoff between binary and biased SVM is that construction of binary SVM requires a far greater amount of training data while biased SVM is more difficult to parameterize. Our results show that with sufficient training data, focal species can be mapped with a high degree of accuracy, in terms of both sensitivity and specificity, in this diverse tropical forest.

  7. Spider Diversity on the Oceanic Island of Fernando De Noronha, Brazil, and Implications for Species Conservation

    PubMed Central

    Freitas, Gilson Carlos da Conceição; Brescovit, Antonio Domingos; Vasconceloslc, Simao Dias

    2013-01-01

    Fernando de Noronha is an oceanic archipelago in Brazil that has been subjected to major alterations in its natural habitat, as it is exposed to increasing rates of tourism. This research aimed at performing the first survey of spider species on the main island, focusing on the environmental occupation and conservation status of local species. Spiders were sampled through pitfall traps, beating sheets, and active collection in the dry (October 2005) and rainy (April 2006) seasons in several parts of the island, such as urban and protected areas. A total of 1,532 adult spiders from 44 species distributed in 20 families were collected. Forty-two species are newly recorded on the archipelago, of which 10 appear to be native. Theridiidae and Salticidae were the richest families, with seven and five species respectively. Hogna sp., probably an endemic Lycosidae species, had the highest abundance throughout the study (17%). Several non-native species were found, especially in the surroundings of human habitations. Areas exposed to human settlements had higher diversity indices and evenness values when compared to preserved areas. Most species were classified as being diurnal space web-weavers. The results suggest that non-native species seemed to be established on the island, due mainly to the traffic of people and goods from the continent.

  8. [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. PMID:20873633

  9. PREVALENCE AND DIVERSITY OF BARTONELLA SPECIES IN WILD SMALL MAMMALS IN ASIA.

    PubMed

    Kim, Kyeong Soon; Inoue, Kai; Kabeya, Hidenori; Sato, Shingo; Takada, Tomoe; Pangjai, Decha; Chiu, Shih-Hui; Fujita, Hiromi; Kawabata, Hiroki; Takada, Nobuhiro; Kariwa, Hiroaki; Maruyama, Soichi

    2016-01-01

    We collected 641 small mammals belonging to 17 species of Rodentia and four species of Soricomorpha in Japan, Korea, Russia, Taiwan, and Thailand and investigated the prevalence and genetic diversity of Bartonella species. Apodemus (field mice) and Rattus (rats) were the most-common genera captured, making up 56.0% and 23.1% of the total specimens, respectively. Bartonellae were isolated from 54.6% of the collected animals, and the prevalence varied depending on the host species and the country of origin. The isolates were identified to the species level based on gltA and rpoB sequences. Although most Bartonella species were shared by more than two host species, the distribution patterns of Bartonella species clearly differed among the four most-common host genera: Apodemus, Rattus, Myodes (voles), and Suncus (shrews). The predominant Bartonella species were Bartonella grahamii in Apodemus, Bartonella tribocorum in Rattus, B. grahamii and Bartonella taylorii in Myodes, and an unclassified Bartonella sp. in Suncus. PMID:26528573

  10. 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. PMID:26206418

  11. 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.

  12. Effect of host species diversity on multiparasite systems in rodent communities.

    PubMed

    Rendón-Franco, Emilio; Muñoz-García, Claudia I; Romero-Callejas, Evangelina; Moreno-Torres, Karla I; Suzán, Gerardo

    2014-01-01

    Reduced species diversity has been suggested to increase transmission rates and prevalence of infectious diseases. While this theory has been studied mostly in single pathogen systems, little is known regarding multiple pathogens systems in vertebrates at the community level. The aim of this study was to evaluate the effect of host richness and diversity on multiple parasite systems on a local scale. We captured small rodents and collected feces in three different vegetation types in a natural protected area in Janos, Chihuahua, Mexico. The flotation technique was used to identify parasite eggs or oocysts. Analysis of linear correlations was conducted between parasite prevalence and host and parasite diversity and richness. Negative correlation was detected between parasite prevalence and host diversity (p = 0.02 r(2) =-0.86), but no significant correlations was detected between parasite prevalence and host richness or parasite diversity or richness. Our study shows that at local scale, host diversity could affect multiple parasite systems in the same way that single pathogens do. Further studies should be performed on larger temporal and spatial scales to more thoroughly investigate the correlation observed in our analysis. PMID:24337614

  13. 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

  14. Helicobacter Pylori Infections

    MedlinePlus

    Helicobacter pylori (H. pylori) is a type of bacteria that causes infection in the stomach. It is found in about two- ... breath or stool to see if it contains H. pylori. The best treatment is a combination of ...

  15. 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. PMID:26046457

  16. Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali.

    PubMed

    Maiga, Mamoudou; Cohen, Keira; Baya, Bocar; Srikrishna, Geetha; Siddiqui, Sophia; Sanogo, Moumine; Somboro, Anou M; Diarra, Bassirou; Diallo, Mariam H; Mazumdar, Varun; Yoder, Christian; Orsega, Susan; Belson, Michael; Kassambara, Hamadoun; Goita, Drissa; Murphy, Robert L; Dao, Sounkalo; Polis, Michael; Diallo, Souleymane; Timmins, Graham S; Dodd, Lori; Earl, Ashlee M; Bishai, William R

    2016-01-01

    Detection of bacterial urease activity has been utilized successfully to diagnose Helicobacter pylori (H. pylori). While Mycobacterium tuberculosis (M. tuberculosis) also possesses an active urease, it is unknown whether detection of mycobacterial urease activity by oral urease breath test (UBT) can be exploited as a rapid point of care biomarker for tuberculosis (TB) in humans. We enrolled 34 individuals newly diagnosed with pulmonary TB and 46 healthy subjects in Bamako, Mali and performed oral UBT, mycobacterial sputum culture and H. pylori testing. Oral UBT had a sensitivity and specificity (95% CI) of 70% (46-88%) and 11% (3-26%), respectively, to diagnose culture-confirmed M. tuberculosis disease among patients without H. pylori, and 100% sensitivity (69-100%) and 11% specificity (3-26%) to diagnose H. pylori among patients without pulmonary TB. Stool microbiome analysis of controls without TB or H. pylori but with positive oral UBT detected high levels of non-H. pylori urease producing organisms, which likely explains the low specificity of oral UBT in this setting and in other reports of oral UBT studies in Africa. PMID:27532494

  17. Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae).

    PubMed

    Goicoechea, Noemí; Padial, José M; Chaparro, Juan C; Castroviejo-Fisher, Santiago; De la Riva, Ignacio

    2012-12-01

    The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals includes all currently recognized species of Proctoporus and 15 additional species representing the most closely related groups to the genus. Maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses recovered a congruent, fully resolved, and strongly supported hypothesis of relationships that challenges previous phylogenetic hypotheses and classifications, and biogeographic scenarios. Our main results are: (i) discovery of a strongly supported clade that includes all species of Proctoporus and within which are nested the monotypic Opipeuter xestus (a genus that we consider a junior synonym of Proctoporus), and two species of Euspondylus, that are therefore transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus with respect to P. subsolanus, which is proposed as a junior synonym of P. bolivianus; (iii) the detection of seven divergent and reciprocally monophyletic lineages (five of them previously assigned to P. bolivianus) that are considered confirmed candidate species, which implies that more candidate species are awaiting formal description and naming than currently recognized species in the genus; (iv) rejection of the hypothesis that Proctoporus diversified following a south to north pattern parallel to the elevation of the Andes; (v) species diversity in Proctoporus is the result of in situ diversification through vicariance in

  18. Documenting and comparing plant species diversity by using numerical and parametric methods in Khaje Kalat, NE Iran.

    PubMed

    Ejtehadi, H; Soltani, R; Zahedi Pour, H

    2007-10-15

    The aim was to examine and document several aspects of numerical diversity such as species richness, species diversity and evenness and to compare diversity in different slope aspects of the area by using numerical and parametric methods. About 193 quadrats of 4 m2 were located according to the nature of vegetation. Species composition and their abundance were recorded in a two-year period (2005 to 2006). The result of field investigation was collecting and identifying of the total 225 plant species belonging to 154 genera and 37 families. The abundance data were subjected to analyses by specific diversity packages to characterize and obtain numerical indices (Shannon, Simpson, Brillouin, McIntosh, etc.,) and parametric families of species diversity. Numerical indices were calculated and documented for monitoring purposes. The results of diversity in main slope aspects (N, S, E, W) showed higher species richness and species diversity indices in the north aspect than in the others but it was not true with evenness indices. About 30 species such as Acanthophyllum glandulosum, Acroptilon repens, Alcea tiliacea, Bromus sericeous, Astragalus turbinatus, Centaurea balsamita etc., were detected exclusively in the north aspect. This can be important in reducing the evenness. Diversity comparing by using rank-abundance plot as well as diversity ordering of Hill, Renyi and Patil and Taillie confirmed high species diversity in the north yet the result of ANOVA showed no significant differences in the four aspects. The result of diversity based on the models revealed that the whole area, the south and the west aspects follow lognormal distribution, north aspect follows logarithmic whereas the east follows both lognormal and logarithmic distribution. In other word, a shift from being lognormal to logarithmic model was observed in the east aspect. PMID:19093482

  19. 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.

  20. Characterization of serum phospholipase a(2) activity in three diverse species of west african crocodiles.

    PubMed

    Merchant, Mark; Juneau, Kate; Gemillion, Jared; Falconi, Rodolfo; Doucet, Aaron; Shirley, Matthew H

    2011-01-01

    Secretory phospholipase A(2), 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 PLA(2) inhibitor, confirming that the activity was a direct result of the presence of serum PLA(2). 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 PLA(2) activities but with slightly different thermal profiles. All three crocodilian species showed high levels of activity against eight different species of bacteria. PMID:22110960

  1. 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. PMID:10849081

  2. Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages.

    PubMed

    Andam, Cheryl P; Choudoir, Mallory J; Vinh Nguyen, Anh; Sol Park, Han; Buckley, Daniel H

    2016-07-01

    Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events. PMID:26849310

  3. 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. PMID:25463151

  4. 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. PMID:27192622

  5. Importance of Diversity in the Oral Microbiota including Candida Species Revealed by High-Throughput Technologies.

    PubMed

    Cho, Tamaki; Nagao, Jun-Ichi; Imayoshi, Rieko; Tanaka, Yoshihiko

    2014-01-01

    Taking advantage of high-throughput technologies, deep sequencing of the human microbiome has revealed commensal bacteria independent of the ability to culture them. The composition of the commensal microbiome is dependent on bacterial diversity and the state of the host regulated by the immune system. Candida species are well known as components of the commensal oral microbiota. Candida species frequently colonize and develop biofilms on medical devices like dentures and catheters. Therefore, Candida biofilm on dentures leads to a decrease in the bacterial diversity and then to a change in the composition of the oral microbiota. A disturbance in the balance between commensal bacteria and the host immune system results in a switch from a healthy state to a diseased state even in the limited oral niche. PMID:24864144

  6. Importance of Diversity in the Oral Microbiota including Candida Species Revealed by High-Throughput Technologies

    PubMed Central

    Cho, Tamaki; Nagao, Jun-ichi; Tanaka, Yoshihiko

    2014-01-01

    Taking advantage of high-throughput technologies, deep sequencing of the human microbiome has revealed commensal bacteria independent of the ability to culture them. The composition of the commensal microbiome is dependent on bacterial diversity and the state of the host regulated by the immune system. Candida species are well known as components of the commensal oral microbiota. Candida species frequently colonize and develop biofilms on medical devices like dentures and catheters. Therefore, Candida biofilm on dentures leads to a decrease in the bacterial diversity and then to a change in the composition of the oral microbiota. A disturbance in the balance between commensal bacteria and the host immune system results in a switch from a healthy state to a diseased state even in the limited oral niche. PMID:24864144

  7. Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.

    PubMed

    Robinson, Christopher J; Vincent, Helen A; Wu, Ming-Cheng; Lowe, Phillip T; Dunstan, Mark S; Leys, David; Micklefield, Jason

    2014-07-30

    Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tunable activation or repression of target gene expression, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, while providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes. PMID:24971878

  8. 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

  9. Species turnover (β-diversity) in ectomycorrhizal fungi linked to NH4+ uptake capacity.

    PubMed

    Kranabetter, J M; Hawkins, B J; Jones, M D; Robbins, S; Dyer, T; Li, T

    2015-12-01

    Ectomycorrhizal (EcM) fungal communities may be shaped by both deterministic and stochastic processes, potentially influencing ecosystem development and function. We evaluated community assembly processes for EcM fungi of Pseudotsuga menziesii among 12 sites up to 400 km apart in southwest British Columbia (Canada) by investigating species turnover (β-diversity) in relation to soil nitrogen (N) availability and physical distance. We then examined functional traits for an N-related niche by quantifying net fluxes of NH4+, NO3- and protons on excised root tips from three contrasting sites using a microelectrode ion flux measurement system. EcM fungal communities were well aligned with soil N availability and pH, with no effect of site proximity (distance-decay curve) on species assemblages. Species turnover was significant (β(1/2) = 1.48) along soil N gradients, with many more Tomentella species on high N than low N soils, in contrast to Cortinarius species. Ammonium uptake was greatest in the spring on the medium and rich sites and averaged over 190 nmol/m(2)/s for Tomentella species. The lowest uptake rates of NH4+ were by nonmycorrhizal roots of axenically grown seedlings (10 nmol/m(2)/s), followed by Cortinarius species (60 nmol/m(2)/s). EcM roots from all sites displayed only marginal uptake of nitrate (8.3 nmol/m(2)/s). These results suggest NH4+ uptake capacity is an important functional trait influencing the assembly of EcM fungal communities. The diversity of EcM fungal species across the region arguably provides critical belowground adaptations to organic and inorganic N supply that are integral to temperate rainforest ecology. PMID:26507980

  10. Host Life History Strategy, Species Diversity, and Habitat Influence Trypanosoma cruzi Vector Infection in Changing Landscapes

    PubMed Central

    Gottdenker, Nicole L.; Chaves, Luis Fernando; Calzada, José E.; Saldaña, Azael; Carroll, C. Ronald

    2012-01-01

    Background Anthropogenic land use may influence transmission of multi-host vector-borne pathogens by changing diversity, relative abundance, and community composition of reservoir hosts. These reservoir hosts may have varying competence for vector-borne pathogens depending on species-specific characteristics, such as life history strategy. The objective of this study is to evaluate how anthropogenic land use change influences blood meal species composition and the effects of changing blood meal species composition on the parasite infection rate of the Chagas disease vector Rhodnius pallescens in Panama. Methodology/Principal Findings R. pallescens vectors (N = 643) were collected in different habitat types across a gradient of anthropogenic disturbance. Blood meal species in DNA extracted from these vectors was identified in 243 (40.3%) vectors by amplification and sequencing of a vertebrate-specific fragment of the 12SrRNA gene, and T. cruzi vector infection was determined by pcr. Vector infection rate was significantly greater in deforested habitats as compared to contiguous forests. Forty-two different species of blood meal were identified in R. pallescens, and species composition of blood meals varied across habitat types. Mammals (88.3%) dominated R. pallescens blood meals. Xenarthrans (sloths and tamanduas) were the most frequently identified species in blood meals across all habitat types. A regression tree analysis indicated that blood meal species diversity, host life history strategy (measured as rmax, the maximum intrinsic rate of population increase), and habitat type (forest fragments and peridomiciliary sites) were important determinants of vector infection with T. cruzi. The mean intrinsic rate of increase and the skewness and variability of rmax were positively associated with higher vector infection rate at a site. Conclusions/Significance In this study, anthropogenic landscape disturbance increased vector infection with T. cruzi, potentially

  11. Intra-species diversity and epidemiology varies among coagulase-negative Staphylococcus species causing bovine intramammary infections.

    PubMed

    Piessens, V; De Vliegher, S; Verbist, B; Braem, G; Van Nuffel, A; De Vuyst, L; Heyndrickx, M; Van Coillie, E

    2012-02-24

    Although many studies report coagulase-negative staphylococci (CNS) as the predominant cause of subclinical bovine mastitis, their epidemiology is poorly understood. In the current study, the genetic diversity within four CNS species frequently associated with bovine intramammary infections, Staphylococcus haemolyticus, S. simulans, S. chromogenes, and S. epidermidis, was determined. For epidemiological purposes, CNS genotypes recovered from bovine milk collected on six Flemish dairy farms were compared with those from the farm environment, and their distribution within the farms was investigated. Genetic diversity was assessed by two molecular typing techniques, amplification fragment length polymorphism (AFLP) and random amplification of polymorphic DNA (RAPD) analysis. Subtyping revealed the highest genetic heterogeneity among S. haemolyticus isolates. A large variety of genotypes was found among environmental isolates, of which several could be linked with intramammary infection, indicating that the environment could act as a potential source for infection. For S. simulans, various genotypes were found in the environment, but a link with IMI was less obvious. For S. epidermidis and S. chromogenes, genetic heterogeneity was limited and the sporadic isolates from environment displayed largely the same genotypes as those from milk. The higher clonality of the S. epidermidis and S. chromogenes isolates from milk suggests that specific genotypes probably disseminate within herds and are more udder-adapted. Environmental sources and cow-to-cow transmission both seem to be involved in the epidemiology of CNS, although their relative importance might substantially vary between species. PMID:21889271

  12. 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.

  13. Multidimensional trade-offs in species responses to disturbance: implications for diversity in a subtropical forest.

    PubMed

    Uriarte, María; Clark, James S; Zimmerman, Jess K; Comita, Liza S; Forero-Montaña, Jimena; Thompson, Jill

    2012-01-01

    Species employ diverse strategies to cope with natural disturbance, but the importance of these strategies for maintaining tree species diversity in forests has been debated. Mechanisms that have the potential to promote tree species coexistence in the context of repeated disturbance include life history trade-offs in colonization and competitive ability or in species' ability to survive at low resource conditions and exploit the temporary resource-rich conditions often generated in the wake of disturbance (successional niche). Quantifying these trade-offs requires long-term forest monitoring and modeling. We developed a hierarchical Bayes model to investigate the strategies tree species employ to withstand and recover from hurricane disturbance and the life history trade-offs that may facilitate species coexistence in forests subject to repeated hurricane disturbance. Unlike previous approaches, our model accommodates temporal variation in process error and observations from multiple sources. We parameterized the model using growth and mortality data from four censuses of a 16-ha plot taken every five years (1990-2005), together with damage data collected after two hurricanes and annual seed production data (1992-2005). Species' susceptibilities to hurricane damage as reflected by changes in diameter growth and fecundity immediately following a storm were weak, highly variable, and unpredictable using traditional life history groupings. The lower crowding conditions (e.g., high light) generated in the wake of storms, however, led to greater gains in growth and fecundity for pioneer and secondary-forest species than for shade-tolerant species, in accordance with expectation of life history. We found moderate trade-offs between survival in high crowding conditions, a metric of competitive ability, and long-distance colonization. We also uncovered a strong trade-off between mean species fecundity in low crowding conditions, a metric of recovery potential, and

  14. Novel gastric helicobacters and oral campylobacters are present in captive and wild cetaceans

    PubMed Central

    Goldman, Cinthia G.; Matteo, Mario J.; Loureiro, Julio D.; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Catalano, Mariana; Heredia, Sergio Rodríguez; Mantero, Paula; Boccio, Jose R.; Zubillaga, Marcela B.; Cremaschi, Graciela A.; Solnick, Jay V.; Perez-Perez, Guillermo I.; Blaser, Martin J.

    2011-01-01

    The mammalian gastric and oral mucosa may be colonized by mixed Helicobacter and Campylobacter species, respectively, in individual animals. To better characterize the presence and distribution of Helicobacter and Campylobacter among marine mammals, we used PCR and 16S rDNA sequence analysis to examine gastric and oral samples from ten dolphins (Tursiops gephyreus), one killer whale (Orcinus orca), one false killer whale (Pseudorca crassidens), and three wild La Plata river dolphins (Pontoporia blainvillei). Helicobacter spp. DNA was widely distributed in gastric and oral samples from both captive and wild cetaceans. Phylogenetic analysis demonstrated two Helicobacter sequence clusters, one closely related to H. cetorum, a species isolated from dolphins and whales in North America. The second related cluster was to sequences obtained from dolphins in Australia and to gastric non-Helicobacter pylori helicobacters, and may represent a novel taxonomic group. Dental plaque sequences from four dolphins formed a third cluster within the Campylobacter genus that likely represents a novel species isolated from marine mammals. Identification of identical Helicobacter spp. DNA sequences from dental plaque, saliva and gastric fluids from the same hosts, suggests that the oral cavity may be involved in transmission. These results demonstrate that Helicobacter and Campylobacter species are commonly distributed in marine mammals, and identify taxonomic clusters that may represent novel species. PMID:21592686

  15. Other Helicobacters and gastric microbiota.

    PubMed

    De Witte, Chloë; Schulz, Christian; Smet, Annemieke; Malfertheiner, Peter; Haesebrouck, Freddy

    2016-09-01

    This article aimed to review the literature from 2015 dealing with gastric and enterohepatic non-Helicobacter pylori Helicobacter species (NHPH). A summary of the gastric microbiota interactions with H. pylori is also presented. An extensive number of studies were published during the last year and have led to a better understanding of the pathogenesis of infections with NHPH. These infections are increasingly reported in human patients, including infections with H. cinaedi, mainly characterized by severe bacteremia. Whole-genome sequencing appears to be the most reliable technique for identification of NHPH at species level. Presence of NHPH in laboratory animals may influence the outcome of experiments, making screening and eradication desirable. Vaccination based on UreB proteins or bacterial lysate with CCR4 antagonists as well as oral glutathione supplementation may be promising strategies to dampen the pathogenic effects associated with gastric NHPH infections. Several virulent factors such as outer membrane proteins, phospholipase C-gamma 2, Bak protein, and nickel-binding proteins are associated with colonization of the gastric mucosae and development of gastritis. The development of high-throughput sequencing has led to new insights in the gastric microbiota composition and its interaction with H. pylori. Alterations in the gastric microbiota caused by the pH-increasing effect of a H. pylori infection may increase the risk for gastric cancer. PMID:27531542

  16. Species diversity and distribution for phytoplankton of the Pearl River estuary during rainy and dry seasons.

    PubMed

    Huang, Liangmin; Jian, Weijun; Song, Xingyu; Huang, Xiaoping; Liu, Sheng; Qian, Peiyuan; Yin, Kedong; Wu, Madeline

    2004-10-01

    Based on data collected at 31 stations and 1 continuous station in the Pearl River estuary during cruises of July 1999 (rainy season) and January 2001 (dry season), this study examined taxonomic composition, abundance, and spatial distribution of phytoplankton. Results indicated 130 species of phytoplankton in the samples from the rainy season, and 132 species in the dry season. Among them, in the rainy season, 82 species of diatom, 39 fresh-water and half-fresh-water species and 41 species of red tide organisms were found. Within these, there were 54 tropical and sub-tropical species, 47 cosmopolitan species and 17 temperate species. The abundance of phytoplankton in the rainy season was higher than that of the dry season, with an average of 6.3 x 10(5) cells x L(-1) and 1.4 x 10(5) cells x L(-1), respectively. Diversity index (H') and evenness (J) were 2.47 and 0.57 in the rainy season, and 2.01 and 0.54 in the dry season. The dominant phytoplankton species in the rainy season was Skeletonema costatum with an average of 2.8 x 10(5) cells x L(-1) and 45.0% of the total phytoplankton abundance. In the dry season, Eucampia zoodiacus became the key dominant species (5.9 x 10(4) cells x L(-1)) when it was 43.47% of the total phytoplankton abundance. Distribution of the dominant species varied with salinity of sea-water, and their amounts correlated negatively with nutrients and zooplankton. PMID:15476837

  17. Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species

    PubMed Central

    Maebe, Kevin; Meeus, Ivan; Ganne, Maarten; De Meulemeester, Thibaut; Biesmeijer, Koos; Smagghe, Guy

    2015-01-01

    Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949–1955 and 1975–1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline. PMID:26061732

  18. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

    PubMed

    Pavan, Ana Carolina; Marroig, Gabriel

    2016-10-01

    A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on

  19. Gastrointestinal nematode species diversity in Soay sheep kept in a natural environment without active parasite control.

    PubMed

    Sinclair, Rona; Melville, Lynsey; Sargison, Fiona; Kenyon, Fiona; Nussey, Dan; Watt, Kathryn; Sargison, Neil

    2016-08-30

    Molecular methods based on ITS2 sequence analysis were used to identify strongylid parasites and describe their diversity in a management intervention and anthelmintic drug treatment-free sheep flock. Fourteen different nematode parasite species were identified in the flock and the results showed a greater level of nematode species diversity than is normally reported in managed farmed flocks, with the presence of parasites such as Bunostomum trigonocephalum, Ostertagia leptospicularis, Spiculopteragia houdemeri and Trichostrongylus retortaeformis that are considered to be absent or rare in sheep kept in comparable localities. The implied prevalences of Haemonchus contortus in lambs, and of Trichostrongylus axei in lambs, ewes and rams, were higher than those in farmed sheep kept in similar regions, while those of Teladorsagia circumcincta and Trichostrongylus vitrinus were lower. Comparison of the patterns of nematode parasite infection between the summer and autumn sampling periods showed differences from the scenarios that are commonplace in comparable managed flocks; with T. vitrinus burdens of the lambs being higher in the summer than in the winter, and Oesophagostomum venulosum being the predominant nematode species in the adult sheep during the summer, while more-or-less absent from these groups during the winter. Rams played an important role in the epidemiology of certain parasitic nematode species. The relatively non-pathogenic O. venulosum was the only parasitic nematode species to predominate in any group during the study. This preliminary characterisation of the nematode parasite burdens of sheep extensively grazed on diverse unimproved pastures will aid in the understanding of the parasitological consequences of intensive grazing management and of the manner in which modern agriculture upsets the equilibrium between parasites and their hosts. These factors must be accounted for when defining the concept of sustainable parasite control and informing

  20. Species diversity of the genus Osmundea (Ceramiales, Rhodophyta) in the Macaronesian region.

    PubMed

    Machín-Sánchez, María; Rousseau, Florence; Le Gall, Line; Cassano, Valéria; Neto, Ana I; Sentíes, Abel; T Fujii, Mutue; Gil-Rodríguez, María Candelaria

    2016-08-01

    Species diversity within the genus Osmundea in the Macaronesian region was explored by conducting a comprehensive sampling in the Azores, the Canary, and the Madeira archipelagos. Toward identification, all specimens were first observed alive to verify the absence of corps en cerise, a diagnostic character for the genus and morphometric data were measured (thallus length and width, first-order branches length and width, branchlets length and width, cortical cell length and width in surface view, cortical cell length and width in transverse section). Specimens were sequenced for COI-5P (39 specimens) and three species delimitation methods (Generalized Mixed Yule Coalescent, Automatic Barcode Gap Discovery method, and Poisson Tree Processes) were used to assess the threshold between infra- and interspecific relationships. Subsequently, one or several sequences of plastid-encoded large subunit of RuBisCO (21 specimens) per delimited species were generated to assess the phylogenetic relationships among Macaronesian Osmundea. Moreover, for each delineated species, vegetative and reproductive anatomy was thoroughly documented and, when possible, specimens were either assigned to existing taxa or described as novel species. This integrative approach has provided data for (i) the presence of O. oederi, O. pinnatifida, and O. truncata in Macaronesia; (ii) the proposal of two novel species, O. prudhommevanreinei sp. nov. and O. silvae sp. nov.; and (iii) evidence of an additional species referred as "Osmundea sp.1," which is a sister taxon of O. hybrida. PMID:27221970

  1. Distribution and diversity of fungal species in and adjacent to the Los Alamos National Laboratory

    SciTech Connect

    Balice, R.G.; Jarmie, N.; Rogers, F.J.

    1997-12-01

    Fungi have demonstrated their ability to diversify and specialize to take advantage of new environments (Murphy 1996). These species are essential to the normal functioning of ecosystems and the impacts of human activities may be harmful to fungi. There is a need to inventory fungi throughout the range of their environments. Previously archived information representing 43 sample locations was used to perform a preliminary evaluation of the distributions and diversity of fungal species at the Los Alamos National Laboratory and in adjacent environments. Presence-absence data for 71 species of fungi in five habitats, pinon-juniper, canyon-bottom ponderosa pine, ponderosa pine, canyon-bottom mixed conifer, and mixed conifer were analyzed. The results indicate that even though fungi occur in each of the habitats, fungal species are not distributed evenly among these habitats. The richness of fungal species is greater in the canyon-bottom mixed conifer and mixed conifer habitats than in the pinon-juniper, canyon-bottom ponderosa pine or ponderosa pine habitats. All but three of the fungal species were recorded in either the canyon-bottom mixed conifer or the mixed conifer habitats, and all but seven of the fungal species were found in the mixed conifer habitat.

  2. Cryptic diversity and habitat partitioning in an economically important aphid species complex.

    PubMed

    Savory, F R; Ramakrishnan, U

    2015-03-01

    Cardamom Bushy Dwarf Virus (CBDV) is an aphid-borne nanovirus which infects large cardamom, Amomum subulatum (Zingiberaceae family), in the Himalayan foothills of Northeast India, Nepal and Bhutan. Two aphid species have been reported to transmit CBDV, including Pentalonia nigronervosa and Micromyzus kalimpongensis (also described as Pentalonia kalimpongensis). However, P. nigronervosa was recently split into two species which exhibit different host plant affiliations. Whilst P. nigronervosa primarily feeds on banana plants, Pentaloniacaladii (previously considered a 'form' of P. nigronervosa) typically feeds on plants belonging to the Araceae, Heliconiaceae and Zingiberaceae families. This raises the possibility that CBDV vectors that were originally described as P. nigronervosa correspond to P. caladii. Accurate identification of vector species is important for understanding disease dynamics and for implementing management strategies. However, closely related species can be difficult to distinguish based on morphological characteristics. In this study, we used molecular markers (two mitochondrial loci and one nuclear locus) and Bayesian phylogenetic analyses to identify aphid specimens collected from 148 CBDV infected plants at a range of locations and elevations throughout Sikkim and the Darjeeling district of West Bengal (Northeast India). Our results revealed the presence of a diversity of lineages, comprising up to six distinct species in at least two related genera. These included the three species mentioned above, an unidentified Pentalonia species and two lineages belonging to an unknown genus. Surprisingly, P. caladii was only detected on a single infected plant, indicating that this species may not play an important role in CBDV transmission dynamics. Distinct elevation distributions were observed for the different species, demonstrating that the community composition of aphids which feed on large cardamom plants changes across an elevation gradient

  3. Freshwater gastropods diversity hotspots: three new species from the Uruguay River (South America)

    PubMed Central

    de Lucía, Micaela

    2016-01-01

    Background: The Atlantic Forest is globally one of the priority ecoregions for biodiversity conservation. In Argentina, it is represented by the Paranense Forest, which covers a vast area of Misiones Province between the Paraná and Uruguay rivers. The Uruguay River is a global hotspot of freshwater gastropod diversity, here mainly represented by Tateidae (genus Potamolithus) and to a lesser extent Chilinidae. The family Chilinidae (Gastropoda, Hygrophila) includes 21 species currently recorded in Argentina, and three species in the Uruguay River. The species of Chilinidae occur in quite different types of habitats, but generally in clean oxygenated water recording variable temperature ranges. Highly oxygenated freshwater environments (waterfalls and rapids) are the most vulnerable continental environments. We provide here novel information on three new species of Chilinidae from environments containing waterfalls and rapids in the Uruguay River malacological province of Argentina. Materials and Methods: The specimens were collected in 2010. We analyzed shell, radula, and nervous and reproductive systems, and determined the molecular genetics. The genetic distance was calculated for two mitochondrial markers (cytochrome c oxidase subunit I–COI- and cytochrome b -Cyt b-) for these three new species and the species recorded from the Misionerean, Uruguay River and Lower Paraná-Río de la Plata malacological provinces. In addition, the COI data were analyzed phylogenetically by the neighbor-joining and Bayesian inference techniques. Results: The species described here are different in terms of shell, radula and nervous and reproductive systems, mostly based on the sculpture of the penis sheath. Phylogenetic analyses grouped the three new species with those present in the Lower Paraná-Río de la Plata and Uruguay River malacological provinces. Discussion: Phylogenetic analyses confirm the separation between the Uruguay River and the Misionerean malacological

  4. Biomechanical Diversity of Mating Structures among Harvestmen Species Is Consistent with a Spectrum of Precopulatory Strategies.

    PubMed

    Burns, Mercedes; Shultz, Jeffrey W

    2015-01-01

    Diversity in reproductive structures is frequently explained by selection acting at individual to generational timescales, but interspecific differences predicted by such models (e.g., female choice or sexual conflict) are often untestable in a phylogenetic framework. An alternative approach focuses on clade- or function-specific hypotheses that predict evolutionary patterns in terms neutral to specific modes of sexual selection. Here we test a hypothesis that diversity of reproductive structures in leiobunine harvestmen (daddy longlegs) of eastern North America reflects two sexually coevolved but non-overlapping precopulatory strategies, a primitive solicitous strategy (females enticed by penis-associated nuptial gifts), and a multiply derived antagonistic strategy (penis exerts mechanical force against armature of the female pregenital opening). Predictions of sexual coevolution and fidelity to precopulatory categories were tested using 10 continuously varying functional traits from 28 species. Multivariate analyses corroborated sexual coevolution but failed to partition species by precopulatory strategy, with multiple methods placing species along a spectrum of mechanical antagonistic potential. These findings suggest that precopulatory features within species reflect different co-occurring levels of solicitation and antagonism, and that gradualistic evolutionary pathways exist between extreme strategies. The ability to quantify antagonistic potential of precopulatory structures invites comparison with ecological variables that may promote evolutionary shifts in precopulatory strategies. PMID:26352413

  5. Biomechanical Diversity of Mating Structures among Harvestmen Species Is Consistent with a Spectrum of Precopulatory Strategies

    PubMed Central

    Burns, Mercedes; Shultz, Jeffrey W.

    2015-01-01

    Diversity in reproductive structures is frequently explained by selection acting at individual to generational timescales, but interspecific differences predicted by such models (e.g., female choice or sexual conflict) are often untestable in a phylogenetic framework. An alternative approach focuses on clade- or function-specific hypotheses that predict evolutionary patterns in terms neutral to specific modes of sexual selection. Here we test a hypothesis that diversity of reproductive structures in leiobunine harvestmen (daddy longlegs) of eastern North America reflects two sexually coevolved but non-overlapping precopulatory strategies, a primitive solicitous strategy (females enticed by penis-associated nuptial gifts), and a multiply derived antagonistic strategy (penis exerts mechanical force against armature of the female pregenital opening). Predictions of sexual coevolution and fidelity to precopulatory categories were tested using 10 continuously varying functional traits from 28 species. Multivariate analyses corroborated sexual coevolution but failed to partition species by precopulatory strategy, with multiple methods placing species along a spectrum of mechanical antagonistic potential. These findings suggest that precopulatory features within species reflect different co-occurring levels of solicitation and antagonism, and that gradualistic evolutionary pathways exist between extreme strategies. The ability to quantify antagonistic potential of precopulatory structures invites comparison with ecological variables that may promote evolutionary shifts in precopulatory strategies. PMID:26352413

  6. Effect of trophic status in lakes on fungal species diversity and abundance.

    PubMed

    Pietryczuk, A; Cudowski, A; Hauschild, T

    2014-11-01

    The objective of this study was to determine the species diversity and abundance of fungi in relation to the hydrochemical conditions, with special emphasis on the trophic status and degree of pollution of lakes. The study was conducted in 14 lakes of the Augustów Lakeland (central Europe, NE Poland) with different hydrological conditions, type of stratification and trophic status. The analyses were performed in the hydrological year 2013. In the waters of the studied lakes, the mean abundance of fungi was 5600±3600 CFU/mL. The minimum value (800 CFU/mL) was recorded for the mesotrophic Płaskie Lake, and the maximum value (14,000 CFU/mL) was recorded for the eutrophic Pobojno Lake. A total of 38 species of fungi were identified, including 11 belonging to the aquatic hyphomycetes; up to 14 species were potentially pathogenic fungi. The potentially pathogenic fungi, particularly Candida albicans and Scopulariopsis fusca, were found in lakes with increased concentrations of chloride and sulphate(VI) ions and may thus serve as indicators of the degree of water pollution. This paper illustrates that the species diversity and abundance of fungi in limnic waters depend on the concentration of organic matter, chlorophyll a concentration, and the degree of water pollution. The results suggest that aquatic fungi can be a valuable indicator of the degree of pollution and the sanitary quality of the water. PMID:25145569

  7. Diversity and associations between Drosophilidae (Diptera) species and Basidiomycetes in a Neotropical forest.

    PubMed

    Valer, Felipe B; Bernardi, Eduardo; Mendes, Mayara F; Blauth, Monica L; Gottschalk, Marco S

    2016-01-01

    Drosophilidae is one of the most representative families of insects that occurs in fungal fruiting bodies of Basidiomycetes; however, the diversity and community structure of mycophagous Drosophilidae in the Neotropical region is poorly known. The aims of the present study were to describe the diversity of mycophagous Drosophilidae and to investigate its colonization of fungal hosts in a forest of southern Brazil. From 120 fungal samples (patches of mushrooms) of 17 Basidiomycetes genera, flies were recorded emerging from 70 samples and collected in adult stages of 25 fungal samples, for a total of 4897 drosophilids belonging to 31 species and 5 genera. Drosophila Fallén was the most species-rich genus, whereas Hirtodrosophila Duda was the dominant genus. Studies performed in the Holarctic region indicate that mycophagous drosophilid have generalist habits; however, our results showed that most drosophilids use fewer than two fungal hosts, and most species of Hirtodrosophila and Leucophenga were restricted to abundant fungal species, suggesting a specialization for these resources. The most specialized fauna emerged from Auricularia, which was the most frequent fungal genus in our collection, and this result supports the assumption that specialization depends on the availability of fungal resources over time. PMID:27142546

  8. Diversity of Variable Number Tandem Repeat Loci in Shigella Species Isolated from Pediatric Patients

    PubMed Central

    Ranjbar, Reza; Memariani, Mojtaba; Memariani, Hamed

    2015-01-01

    Multilocus variable number tandem repeat (VNTR) analysis (MLVA) is a new typing method with several advantages compared to other methods. Dissemination of Shigella is highly significant in developing countries. Whilst Shigella is becoming increasingly important as an etiologic agent of pediatric shigellosis in Iran, little is known about the genetic diversity of the local strains. Therefore, the aim of this study was to describe the genetic diversity of Shigella species isolated from pediatric patients in Tehran, Iran. A total of 53 Shigella isolates were obtained from 1070 patients with diarrhea (less than 12 years of age). All isolates were identified by routine biochemical and serological tests. The confirmed Shigella isolates were further serogrouped (by the slide agglutination) using slide agglutination method. MLVA assay with the seven loci resolved 53 Shigella isolates into 36 different genotypes. Almost all the isolates were classified into five clonal complexes. Furthermore, our MLVA assay could effectively distinguish the four Shigella species. This study has provided valuable insights into the genetic heterogeneity of Shigella species in Tehran, Iran. Our findings can be helpful for further epidemiological surveillance of Shigella species in this country in the future. PMID:26629486

  9. Gonadal expression of Foxo1, but not Foxo3, is conserved in diverse Mammalian species.

    PubMed

    Tarnawa, Edward D; Baker, Michael D; Aloisio, Gina M; Carr, Bruce R; Castrillon, Diego H

    2013-04-01

    The Foxos are key effectors of the PI3K/Akt signaling pathway and regulate diverse physiologic processes. Two of these factors, Foxo1 and Foxo3, serve specific roles in reproduction in the mouse. Foxo3 is required for suppression of primordial follicle activation in females, while Foxo1 regulates spermatogonial stem cell maintenance in males. In the mouse ovary, Foxo1 is highly expressed in somatic cells (but not in oocytes), suggesting an important functional role for Foxo1 in these cells. Given that invertebrate model species such as Caenorhabditis elegans and Drosophila melanogaster harbor a single ancestral Foxo homolog, these observations suggest that gene duplication conferred a selective advantage by permitting the Foxos to adopt distinct roles in oogenesis and spermatogenesis. Our objective was to determine if the remarkably specific expression patterns of Foxo1 and Foxo3 in mouse gonads (and, by inference, Foxo function) are conserved in diverse mammalian species. Western blotting was used to validate isoform-specific antibodies in rodents, companion animals, farm animals, nonhuman primates, and humans. Following validation of each antibody, immunohistochemistry was performed to ascertain Foxo1 and Foxo3 gonadal expression patterns. While Foxo1 expression in spermatogonia and granulosa cells was conserved in each species evaluated, Foxo3 expression in oocytes was not. Our findings suggest that Foxo3 is not uniquely required for primordial follicle maintenance in nonrodent species and that other Foxos, particularly Foxo1, may contribute to oocyte maintenance in a functionally redundant manner. PMID:23486915

  10. Culicoides monitoring in Belgium in 2011: analysis of spatiotemporal abundance, species diversity and Schmallenberg virus detection.

    PubMed

    DE Regge, N; DE Deken, R; Fassotte, C; Losson, B; Deblauwe, I; Madder, M; Vantieghem, P; Tomme, M; Smeets, F; Cay, A B

    2015-09-01

    In 2011, Culicoides (Diptera: Ceratopogonidae) were collected at 16 locations covering four regions of Belgium with Onderstepoort Veterinary Institute (OVI) traps and at two locations with Rothamsted suction traps (RSTs). Quantification of the collections and morphological identification showed important variations in abundance and species diversity between individual collection sites, even for sites located in the same region. However, consistently higher numbers of Culicoides midges were collected at some sites compared with others. When species abundance and diversity were analysed at regional level, between-site variation disappeared. Overall, species belonging to the subgenus Avaritia together with Culicoides pulicaris (subgenus Culicoides) were the most abundant, accounting for 80% and 96% of all midges collected with RSTs and OVI traps, respectively. Culicoides were present during most of the year, with Culicoides obsoletus complex midges found from 9 February until 27 December. Real-time reverse-transcription polymerase chain reaction screening for Schmallenberg virus in the heads of collected midges resulted in the first detection of the virus in August 2011 and identified C. obsoletus complex, Culicoides chiopterus and Culicoides dewulfi midges as putative vector species. At Libramont in the south of Belgium, no positive pools were identified. PMID:25761054

  11. Genetic diversity in three invasive clonal aquatic species in New Zealand

    PubMed Central

    2010-01-01

    Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946) and L. major (1950). Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient. PMID:20565861

  12. 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. PMID:24783800

  13. Incorporating biodiversity into rangeland health: Plant species richness and diversity in great plains grasslands

    USGS Publications Warehouse

    Symstad, A.J.; Jonas, J.L.

    2011-01-01

    Indicators of rangeland health generally do not include a measure of biodiversity. Increasing attention to maintaining biodiversity in rangelands suggests that this omission should be reconsidered, and plant species richness and diversity are two metrics that may be useful and appropriate. Ideally, their response to a variety of anthropogenic and natural drivers in the ecosystem of interest would be clearly understood, thereby providing a means to diagnose the cause of decline in an ecosystem. Conceptual ecological models based on ecological principles and hypotheses provide a framework for this understanding, but these models must be supported by empirical evidence if they are to be used for decision making. To that end, we synthesize results from published studies regarding the responses of plant species richness and diversity to drivers that are of management concern in Great Plains grasslands, one of North America's most imperiled ecosystems. In the published literature, moderate grazing generally has a positive effect on these metrics in tallgrass prairie and a neutral to negative effect in shortgrass prairie. The largest published effects on richness and diversity were caused by moderate grazing in tallgrass prairies and nitrogen fertilization in shortgrass prairies. Although weather is often cited as the reason for considerable annual fluctuations in richness and diversity, little information about the responses of these metrics to weather is available. Responses of the two metrics often diverged, reflecting differences in their sensitivity to different types of changes in the plant community. Although sufficient information has not yet been published for these metrics to meet all the criteria of a good indicator in Great Plains Grasslands, augmenting current methods of evaluating rangeland health with a measure of plant species richness would reduce these shortcomings and provide information critical to managing for biodiversity. ?? Society for Range

  14. Deep-sea benthic foraminiferal species diversity in the NE Atlantic and NW Arabian sea: a synthesis

    NASA Astrophysics Data System (ADS)

    Gooday, Andrew J.; Bett, Brian J.; Shires, Rizpah; Lambshead, P. John D.

    1998-01-01

    We present a synthesis of species diversity data (Fishers' alpha index, Shannon-Wiener (log 2), ES(100), Rank 1 Dominance) for "live" (stained) foraminifera from five bathyal (1340 m depth) and abyssal (4450-4950 m depth) sites in the NE Atlantic and a 3400 m-deep site in the Arabian Sea. Three Atlantic sites (Porcupine Seabight, BIOTRANS, Porcupine Abyssal Plain) are subject to seasonal phytodetritus inputs that support low diversity populations (8-17 species). In other respects the foraminifera are highly diverse. The meiofaunal fractions (>45 or >63 μm; including fragmented and phytodetritus species) of abyssal Atlantic samples yielded >110 and >170 species in the 0-1 cm and 0-10 cm layers, respectively; the Arabian Sea sample (0-1 cm layer only) yielded 232 species. In both cases, values for diversity measures were very high. Diversity was rather lower in bathyal Porcupine Seabight samples (0-1 cm layer), which yielded <100 species. The foraminiferal macrofauna (>500 μm; Porcupine and Madeira Abyssal Plains) was also speciose (113-133 species), but diversity measures were lower and dominance higher than for the meiofauna. All assemblages contained numerous undescribed species, many belonging to poorly known monothalamous, soft-bodied taxa. Sample diversity was influenced by several factors. Combining phytodetrital and sediment populations reduced diversity and increased dominance slightly; the inclusion of deeper sediment layers and finer sieve fractions had the opposite effect. The inclusion of fragments had more impact on macrofaunal than on meiofaunal diversity, although in both cases the effect was inconsistent (either positive or negative). Porcupine and Madeira Abyssal Plain multicore samples (>63 μm fraction) contained substantially more foraminiferal species than nematode species; the numbers of foraminiferal species in boxcore samples (>500 μm fraction) were comparable to, or greater than, literature values for macrofaunal taxa such as polychaetes

  15. Gains to species diversity in organically farmed fields are not propagated at the farm level.

    PubMed

    Schneider, Manuel K; Lüscher, Gisela; Jeanneret, Philippe; Arndorfer, Michaela; Ammari, Youssef; Bailey, Debra; Balázs, Katalin; Báldi, András; Choisis, Jean-Philippe; Dennis, Peter; Eiter, Sebastian; Fjellstad, Wendy; Fraser, Mariecia D; Frank, Thomas; Friedel, Jürgen K; Garchi, Salah; Geijzendorffer, Ilse R; Gomiero, Tiziano; Gonzalez-Bornay, Guillermo; Hector, Andy; Jerkovich, Gergely; Jongman, Rob H G; Kakudidi, Esezah; Kainz, Max; Kovács-Hostyánszki, Anikó; Moreno, Gerardo; Nkwiine, Charles; Opio, Julius; Oschatz, Marie-Louise; Paoletti, Maurizio G; Pointereau, Philippe; Pulido, Fernando J; Sarthou, Jean-Pierre; Siebrecht, Norman; Sommaggio, Daniele; Turnbull, Lindsay A; Wolfrum, Sebastian; Herzog, Felix

    2014-01-01

    Organic farming is promoted to reduce environmental impacts of agriculture, but surprisingly little is known about its effects at the farm level, the primary unit of decision making. Here we report the effects of organic farming on species diversity at the field, farm and regional levels by sampling plants, earthworms, spiders and bees in 1470 fields of 205 randomly selected organic and nonorganic farms in twelve European and African regions. Species richness is, on average, 10.5% higher in organic than nonorganic production fields, with highest gains in intensive arable fields (around +45%). Gains to species richness are partly caused by higher organism abundance and are common in plants and bees but intermittent in earthworms and spiders. Average gains are marginal +4.6% at the farm and +3.1% at the regional level, even in intensive arable regions. Additional, targeted measures are therefore needed to fulfil the commitment of organic farming to benefit farmland biodiversity. PMID:24958283

  16. High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States

    PubMed Central

    Holguin, Claudia M; Baeza, Juan A; Mueller, John D; Agudelo, Paula

    2015-01-01

    Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group. PMID:26306177

  17. Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato.

    PubMed

    Obase, Keisuke; Douhan, Greg W; Matsuda, Yosuke; Smith, Matthew E

    2016-08-01

    The fungus Cenococcum geophilum Fr. (Dothideomycetes, Ascomycota) is one of the most common ectomycorrhizal fungi in boreal to temperate regions. A series of molecular studies has demonstrated that C. geophilum is monophyletic but a heterogeneous species or a species complex. Here, we revisit the phylogenetic diversity of C. geophilum sensu lato from a regional to intercontinental scale by using new data from Florida (USA) along with existing data in GenBank from Japan, Europe, and North America. The combination of internal transcribed spacer (ITS) ribosomal DNA and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene resolved six well-supported lineages (87-100 % bootstrap values) that are closely related to each other and a seventh lineage that is phylogenetically distinct. A multi-locus analysis (small subunit (SSU), large subunit (LSU), translational elongation factor (TEF), and the largest and second-largest subunits of RNA polymerase II (RPB1 and RPB2)) revealed that the divergent lineage is the sister group to all other known Cenococcum isolates. Isolates of the divergent lineage grow fast on nutrient media and do not form ectomycorrhizas on seedlings of several pine and oak species. Our results indicate that C. geophilum sensu lato includes more phylogenetically distinct cryptic species than have previously been reported. Furthermore, the divergent lineage appears to be a non-mycorrhizal sister group. We discuss the phylogenetic diversity of C. geophilum sensu lato and argue in favor of species recognition based on phylogenetic and ecological information in addition to morphological characteristics. A new genus and species (Pseudocenococcum floridanum gen. et sp. nov.) is proposed to accommodate a divergent and putatively non-mycorrhizal lineage. PMID:26968743

  18. Species diversity and cytotoxic potency of airborne sterigmatocystin-producing Aspergilli from the section Versicolores.

    PubMed

    Despot, Daniela Jakšić; Kocsubé, Sandor; Bencsik, Ottó; Kecskeméti, Anita; Szekeres, András; Vágvölgyi, Csaba; Varga, Janos; Klarić, Maja Šegvić

    2016-08-15

    This study presents the distribution and species diversity of sterigmatocystin-producing Aspergilli from the section Versicolores in the indoor air of apartment-AP, basements-BS and grain mill-GM in Croatia, as well as the cytotoxic potency of isolates. The species comprised 0.7-20% of total airborne fungi detected in the AP, 11-55% in the BS, and 0-2% in the GM. Based on CaM sequences, seven species were identified; dominant were Aspergillus jensenii and Aspergillus creber, followed by Aspergillus protuberus, Aspergillus venenatus, Aspergillus tennesseensis, Aspergillus amoenus, Aspergillus griseoaurantiacus and three undescribed species. All of the identified species produced sterigmatocystin-STC (HPLC/UV-VIS); A. griseoaurantiacus (208.29μg/mL) and A. jensenii (1.192-133.63μg/mL) produced the highest levels, the lowest were detected in A. protuberus and A. tennesseensis (0.117-2.749μg/mL). Lower species diversity was obtained in the GM due to overgrowth with more propulsive fungi. Relatively high STC levels (0.06-2.35μg/g) detected in 52% of GM dust samples confirmed the presence of STC-producers, although this STC cannot be exclusively attributed to Aspergilli (Versicolores). STC and the majority of STC-producing Aspergilli were cytotoxic to human lung A549 cells (IC50 0.9-2.3μg/mL) and THP-1 macrophage-like cells (IC50 0.3-0.6μg/mL) in relatively low concentrations suggesting that humans can be at high risk during chronic exposure. PMID:27100010

  19. Reconstructed Homo habilis type OH 7 suggests deep-rooted species diversity in early Homo.

    PubMed

    Spoor, Fred; Gunz, Philipp; Neubauer, Simon; Stelzer, Stefanie; Scott, Nadia; Kwekason, Amandus; Dean, M Christopher

    2015-03-01

    Besides Homo erectus (sensu lato), the eastern African fossil record of early Homo has been interpreted as representing either a single variable species, Homo habilis, or two species. In the latter case, however, there is no consensus over the respective groupings, and which of the two includes OH 7, the 1.8-million-year-old H. habilis holotype. This partial skull and hand from Olduvai Gorge remains pivotal to evaluating the early evolution of the Homo lineage, and by priority names one or other of the two taxa. However, the distorted preservation of the diagnostically important OH 7 mandible has hindered attempts to compare this specimen with other fossils. Here we present a virtual reconstruction of the OH 7 mandible, and compare it to other early Homo fossils. The reconstructed mandible is remarkably primitive, with a long and narrow dental arcade more similar to Australopithecus afarensis than to the derived parabolic arcades of Homo sapiens or H. erectus. We find that this shape variability is not consistent with a single species of early Homo. Importantly, the jaw morphology of OH 7 is incompatible with fossils assigned to Homo rudolfensis and with the A.L. 666-1 Homo maxilla. The latter is morphologically more derived than OH 7 but 500,000 years older, suggesting that the H. habilis lineage originated before 2.3 million years ago, thus marking deep-rooted species diversity in the genus Homo. We also reconstructed the parietal bones of OH 7 and estimated its endocranial volume. At between 729 and 824 ml it is larger than any previously published value, and emphasizes the near-complete overlap in brain size among species of early Homo. Our results clarify the H. habilis hypodigm, but raise questions about its phylogenetic relationships. Differences between species of early Homo appear to be characterized more by gnathic diversity than by differences in brain size, which was highly variable within all taxa. PMID:25739632

  20. Revisiting the age, evolutionary history and species level diversity of the genus Hydra (Cnidaria: Hydrozoa).

    PubMed

    Schwentner, Martin; Bosch, Thomas C G

    2015-10-01

    The genus Hydra has long served as a model system in comparative immunology, developmental and evolutionary biology. Despite its relevance for fundamental research, Hydra's evolutionary origins and species level diversity are not well understood. Detailed previous studies using molecular techniques identified several clades within Hydra, but how these are related to described species remained largely an open question. In the present study, we compiled all published sequence data for three mitochondrial and nuclear genes (COI, 16S and ITS), complemented these with some new sequence data and delimited main genetic lineages (=hypothetical species) objectively by employing two DNA barcoding approaches. Conclusions on the species status of these main lineages were based on inferences of reproductive isolation. Relevant divergence times within Hydra were estimated based on relaxed molecular clock analyses with four genes (COI, 16S, EF1α and 28S) and four cnidarians fossil calibration points All in all, 28 main lineages could be delimited, many more than anticipated from earlier studies. Because allopatric distributions were common, inferences of reproductive isolation often remained ambiguous but reproductive isolation was rarely refuted. Our results support three major conclusions which are central for Hydra research: (1) species level diversity was underestimated by molecular studies; (2) species affiliations of several crucial 'workhorses' of Hydra evolutionary research were wrong and (3) crown group Hydra originated ∼200mya. Our results demonstrate that the taxonomy of Hydra requires a thorough revision and that evolutionary studies need to take this into account when interspecific comparisons are made. Hydra originated on Pangea. Three of four extant groups evolved ∼70mya ago, possibly on the northern landmass of Laurasia. Consequently, Hydra's cosmopolitan distribution is the result of transcontinental and transoceanic dispersal. PMID:26014206

  1. Species-Specific Diversity of a Fixed Motor Pattern: The Electric Organ Discharge of Gymnotus

    PubMed Central

    Rodríguez-Cattaneo, Alejo; Pereira, Ana Carolina; Aguilera, Pedro A.; Crampton, William G. R.; Caputi, Angel A.

    2008-01-01

    Understanding fixed motor pattern diversity across related species provides a window for exploring the evolution of their underlying neural mechanisms. The electric organ discharges of weakly electric fishes offer several advantages as paradigmatic models for investigating how a neural decision is transformed into a spatiotemporal pattern of action. Here, we compared the far fields, the near fields and the electromotive force patterns generated by three species of the pulse generating New World gymnotiform genus Gymnotus. We found a common pattern in electromotive force, with the far field and near field diversity determined by variations in amplitude, duration, and the degree of synchronization of the different components of the electric organ discharges. While the rostral regions of the three species generate similar profiles of electromotive force and local fields, most of the species-specific differences are generated in the main body and tail regions of the fish. This causes that the waveform of the field is highly site dependant in all the studied species. These findings support a hypothesis of the relative separation of the electrolocation and communication carriers. The presence of early head negative waves in the rostral region, a species-dependent early positive wave at the caudal region, and the different relationship between the late negative peak and the main positive peak suggest three points of lability in the evolution of the electrogenic system: a) the variously timed neuronal inputs to different groups of electrocytes; b) the appearance of both rostrally and caudally innervated electrocytes, and c) changes in the responsiveness of the electrocyte membrane. PMID:18461122

  2. Latitudinal species diversity gradient of mushroom corals off eastern Australia: a baseline from the 1970s

    NASA Astrophysics Data System (ADS)

    Hoeksema, Bert W.

    2015-11-01

    Based on a study of mushroom coral species of eastern Australia, a decrease in species richness can be discerned from north to south. Eastern Australia, including the Great Barrier Reef (GBR), is one of only few coral reef areas suitable for studies on large-scale latitudinal biodiversity patterns. Such patterns may help to recognize biogeographic boundaries and factors regulating biodiversity. Owing to the eastern Australian long coastline, such studies are a logistic challenge unless reliable distribution data are already available, as in museum collections. A large coral collection predominantly sampled from this area in the 1970s is present in the Museum of Tropical Queensland (MTQ). The scleractinian family Fungiidae (mushroom corals), representing about 10% of Indo-Pacific reef coral species, was selected as proxy. It was represented by 1289 specimens belonging to 34 species with latitudinal ranges between 09°09‧S and 31°28‧S. The fauna of the northernmost reefs in the Gulf of Papua and the Torres Strait, and north of the Great Barrier Reef Marine Park (GBRMP), was represented by a maximum of 30 fungiids. From here a southward decline in species number was observed, down to Lord Howe Island with only one species. Together with previous records, the mushroom coral fauna of eastern Australia consists of 37 species, which is more diverse than hitherto known and similar to numbers found in the Coral Triangle. Future field surveys in the GBR should specifically target rarely known species, which are mainly small and found at depths >25 m. In the light of global climate change, they may also show whether previously recorded species are still present and whether their latitudinal ranges have shifted, using the 1970s records as a baseline.

  3. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    PubMed

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. PMID:26484942

  4. Karyotypic diversity among three species of the genus Astyanax (Characiformes: Characidae).

    PubMed

    Nishiyama, P B; Vieira, M M R; Porto, F E; Borin, L A; Portela-Castro, A L B; Santos, I C M

    2016-06-01

    The group Incertae sedis within the Characidae family currently includes 88 genera, previously included in the subfamily Tetragonopterinae. Among them is the genus Astyanax comprising a group of species with similar morphology and widely distributed in the Neotropics. Thus, the present study aimed to analyze the karyotype diversity in Astyanax species from different watersheds by conventional Giemsa staining, C-banding and fluorescence in situ hybridization (FISH rDNA 18S) probe.specimens of Astyanax aff. paranae belonging to the "scabripinnis complex", Astyanax asunsionensis and Astyanax aff. bimaculatus were analyzed". Two sympatric karyomorphs were observed in Astyanax.aff paranae, one of them having2n=48andthe other one with 2n=50 chromosomes. Other population of this same species also presented 2n=50 chromosomes, but differing in the karyotype formula and with macro supernumerary chromosome found in 100% of the cells in about 80%of females analyzed. Two population of A. asuncionensis and one population of Astyanax. aff. bimaculatus, also showed a diploid number of 50 chromosomes, but also differing in their karyotype formulas. Therefore, A. asuncionensis was also characterized by intraspecific chromosome diversity. The C-banding analysis was able to demonstrate a distinctable to demonstrate a distinct pattern of heterochromatin differing A. asuncionensis from Astyanax aff. paranae and Astyanax aff. bimaculatus. The supernumerary chromosome of Astyanax aff. paranae proved completely heterochromatic. Only Astyanax.aff. bimaculatus multiple showed multiple sites of nucleolar organizing regions. The other species were characterized by having a simple system of NOR. These data contributes to the know ledge of the existing biodiversity in our fish fauna, here highlighted by the inter- and intraspecific chromosomal diversity in the genus Astyanax. PMID:26934153

  5. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes

    PubMed Central

    Iftikhar, Romana; Ashfaq, Muhammad; Rasool, Akhtar; Hebert, Paul D. N.

    2016-01-01

    Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5ʹ (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips. PMID:26741134

  6. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes.

    PubMed

    Iftikhar, Romana; Ashfaq, Muhammad; Rasool, Akhtar; Hebert, Paul D N

    2016-01-01

    Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips. PMID:26741134

  7. Density dynamics of diverse Spiroplasma strains naturally infecting different species of Drosophila

    PubMed Central

    Haselkorn, Tamara S; Watts, Thomas D; Markow, Therese A

    2013-01-01

    Facultative heritable bacterial endosymbionts can have dramatic effects on their hosts, ranging from mutualistic to parasitic. Within-host bacterial endosymbiont density plays a critical role in maintenance of a symbiotic relationship, as it can affect levels of vertical transmission and expression of phenotypic effects, both of which influence the infection prevalence in host populations. Species of genus Drosophila are infected with Spiroplasma, whose characterized phenotypic effects range from that of a male-killing reproductive parasite to beneficial defensive endosymbiont. For many strains of Spiroplasma infecting at least 17 species of Drosophila, however, the phenotypic effects are obscure. The infection prevalence of these Spiroplasma vary within and among Drosophila species, and little is known about the within-host density dynamics of these diverse strains. To characterize the patterns of Spiroplasma density variation among Drosophila we used quantitative PCR to assess bacterial titer at various life stages of three species of Drosophila naturally-infected with two different types of Spiroplasma. For naturally infected Drosophila species we found that non-male-killing infections had consistently lower densities than the male-killing infection. The patterns of Spiroplasma titer change during aging varied among Drosophila species infected with different Spiroplasma strains. Bacterial density varied within and among populations of Drosophila, with individuals from the population with the highest prevalence of infection having the highest density. This density variation underscores the complex interaction of Spiroplasma strain and host genetic background in determining endosymbiont density. PMID:23846301

  8. Genetic Diversity in Passiflora Species Assessed by Morphological and ITS Sequence Analysis

    PubMed Central

    Ramaiya, Shiamala Devi; Bujang, Japar Sidik; Zakaria, Muta Harah

    2014-01-01

    This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level. PMID:25050402

  9. How Many Parasites Species a Frog Might Have? Determinants of Parasite Diversity in South American Anurans

    PubMed Central

    Campião, Karla Magalhães; Ribas, Augusto Cesar de Aquino; Morais, Drausio Honorio; da Silva, Reinaldo José; Tavares, Luiz Eduardo Roland

    2015-01-01

    There is an increasing interest in unveiling the dynamics of parasite infection. Understanding the interaction patterns, and determinants of host-parasite association contributes to filling knowledge gaps in both community and disease ecology. Despite being targeted as a relevant group for conservation efforts, determinants of the association of amphibians and their parasites in broad scales are poorly understood. Here we describe parasite biodiversity in South American amphibians, testing the influence of host body size and geographic range in helminth parasites species richness (PSR). We also test whether parasite diversity is related to hosts’ phylogenetic diversity. Results showed that nematodes are the most common anuran parasites. Host-parasite network has a nested pattern, with specialist helminth taxa generally associated with hosts that harbour the richest parasite faunas. Host size is positively correlated with helminth fauna richness, but we found no support for the association of host geographic range and PSR. These results remained consistent after correcting for uneven study effort and hosts’ phylogenic correlation. However, we found no association between host and parasite diversity, indicating that more diversified anuran clades not necessarily support higher parasite diversity. Overall, considering both the structure and the determinants of PRS in anurans, we conclude that specialist parasites are more likely to be associated with large anurans, which are the ones harbouring higher PSR, and that the lack of association of PSR with hosts’ clade diversification suggests it is strongly influenced by ecological and contemporary constrains. PMID:26473593

  10. Community maturity, species saturation and the variant diversity- productivity relationships in grasslands

    USGS Publications Warehouse

    Guo, Q.; Shaffer, T.; Buhl, T.

    2006-01-01

    Detailed knowledge of the relationship between plant diversity and productivity is critical for advancing our understanding of ecosystem functioning and for achieving success in habitat restoration efforts. However, effects and interactions of diversity, succession and biotic invasions on productivity remain elusive. We studied newly established communities in relation to preexisting homogeneous vegetation invaded by exotic plants in the northern Great Plains, USA, at four study sites for 3 years. We observed variant diversity-productivity relationships for the seeded communities (generally positive monotonic at three sites and non-monotonic at the other site) but no relationships for the resident community or the seeded and resident communities combined at all sites and all years. Community richness was enhanced by seeding additional species but productivity was not. The optimal diversity (as indicated by maximum productivity) changed among sites and as the community developed. The findings shed new light on ecosystem functioning of biodiversity under different conditions and have important implications for restoration. ?? 2006 Blackwell Publishing Ltd/CNRS.

  11. Distinct Diversity of vacA, cagA, and cagE Genes of Helicobacter pylori Associated with Peptic Ulcer in Japan

    PubMed Central

    Yamazaki, Shiho; Yamakawa, Akiyo; Okuda, Tomoyuki; Ohtani, Masahiro; Suto, Hiroyuki; Ito, Yoshiyuki; Yamazaki, Yukinao; Keida, Yoshihide; Higashi, Hideaki; Hatakeyama, Masanori; Azuma, Takeshi

    2005-01-01

    Colonization of the stomach mucosa by Helicobacter pylori is a major cause of acute and chronic gastric pathologies in humans. Several H. pylori virulence genes that may play a role in its pathogenicity have been identified. The most important determinants are vacA and cagA in the cag pathogenicity island (cagPAI) genes. In the present study, to consider the association of molecular genetics between vacA and the cagPAI regarding clinical outcome, we selected H. pylori strains with various genotypes of vacA in Japan and sequenced full-length vacA, cagA, and cagE genes. Sequencing of vacA and cagA genes revealed variable size, whereas the cagE gene was well conserved among strains. Each of the phylogenetic trees based on the deduced amino acid sequences of VacA, CagA, and CagE indicated that all three proteins were divided into two major groups, a Western group and an East Asian group, and the distributions of isolates exhibited similar patterns among the three proteins. The strains with s2 and s1a/m1a vacA genotypes and the Western-type 3′ region cagA genotype were classified into the Western group, and the strains with the s1c/m1b vacA genotype and the East Asian-type 3′ cagA genotype were included in the East Asian group. In addition, the prevalence of infection with the Western group strain was significantly higher in patients with peptic ulcer (90.0%, 9/10) than in patients with chronic gastritis (22.7%, 5/22) (χ2 = 12.64, P = 0.00057). These data suggest that the molecular genetics of vacA and cagPAI are associated and that the Western group with vacA and cagPAI genes is associated with peptic ulcer disease. PMID:16081930

  12. Distinct diversity of vacA, cagA, and cagE genes of Helicobacter pylori associated with peptic ulcer in Japan.

    PubMed

    Yamazaki, Shiho; Yamakawa, Akiyo; Okuda, Tomoyuki; Ohtani, Masahiro; Suto, Hiroyuki; Ito, Yoshiyuki; Yamazaki, Yukinao; Keida, Yoshihide; Higashi, Hideaki; Hatakeyama, Masanori; Azuma, Takeshi

    2005-08-01

    Colonization of the stomach mucosa by Helicobacter pylori is a major cause of acute and chronic gastric pathologies in humans. Several H. pylori virulence genes that may play a role in its pathogenicity have been identified. The most important determinants are vacA and cagA in the cag pathogenicity island (cagPAI) genes. In the present study, to consider the association of molecular genetics between vacA and the cagPAI regarding clinical outcome, we selected H. pylori strains with various genotypes of vacA in Japan and sequenced full-length vacA, cagA, and cagE genes. Sequencing of vacA and cagA genes revealed variable size, whereas the cagE gene was well conserved among strains. Each of the phylogenetic trees based on the deduced amino acid sequences of VacA, CagA, and CagE indicated that all three proteins were divided into two major groups, a Western group and an East Asian group, and the distributions of isolates exhibited similar patterns among the three proteins. The strains with s2 and s1a/m1a vacA genotypes and the Western-type 3' region cagA genotype were classified into the Western group, and the strains with the s1c/m1b vacA genotype and the East Asian-type 3' cagA genotype were included in the East Asian group. In addition, the prevalence of infection with the Western group strain was significantly higher in patients with peptic ulcer (90.0%, 9/10) than in patients with chronic gastritis (22.7%, 5/22) (chi2 = 12.64, P = 0.00057). These data suggest that the molecular genetics of vacA and cagPAI are associated and that the Western group with vacA and cagPAI genes is associated with peptic ulcer disease. PMID:16081930

  13. Species presence frequency and diversity in different patch types along an altitudinal gradient: Larix chinensis Beissn in Qinling Mountains (China).

    PubMed

    Huang, Minyi; Duan, Renyan; Wang, Shixiong; Wang, Zhigao; Fan, Weiyi

    2016-01-01

    Forest communities are mosaic systems composed of patches classified into four different developmental patch types: gap patch (G), building patch (B), mature patch (M) and degenerate patch (D). To study the mechanisms maintaining diversity in subalpine coniferous forests, species presence frequency and diversity in the four distinct patch types (G, B, M and D) of Larix chinensis conifer forests at three altitudinal gradients in the Qinling Mountains were analyzed. Our results were as follows: (1) Different species (or functional groups) had distinct presence frequencies in the four different patch types along the altitudinal gradient; (2) Some species or functional groups (species groups sharing similar traits and responses to the environment) only occurred in some specific patches. For seed dispersal, species using wind mainly occurred in G and D, while species using small animals mainly occurred in B and M; (3) Species composition of adjacent patch types was more similar than non-adjacent patch types, based on the lower β diversity index of the former; (4) The maximum numbers of species and two diversity indices (D' and H') were found in the middle altitudes. Various gap-forming processes and dispersal limitation may be the two major mechanisms determining species diversity in Larix chinensis coniferous forests at the patch scale. PMID:26998409

  14. Species presence frequency and diversity in different patch types along an altitudinal gradient: Larix chinensis Beissn in Qinling Mountains (China)

    PubMed Central

    Huang, Minyi; Wang, Shixiong; Wang, Zhigao; Fan, Weiyi

    2016-01-01

    Forest communities are mosaic systems composed of patches classified into four different developmental patch types: gap patch (G), building patch (B), mature patch (M) and degenerate patch (D). To study the mechanisms maintaining diversity in subalpine coniferous forests, species presence frequency and diversity in the four distinct patch types (G, B, M and D) of Larix chinensis conifer forests at three altitudinal gradients in the Qinling Mountains were analyzed. Our results were as follows: (1) Different species (or functional groups) had distinct presence frequencies in the four different patch types along the altitudinal gradient; (2) Some species or functional groups (species groups sharing similar traits and responses to the environment) only occurred in some specific patches. For seed dispersal, species using wind mainly occurred in G and D, while species using small animals mainly occurred in B and M; (3) Species composition of adjacent patch types was more similar than non-adjacent patch types, based on the lower β diversity index of the former; (4) The maximum numbers of species and two diversity indices (D′ and H′) were found in the middle altitudes. Various gap-forming processes and dispersal limitation may be the two major mechanisms determining species diversity in Larix chinensis coniferous forests at the patch scale. PMID:26998409

  15. Parallel responses of species and genetic diversity to El Niño Southern Oscillation-induced environmental destruction.

    PubMed

    Cleary, Daniel F R; Fauvelot, Cécile; Genner, Martin J; Menken, Steph B J; Mooers, Arne Ø

    2006-03-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to suggest a novel macro-ecological pattern termed the species-genetic diversity correlation. We tested whether this prediction holds for areas affected by recent habitat disturbance using butterfly communities in east Kalimantan, Indonesia. Here, we show that both strong spatial and temporal correlations exist between species and allelic richness across rainforest habitats affected by El Niño Southern Oscillation-induced disturbance. Coupled with evidence that changes in species richness are a direct result of local extirpation and lower recruitment, these data suggest that forces governing variation at the two levels operate over parallel and short timescales, with implications for biodiversity recovery following disturbance. Remnant communities may be doubly affected, with reductions in species richness being associated with reductions in genetic diversity within remnant species. PMID:16958896

  16. Vast assembly of vocal marine mammals from diverse species on fish spawning ground.

    PubMed

    Wang, Delin; Garcia, Heriberto; Huang, Wei; Tran, Duong D; Jain, Ankita D; Yi, Dong Hoon; Gong, Zheng; Jech, J Michael; Godø, Olav Rune; Makris, Nicholas C; Ratilal, Purnima

    2016-03-17

    Observing marine mammal (MM) populations continuously in time and space over the immense ocean areas they inhabit is challenging but essential for gathering an unambiguous record of their distribution, as well as understanding their behaviour and interaction with prey species. Here we use passive ocean acoustic waveguide remote sensing (POAWRS) in an important North Atlantic feeding ground to instantaneously detect, localize and classify MM vocalizations from diverse species over an approximately 100,000 km(2) region. More than eight species of vocal MMs are found to spatially converge on fish spawning areas containing massive densely populated herring shoals at night-time and diffuse herring distributions during daytime. We find the vocal MMs divide the enormous fish prey field into species-specific foraging areas with varying degrees of spatial overlap, maintained for at least two weeks of the herring spawning period. The recorded vocalization rates are diel (24 h)-dependent for all MM species, with some significantly more vocal at night and others more vocal during the day. The four key baleen whale species of the region: fin, humpback, blue and minke have vocalization rate trends that are highly correlated to trends in fish shoaling density and to each other over the diel cycle. These results reveal the temporospatial dynamics of combined multi-species MM foraging activities in the vicinity of an extensive fish prey field that forms a massive ecological hotspot, and would be unattainable with conventional methodologies. Understanding MM behaviour and distributions is essential for management of marine ecosystems and for accessing anthropogenic impacts on these protected marine species. PMID:26934221

  17. Molecular Diversity of Seed-borne Fusarium Species Associated with Maize in India.

    PubMed

    Aiyaz, Mohammed; Divakara, Shetty Thimmappa; Mudili, Venkataramana; Moore, Geromy George; Gupta, Vijai Kumar; Yli-Mattila, Tapani; Nayaka, Siddaiah Chandra; Niranjana, Siddapura Ramachandrappa

    2016-04-01

    A total of 106 maize seed samples were collected from different agro-climatic regions of India. Sixty-two Fusarium isolates were recovered, 90% of which were identified as Fusarium verticillioides based on morphological and molecular characters. Use of the tef-1α gene corrected/refined the morphological species identifications of 11 isolates, and confirmed those of the remaining isolates. Genetic diversity among the Fusarium isolates involved multilocus fingerprinting profiles by Inter Simple Sequence Repeats (ISSR) UPGMA and tef-1α gene phenetic analyses; for which, we observed no significant differences among the isolates based on geographic origin or fumonisin production; most of the subdivision related to species. Genotyping was performed on the F. verticillioides isolates, using 12 primer sets from the fumonisin pathway, to elucidate the molec-ular basis of fumonisin production or non-production. One fumonisin-negative isolate, UOMMF-16, was unable to amplify nine of the 12 fumonisin cluster genes tested. We also used the CD-ELISA method to confirm fumonisin production for our 62 Fusarium isolates. Only 15 isolates were found to be fumonisin-negative. Interestingly, genotypic characterization re-vealed six isolates with various gene deletion patterns that also tested positive for the production of fumonisins via CD-ELISA. Our findings confirm the importance of molecular studies for species delimitation, and for observing genetic and phenotypic diversity, among the Fusaria. PMID:27226769

  18. Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis.

    PubMed Central

    Laguerre, G; van Berkum, P; Amarger, N; Prévost, D

    1997-01-01

    The genetic diversity of 44 rhizobial isolates from Astragalus, Oxytropis, and Onobrychis spp. originating from different geographic locations was evaluated by mapped restriction site polymorphism (MRSP) analysis of 16S rRNA genes and by PCR DNA fingerprinting with repetitive sequences (REP-PCR). A comparison of tree topologies of reference strains constructed with data obtained by MRSP and by 16S rRNA gene sequence analyses showed that the topologies were in good agreement, indicating that the MSRP approach results in reasonable estimates of rhizobial phylogeny. The isolates were distributed into 14 distinct 16S rRNA gene types clustering into three major groups which corresponded with three of the genera within the legume symbionts. Most of the isolates were within the genus Mesorhizobium. Five were identified with different genomic species nodulating Lotus spp. and Cicer arietinum. Three Astragalus isolates were classified as Bradyrhizobium, one being similar to Bradyrhizobium elkanii and another being similar to Bradyrhizobium japonicum. Six of the isolates were related to species within the genus Rhizobium. Two were similar to Rhizobium leguminosarum, and the remainder were identified as Rhizobium gallicum. DNA fingerprinting by REP-PCR revealed a high level of diversity within single 16S ribosomal DNA types. The 44 isolates were distributed into 34 REP groups. Rhizobial classification at the genus and probably also the species levels was independent of geographic origin and host plant affinity. PMID:9406393

  19. Prevalence and characterization of influenza viruses in diverse species in Los Llanos, Colombia.

    PubMed

    Karlsson, Erik A; Ciuoderis, Karl; Freiden, Pamela J; Seufzer, Bradley; Jones, Jeremy C; Johnson, Jordan; Parra, Rocio; Gongora, Agustin; Cardenas, Dario; Barajas, Diana; Osorio, Jorge E; Schultz-Cherry, Stacey

    2013-04-01

    While much is known about the prevalence of influenza viruses in North America and Eurasia, their prevalence in birds and mammals in South America is largely unknown. To fill this knowledge gap and provide a baseline for future ecology and epidemiology studies, we conducted 2 years of influenza surveillance in the eastern plains (Los Llanos) region of Colombia. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) identified influenza viruses in wild birds, domestic poultry, swine and horses. Prevalence ranged from 2.6% to 13.4% across species. Swine showed the highest prevalence and were infected primarily with 2009 pandemic H1N1 (pH1N1) viruses genetically related to those in humans. In addition, we isolated H5N2 viruses from two resident species of whistling ducks (genus Dendrocygna) that differed completely from previous South American isolates, instead genetically resembling North American wild bird viruses. Both strains caused low pathogenicity in chickens and mammals. The prevalence and subtype diversity of influenza viruses isolated from diverse species within a small area of Colombia highlights the need for enhanced surveillance throughout South America, including monitoring of the potential transmissibility of low-pathogenic H5N2 viruses from wild birds to domestic poultry and the emergence of reassortant viruses in domestic swine. PMID:26038461

  20. Prevalence and characterization of influenza viruses in diverse species in Los Llanos, Colombia

    PubMed Central

    Karlsson, Erik A; Ciuoderis, Karl; Freiden, Pamela J; Seufzer, Bradley; Jones, Jeremy C; Johnson, Jordan; Parra, Rocio; Gongora, Agustin; Cardenas, Dario; Barajas, Diana; Osorio, Jorge E; Schultz-Cherry, Stacey

    2013-01-01

    While much is known about the prevalence of influenza viruses in North America and Eurasia, their prevalence in birds and mammals in South America is largely unknown. To fill this knowledge gap and provide a baseline for future ecology and epidemiology studies, we conducted 2 years of influenza surveillance in the eastern plains (Los Llanos) region of Colombia. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) identified influenza viruses in wild birds, domestic poultry, swine and horses. Prevalence ranged from 2.6% to 13.4% across species. Swine showed the highest prevalence and were infected primarily with 2009 pandemic H1N1 (pH1N1) viruses genetically related to those in humans. In addition, we isolated H5N2 viruses from two resident species of whistling ducks (genus Dendrocygna) that differed completely from previous South American isolates, instead genetically resembling North American wild bird viruses. Both strains caused low pathogenicity in chickens and mammals. The prevalence and subtype diversity of influenza viruses isolated from diverse species within a small area of Colombia highlights the need for enhanced surveillance throughout South America, including monitoring of the potential transmissibility of low-pathogenic H5N2 viruses from wild birds to domestic poultry and the emergence of reassortant viruses in domestic swine. PMID:26038461

  1. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

    PubMed

    Laureys, David; De Vuyst, Luc

    2014-04-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  2. Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

    PubMed Central

    Laureys, David

    2014-01-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  3. Recent "omics" advances in Helicobacter pylori.

    PubMed

    Berthenet, Elvire; Sheppard, Sam; Vale, Filipa F

    2016-09-01

    The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health. PMID:27531533

  4. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

    PubMed Central

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  5. Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

    USGS Publications Warehouse

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  6. Community structure, diversity and total biomass of tree species at Kapur dominated forests in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Norafida, N. A. Nik; Nizam, M. S.; Juliana, W. A. Wan

    2013-11-01

    A study was conducted to determine the species composition, diversity and biomass of Kapur (Dryobalanops aromatica Gaertn.f.) dominated forests in Peninsular Malaysia. Three forests were selected in different geographical zones, namely Bukit Bauk Virgin Jungle Reserve (BBVJR), Terengganu, Lesong Forest Reserve (LFR), Pahang and Gunung Belumut Recreational Forest (GBRF), Johor. Thirty plots of 0.1 ha (50 m × 20 m) were established with a total sampling area of 1.0 ha at each forest site. All trees with ≥5 cm diameter at breast height (dbh) were tagged, measured and voucher specimens were collected. Floristic composition in the study plot at BBVJR recorded 55 families, 147 genera and 336 species. In LFR, there were 52 families, 138 genera and 288 species, whereas in GBRF there were 52 families, 132 genera and 271 species. D. aromatica was the most important species in all study plots with the Importance Value Index (IVi) of 17.81%, 23.01% and 16.25% in BBVJR, LFR and GBRF, respectively. Similar trend at family level showed the Dipterocarpaceae was the most important family in each of the areas with the family Importance Value Index (FIVi) of 27.95% (BBVJR), 26.09% (LFR) and 27.16% (GBRF). Shannon diversity index (H'f) and Shannon evenness index (J'f) of trees at BBVJR was 5.02 and 0.86; LFR was 4.63 and 0.82; and GBRF was 4.82 and 0.86, respectively. Sorensen's community similarity coefficient (CCs) showed that tree communities between BBVJR, LFR and GBRF had low similarities with values of 0.3 to 0.4. The highest total biomass estimated was in LFR with a value of 739.44 t/ha, followed by BBVJR at 701.34 t/ha and GBRF at 606.29 t/ha.

  7. Urban habitat complexity affects species richness but not environmental filtering of morphologically-diverse ants

    PubMed Central

    Nash, Michael A.; Christie, Fiona J.; Hahs, Amy K.; Livesley, Stephen J.

    2015-01-01

    Habitat complexity is a major determinant of structure and diversity of ant assemblages. Following the size-grain hypothesis, smaller ant species are likely to be advantaged in more complex habitats compared to larger species. Habitat complexity can act as an environmental filter based on species size and morphological traits, therefore affecting the overall structure and diversity of ant assemblages. In natural and semi-natural ecosystems, habitat complexity is principally regulated by ecological successions or disturbance such as fire and grazing. Urban ecosystems provide an opportunity to test relationships between habitat, ant assemblage structure and ant traits using novel combinations of habitat complexity generated and sustained by human management. We sampled ant assemblages in low-complexity and high-complexity parks, and high-complexity woodland remnants, hypothesizing that (i) ant abundance and species richness would be higher in high-complexity urban habitats, (ii) ant assemblages would differ between low- and high-complexity habitats and (iii) ants living in high-complexity habitats would be smaller than those living in low-complexity habitats. Contrary to our hypothesis, ant species richness was higher in low-complexity habitats compared to high-complexity habitats. Overall, ant assemblages were significantly different among the habitat complexity types investigated, although ant size and morphology remained the same. Habitat complexity appears to affect the structure of ant assemblages in urban ecosystems as previously observed in natural and semi-natural ecosystems. However, the habitat complexity filter does not seem to be linked to ant morphological traits related to body size. PMID:26528416

  8. Urban habitat complexity affects species richness but not environmental filtering of morphologically-diverse ants.

    PubMed

    Ossola, Alessandro; Nash, Michael A; Christie, Fiona J; Hahs, Amy K; Livesley, Stephen J

    2015-01-01

    Habitat complexity is a major determinant of structure and diversity of ant assemblages. Following the size-grain hypothesis, smaller ant species are likely to be advantaged in more complex habitats compared to larger species. Habitat complexity can act as an environmental filter based on species size and morphological traits, therefore affecting the overall structure and diversity of ant assemblages. In natural and semi-natural ecosystems, habitat complexity is principally regulated by ecological successions or disturbance such as fire and grazing. Urban ecosystems provide an opportunity to test relationships between habitat, ant assemblage structure and ant traits using novel combinations of habitat complexity generated and sustained by human management. We sampled ant assemblages in low-complexity and high-complexity parks, and high-complexity woodland remnants, hypothesizing that (i) ant abundance and species richness would be higher in high-complexity urban habitats, (ii) ant assemblages would differ between low- and high-complexity habitats and (iii) ants living in high-complexity habitats would be smaller than those living in low-complexity habitats. Contrary to our hypothesis, ant species richness was higher in low-complexity habitats compared to high-complexity habitats. Overall, ant assemblages were significantly different among the habitat complexity types investigated, although ant size and morphology remained the same. Habitat complexity appears to affect the structure of ant assemblages in urban ecosystems as previously observed in natural and semi-natural ecosystems. However, the habitat complexity filter does not seem to be linked to ant morphological traits related to body size. PMID:26528416

  9. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    PubMed

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  10. High-throughput genotyping for species identification and diversity assessment in germp