scholarly journals The Use of DNA Barcoding to Assess Phylogenetic β-Diversity in Mid-Subtropical Evergreen Broad-Leaved Forests of China

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 923
Author(s):  
Liu ◽  
Liu ◽  
Ge ◽  
Huang ◽  
Zhou ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Environmental Gradients ◽  
Environmental Filtering ◽  
Nuclear Region ◽  
Dna Barcodes ◽  
Subtropical Forests ◽  
Construction Methods ◽  
Β Diversity ◽  
Nuclear Its ◽  
Analysis Of Variation

The application of quantifying phylogenetic information into measures of forest β-diversity is increasing for investigating the underlying drivers of community assembly along environmental gradients. In terms of assessing evolutionary inferences of community processes, a variety of plant DNA barcodes has been widely used in phylogenetic diversity measurements. However, relatively few studies have evaluated the effectiveness of DNA barcodes with using nuclear region in estimating phylogenetic β-diversity, particularly for communities in tropical or subtropical forests. In this study, we employed DNA barcodes combing with the nuclear region to construct the community phylogeny and examined the patterns of phylogenetic β-diversity of three mid-subtropical evergreen broad-leaved forests (EBLFs) in South China. Three phylogenetic construction methods were performed, including a Phylomatic-generated tree and two ML trees based on the combination of rbcL +matK +ITS with or without a constrained tree. Our results showed that the DNA barcodes including nuclear ITS constructed a highly resolved phylogenetic tree, but the application of a constrained tree had little influence on estimation of phylogenetic diversity metrics (mean pairwise distances and mean nearest taxon distances) based on branch lengths. Using both metrics and their standardized effect size metrics, we found that the patterns of phylogenetic β-diversity in mid-subtropical forests were non-random. There was a slight decline of phylogenetic β-diversity with increasing latitudes, but no trend was found along the altitude gradient. According to the analysis of variation partition, both environmental filtering and dispersion limitation could explain the variation of phylogenetic dissimilarity between communities in mid-subtropical EBLFs of China. Our results highlight the importance of neutrality and the niche conservatism in structuring the patterns of species diversity in subtropical woody communities.

scholarly journals Distinguishing the signatures of local environmental filtering and regional trait range limits in the study of trait-environment relationships

2019 ◽  
Author(s):  
Pierre Denelle ◽  
Cyrille Violle ◽  
François Munoz
Keyword(s):  
Community Assembly ◽  
Environmental Gradients ◽  
Boundary Effect ◽  
Extreme Environments ◽  
Environmental Filtering ◽  
Range Limits ◽  
Species Pool ◽  
Statistical Tool ◽  
Leaf Trait ◽  
Trait Convergence

AbstractUnderstanding the imprint of environmental filtering on community assembly along environmental gradients is a key objective of trait-gradient analyses. Depending on local constraints, this filtering generally entails that species departing from an optimum trait value have lower abundances in the community. The Community-Weighted Mean (CWM) and Variance (CWV) of trait values are then expected to depict the optimum and intensity of filtering, respectively. However, the trait distribution within the regional species pool and its limits can also affect local CWM and CWV values apart from the effect of environmental filtering. The regional trait range limits are more likely to be reached in communities at the extremes of environmental gradients. Analogous to the mid-domain effect in biogeography, decreasing CWV values in extreme environments can then represent the influence of regional trait range limits rather than stronger filtering in the local environment. We name this effect the “Trait-Gradient Boundary Effect” (TGBE). First, we use a community assembly framework to build simulated communities along a gradient from a species pool and environmental filtering with either constant or varying intensity while accounting for immigration processes. We demonstrate the significant influence of TGBE, in parallel to environmental filtering, on CWM and CWV at the extremes of the environmental gradient. We provide a statistical tool based on Approximate Bayesian Computation to decipher the respective influence of local environmental filtering and regional trait range limits. Second, as a case study, we reanalyze the functional composition of alpine plant communities distributed along a gradient of snow cover duration. We show that leaf trait convergence found in communities at the extremes of the gradient reflect an influence of trait range limits rather than stronger environmental filtering. These findings challenge correlative trait-environment relationships and call for more explicitly identifying the mechanisms responsible of trait convergence/divergence along environmental gradients.

scholarly journals Genome size mediates the effect of environmental filtering in determining plant β-diversity across temperate grasslands

2021 ◽  
Author(s):  
Hai-Yang Zhang ◽  
Xiaotao Lü ◽  
cunzheng wei ◽  
Jeff Powell ◽  
Xiaobo Wang ◽  
...  
Keyword(s):  
Genome Size ◽  
Community Assembly ◽  
Nuclear Dna ◽  
Environmental Filtering ◽  
Nuclear Dna Content ◽  
Mean Annual Precipitation ◽  
Mean Annual Temperature ◽  
Nitrogen And Phosphorus ◽  
Temperate Grasslands ◽  
Β Diversity

Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS, i.e. nuclear DNA content) determines species’ capacity to tolerate environmental stress or to exploit new environments and therefore potentially drive community assembly. However, its role in driving β-diversity (i.e., the site-to-site variability in species composition) remains unclear. We measured GS for 169 plant species and investigated their occurrences within plant communities across 52 sites spanning a 3200-km transect in the temperate grasslands of China. We found environmental factors showed larger effects on β-diversity of large-GS than that of small-GS species. Community weighted mean GS increased with mean annual precipitation, soil total nitrogen and phosphorus concentrations, but decreased with mean annual temperature, suggesting a negative selection against species with large GS in resources-limited or warmer climates. These findings highlight the roles for GS in driving community assembly and predicting species responses to climate change.

Quercus ngochoaensis (Fagaceae), a new species from Ba Vi National Park, northern, Vietnam

Phytotaxa ◽  
2021 ◽  
Vol 516 (3) ◽  
Author(s):  
HOANG THI BINH ◽  
NGUYEN VAN NGOC ◽  
HOANG THANH SON ◽  
SHUICHIRO TAGANE ◽  
TETSUKAZU YAHARA
Keyword(s):  
New Species ◽  
National Park ◽  
Nuclear Region ◽  
Dna Barcodes ◽  
Leaf Base ◽  
Northern Vietnam ◽  
Entire Margin ◽  
A New Species

A new species of Quercus (Fagaceae), Q. ngochoaensis, from Ba Vi National Park, Ha Noi, northern Vietnam is described and illustrated. This species is morphologically similar to Q. glauca in having glabrous twigs, cuneate leaf base, two or three fruits per infructescence, almost entire margin of lamellate rings on cupule except the lowest three rings, slightly convex scar at the base of a nut. However, it differs from Q. glauca in having smaller leaves, cup-shaped cupule enclosing 1/2–2/3 of the nut, 7–8 lamellate rings on cupule, and subglobose nut. In addition to the description, DNA barcodes of the two partial plastid regions of matK, rbcL and the nuclear region of ITS of the new species are provided.

scholarly journals Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140008 ◽  
Author(s):  
Hironori Toyama ◽  
Tsuyoshi Kajisa ◽  
Shuichiro Tagane ◽  
Keiko Mase ◽  
Phourin Chhang ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Tropical Rainforest ◽  
Deciduous Forests ◽  
Ecological Communities ◽  
Illegal Logging ◽  
Phylogenetic Structure ◽  
Evergreen Forests ◽  
Phylogenetic Community Structure ◽  
Β Diversity ◽  
Made In

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging.

scholarly journals Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities

2015 ◽  
Vol 282 (1809) ◽  
pp. 20142630 ◽  
Author(s):  
Jordan G. Okie ◽  
David J. Van Horn ◽  
David Storch ◽  
John E. Barrett ◽  
Michael N. Gooseff ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Negative Relationship ◽  
Low Complexity ◽  
Biodiversity Patterns ◽  
Soil Bacterial Communities ◽  
Β Diversity ◽  
Α Diversity ◽  
Magnitude Variation ◽  
Effects Of Temperature

The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower temperatures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to contrasting α- and β-diversity patterns. In accord with the predictions, α-diversity, niche widths and occupancies decreased while β-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between α-diversity and pH and a negative relationship between α-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms.

scholarly journals Two new species and a new species record of Aglaia (Meliaceae) from Indonesia

PhytoKeys ◽  
2020 ◽  
Vol 155 ◽  
pp. 33-51
Author(s):  
Caroline M. Pannell ◽  
Jan Schnitzler ◽  
Alexandra N. Muellner-Riehl
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Geographic Range ◽  
Dna Barcodes ◽  
Dichotomous Key ◽  
West Papua ◽  
Two New Species ◽  
Nuclear Its ◽  
Sabah And Sarawak ◽  
A New Species

Two new species of Aglaia from Indonesia are described, Aglaia monocaula restricted to West Papua, and Aglaia nyaruensis occurring on Borneo (Kalimantan, Brunei, Sabah and Sarawak). A phylogenetic analysis using nuclear ITS and ETS, and plastid rps15-ycf1 sequence data indicates that the two new species of Aglaia are also genetically distinct. Aglaia monocaula belongs to sectionAmoora, while A. nyaruensis is included in section Aglaia. A dichotomous key, drawings and three-locus DNA barcodes are provided as aids for the identification of the two new species of Aglaia. In addition, the geographic range of Aglaia mackiana (section Amoora) is expanded from a single previously known site in Papua New Guinea to West Papua, Indonesia.

scholarly journals Different environmental gradients affect different measures of snake β-diversity in the Amazon rainforests

2018 ◽  
Author(s):  
Rafael de Fraga ◽  
Miquéias Ferrão ◽  
Adam J Stow ◽  
William E Magnusson ◽  
Albertina P Lima
Keyword(s):  
Amazon Basin ◽  
Prey Availability ◽  
Environmental Gradients ◽  
Geographic Distance ◽  
Clay Content ◽  
Tree Cover ◽  
Β Diversity ◽  
Temperature And Precipitation ◽  
Nesting Sites ◽  
Conservation Actions

Mechanisms generating and maintaining biodiversity at regional scales may be evaluated by quantifying β-diversity along environmental gradients. Differences in assemblages result in biotic complementarities and redundancies among sites, which may be quantified through multi-dimensional approaches incorporating taxonomic β-diversity (TBD), functional β-diversity (FBD) and phylogenetic β-diversity (PBD). Here we test the hypothesis that snake TBD, FBD and PBD are influenced by environmental gradients, independently of geographic distance. The gradients tested are expected to affect snake assemblages indirectly, such as clay content in the soil determining primary production and Height Above the Nearest Drainage (HAND) determining prey availability, or directly, such as percentage of tree cover determining availability of resting and nesting sites, and climate (temperature and precipitation) causing physiological filtering. We sampled snakes in 21 sampling plots, each covering 5 km2, distributed over 880 km in the central-southern Amazon Basin. We used dissimilarities between sampling sites to quantify TBD, FBD and PBD, which were response variables in multiple-linear-regression and RDA models. We show that patterns of snake community composition based on TBD, FBD and PBD are associated with environmental heterogeneity in the Amazon. Despite positive correlations between all β-diversity measures, TBD responded to different environmental gradients compared to FBD and PBD. Our findings suggest that multi-dimensional approaches are more informative for ecological studies and conservation actions compared to a single diversity measure.

scholarly journals Roads as conduits of taxonomic, functional and phylogenetic degradation in caatinga vegetation

2020 ◽  
Author(s):  
Nayara Mesquita Mota ◽  
Markus Gastauer ◽  
Juan Fernando Carrión ◽  
João Augusto Alves Meira-Neto
Keyword(s):  
Plant Communities ◽  
Phylogenetic Diversity ◽  
Plant Traits ◽  
Environmental Filtering ◽  
Maximum Diameter ◽  
Maximum Height ◽  
Phylogenetic Structure ◽  
Caatinga Vegetation ◽  
Phylogenetic Lineages ◽  
Functional And Phylogenetic Diversity

AbstractRoad networks cause disturbances that can alter the biodiversity and the functioning of the Caatinga ecosystems. We tested the hypotheses that (i) Caatinga vegetation near roads is less taxonomically, functionally and phylogenetically diverse, (ii) phylogenetically and functionally more clustered than vegetation further from roads, (iii) plant traits associated with herbivory deterrence are conserved within the phylogenetic lineages, and (iv) Caatinga vegetation near roads selects for disturbance-related traits. We sampled herbaceous and woody component of vegetation in four plots near roads and four plots further from roads to test these hypothesis. Sampled species were classified according to their resprouting capacity, nitrogen fixation, succulence/spines, urticancy/toxicity, lifeform, endozoochory, maximum height and maximum diameter, before we calculated the taxonomic, functional and phylogenetic diversity of plant communities. Species richness, taxonomic, functional and phylogenetic diversities were lower in plots close to the roads, confirming roads as sources of disturbances. The phylogenetic structure of the Caatinga vegetation near roads was clustered, indicating environmental filtering by herbivory as the main pervasive disturbance in Caatinga ecosystems, since traits related to herbivory deterrence were conserved within phylogenetic lineages and were filtered in near roads. Thus, roads should be considered degradation conduits causing taxonomic, phylogenetic and functional impoverishment of Caatinga vegetation.

scholarly journals The role of environmental filtering, geographic distance and dispersal barriers in shaping the turnover of plant and animal species in Amazonia

2020 ◽  
Vol 29 (13) ◽  
pp. 3609-3634 ◽  
Author(s):  
Cristian Dambros ◽  
Gabriela Zuquim ◽  
Gabriel M. Moulatlet ◽  
Flávia R. C. Costa ◽  
Hanna Tuomisto ◽  
...  
Keyword(s):  
Community Composition ◽  
Environmental Conditions ◽  
Environmental Gradients ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Multivariate Techniques ◽  
Time Period ◽  
Dispersal Barriers

Abstract To determine the effect of rivers, environmental conditions, and isolation by distance on the distribution of species in Amazonia. Location: Brazilian Amazonia. Time period: Current. Major taxa studied: Birds, fishes, bats, ants, termites, butterflies, ferns + lycophytes, gingers and palms. We compiled a unique dataset of biotic and abiotic information from 822 plots spread over the Brazilian Amazon. We evaluated the effects of environment, geographic distance and dispersal barriers (rivers) on assemblage composition of animal and plant taxa using multivariate techniques and distance- and raw-data-based regression approaches. Environmental variables (soil/water), geographic distance, and rivers were associated with the distribution of most taxa. The wide and relatively old Amazon River tended to determine differences in community composition for most biological groups. Despite this association, environment and geographic distance were generally more important than rivers in explaining the changes in species composition. The results from multi-taxa comparisons suggest that variation in community composition in Amazonia reflects both dispersal limitation (isolation by distance or by large rivers) and the adaptation of species to local environmental conditions. Larger and older river barriers influenced the distribution of species. However, in general this effect is weaker than the effects of environmental gradients or geographical distance at broad scales in Amazonia, but the relative importance of each of these processes varies among biological groups.

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