Browsing by Subject "BIOGEOGRAPHY"
Now showing items 1-20 of 20
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(2016)The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
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(2021)Background Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs -Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015-2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only. New information We enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoologia of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.
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Co-occurrences of tropical trees in eastern South America : disentangling abiotic and biotic forces (2021)Species co-occurrences in local communities can arise independent or dependent on species' niches. However, the role of niche-dependent processes has not been thoroughly deciphered when generalized to biogeographical scales, probably due to combined shortcomings of data and methodology. Here, we explored the influence of environmental filtering and limiting similarity, as well as biogeographical processes that relate to the assembly of species' communities and co-occurrences. We modelled jointly the occurrences and co-occurrences of 1016 tropical tree species with abundance data from inventories of 574 localities in eastern South America. We estimated species co-occurrences as raw and residual associations with models that excluded and included the environmental effects on the species' co-occurrences, respectively. Raw associations indicate co-occurrence of species, whereas residual associations indicate co-occurrence of species after accounting for shared responses to environment. Generally, the influence of environmental filtering exceeded that of limiting similarity in shaping species' co-occurrences. The number of raw associations was generally higher than that of the residual associations due to the shared responses of tree species to the environmental covariates. Contrary to what was expected from assuming limiting similarity, phylogenetic relatedness or functional similarity did not limit tree co-occurrences. The proportions of positive and negative residual associations varied greatly across the study area, and we found a significant tendency of some biogeographical regions having higher proportions of negative associations between them, suggesting that large-scale biogeographical processes limit the establishment of trees and consequently their co-occurrences.
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(2021)Background Freshwater diversity, and diatoms in particular, from Desertas Islands (Madeira Archipelago, Portugal) is poorly known, although the Islands are protected and became a Natural Reserve in 1995. During two field expeditions in 2013 and 2014 to Deserta Grande Island, several freshwater and terrestrial habitats were sampled. The analysis of these samples aims to contribute to the biodiversity assessment of the freshwater biota present in Deserta Grande Island. Here, we present the diatom diversity in Deserta Grande Island resulting from that survey. This study contributes to improve the knowledge of Madeira Archipelago freshwater diversity, particularly in the Desertas sub-archipelago. New information To our knowledge, we present the first diatom data for the Desertas sub-archipelago. This work resulted in a list of 60 diatom taxa for Deserta Grande, from which 57 were identified to species level. From the 60 new records for Desertas sub-archipelago, 30 of them were also new records for Madeira Archipelago. Several specimens could not be assigned to a known species and may be new diatom species not yet described.
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(2012)Background The regression of similarity against distance unites several ecological phenomena, and thus provides a highly useful approach for illustrating the spatial turnover across sites. Our aim was to test whether the rates of decay in community similarity differ between diatom growth forms suggested to show different dispersal ability. We hypothesized that the diatom group with lower dispersal ability (i.e. periphyton) would show higher distance decay rates than a group with higher dispersal ability (i.e. plankton). Methods/Principal findings Periphyton and phytoplankton samples were gathered at sites distributed over an area of approximately 800 km length in the Negro River, Amazon basin, Brazil, South America (3°08′00″S; 59°54′30″W). Distance decay relationships were then estimated using distance-based regressions, and the coefficients of these regressions were compared among the groups with different dispersal abilities to assess our predictions. We found evidence that different tributaries and reaches of the Negro River harbor different diatom communities. As expected, the rates of distance decay in community similarity were higher for periphyton than for phytoplankton indicating the lower dispersal ability of periphytic taxa. Conclusions/Significance Our study demonstrates that the comparison of distance decay relationships among taxa with similar ecological requirements, but with different growth form and thus dispersal ability provides a sound approach to evaluate the effects of dispersal ability on beta diversity patterns. Our results are also in line with the growing body of evidence indicating that microorganisms exhibit biogeographic patterns. Finally, we underscore that clumbing all microbial taxa into one group may be a flawed approach to test whether microbes exhibit biogeographic patterns.
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(2019)Dendrocincla woodcreepers are ant-following birds widespread throughout tropical America. Species in the genus are widely distributed and show little phenotypic variation. Notwithstanding, several subspecies have been described, but the validity of some of these taxa and the boundaries among them have been discussed for decades. Recent genetic evidence based on limited sampling has pointed to the paraphyly of D. fuliginosa, showing that its subspecies constitute a complex that also includes D. anabatina and D. turdina. In this study we sequenced nuclear and mitochondrial markers for over two hundred individuals belonging to the D. fuliginosa complex to recover phylogenetic relationships, describe intraspecific genetic diversity and provide historical biogeographic scenarios of diversification. Our results corroborate the paraphyly of D. fuliginosa, with D. turdina and D. anabatina nested within its recognized subspecies. Recovered genetic lineages roughly match the distributions of described subspecies and congruence among phylogenetic structure, phenotypic diagnosis and distribution limits were used to discuss current systematics and taxonomy within the complex, with special attention to Northern South America. Our data suggest the origin of the complex in western Amazonia, associated with the establishment of upland forests in the area during the early Pliocene. Paleoclimatic cycles and river rearrangements during the Pleistocene could have, at different times, both facilitated dispersal across large Amazonian rivers and the Andes and isolated populations, likely playing an important role in differentiation of extant species. Previously described hybridization in the headwaters of the Tapajós river represents a secondary contact of non-sister lineages that cannot be used to test the role of the river as primary source of diversification. Based on comparisons of D. fuliginosa with closely related understory upland forest taxa, we suggest that differential habitat use could influence diversification processes in a historically changing landscape, and should be considered for proposing general mechanisms of diversification.
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(2022)The Laccophilus alluaudi species group is an interesting case of an endemic species radiation of Madagascar and the Comoros. To date, a single species, Laccophilus tigrinus Guignot, 1959 (Anjouan), is known from the Comoro Islands, with eight other species known from Madagascar. Here we review the Laccophilus alluaudi species group from the Comoro Islands based on partly new material. We recognize five species, out of which four are here described as new: L. mohelicus n. sp. (Moheli), L. denticulatus n. sp. (Grande Comore), L. michaelbalkei n. sp. (Mayotte) and L. mayottei n. sp. (Mayotte). Based on morphology of male genitalia, we hypothesize that the five species form a monophyletic group and originated from a single colonization event from Madagascar. If confirmed, this would constitute one of the few examples of intra-archipelago diversification in the Comoros. The knowledge of species limits in relation to their distribution in the Comoros archipelago is also urgently needed in the face of rapid habitat degradation.
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(2020)In total 196 bacterial isolates were obtained from root nodules of lentil (Lens culinaris) and faba bean (Vicia faba) grown on soil samples collected from 10 different sites in central and southern parts of Ethiopia. All isolates were identified as members of the genus Rhizobium by using recA gene sequence analysis. In the recA phylogenetic tree 195 rhizobial strains were classified into nine genospecies. The phylogeny of symbiotic genes nodC and nifH revealed five and six distinct groups respectively, largely dominated by symbiovar viciae. A multivariate analysis showed that environmental variables of the sampling sites considered in this study had more effect on the distribution and composition of the genospecies than the host legumes of the strains. Twenty representative strains, selected based on their isolation site, host plant and nodC group, were able to nodulate all lentil, faba bean, field pea (Pisum abyssinicum) and grass pea (Lathyrus sativus) plants in a greenhouse test in axenic conditions. The majority of the rhizobial strains were effective nitrogen-fixing symbionts for all tested legumes, indicating their potential to serve as broad host-range inoculants in agriculture. The present work suggests the presence of taxonomically and symbiotically diverse rhizobial species for legumes in the Viciae tribe in Ethiopia.
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(2021)In this study, we test and corroborate the phylogenetic position of Heterosyphus within Helictopleurus using mitogenomes and nuclear loci. Our recent samplings revealed that males of the former Heterosyphus sicardi Paulian, 1975 (today under Helictopleurus d'Orbigny, 1915) have extraordinary bilateral clypeal horns which are exclusive within the genus. We provide a taxonomic review of the fungicola species group of Helictopleurus and discuss the systematic position of H. sicardi within the group. The male phenotype of H. sicardi is described and photographs of the body and genitalia of the members of the fungicola group are given, as well as a diagnostic key to species of the group. Helictopleurus fungicola peyrierasi is considered to be a distinct species within the genus (H. peyrierasi stat. rest.). Helictopleurus pluristriatus d'Orbigny, 1915 syn. nov. is established as a junior synonym of H. fungicola (Fairmaire, 1899).
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(2019)Different metacommunity perspectives have been developed to describe the relationship between environmental and spatial factors and their relative roles for local communities. However, only little is known about temporal variation in metacommunities and their underlying drivers. We examined temporal variation in the relative roles of environmental and spatial factors for diatom community composition among brackish-watered rock pools on the Baltic Sea coast over a 3-month period. We used a combination of direct ordination, variation partition, and Mantel tests to investigate the metacommunity patterns. The studied communities housed a mixture of freshwater, brackish, and marine species, with a decreasing share of salinity tolerant species along both temporal and spatial gradients. The community composition was explained by both environmental and spatial variables (especially conductivity and distance from the sea) in each month; the joint effect of these factors was consistently larger than the pure effects of either variable group. Community similarity was related to both environmental and spatial distance between the pools even when the other variable group was controlled for. The relative influence of environmental factors increased with time, accounting for the largest share of the variation in species composition and distance decay of similarity in July. Metacommunity organization in the studied rock pools was probably largely explained by a combination of species sorting and mass effect given the small spatial study scale. The found strong distance decay of community similarity indicates spatially highly heterogeneous diatom communities mainly driven by temporally varying conductivity gradient at the marine-freshwater transition zone.
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(2020)How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.
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(2019)Aim We use cluster analysis to delimit climatically and functionally distinct mammalian faunal clusters. These entities form regional species pools and are relevant to community assembly processes. Similar clusters can be differentiated in the fossil record, offering the potential for use as palaeoenvironmental proxies. Location North America within W178 degrees, W14 degrees, N83 degrees, N7 degrees and Europe within W32 degrees, E35 degrees, N80 degrees, N35 degrees. Major taxa studied 575 and 124 land mammal species from North America and Europe. Methods K-means clustering was used to subdivide North America and Europe into distinct faunas ranging in number from 3 (largest scale) to 21 (smallest scale). Each set of faunas was tested for significant differences in climate (mean annual precipitation, mean annual temperature) and functional traits (body mass, locomotion and diet). Results In North America, climatic differentiation exists at the scale where mammals are divided into 11 or fewer distinct faunas and, in Europe, at the scale where there are five or fewer faunas. Functional trait differentiation in body mass occurs at a larger spatial scale in North America (8 distinct faunas), but locomotor differentiation is present at all spatial scales, and dietary differentiation is not present at any scale. No significant differentiation in any functional trait at any scale was found in Europe. Main conclusions Faunal clusters can be constructed at any spatial scale, but clusters are climatically and functionally meaningful only at larger scales. Climatic (and environmental) differences and their associated functional trait specialisations are likely to be barriers to large-scale mixing. We argue, therefore, that functionally and climatically distinct faunal clusters are the entities that form regional species pools for community assembly processes. In North America, there are eight such mammal pools, but only one in Europe. Since the functional traits in our study are observable in the fossil record, functional trait analysis can potentially be used to diagnose climatically distinct regions in the past.
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(2020)The Geomitrini is the most species-rich group of land snails in the Madeiran Archipelago. The phylogeny of the group is reconstructed based on mitochondrial and nuclear genetic markers. The timing of diversification, the colonisation history of the islands of the Madeiran Archipelago and the evolution of characters of the dart apparatus are studied. The results of the phylogenetic analyses confirm the sister group relationship of Geomitrini and Cochlicellini, but also show that several previously accepted genus-group taxa are not monophyletic. A new classification for the Geomitrini is proposed, including the description of two new genera, Domunculifex Brozzo, De Mattia, Harl & Neiber, n. gen. and Testudodiscula Brozzo, De Mattia, Harl & Neiber, n. gen. The onset of diversification of Geomitrini was dated in our analysis at 13 Ma, which largely coincides with the emergence of the present-day islands. The ancestral state estimation recovered the presence of two appendiculae in the reproductive system as the ancestral state in Geomitrini. One appendicula was lost three times independently within the tribe and is even missing completely in one group. The ancestral area estimation suggests recurrent colonisations of Madeira (and the Ilhas Desertas) from the older island Porto Santo.
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(2021)Molecular studies have shown that many polytypic species of birds are paraphyletic and may actually consist of multiple independent species, some of them phenotypically cryptic. One of such cases is Dendrocolaptes picumnus, which was found to be a paraphyletic species, with Dendrocolaptes hoffmannsi nested in it. Recent evidence also showed that multiple independent evolutionary lineages exist in the polytypic D. picumnus that may be characterized as distinct species, however, conclusions were weakened due to small sample sizes. To further evaluate phylogenetic relationships, species limits, and the diversification history of the D. picumnus species complex, herein we performed the densest sampling ever registered for the complex, and analyzed sequences of mitochondrial and nuclear genes from 106 specimens, belonging to all but four taxa grouped in the complex. Our phylogenetic analyses confirmed the monophyly of D. hoffmannsi and D. platyrostris, as well as the paraphyly of the polytypic D. picumnus. A combination of coalescent and population genetic structure analyses further supported an evolutionary independent status for D. picumnus transfasciatus, but were ambiguous with respect to the statuses of nominate D. picumnus, D. picumnus pallescens, D. picumnus validus, and D. picumnus costaricensis. In contrast, D. picumnus olivaceus and D. platyrostris intermedius were polyphyletic and not genetically structured with respect to D. picumnus pallescens and D. platyrostris platyrostris, respectively. Our results did not support the monophyly of the previously defined ‘Amazonian' and ‘montane' subspecies groups of D. picumnus, further indicating that at least one ‘montane' taxon may actually belong to the ‘Chaco' group, a relationship that highlights a close historical connection between the Andean and Chacoan biotas. When interpreted together with previous morphological studies, our results support the split of the polytypic D. picumnus into at least two species, while keeping the status of D. hoffmannsi and D. platyrostris as distinct species.
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Priors and Posteriors in Bayesian Timing of Divergence Analyses : The Age of Butterflies Revisited (2019)The need for robust estimates of times of divergence is essential for downstream analyses, yet assessing this robustness is still rare. We generated a time-calibrated genus-level phylogeny of butterflies (Papilionoidea), including 994 taxa, up to 10 gene fragments and an unprecedented set of 12 fossils and 10 host-plant node calibration points. We compared marginal priors and posterior distributions to assess the relative importance of the former on the latter. This approach revealed a strong influence of the set of priors on the root age but for most calibrated nodes posterior distributions shifted from the marginal prior, indicating significant information in the molecular data set. Using a very conservative approach we estimated an origin of butterflies at 107.6 Ma, approximately equivalent to the latest Early Cretaceous, with a credibility interval ranging from 89.5 Ma (mid Late Cretaceous) to 129.5 Ma (mid Early Cretaceous). In addition, we tested the effects of changing fossil calibration priors, tree prior, different sets of calibrations and different sampling fractions but our estimate remained robust to these alternative assumptions. With 994 genera, this tree provides a comprehensive source of secondary calibrations for studies on butterflies.
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(2018)Despite much interest in the ecology and origins of the extensive grassland ecosystems of the modern world, the biogeographic relationships of savannah palaeobiomes of Africa, India and mainland Eurasia have remained unclear. Here we assemble the most recent data from the Neogene mammal fossil record in order to map the biogeographic development of Old World mammalian faunas in relation to palaeoenvironmental conditions. Using genus-level faunal similarity and mean ordinated hypsodonty in combination with palaeoclimate modelling, we show that savannah faunas developed as a spatially and temporally connected entity that we term the Old World savannah palaeobiome. The Old World savannah palaeobiome flourished under the influence of middle and late Miocene global cooling and aridification, which resulted in the spread of open habitats across vast continental areas. This extensive biome fragmented into Eurasian and African branches due to increased aridification in North Africa and Arabia during the late Miocene. Its Eurasian branches had mostly disappeared by the end of the Miocene, but the African branch survived and eventually contributed to the development of Plio-Pleistocene African savannah faunas, including their early hominins. The modern African savannah fauna is thus a continuation of the extensive Old World savannah palaeobiome.
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(2022)Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.
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(2019)Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (>1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The -diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.
