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At least 415 records · Page 23Linked to original sources
PubMed2006

Spatial stratification of soil bacterial populations in aggregates of diverse soils.

Most soil microbial community studies to date have focused on homogenized bulk soil samples. However, it is likely that many important microbial processes occur in spatially segregated microenvironments in the soil leading to a microscale biogeography. This study attempts to localize specific microbial populations to different fractions or compartments within the soil matrix. Microbial populations associated with macroaggregates and inner- versus total-microaggregates of three diverse soils were characterized using culture-independent, molecular methods. Despite their relative paucity in most surveys of soil diversity, representatives of Gemmatimonadetes and Actinobacteria subdivision Rubrobacteridae were found to be highly abundant in inner-microaggregates of most soils analyzed. By contrast, clones affiliated with Acidobacteria were found to be relatively enriched in libraries derived from macroaggregate fractions of nearly all soils, but poorly represented in inner-microaggregate fractions. Based upon analysis of 16S rRNA, active community members within microaggregates of a Georgian Ultisol were comprised largely of Gemmatimonadetes and Rubrobacteridae, while within microaggregates of a Nebraska Mollisol, Rubrobacteridae and Alphaproteobacteria were the predominant active bacterial lineages. This work suggests that microaggregates represent a unique microenvironment that selects for specific microbial lineages across disparate soils.

Actinobacteria↗
PubMed2000

Problems in Extinction Model Selection and Parameter Estimation.

It is a vexing problem to achieve a consensus about the proper scientific way to assess population viability for habitat conservation plans. Rather than a hypothesis-testing approach, here it is proposed to select population models, estimate extinction parameters, and assess prediction uncertainty using a pragmatic, empirical Bayesian approach. The simplest usable models include the effects of population growth, r; carrying capacity, K; Allee threshold, N(A); and environmental stochasticity, v(r). Analytic predictions of expected extinction times are available for such models. Models that are more complex can be elaborated from this basis. Selection from a hierarchy of nesting population models can often be done through the evaluation of parameters. The estimation of the most important extinction parameters can be undertaken in a variety of ways. Time series can be analyzed to estimate r(d), v(r), rho, and K. Habitat models and individualistic population models may help estimate N(A) and K and demographic stochasticity. Fine-scale biogeography and climatological data may be useful in the estimation of a variety of parameters. Because it takes many years to estimate extinction parameters accurately for a given population of interest, the most efficient estimation procedures are desirable. I propose the use of prior information from an (as yet nonexistent) population biology database. The accumulation of local information through monitoring will improve our estimates allowing adaptive management. Uncertainty in the estimates will always remain, but it may be quantified by the posterior distributions. A crude example is discussed using treefrog population data. Although the motivations, beliefs, and biases of competing stakeholders will differ, a habitat conservation plan could accommodate this variation in the prior distributions. Field experience from monitoring will increasingly clear up any discrepancies between the opposing beliefs and the real ecosystem. As the world is an uncertain place and because there is no universal scientific method, there will always be controversy and surprises. The best we can do is (1) agree about our prior information, (2) agree about the strategy of model selection and parameter estimation, and (3) agree about our strategy for adaptive management. Perhaps the greatest impediment to such prior agreements for HCPs is the likely paranoia inspired by the use of unfamiliar statistical methodology. We need to train students of ecology in a more flexible and deeper understanding of statistics and philosophy of science.

Journal Article↗
PubMed2001

The interior-to-edge breakpoint distance as a guideline for nature conservation policy.

A method is proposed to quantify disturbance impact on isolated habitats. For every landscape patch, the breakpoint distance, defined as the penetration distance for which equality of interior and edge habitat is observed, can be calculated. Disturbance with equal impact at all patch sides is assumed. Effects of patch compactness, size, convolution, and perforation are discussed. The potential use of the measure for nature reserve design is discussed. The breakpoint distance follows the reserve design guidelines for individual patches, based on island biogeography and is consistent with the form and function principle. A large breakpoint distance is preferred for natural habitats. Small size, small compactness, intense convolution, and the occurrence of many gaps depress the breakpoint distance.

Animals↗
PubMed1998

ENVIRONMENTAL AUDITING: Butterflies (Lepidoptera: Papilionoidea and Hesperioidea) of Roxborough State Park, Colorado, USA: Baseline Inventory, Community Attributes, and Monitoring Plan

/ Roxborough State Park in Colorado's Front Range was established in 1975 following a history of cattle and sheep ranching by private ownership. Survey work conducted from 1979 to 1995 resulted in the documentation of 93 species of butterflies. A variety of factors are responsible for the composition of the butterfly community: (1) overgrazing and its effect on the presence or absence of specific butterfly host plants; (2) habitat differences resulting from topographical and geological features; and (3) ecological and historical biogeography. This study provides data on community sampling adequacy, along with estimates of effort needed to monitor trends in abundance by using a community self-similarity curve and power analysis. An annual monitoring plan is proposed to assess trends in community composition. The plan includes collection of presence/absence and abundance data for select butterflies based on natural history information.KEY WORDS: Butterfly communities; Grazing; Inventory; Monitoring; Natural history

Journal Article↗
PubMed2004

Four-year monitoring of parasite communities in gobiid fishes of the southwest Baltic: III. parasite species diversity and applicability of monitoring.

The parasite infrapopulations of five goby species (Pomatoschistus minutus, P. pictus, P.microps, Gobiusculus flavescens and Gobius niger) were investigated during spring, summer and autumn of the years 1997-2000. In total, 34 parasite species were found: 17 Digenea, 6 Nematoda, 5 Cestoda, 3 Acanthocephala, 2 Protozoa, and 1 Monogenea. The dominant parasites were the digeneans Podocotyle atomon and Cryptocotyle concavum, which represent different ecological groups in terms of their modes of transmission, either indirectly by prey or directly by larvae. The relationship between the parasite Cryptocotyle concavum and the host P. microps is a special one which results in a mean intensity of several hundred cysts (max. 1,329) which settle in the kidney. The diversity of the parasite component community was highest in autumn, but low in spring and summer, with the exception of P. microps for which high values were already found in spring when direct parasites were disregarded. These results depend on the respective seasonal variation in species, some of which occur in huge numbers in some hosts. The diversity of the prey parasite assemblage is higher in Pomatoschistus microps and Gobius niger than in the whole parasite spectrum; the other hosts present the opposite trend. A combination of the island theory of biogeography as modified for parasite infection with the theory of screens and filters leads to a model which considers three handicaps or distances for parasite colonisation: genetic, phylogenetic and ecological. Long-term investigations, as performed here over a time-span of 4 years, can detect more than 80% of parasite species in single hosts after 3 years, and in the whole goby guild after 2 years. Long-term investigations can be useful for finding rare parasites, in analysing parasite diversity, and for determining the seasonality of parasites.

Acanthocephala↗
PubMed2005

Nested communities, invasive species and Holocene extinctions: evaluating the power of a potential conservation tool.

General ecological methods and models that require a minimum amount of information yet are still able to inform conservation planning are particularly valuable. Nested subset analysis has been advocated as such a tool for the prediction of extinction-prone species and populations. However, such advocacy has not been without skepticism and debate, and in the majority of published examples assessing extinction vulnerability, actual extinctions are based on assumptions rather than direct evidence. Here, we empirically test the power of nested subset analysis to predict extinction-prone species, using documented Holocene insular mammal extinctions on three island archipelagos off the west coast of North America. We go on to test whether the introduction of invasive mammals promotes nestedness on islands via extinction. While all three archipelagos were significantly nested before and after the extinction events, nested subset analysis largely failed to predict extinction patterns. We also failed to detect any correlations between the degree of nestedness at the genus-level with area, isolation, or species richness and extinction risk. Biogeography tools, such as nested subset analysis, must be critically evaluated before they are prescribed widely for conservation planning. For these island archipelagos, it appears detailed natural history and taxa-specific ecology may prove critical in predicting patterns of extinction risk.

Animals↗
PubMed2006

Small-scale experimental habitat fragmentation reduces colonization rates in species-rich grasslands.

Habitat fragmentation is one of the most important threats to biodiversity. Decreasing patch size may lead to a reduction in the size of populations and to an increased extinction risk of remnant populations. Furthermore, colonization rates may be reduced in isolated patches. To investigate the effects of isolation and patch size on extinction and colonization rates of plant species, calcareous grasslands at three sites in the Swiss Jura Mountains were experimentally fragmented into patches of 0.25, 2.25, and 20.25 m2 by frequent mowing of the surrounding area from 1993 to 1999. Species richness in the fragment plots and adjacent control plots of the same sizes was recorded during these 7 years. In agreement with the theory of island biogeography, colonization rate was reduced by 30% in fragments versus non-isolated controls, and extinction increased in small versus large plots. Habitat specialists, in contrast to generalists, were less likely to invade fragments. In the last 4 years of the experiment, extinction rates tended to be higher in fragment than in control plots at two of the three sites. Despite reduced colonization rates and a tendency of increased extinction rates in fragments, fragmented plots had only marginally fewer species than control plots after 7 years. Hence, rates were a more sensitive measure for community change than changes in species richness per se. From a conservation point of view, the detected reduced colonization rates are particularly problematic in small fragments, which are more likely to suffer from high extinction rates in the long run.

Biodiversity↗
PubMed2026

A new southern limit for the distribution of African great apes: sympatric western lowland gorilla (Gorilla gorilla gorilla) and central chimpanzee (Pan troglodytes troglodytes) confirmed in Mayombe National Park, Angola.

The distribution of African great apes has remained unconfirmed regarding their southern limit, particularly on the western side of the continent. IUCN maps include the Mayombe forest of Angola as part of the estimated distribution of western lowland gorillas (Gorilla gorilla gorilla) and central chimpanzees (Pan troglodytes troglodytes). However, until now no published evidence-based records had confirmed the continued presence of both species. The Mayombe forest is a key biodiversity hotspot and a potentially important stronghold for the conservation of great ape populations in Africa. Here, we report the first systematic evidence of both species in the Mayombe National Park, Cabinda, Angola. In 2023, a grid of camera traps was systematically deployed, producing the first visual records of gorillas and chimpanzees. Building on these findings, in 2024, a pilot survey including ad libitum field observations was carried out along exploratory trails to maximise data collection. The combination of these records identified a hotspot of great ape activity where six transects were established, and systematic direct and indirect evidence was documented. Chimpanzees were recorded more times across a broader range of evidence categories, while gorillas appeared less and seemed more spatially restricted. Notably, both species were detected at overlapping sites but never simultaneously, indicating sympatric coexistence with spatio-temporal partitioning. These findings confirm the southernmost predicted distribution of both species for this part of Africa, filling critical gaps in the understanding of great ape evolution and biogeography, and providing a baseline for the first demographic and ecological census of great apes in Angola.

Animals↗
PubMed2005

Species of Pseudorhabdosynochus Yamaguti, 1958 (Monogenea: Diplectanidae) from Epinephelus fasciatus and E. merra (Perciformes: Serranidae) off New Caledonia and other parts of the Indo-Pacific Ocean, with a comparison of measurements of specimens prepared using different methods, and a description of P. caledonicus n. sp.

Species of Pseudorhabdosynochus were studied from fresh specimens collected from Epinephelus fasciatus and E. merra off New Caledonia, South Pacific, and specimens deposited in Museums. Experiments on two species demonstrated that the sclerotised hollow organs, such as the quadriloculate male copulatory organ and the vagina, may show differences in measurements of up to 50% when flattened. P. caledonicus n. sp. is described from E. fasciatus in New Caledonia, on which it is relatively rare; it is distinguished on the basis of the quadriloculate organ, which has a very thin anterior wall, the sclerotised parts of the vagina in form of a straight tube with a star-shaped lateral structure, and the squamodiscs composed of 11 open rows of rodlets. P. cupatus (Young, 1969) is redescribed from abundant material from E. fasciatus off New Caledonia (new geographical record) and compared with paratype specimens from Australia (from E. fasciatus and E. merra) and specimens from E. fasciatus in the Red Sea (both herein redescribed and figured); a specimen was also found on a slide from E. merra off Vanuatu. P. melanesiensis (Laird, 1958) is redescribed from material from E. merra off New Caledonia (new geographical record) and compared with type-specimens (herein redescribed and figured) from the same host off Vanuatu. The structure of the sclerotised vagina in P. cupatus and P. melanesiensis is very similar, with a thin-walled tube and a heavily sclerotised structure with three loculi. P. vagampullum (Young, 1969) is redescribed from the paratypes from E. merra from Australia, but was not found in New Caledonia; specimens included among its paratypes (from E. merra in Australia), but different, are herein attributed to Pseudorhabdosynochus sp. 3. P. lantauensis (Beverley-Burton & Suriano, 1981) is redescribed from the paratype specimens from E. longispinis off Hong-Kong. A specimen found among the paratypes of P. cupatus belongs to a different species, herein designated as Pseudorhabdosynochus sp. 1. Specimens from E. longispinis off Hong-Kong, previously attributed to P. cupatus, are attributed to another species, Pseudorhabdosynochus sp. 2. The three species P. cupatus, Pseudorhabdosynochus sp. 1 and Pseudorhabdosynochus sp. 2 have in common a 'lamellosquamodisc' composed of central telescopic lamellae and peripheral rows of rodlets; they can be distinguished by the shape of the sclerotised vagina and measurements of the haptoral hard-parts. Specimens from E. longispinis off Hong-Kong, previously attributed to P. vagampullum, probably belong to a different species. Consequently, after these modified determinations, P. cupatus parasitises only E. fasciatus and E. merra, and P. melanesiensis and P. vagampullum parasitise only E. merra. With their wide geographical distribution and different species of Pseudorhabdosynochus in different localities, E. fasciatus and E. merra appear to represent excellent models for investigating monogenean biogeography in the Indo-Pacific Ocean.

Animals↗
PubMed2025

Picocyanobacteria in the Chesapeake Bay: isolation, diversity, and adaptation.

Tiny unicellular cyanobacteria or picocyanobacteria (0.5-3 µm) are important due to their ecological significance. Chesapeake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria. Studies of Chesapeake Bay picocyanobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus. They laid the foundation for revealing the ecophysiology, biogeography, genomics, and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries. The Bay picocyanobacteria are known to better tolerate the changes in temperature, salinity, and heavy metals compared to their coastal and open-ocean counterparts. Many picocyanobacteria isolated from the Bay contain rich toxin-antitoxin (TA) genes, suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments. Distinct winter and summer picocyanobacteria are present in the Bay, suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary. While the Bay contains subcluster 5.2 Synechococcus, it also contains freshwater Synechococcus, Cyanobium, and marine Synechococcus due to river influx and the ocean's tidal influence. Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea, showing a link between the Bay and polar picocyanobacteria. Genomic sequences of estuarine picocyanobacteria provide new insight into the taxonomy and evolution of freshwater, estuarine, and marine unicellular cyanobacteria. Estuaries connect freshwater and marine ecosystems. This overview attempts to extend what we learned from Chesapeake Bay picocyanobacteria to picocyanobacteria in freshwater and marine waters.

Chesapeake Bay↗
PubMed1993

Speciation patterns of ectoparasites and "straggling" lice.

Two competing views have been expressed to explain ectoparasite speciation patterns, one emphasizing co-speciation and one emphasizing host-switching. Though recent authors preferred a combination of these views, the available phylogenetic trees cannot be interpreted without revisiting island biogeography theory. Parasite extinction due to a temporal decline in host population size seems to be a prerequisite of subsequent speciation by host-switch. The need for a re-evaluation of "stragglers" (ectoparasites found on non-specific hosts) is emphasized.

Animals↗
PubMed1996

Parasites as host [corrected] evolutionary prints: insights into host evolution from parasitological data.

The close relationships which link parasitic organisms to their hosts have led to the use of parasites as biological tags. Most studies on this topic refer to parasites as host ecological tags. Recent development of molecular methods which give access to the genomic structures of populations have provided new information on the evolutionary biology of parasites. In this paper, we have attempted to review whether parasites can be considered as "host evolutionary prints", and focus our discussion on host biodiversity and biogeography.

Animals↗
PubMed1982

[The "nivrées", or ichthyotoxic plants of French Guyana].

An attempt to clarify the taxonomy, the biogeography and the ethnobotany of the fishing poisons of Guiana and adjacent countries is presented. Collections have been made for every drug and field-notes concerning all ethnic groups of Guiana. Data are compared with published sources, particularly those of the past centuries. Ichthyotoxic plants have been classified into three groups: rotenone-yielding plants (Lonchocarpus, Derris, Tephrosia), saponin-yielding plants (Sapindaceae), and the "kunami" group of plants (Compositae, Euphorbiaceae). For each drug the vernacular names, the synonyms still used, the most notable morphological characteristics are specified, as well as ethnological observations and active constituents when known. Drugs and fishing-related techniques were selected long ago by Amerindians then often diffused through Amazonian countries by mixed-blood populations.

Animals↗
PubMed2025

From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.

Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.

Humans↗
PubMed2005

Humicolous buthoid scorpions: a new species from Brazilian Amazon.

A new species of humicolous buthid scorpion is described on the basis of a single specimen collected in the Brazilian Amazonia. New considerations on the taxonomy and biogeography of some micro-scorpions of the subfamily Ananterinae Pocock, 1900 are proposed in relation to their possible evolution from endogeous to epygean environments.

Animals↗
PubMed2026

Phylogenomics and museomics reveal five distinct species of tiger cats in South America.

The evolutionary history of elusive organisms can be characterized through genomic analyses, which have the power to reveal previously unknown taxa even in groups assumed to be well studied, such as cats. We have analyzed complete genomes of 38 individuals from the Neotropical cat genus Leopardus, including 26 individuals representing multiple evolutionary units of the contentious tiger cat (Leopardus tigrinus) species complex. Eight genomes were generated from museum specimens, which allowed the first genetic assessment of the type locality for L. tigrinus in the Guiana Shield. We found that this complex comprises five distinct species, including a novel cat species, discovered in the Bolivian Yungas and described in this study as L. tilcayo. The Peruvian Yungas unit of this complex also represents a distinct taxonomic entity, which we describe here as a novel subspecies, L. tigrinus antisuyo. Our phylogenomic analyses resolve the evolutionary relationships among the tiger cat geographic units, thus stabilizing their recalcitrant taxonomy and enabling adequate conservation assessment of these threatened felids. We also address other aspects of their evolution, including biogeography, past episodes of interspecies admixture, demographic history of each taxonomic unit, and temporal changes in genetic diversity. Altogether, our results clarify the evolutionary history of a complex radiation of wild cats, reveal novel taxa, and serve as a basis for conservation planning on behalf of these elusive wild cats.

Bolivian Yungas↗
PubMed2005

The use of predatory soil mites in ecological soil classification and assessment concepts, with perspectives for oribatid mites.

Gamasina are the main predators among the soil mesofauna and, therefore, have a crucial position in the soil food web and contribute significantly to energy and matter turnover. Ecological concepts including predatory mites in soil assessment have not yet been established, while standardized sampling, extraction, and conservation methods are available. There are reliable keys for Europe that cover most families. Few species in low dominance ranks correlate well with soil properties like soil texture and pH. Meaningful endpoints for soil assessment are community parameters that are based on the life history of the species (e.g., Maturity Index). It has been shown that the predatory mites, as well as the oribatids as a second common and widespread group of mites, fit well into a soil assessment concept comparable to RIVPACS, which was established for aquatic systems. Perspectives for future research are the development of a computer-aided identification key and the creation of a database with information on the ecology and biogeography of important species.

Animals↗
PubMed2004

Global distribution of nearly identical phage-encoded DNA sequences.

Phages, the most abundant biological entities on the planet, play important roles in biogeochemical cycling, horizontal gene transfer, and defining microbial community composition. However, very little is known about phage diversity or biogeography, and there has not yet been a systematic effort to compare the phages found in different ecosystems. Here, we report that T7-like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan-associated. The majority of these sequences belong to a unique clade that is only distantly related to cultured isolates. Some identical T7-like phage-encoded DNA polymerase genes from this clade were >99% conserved at the nucleotide level in multiple different environments, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T7-like phages may be smaller than previously hypothesized.

Conserved Sequence↗