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Phylogenetic Diversity (phylogenetic + diversity)
Selected AbstractsPhylogenetic diversity and metagenomics of candidate division OP3ENVIRONMENTAL MICROBIOLOGY, Issue 5 2010Jana Glöckner Summary Except for environmental 16S rRNA gene sequences, no information is available for members of the candidate division OP3. These bacteria appear to thrive in anoxic environments, such as marine sediments, hypersaline deep sea, freshwater lakes, aquifers, flooded paddy soils and methanogenic bioreactors. The 16S rRNA phylogeny suggests that OP3 belongs to the Planctomycetes/Verrucomicrobia/Chlamydiae (PVC) superphylum. Metagenomic fosmid libraries were constructed from flooded paddy soil and screened for 16S rRNA gene-containing fragments affiliated with the PVC superphylum. The screening of 63 000 clones resulted in 23 assay-positive fosmids, of which three clones were affiliated with OP3. The 16S rRNA gene sequence divergence between the fragments OP3/1, OP3/2 and OP3/3 ranges from 18% to 25%, indicating that they belong to different OP3 subdivisions. The 23S rRNA phylogeny confirmed the membership of OP3 in the PVC superphylum. Sequencing the OP3 fragments resulted in a total of 105 kb of genomic information and 90 ORFs, of which 47 could be assigned a putative function and 11 were conserved hypothetical. Using BLASTP searches, a high proportion of ORFs had best matches to homologues from Deltaproteobacteria, rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of nine ORFs was predicted to encode the bacterial NADH dehydrogenase I. Given the high proportion of homologues present in deltaproteobacteria and anoxic conditions in the natural environment of OP3 bacteria, the detection of NADH dehydrogenase I may suggest an anaerobic respiration mode. Oligonucleotide frequencies calculated for OP3/1, OP3/2 and OP/3 show high intraphylum correlations. This novel sequence information could therefore be used to identify OP3-related fragments in large metagenomic data sets using marker gene-independent procedures in the future. In addition to the OP3 fragments, a single metagenomic fragment affiliated with the candidate division BRC1 was obtained and analysed. [source] Phylogenetic diversity of non-nodulating Rhizobium associated with pine ectomycorrhizaeFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Megumi Tanaka Abstract Most Rhizobium species described are symbionts that form nodules on legume roots; however, non-nodulating strains of Rhizobium are also widespread in nature. Unfortunately, knowledge of non-nodulating Rhizobium is quite limited compared with nodulating Rhizobium. Here, we studied the phylogenetic diversity of Rhizobium species that inhabit Japanese red pine roots (Pinus densiflora). Because fine roots of pine trees are usually colonized by ectomycorrhizal fungi in nature, we mainly used ectomycorrhizal root tips for bacterial isolation. Out of 1195 bacteria isolated from 75 independent root samples from the field and greenhouse experiments, 102 isolates were confirmed to be Rhizobium following partial 16S rRNA gene analysis. Rhizobium species were occasionally dominant in culturable bacterial communities, whereas no Rhizobium species were isolated from the soil itself. Molecular phylogenetic analyses using 16S rRNA, atpD, and recA gene sequences revealed that isolated Rhizobium strains were phylogenetically diverse and that several were distantly related to known Rhizobium species. Considering that a single species of pine is associated with unique and phylogenetically diverse Rhizobium populations, we should pay more attention to non-nodulating strains to better understand the diversity, ecology, and evolution of the genus Rhizobium and plant,Rhizobium associations. [source] Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East SeaFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Dong Han Choi Abstract Phylogenetic relationships among 33 Synechococcus strains isolated from the East China Sea (ECS) and the East Sea (ES) were studied based on 16S rRNA gene sequences and 16S,23S rRNA gene internal transcribed spacer (ITS) sequences. Pigment patterns of the culture strains were also examined. Based on 16S rRNA gene and ITS sequence phylogenies, the Synechococcus isolates were clustered into 10 clades, among which eight were previously identified and two were novel. Half of the culture strains belonged to clade V or VI. All strains that clustered into novel clades exhibited both phycoerythrobilin and phycourobilin. Interestingly, the pigment compositions of isolates belonging to clades V and VI differed from those reported for other oceanic regions. None of the isolates in clade V showed phycourobilin, whereas strains in clade VI exhibited both phycourobilin and phycoerythrobilin, which is in contrast to previous studies. The presence of novel lineages and the different pigment patterns in the ECS and the ES suggests the possibility that some Synechococcus lineages are distributed only in geographically restricted areas and have evolved in these regions. Therefore, further elucidation of the physiological, ecological, and genetic characteristics of the diverse Synechococcus strains is required to understand their spatial and geographical distribution. [source] Phylogenetic diversity of T4-like bacteriophages in Lake Baikal, East SiberiaFEMS MICROBIOLOGY LETTERS, Issue 2 2010Tatyana Vladimirovna Butina Abstract Among the tailed phages, the myoviruses, those with contractile tails, are widespread and diverse. An important component of the Myoviridae family is the genus ,T4-like viruses'. The present study was aimed at elucidating the molecular diversity of T4-type bacteriophages in Lake Baikal by partial sequencing of g23 genes of T4-type bacteriophages. Our study revealed that the g23 gene sequences investigated were highly diverse and different from those of T4-like bacteriophages and from g23 clones obtained from different environments. Phylogenetic analysis showed that all g23 fragments from Lake Baikal, except for the one sequence, were more closely related to marine T4 cyanophages and to previously described subgroups of uncultured T4 phages from marine and rice field environments. [source] Biodiverse, a tool for the spatial analysis of biological and related diversityECOGRAPHY, Issue 4 2010Shawn W. Laffan Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix (e.g. genetic dissimilarity) relationships. The explosion in georeferenced biological specimen and survey data means there is an increasing need for such tools. Biodiverse supports four processes: 1) linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces; 2) spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity; 3) spatially constrained agglomerative cluster analyses; and 4) randomisations for hypothesis testing. Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface and scripts. Biodiverse can be downloaded from Facilitation can increase the phylogenetic diversity of plant communitiesECOLOGY LETTERS, Issue 11 2007Alfonso Valiente-Banuet Abstract With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity. [source] Long-term reproductive behaviour of woody plants across seven Bornean forest types in the Gunung Palung National Park (Indonesia): suprannual synchrony, temporal productivity and fruiting diversityECOLOGY LETTERS, Issue 10 2007Charles H. Cannon Abstract For 68 months, we observed the reproductive behaviour of 7288 woody plants (172 figs, 1457 climbers and 5659 trees) spanning major soil and elevational gradients. Two 2,3 month community-wide supra-annual fruiting events were synchronized across five forest types, coinciding with ENSO events. At least 27 genera in 24 families restricted their reproduction to these events, which involved a substantial proportion of tree diversity (> 80% of phylogenetic diversity). During these events, mean reproductive levels (8.5%) represented an almost four-fold increase compared with other months. These patterns indicate a strong behavioural advantage to this unusual reproductive behaviour. Montane forest experienced a single, separate fruiting peak while the peat swamp forest did not participate. Excluding these events, no temporal reproductive pattern was detectible, at either the landscape or forest type. These phenological patterns have major implications for the conservation of frugivore communities, with montane and swamp forests acting as ,keystone' forests. [source] Distribution, phylogenetic diversity and physiological characteristics of epsilon- Proteobacteria in a deep-sea hydrothermal fieldENVIRONMENTAL MICROBIOLOGY, Issue 10 2005Satoshi Nakagawa Summary Epsilon- Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon- Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon -Proteobacteria. Energy metabolism of epsilon- Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon- Proteobacteria. Nevertheless, culturability of epsilon- Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon- Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes. [source] Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugationENVIRONMENTAL MICROBIOLOGY, Issue 7 2001Sophie Courtois All molecular analyses of soil bacterial diversity are based on the extraction of a representative fraction of cellular DNA. Methods of DNA extraction for this purpose are divided into two categories: those in which cells are lysed within the soil (direct extraction) and those in which cells are first removed from soil (cell extraction) and then lysed. The purpose of this study was to compare a method of direct extraction with a method in which cells were first separated from the soil matrix by Nycodenz gradient centrifugation in order to evaluate the effect of these different approaches on the analysis of the spectrum of diversity in a microbial community. We used a method based on polymerase chain reaction (PCR) amplification of a 16S rRNA gene fragment, followed by hybridization of the amplified fragments to a set of specific probes to assess the phylogenetic diversity of our samples. Control parameters, such as the relationship between amount of DNA template and amount of PCR product and the influence of competing DNA on PCR amplification, were first examined. Comparison between extraction methods showed that less DNA was extracted when cells were first separated from the soil matrix (0.4 µg g,1 dry weight soil versus 38,93 µg g,1 obtained by in situ lysis methods). However, with the exception of the ,-subclass of Proteobacteria, there was no significant difference in the spectrum of diversity resulting from the two extraction strategies. [source] Phylogenetic diversity of non-nodulating Rhizobium associated with pine ectomycorrhizaeFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Megumi Tanaka Abstract Most Rhizobium species described are symbionts that form nodules on legume roots; however, non-nodulating strains of Rhizobium are also widespread in nature. Unfortunately, knowledge of non-nodulating Rhizobium is quite limited compared with nodulating Rhizobium. Here, we studied the phylogenetic diversity of Rhizobium species that inhabit Japanese red pine roots (Pinus densiflora). Because fine roots of pine trees are usually colonized by ectomycorrhizal fungi in nature, we mainly used ectomycorrhizal root tips for bacterial isolation. Out of 1195 bacteria isolated from 75 independent root samples from the field and greenhouse experiments, 102 isolates were confirmed to be Rhizobium following partial 16S rRNA gene analysis. Rhizobium species were occasionally dominant in culturable bacterial communities, whereas no Rhizobium species were isolated from the soil itself. Molecular phylogenetic analyses using 16S rRNA, atpD, and recA gene sequences revealed that isolated Rhizobium strains were phylogenetically diverse and that several were distantly related to known Rhizobium species. Considering that a single species of pine is associated with unique and phylogenetically diverse Rhizobium populations, we should pay more attention to non-nodulating strains to better understand the diversity, ecology, and evolution of the genus Rhizobium and plant,Rhizobium associations. [source] Diversity of endophytic bacterial communities in poplar grown under field conditionsFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Kristina Ulrich Abstract Bacterial endophytes may be important for plant health and other ecologically relevant functions of poplar trees. The composition of endophytic bacteria colonizing the aerial parts of poplar was studied using a multiphasic approach. The terminal restriction fragment length polymorphism analysis of 16S rRNA genes demonstrated the impact of different hybrid poplar clones on the endophytic community structure. Detailed analysis of endophytic bacteria using cultivation methods in combination with cloning of 16S rRNA genes amplified from plant tissue revealed a high phylogenetic diversity of endophytic bacteria with a total of 53 taxa at the genus level that included Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The community structure displayed clear differences in terms of the presence and relative proportions of bacterial taxa between the four poplar clones studied. The results showed that the genetic background of the hybrid poplar clones corresponded well with the endophytic community structure. Out of the 513 isolates and 209 clones identified, Actinobacteria, in particular the family Microbacteriaceae, made up the largest fraction of the isolates, whereas the clone library was dominated by Alpha - and Betaproteobacteria. The most abundant genera among the isolates were Pseudomonas and Curtobacterium, while Sphingomonas prevailed among the clones. [source] Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeoteFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Hélčne Moussard Abstract The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents. [source] Soil parent material is a key determinant of the bacterial community structure in arable soilsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Andreas Ulrich Abstract The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes. [source] Influence of long-term land application of Class B biosolids on soil bacterial diversityJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2010H. Zerzghi Abstract Aim:, To evaluate the effect of long-term annual land applications of Class B biosolids on soil bacterial diversity at University of Arizona Marana Agricultural Field Center, Tucson, Arizona. Methods and Results:, Following the final of 20 consecutive years of application of Class B biosolids in March 2005, followed by cotton growth from April to November 2005 surface soil samples (0,30 cm) were collected from control (unamended) and biosolid-amended plots. Total bacterial community DNA was extracted, amplified using 16S rRNA primers, cloned, and sequenced. All 16S rRNA sequences were identified by 16S rRNA sequence analysis and comparison to known sequences in GenBank (NCBI BlastN and Ribosomal Database Project II, RDP). Results showed that the number of known genera (identifiable > 96%) increased in the high rate biosolid plots compared to control plots. Biosolids-amended soils had a broad phylogenetic diversity comprising more than four major phyla: Proteobacteria (32%), Acidobacteria (21%), Actinobacteria (16%), Firmicutes (7%), and Bacteroidetes (6%) which were typical to bacterial diversity found in the unamended arid southwestern soils. Conclusion:, Bacterial diversity was either enhanced or was not negatively impacted following 20 years of land application of Class B biosolids. Significance and Impact of the Study:, This study illustrates that long-term land application of biosolids to arid southwestern desert soils has no deleterious effect on soil microbial diversity. [source] Additive partitioning of diversity including species differences: a comment on Hardy & Senterre (2007)JOURNAL OF ECOLOGY, Issue 5 2008Sébastien Villéger Summary 1The distribution of biodiversity at multiple spatial scales has been traditionally investigated through the additive partitioning of ,-biodiversity (regional) into ,-(within-site) and ,-(among-site) components. 2However, this decomposition is almost exclusively applied using species turnover among communities while two communities with no species in common can be very similar because they share some ,biological' similarity. 3To overcome this limitation, Hardy & Senterre (2007) (J. Ecol., 95, 493,506) presented a new statistical framework partitioning the phylogenetic diversity into ,- and ,-components using the Rao's quadratic entropy. 4We show that their decomposition is correct only when sites have the same total abundance, otherwise it may lead to negative ,-diversity values. As an alternative, we provided a general decomposition of the quadratic entropy into ,-, ,- and ,-diversities. 5Synthesis. We suggest that the ,biological' turnover quantified by the ,-component of the regional quadratic entropy may help, at least, to disentangle dispersal vs. niche influences on biodiversity patterns. [source] Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversityJOURNAL OF ECOLOGY, Issue 3 2007OLIVIER J. HARDY Summary 1Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities. 2Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within-site) and beta (among-site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. IST, PST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. FST, NST). 3Two coefficients which express community differentiation among sites from species identity (IST) or species phylogeny (PST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (,ST) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site). 4We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (PST > IST or ,ST > 0) or phylogenetic overdispersion (PST < IST or ,ST < 0). In addition, we propose a novel approach to detect phylogenetic clustering or overdispersion in different clades or at different evolutionary time depths using partial randomizations. 5IST, PST or ,ST can also be used as distances between community samples and regressed on ecological or geographical distances, allowing us to investigate the factors responsible for the phylogenetic signal and the critical scales at which it appears. 6We illustrate the approach on forest tree communities in Equatorial Guinea, where a phylogenetic clustering signal was probably due to phylogenetically conserved adaptations to the elevation gradient and was mostly contributed to by ancient clade subdivisions. 7The approach presented should find applications for comparing quantitatively phylogenetic patterns of different communities, of similar communities in different regions or continents, or of populations (within species) vs. communities (among species). [source] 16S rRNA GENE HETEROGENEITY IN THE FILAMENTOUS MARINE CYANOBACTERIAL GENUS LYNGBYA,JOURNAL OF PHYCOLOGY, Issue 3 2010Niclas Engene The SSU (16S) rRNA gene was used to investigate the phylogeny of the cyanobacterial genus Lyngbya as well as examined for its capacity to discriminate between different marine species of Lyngbya. We show that Lyngbya forms a polyphyletic genus composed of a marine lineage and a halophilic/brackish/freshwater lineage. In addition, we found morphological and genetic evidence that Lyngbya spp. often grow in association with other microorganisms, in particular smaller filamentous cyanobacteria such as Oscillatoria, and propose that these associated microorganisms have led to extensive phylogenetic confusion in identification of Lyngbya spp. At the species level, the phylogenetic diversity obtained from the comparison of 16S rRNA genes exceeded morphological diversity in Lyngbya. However, the expectation that this improved phylogeny would be useful to species and subspecies identification was eliminated by the fact that phylogenetic species did not correlate in any respect with the species obtained from current taxonomic systems. In addition, phylogenetic identification was adversely affected by the presence of multiple gene copies within individual Lyngbya colonies. Analysis of clonal Lyngbya cultures and multiple displacement amplified (MDA) single-cell genomes revealed that Lyngbya genomes contain two 16S rRNA gene copies, and that these typically are of variable sequence. Furthermore, intragenomic and interspecies 16S rRNA gene heterogeneity was approximately of the same magnitude. Hence, the intragenomic heterogeneity of the 16S rRNA gene overestimates the microdiversity of different strains and does not accurately reflect speciation within cyanobacteria, including the genus Lyngbya. [source] INCREASED SAMPLING FOR INFERRING PHYLOGEOGRAPHIC PATTERNS IN BOSTRYCHIA RADICANS/B.JOURNAL OF PHYCOLOGY, Issue 6 2006MORITZIANA (RHODOMELACEAE, RHODOPHYTA) IN THE EASTERN USA Zuccarello and West (2003) reported on the phylogenetic diversity of algae identified as Bostrychia radicans (Montagne) Montagne and B. moritziana (Sonder ex Kützing) J. Agardh from around the world. They showed that the species complex consisted of seven distinct lineages, of which two lineages were common on the East Coast of the USA and eastern Gulf of Mexico. The distribution of haplotypes within these lineages on the East Coast of the USA showed a general north,south distribution. One haplotype of lineage 5 (B) was mostly collected in northern areas, while the other common haplotype (C) was more southerly in distribution. Samples in lineage 6 (haplotype D) were not found north of Sapelo Island, Georgia. Increased sampling from the eastern USA over 5 years later has revealed an altered pattern. Haplotype D is distributed in North Carolina and is common in some populations. Haplotype C is rare or absent in many sampled populations. Haplotype B is only observed in the northern sampled sites on both sides of the Florida peninsula. This disjunct distribution agrees with geological scenarios for a strait between the western Gulf of Mexico and southern Georgia in the Miocene/Pliocene, which closed in the late Pliocene. This paper highlights the importance of increased sampling to determine phylogeographic patterns and hypotheses of dispersal scenarios in algae. [source] Fate of epiphytes on phorophytes with different architectural characteristics along the perturbation gradient of Sabal mexicana forests in Veracruz, MexicoJOURNAL OF VEGETATION SCIENCE, Issue 1 2010A. Aguirre Abstract Question: Vascular epiphytes and hemiepiphytes (E/HE) in neotropical forests account for a large fraction of plant richness, but little is known of how the interplay between phorophyte architectural characteristics and habitat perturbation affect communities of E/HE. Location: Sabal mexicana forests in a coastal area of Veracruz, Mexico. Methods: We compared communities of E/HE on phorophytes with different architectural characteristics , the palm S. mexicana and non-palm phorophytes , in three environments: conserved sites, perturbed sites and small regenerated forest fragments. We combined traditional (abundance, species richness, similarity and complementarity indices) and more recent (phylogenetic diversity) metrics to describe the communities of E/HE. Results: Overall, we recorded 924 E/HE individuals (nine families, 16 genera and 21 species). The abundance and species richness of E/HE was higher on palms than on non-palm phorophytes. Abundance-based complementarities between phorophytes and sites were high. We detected clear changes in community structure of E/HE with habitat perturbation, but there were no effects on the phylogenetic diversity of the E/HE community. Palm phorophytes hosted a more phylogenetically diverse community of E/HE than did non-palm phorophytes. Conclusions: Palm phorophytes are key elements supporting the conservation of resilient communities of E/HE in S. mexicana forest. Habitat fragmentation has a strong effect on the structure of the E/HE community in S. mexicana forests. Ferns are the group of epiphytes most severely affected by habitat perturbation, but we detected no significant effect on the phylogenetic diversity of the community. [source] Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscapeMOLECULAR ECOLOGY, Issue 7 2010IVAN P. EDWARDS Abstract The Agaricomycotina are a phylogenetically diverse group of fungi that includes both saprotrophic and mycorrhizal species, and that form species , rich communities in forest ecosystems. Most species are infrequently observed, and this hampers assessment of the role that environmental heterogeneity plays in determining local community composition and in driving ,-diversity. We used a combination of phenetic (TRFLP) and phylogenetic approaches [Unifrac and Net Relatedness Index (NRI)] to examine the compositional and phylogenetic similarity of Agaricomycotina communities in forest floor and surface soil of three widely distributed temperate upland forest ecosystems (one, xeric oak , dominated and two, mesic sugar maple dominated). Generally, forest floor and soil communities had similar phylogenetic diversity, but there was little overlap of species or evolutionary lineages between these two horizons. Forest floor communities were dominated by saprotrophic species, and were compositionally and phylogenetically similar in all three ecosystems. Mycorrhizal species represented 30% to 90% of soil community diversity, and these communities differed compositionally and phylogenetically between ecosystems. Estimates of NRI revealed significant phylogenetic clustering in both the forest floor and soil communities of only the xeric oak-dominated forest ecosystem, and may indicate that this ecosystem acts as a habitat filter. Our results suggest that environmental heterogeneity strongly influences the phylogenetic ,-diversity of soil inhabiting Agaricomycotina communities, but has only a small influence on forest floor ,-diversity. Moreover, our results suggest that the strength of community assembly processes, such as habitat filtering, may differ between temperate forest ecosystems. [source] Parallel habitat-driven differences in the phylogeographical structure of two independent lineages of Mediterranean saline water beetlesMOLECULAR ECOLOGY, Issue 18 2009P. ABELLÁN Abstract It has been hypothesized that species living in small lentic water bodies, because of the short-term geological persistence of their habitat, should show higher dispersal ability, with increased gene flow among populations and a less pronounced phylogeographical structure. Conversely, lotic species, living in more geologically stable habitats, should show reduced dispersal and an increased phylogeographical structure at the same geographical scales. In this work we tested the influence of habitat type in two groups of aquatic Coleoptera (Nebrioporus ceresyi and Ochthebius notabilis groups, families Dytiscidae and Hydraenidae respectively), each of them with closely related species typical of lotic and lentic saline Western Mediterranean water bodies. We used mitochondrial cox1 sequence data of 453 specimens of 77 populations through the range of nine species to compare a lotic vs. a lentic lineage in each of the two groups. Despite the differences in biology (predators vs. detritivorous) and evolutionary history, in both lotic lineages there was a higher proportion of nucleotide diversity among than within groups of populations, and a faster rate of accumulation of haplotype diversity (as measured by rarefaction curves) than in the lentic lineages. Similarly, lotic lineages had a higher absolute phylogenetic diversity, more remarkable considering their smaller absolute geographical ranges. By comparing closely related species, we were able to show the effect of contrasting habitat preferences in two different groups, in agreement with predictions derived from habitat stability. [source] Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environmentsOIKOS, Issue 3 2004Paul S. Giller Recent experiments, mainly in terrestrial environments, have provided evidence of the functional importance of biodiversity to ecosystem processes and properties. Compared to terrestrial systems, aquatic ecosystems are characterised by greater propagule and material exchange, often steeper physical and chemical gradients, more rapid biological processes and, in marine systems, higher metazoan phylogenetic diversity. These characteristics limit the potential to transfer conclusions derived from terrestrial experiments to aquatic ecosystems whilst at the same time provide opportunities for testing the general validity of hypotheses about effects of biodiversity on ecosystem functioning. Here, we focus on a number of unique features of aquatic experimental systems, propose an expansion to the scope of diversity facets to be considered when assessing the functional consequences of changes in biodiversity and outline a hierarchical classification scheme of ecosystem functions and their corresponding response variables. We then briefly highlight some recent controversial and newly emerging issues relating to biodiversity-ecosystem functioning relationships. Based on lessons learnt from previous experimental and theoretical work, we finally present four novel experimental designs to address largely unresolved questions about biodiversity-ecosystem functioning relationships. These include (1) investigating the effects of non-random species loss through the manipulation of the order and magnitude of such loss using dilution experiments; (2) combining factorial manipulation of diversity in interconnected habitat patches to test the additivity of ecosystem functioning between habitats; (3) disentangling the impact of local processes from the effect of ecosystem openness via factorial manipulation of the rate of recruitment and biodiversity within patches and within an available propagule pool; and (4) addressing how non-random species extinction following sequential exposure to different stressors may affect ecosystem functioning. Implementing these kinds of experimental designs in a variety of systems will, we believe, shift the focus of investigations from a species richness-centred approach to a broader consideration of the multifarious aspects of biodiversity that may well be critical to understanding effects of biodiversity changes on overall ecosystem functioning and to identifying some of the potential underlying mechanisms involved. [source] Distribution and correlates of carnivore phylogenetic diversity across the AmericasANIMAL CONSERVATION, Issue 3 2005Alvaro Soutullo Digital maps and a dated supertree of global carnivore species were used to assess the distribution of American carnivores' phylogenetic diversity (PD, measured in millions of years) both from a geopolitical perspective (,evolutionary heritage' or EH) and on the basis of species' range size and conservation status. A new measure, range-weighted EH, is introduced. This measure partitions the total PD of the tree between countries based on the proportion of species' ranges within each country. Sociopolitical correlates of these measures were explored. Only 3% of the total PD in the Americas is endemic to any one country. As expected, the measures of PD are positively correlated with each other and with species richness. The USA contains the most species, the most EH and the second most range-weighted EH after Brazil. Indeed, larger and richer countries, and those with the lowest state-corruption-rate hold most EH. No significant differences were observed in the amount of PD remaining if species are removed at random, or following more plausible sequences based on IUCN conservation status and range size. Eighty percent of the American carnivores' PD would remain safe if only the set of not threatened species were to remain. Roughly the same is true if only the 50% most widespread species were to persist. Samples of wide-ranging species represent more of the entire tree than do samples of narrow-ranging species, highlighting the importance of the former for conservation strategies. We suggest that similar approaches be applied to more groups across the globe to assess which countries and areas steward the most PD, as well as which species and taxa do, in order to plan conservation actions consequently. [source] Mantophasmatodea and phylogeny of the lower neopterous insectsCLADISTICS, Issue 3 2005Matthew D. Terry Polyneoptera is a name sometimes applied to an assemblage of 11 insect orders comprising the lower neopterous or "orthopteroid" insects. These orders include familiar insects such as Orthoptera (grasshoppers), Blattodea (roaches), Isoptera (termites) (Mantodea) praying mantises, Dermaptera (earwigs), Phasmatodea (stick insects), Plecoptera (stoneflies), as well as the more obscure, Embiidina (web-spinners), Zoraptera (angel insects) and Grylloblattodea (ice-crawlers). Many of these insect orders exhibit a high degree of morphological specialization, a condition that has led to multiple phylogenetic hypotheses and little consensus among investigators. We present a phylogenetic analysis of the polyneopteran orders representing a broad range of their phylogenetic diversity and including the recently described Mantophasmatodea. These analyses are based on complete 18S rDNA, 28S rDNA, Histone 3 DNA sequences, and a previously published morphology matrix coded at the ordinal level. Extensive analyses utilizing different alignment methodologies and parameter values across a majority of possible ranges were employed to test for sensitivity of the results to ribosomal alignment and to explore patterns across the theoretical alignment landscape. Multiple methodologies support the paraphyly of Polyneoptera, the monophyly of Dictyoptera, Orthopteroidea (sensu Kukalova-Peck; i.e. Orthoptera + Phasmatodea + Embiidina), and a group composed of Plecoptera + Dermaptera + Zoraptera. Sister taxon relationships between Embiidina + Phasmatodea in a group called "Eukinolabia", and Dermaptera + Zoraptera ("Haplocercata") are also supported by multiple analyses. This analysis also supports a sister taxon relationship between the newly described Mantophasmatodea, which are endemic to arid portions of southern Africa, and Grylloblattodea, a small order of cryophilic insects confined to the north-western Americas and north-eastern Asia, in a group termed "Xenonomia". This placement, coupled with the morphological disparity of the two groups, validates the ordinal status of Mantophasmatodea. © The Willi Hennig Society 2005. [source]
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