scholarly journals Phylogenetic diversity patterns in Himalayan forests reveal evidence for environmental filtering of distinct lineages

Ecosphere ◽  
2018 ◽  
Vol 9 (5) ◽  
pp. e02157 ◽  
Author(s):  
Stephanie Shooner ◽  
T. Jonathan Davies ◽  
Purabi Saikia ◽  
Jyotishman Deka ◽  
Sanjeeb Bharali ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Environmental Filtering ◽  
Diversity Patterns ◽  
Himalayan Forests

Phylogenetic diversity patterns in forests of a putative refugial area in Greece: A community level analysis

2019 ◽  
Vol 446 ◽  
pp. 226-237 ◽  
Author(s):  
Anna Mastrogianni ◽  
Athanasios S. Kallimanis ◽  
Milan Chytrý ◽  
Ioannis Tsiripidis
Keyword(s):  
Phylogenetic Diversity ◽  
Community Level ◽  
Diversity Patterns ◽  
Refugial Area ◽  
Level Analysis

Diversity patterns among early gastropods: contrasting taxonomic and phylogenetic descriptions

Paleobiology ◽  
1995 ◽  
Vol 21 (4) ◽  
pp. 410-439 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Phylogenetic Diversity ◽  
Logistic Growth ◽  
Test Case ◽  
Data Sets ◽  
Diversity Patterns ◽  
Phylogenetic Data ◽  
Systematic Philosophy ◽  
Generic Data ◽  
Traditional Taxonomy ◽  
Diversity Studies

Paleobiologists have used taxonomic data for several types of diversity studies. Some systematists have charged that this practice obfuscates actual historical patterns of clades because many traditionally defined higher taxa are not monophyletic. Some have questioned whether ranked taxa ever represent comparable units, even when monophyletic. This study contrasts diversity patterns implied by phylogenetic estimates with those implied by ranked taxa. Early Paleozoic gastropods are useful as a test case because their generic taxonomy does not reflect the phylogenetic systematic philosophy, and fewer than one third of the genera represent monophyletic clades. Phylogenetic diversity is described in two ways: (1) numbers of lineages (i.e., observed plus phylogenetically implied “ghost lineages”), and (2) numbers of monophyla (i.e., clades whose sister taxa are other clades rather than species). “Monophyla” as tallied here are monophyletic relative to their contemporaries and older clades; however, they can be paraphyletic relative to “future” monophyla. Phylogenetic diversity is tallied with both maximum and minimum “ghost lineage” interpolations in order to reflect different possible speciation patterns and timings of speciation. Phylogenetic diversity as implied by a stricter cladistic criterion (i.e., taxa that are monophyletic relative to their contemporaries, older taxa and younger taxa) is discussed also.First differences between substage-to-substage standing diversities reveal significant congruence between generic data and both types of phylogenetic data. Taxonomic and phylogenetic data imply a major extinction event at the end of the Ordovician, although the phylogenetic data suggest greater extinction levels than do the taxonomic data. Both data sets also suggest diversity-dependent diversification reminiscent of logistic growth, which is the pattern predicted if one or a few major ecologic factors were constraining the diversification of gastropods. However, diversity described by strict Hennigian taxa is not highly congruent with diversity as described by either lineages or monophyla. Comparing subclade dynamics requires extensive redefinition of traditional orders, but lineages, monophyla and genera all suggest that the two major subclades had different logistic diversification patterns, with one (“murchisonioids”) having a higher K than the other (“euomphaloids”). The concern that phylogenetic and taxonomic data might imply very different evolutionary histories is not borne out by gastropods, despite the nonphylogenetic nature of their traditional taxonomy.

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 Plant diversity patterns and conservation status of eastern Himalayan forests in Arunachal Pradesh, Northeast India

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
P. Saikia ◽  
J. Deka ◽  
S. Bharali ◽  
Amit Kumar ◽  
O. P. Tripathi ◽  
...  
Keyword(s):  
Plant Diversity ◽  
Conservation Status ◽  
Northeast India ◽  
Arunachal Pradesh ◽  
Diversity Patterns ◽  
Himalayan Forests

scholarly journals Community metabarcoding reveals the relative role of environmental filtering and dispersal in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

2021 ◽  
Author(s):  
Victor Noguerales ◽  
Emmanouil Meramveliotakis ◽  
Adrián Castro-Insua ◽  
Carmelo Andujar ◽  
Paula Arribas ◽  
...  
Keyword(s):  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Mountain Range ◽  
Relative Role ◽  
Primary Role ◽  
Soil Microarthropods ◽  
Diversity Patterns ◽  
Mountainous Regions ◽  
Metacommunity Structure

Disentangling the relative role of environmental filtering and dispersal limitation in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical datasets are required to account for taxon- and context-dependency but relevant research is often compromised by coarse taxonomic resolution. We here employed haplotype-level community DNA metabarcoding, enabled by stringent filtering of Amplicon Sequence Variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, Operational Taxonomic Unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Golden Oak habitat, we also detected a major role of dispersal limitation imposed by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterising metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.

scholarly journals Do forest over- and understory respond to the same environmental variables when viewed at the taxonomic and trait level?

2021 ◽  
Author(s):  
Kenny Helsen ◽  
Yeng-Chen Shen ◽  
Tsung-Yi Lin ◽  
Chien-Fan Chen ◽  
Chu-Mei Huang ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Environmental Filtering ◽  
Soil Nutrient ◽  
Woody Species ◽  
Elevational Gradient ◽  
Functional Trait ◽  
Environmental Drivers ◽  
Small Scale ◽  
Diversity Patterns ◽  
Soil Variation

While the relative importance of climate filtering is known to be higher for woody species assemblages than herbaceous assemblage, it remains largely unexplored whether this pattern is also reflected between the woody overstory and herbaceous understory of forests. While climatic variation will be more buffered by the tree layer, the understory might also respond more to small-scale soil variation, next to experiencing additional environmental filtering due to the overstory's effects on light and litter quality. For (sub)tropical forests, the understory often contains a high proportion of fern and lycophyte species, for which environmental filtering is even less well understood. We explored the proportional importance of climate proxies and soil variation on the species, functional trait and (functional) diversity patterns of both the forest overstory and fern and lycophyte understory along an elevational gradient from 850 to 2100 m a.s.l. in northern Taiwan. We selected nine functional traits expected to respond to soil nutrient or climatic stress for this study and furthermore verified whether they were positively related across vegetation layers, as expected when driven by similar environmental drivers. We found that climate was a proportionally more important predictor than soil for the species composition of both vegetation layers and trait composition of the understory. The stronger than expected proportional effect of climate for the understory was likely due to fern and lycophytes' higher vulnerability to drought, while the high importance of soil for the overstory seemed driven by deciduous species. The environmental drivers affected different response traits in both vegetation layers, however, which together with additional overstory effects on understory traits, resulted in a strong disconnection of community-level trait values across layers. Interestingly, species and functional diversity patterns could be almost exclusively explained by climate effects for both vegetational layers, with the exception of understory species richness. This study illustrates that environmental filtering can differentially affect species, trait and diversity patterns and can be highly divergent for forest overstory and understory vegetation, and should consequently not be extrapolated across vegetation layers or between composition and diversity patterns.

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.

Interactive effects of environmental filtering predict beta-diversity patterns in a subtropical forest metacommunity

2015 ◽  
Vol 17 (2) ◽  
pp. 96-106 ◽  
Author(s):  
Anita Stival dos Santos ◽  
Daniel Dutra Saraiva ◽  
Sandra Cristina Müller ◽  
Gerhard Ernst Overbeck
Keyword(s):  
Beta Diversity ◽  
Environmental Filtering ◽  
Subtropical Forest ◽  
Interactive Effects ◽  
Diversity Patterns

Phylogenetic diversity in the Western Ghats biodiversity hotspot reflects environmental filtering and past niche diversification of trees

2018 ◽  
Vol 46 (1) ◽  
pp. 145-157 ◽  
Author(s):  
Ruksan Bose ◽  
Brahmasamudra Ranganna Ramesh ◽  
Raphaël Pélissier ◽  
François Munoz
Keyword(s):  
Western Ghats ◽  
Phylogenetic Diversity ◽  
Environmental Filtering ◽  
Biodiversity Hotspot ◽  
The Western Ghats ◽  
Niche Diversification
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