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Total Diversity (total + diversity)
Selected AbstractsEstimating Diversity in Unsampled Habitats of a Biogeographical ProvinceCONSERVATION BIOLOGY, Issue 3 2003Michael L. Rosenzweig A number of methods have been developed to overcome sample-size limits within a single habitat. We evaluated six of these methods to see whether they could also compensate for incomplete habitat samples. We applied them to the butterfly species of the 110 ecoregions of Canada and the United States. Two of the methods use the frequency of species that occur in a few of the sampled ecoregions. These two methods did not work. The other four methods estimate the asymptote of the species-accumulation curve ( the graph of "number of species in a set of samples" versus "number of species occurrences in those samples" ). The asymptote of this curve is the actual number of species in the system. Three of these extrapolation estimators produced good estimates of total diversity even when limited to 10% of the ecoregions. Good estimates depend on sampling ecoregions that are hyperdispersed in space. Clustered sampling designs ruin the usefulness of the three successful methods. To ascertain their generality, our results must be duplicated at other scales and for other taxa and in other provinces. Resumen: La estimación del número de especies en una provincia biogeográfica puede ser problemático. Se ha desarrollado un número de métodos para superar los límites del tamaño de muestra dentro de un solo hábitat. Evaluamos seis de estos métodos para ver si podrían compensar por muestras incompletas de hábitat. Aplicamos estos métodos a especies de mariposas de las 110 ecoregiones de Canadá y los Estados Unidos. Dos de los métodos usan la frecuencia de las especies que ocurren en algunas de las ecoregiones muestreadas. Estos dos métodos no sirvieron. Los otros cuatro métodos estimaron la asíntota de la curva de acumulación de especies ( la gráfica de "el número de especies en un juego de muestras" contra el "número de ocurrencias de especies en éstas muestras" ). La asíntota de ésta curva es el número real de especies en el sistema. Tres de éstos estimadores de extrapolación produjeron buenas estimaciones de la diversidad total aún cuando se limitaron al 10% de las ecoregiones. Las buenas estimaciones dependen del muestreo de ecoregiones altamente dispersas en el espacio. Los diseños de muestreos en agrupamientos arruinan la utilidad de los tres métodos exitosos. Para asegurar su generalidad, nuestros resultados deben ser duplicados a otras escalas y para otros taxones en otras provincias. [source] Effect of PCR amplicon size on assessments of clone library microbial diversity and community structureENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Julie A. Huber Summary PCR-based surveys of microbial communities commonly use regions of the small-subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using operational taxonomic unit (OTU)- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of c. 100, 400 and 1000 base pairs (bp) from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias and mispriming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities. [source] It's all relative: ranking the diversity of aquatic bacterial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 9 2008Allison K. Shaw Summary The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples. [source] Ordovician graptolite evolutionary radiation: a reviewGEOLOGICAL JOURNAL, Issue 3-4 2006Chen Xu Abstract Based on the global graptolite genera and higher rank taxa, we propose three radiation stages through the Ordovician. The isograptid type of development is present within anisograptids predominating in the Tremadocian. Thus, the evolutionary radiation of the Anisograptid fauna from Tremadocian is proposed as the beginning of the Ordovician graptolite radiation. The second graptolite radiation event is the radiation of the Dichograptid fauna, which began from the T. fruticosus Biozone. The third radiation event, the radiation of Diplograptid fauna began immediately after that of the dichograptids. This radiation includes the peak in total diversity of all the Ordovician graptoloids in the Nemagraptus gracilis Biozone. The radiation extended through the Sandbian and Katian and then was interrupted by a major extinction during the early Hirnantian. Thus, the Ordovician graptolite radiation events coincide with those of the three graptolite faunas proposed by Bulman. The distribution and expansion of the Ordovician graptolites in South China may exemplify the graptolite origination pattern, which begins from the slope belt and expanded into both the shelf and oceanic zones. Copyright © 2006 John Wiley & Sons, Ltd. [source] Alpha and beta diversity of arthropods and plants in organically and conventionally managed wheat fieldsJOURNAL OF APPLIED ECOLOGY, Issue 4 2007YANN CLOUGH Summary 1Most studies in applied ecology use measures of ,-diversity measures, i.e. the mean diversity on a site, to compare biodiversity effects of different management schemes. The total or ,-diversity within a region, however, need not be correlated with the mean ,-diversity within any site of the region. Thus, analyses of ,-diversity alone may misrepresent the contributions of other diversity components (,) to total diversity (,). 2We apply a biodiversity-partitioning approach to species richness from a comparison between paired organic and conventional wheat fields in 21 sites from three regions in Germany, where we recorded plants, bees, carabids, staphylinids and spiders in the centre and edge of the fields. 3Relative values of ,- and ,-diversity depended on taxon. Both between-site and between-region ,-diversity were very high (in total 60,85%). ,-Diversity and between-site ,-diversity was larger on the edge than in the centre of fields for all taxa. 4,-Diversity, between-site ,-diversity of plants and bees and between-region ,-diversity of bees were higher in organic than in conventional fields, providing local as well as larger-scale species richness benefits. ,-Diversity did not differ between management types for the epigaeic arthropods. Lower between-site ,-diversity was found for spiders in organic fields than in conventional fields, resulting in higher total species richness in conventionally managed wheat. 5Similarity in composition of landscapes surrounding the study fields was correlated with similarity in species composition for epigaeic arthropods in conventional fields. For this group of organisms the variability of landscapes in the sample contributed to increasing ,-diversity. 6Synthesis and applications.,-Diversity accounts for the major part of species richness in agro-ecosystems. Implementing an agri-environment scheme such as organic agriculture may result in either an additional increase of total diversity, as could be shown for plants and bees, or in a decrease in total diversity as was the case for the spiders. Therefore, ,-diversity needs to be included in the evaluation of different management schemes for conservation. For plant and bees it is recommended to implement agri-environment schemes in contrasting landscapes and in different regions to maximize total species richness benefits. [source] Phylogenetic analysis of intestinal bacteria in the Chinese mitten crab (Eriocheir sinensis)JOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2007K. Li Abstract Aims:, To identify the dominant intestinal bacteria in the Chinese mitten crab, and to investigate the differences in the intestinal bacteria between pond-raised and wild crabs. Methods and Results:, The diversity of intestinal bacteria in the Chinese mitten crabs was investigated by denaturing gradient gel electrophoresis (DGGE) fingerprinting, 16S rRNA gene clone library analysis and real-time quantitative PCR. The principal component analysis of DGGE profiles indicated that substantial intersubject variations existed in intestinal bacteria in pond-raised crab. The sequencing of 16S rRNA genes revealed that 90,95% of the phylotypes in the clone libraries were affiliated with Proteobacteria and Bacteroidetes. Some genera were identified as unique in wild crabs and in pond-raised crabs, whereas Bacteroidetes was found to be common in all sampled crab groups. Real-time quantitative PCR indicated that the abundance of Bacteroides and the total bacterial load were approximately four-to-10 times higher in pond-raised crabs than in wild crabs. A significant portion of the phylotypes shared low similarity with previously sequenced organisms, indicating that the bacteria in the gut of Chinese mitten crabs are yet to be described. Conclusions:, The intestinal bacteria of pond-raised crabs showed higher intersubject variation, total diversity and abundance than that observed in wild crabs. The high proportion of the clones of Proteobacteria and Bacteroidetes in the clone library is an indication that these bacteria may be the dominant population in the gut of the Chinese mitten crab. Significance and Impact of the Study:, This study demonstrated obvious differences in the intestinal bacterial composition of pond-raised crabs and wild crabs. This knowledge will increase our understanding of the effects of aquaculture operations on bacterial community composition in the crab gut and provide necessary data for the development of probiotic products for crab cultivation. [source] Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in TaiwanJOURNAL OF BIOGEOGRAPHY, Issue 5 2006Su-Hwa Wu Abstract Aim, The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location, The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods, The range-wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer program tcs. Nested clade analysis was conducted with the computer program ceodis, and various parameters of genetic diversity were calculated and neutrality tested by the computer program DnaSP. Population differentiation was estimated using the programs arlequin and hapstep. The contribution of the populations to gene diversity and to allelic richness was calculated using the software contrib. The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise FST for each population against the rest of the populations. Results, Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low-temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north-central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean FST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions, This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north-central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern-edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes. [source] Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markersANIMAL GENETICS, Issue 4 2009N. Bodzsar Summary Six local chicken breeds are registered in Hungary and are regarded as Hungarian national treasures: Hungarian White, Yellow and Speckled, and Transylvanian Naked Neck White, Black and Speckled. Three Hungarian academic institutes have maintained these genetic resources for more than 30 years. The Hungarian Yellow, the Hungarian Speckled and the Transylvanian Naked Neck Speckled breeds were kept as duplicates in two separate subpopulations since time of formation of conservation flocks at different institutes. In this study, we investigated genetic diversity of these nine Hungarian chicken populations using 29 microsatellite markers. We assessed degree of polymorphism and relationships within and between Hungarian breeds on the basis of molecular markers, and compared the Hungarian chicken populations with commercial lines and European local breeds. In total, 168 alleles were observed in the nine Hungarian populations. The FST estimate indicated that about 22% of the total variation originated from variation between the Hungarian breeds. Clustering using structure software showed clear separation between the Hungarian populations. The most frequent solutions were found at K = 5 and K = 6, respectively, classifying the Transylvanian Naked Neck breeds as a separate group of populations. To identify genetic resources unique to Hungary, marker estimated kinships were estimated and a safe set analysis was performed. We show that the contribution of all Hungarian breeds together to the total diversity of a given set of populations was lower when added to the commercial lines than when added to the European set of breeds. [source] | ||||||||||