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 Phylogenetic structure of angiosperm communities during tropical forest succession

2009 ◽  
Vol 277 (1678) ◽  
pp. 97-104 ◽  
Author(s):  
Susan G. Letcher
Keyword(s):  
Multiple Scales ◽  
Forest Succession ◽  
Species Pool ◽  
Ecological Communities ◽  
Phylogenetic Structure ◽  
Stem Size ◽  
Size Classes ◽  
Phylogenetic Community Structure ◽  
Phylogenetic Overdispersion ◽  
Age Category

The phylogenetic structure of ecological communities can shed light on assembly processes, but the focus of phylogenetic structure research thus far has been on mature ecosystems. Here, I present the first investigation of phylogenetic community structure during succession. In a replicated chronosequence of 30 sites in northeastern Costa Rica, I found strong phylogenetic overdispersion at multiple scales: species present at local sites were a non-random assemblage, more distantly related than chance would predict. Phylogenetic overdispersion was evident when comparing the species present at each site with the regional species pool, the species pool found in each age category to the regional pool or the species present at each site to the pool of species found in sites of that age category. Comparing stem size classes within each age category, I found that during early succession, phylogenetic overdispersion is strongest in small stems. Overdispersion strengthens and spreads into larger size classes as succession proceeds, corroborating an existing model of forest succession. This study is the first evidence that succession leaves a distinct signature in the phylogenetic structure of communities.

scholarly journals Conspicuousness, phylogenetic structure, and origins of Müllerian mimicry in 4000 lycid beetles from all zoogeographic regions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michal Motyka ◽  
Dominik Kusy ◽  
Michal Masek ◽  
Matej Bocek ◽  
Yun Li ◽  
...  
Keyword(s):  
Simple Model ◽  
Phylogenetic Diversity ◽  
Single Species ◽  
Visual Signals ◽  
South East Asia ◽  
Phylogenetic Information ◽  
Phylogenetic Structure ◽  
Chemical Defences ◽  
Single Region ◽  
General Appearance

AbstractBiologists have reported on the chemical defences and the phenetic similarity of net-winged beetles (Coleoptera: Lycidae) and their co-mimics. Nevertheless, our knowledge has remained fragmental, and the evolution of mimetic patterns has not been studied in the phylogenetic context. We illustrate the general appearance of ~ 600 lycid species and ~ 200 co-mimics and their distribution. Further, we assemble the phylogeny using the transcriptomic backbone and ~ 570 species. Using phylogenetic information, we closely scrutinise the relationships among aposematically coloured species, the worldwide diversity, and the distribution of aposematic patterns. The emitted visual signals differ in conspicuousness. The uniform coloured dorsum is ancestral and was followed by the evolution of bicoloured forms. The mottled patterns, i.e. fasciate, striate, punctate, and reticulate, originated later in the course of evolution. The highest number of sympatrically occurring patterns was recovered in New Guinea and the Andean mountain ecosystems (the areas of the highest abundance), and in continental South East Asia (an area of moderate abundance but high in phylogenetic diversity). Consequently, a large number of co-existing aposematic patterns in a single region and/or locality is the rule, in contrast with the theoretical prediction, and predators do not face a simple model-like choice but cope with complex mimetic communities. Lycids display an ancestral aposematic signal even though they sympatrically occur with differently coloured unprofitable relatives. We show that the highly conspicuous patterns evolve within communities predominantly formed by less conspicuous Müllerian mimics and, and often only a single species displays a novel pattern. Our work is a forerunner to the detailed research into the aposematic signalling of net-winged beetles.

scholarly journals Spatial analysis of phylogenetic community structure: New version of a classical method

2015 ◽  
Author(s):  
Carlo Ricotta ◽  
Eszter EA Ari ◽  
Giuliano Bonanomi ◽  
Francesco Giannino ◽  
Duncan Heathfield ◽  
...  
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Point Pattern ◽  
Maximum Deviation ◽  
Individual Plant ◽  
Phylogenetic Distance ◽  
Phylogenetic Structure ◽  
Phylogenetic Community Structure ◽  
Point Patterns ◽  
Wide Range

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

scholarly journals Phylogenetic overdispersion of plant species in southern Brazilian savannas

2009 ◽  
Vol 69 (3) ◽  
pp. 843-849 ◽  
Author(s):  
IA. Silva ◽  
MA. Batalha
Keyword(s):  
Phylogenetic Relationships ◽  
Plant Traits ◽  
Environmental Filtering ◽  
Southeastern Brazil ◽  
Ecological Communities ◽  
Ecological Interactions ◽  
Ecological Processes ◽  
Phylogenetic Structure ◽  
History Of ◽  
Phylogenetic Overdispersion

Ecological communities are the result of not only present ecological processes, such as competition among species and environmental filtering, but also past and continuing evolutionary processes. Based on these assumptions, we may infer mechanisms of contemporary coexistence from the phylogenetic relationships of the species in a community. We studied the phylogenetic structure of plant communities in four cerrado sites, in southeastern Brazil. We calculated two raw phylogenetic distances among the species sampled. We estimated the phylogenetic structure by comparing the observed phylogenetic distances to the distribution of phylogenetic distances in null communities. We obtained null communities by randomizing the phylogenetic relationships of the regional pool of species. We found a phylogenetic overdispersion of the cerrado species. Phylogenetic overdispersion has several explanations, depending on the phylogenetic history of traits and contemporary ecological interactions. However, based on coexistence models between grasses and trees, density-dependent ecological forces, and the evolutionary history of the cerrado flora, we argue that the phylogenetic overdispersion of cerrado species is predominantly due to competitive interactions, herbivores and pathogen attacks, and ecological speciation. Future studies will need to include information on the phylogenetic history of plant traits.

scholarly journals Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 288
Author(s):  
Nuria Macías-Hernández ◽  
Marc Domènech ◽  
Pedro Cardoso ◽  
Brent C. Emerson ◽  
Paulo Alexandre Vieira Borges ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Local Communities ◽  
Background Information ◽  
Ecological Processes ◽  
Phylogenetic Structure ◽  
Topological Constraint ◽  
Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

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.

A Strategy for Conserving the Biodiversity of the Uttara Kannada District in South India

1993 ◽  
Vol 20 (2) ◽  
pp. 131-138 ◽  
Author(s):  
R. J. Ranjit Daniels ◽  
M. D. Subash Chandran ◽  
Madhav Gadgil
Keyword(s):  
Rural Economy ◽  
South India ◽  
Action Plan ◽  
Bird Species ◽  
Deciduous Forests ◽  
Conservation Strategy ◽  
Cultivated Plants ◽  
Mangrove Forests ◽  
Sacred Groves ◽  
Evergreen Forests

Taking the various values ascribed to biodiversity as its point of departure rather many years ago, the present study aims at deriving a conservation strategy for Uttara Kannada. This hilly district, with the highest proportion of its area under forests in South India, is divided into five ecological zones: coastal, northern evergreen, southern evergreen, moist deciduous, and dry deciduous. The heavily-populated coastal zone includes mangrove forests and estuarine wetlands. The evergreen forests are particularly rich in the diversity of plant species which they support — including wild relatives of a number of cultivated plants. They also serve a vital function in watershed conservation. The moist deciduous forests are rich in bird species; both moist and dry deciduous forests include a number of freshwater ponds and lakes that support a high diversity of aquatic birds.Reviewing the overall distribution of biodiversity, we identify specific localities — including estuaries, evergreen forests, and moist deciduous forests — which should be set aside as Nature reserves. These larger reserves must be complemented by a network of traditionally-protected sacred groves and sacred trees that are distributed throughout the district and that protect today, for instance, the finest surviving stand of dipterocarp trees.We also spell out the necessary policy-changes in overall development strategy that should stem the ongoing decimation of biodiversity. These include (1) revitalizing community-based systems of sustainable management of village forests and protection of sacred groves and trees; (2) reorienting the usage-pattern of reserve forests from production of a limited variety of timber and softwood species for industrial consumers, to production of a larger diversity of non-wood forest produce of commercial value to support the rural economy; (3) utilizing marginal lands under private ownership for generating industrial wood supplies; and (4) provision of incentives for in situ maintenance of land-races of cultivated plants — especially evergreen, fruit-yielding trees — by the local people.It is proposed that this broad framework be now taken to the local communities, and that an action-plan be developed on the basis of inputs provided — and initiatives taken — by them.

Phytophthora cinnamomi and Australia's biodiversity: impacts, predictions and progress towards control

2008 ◽  
Vol 56 (4) ◽  
pp. 279 ◽  
Author(s):  
David M. Cahill ◽  
James E. Rookes ◽  
Barbara A. Wilson ◽  
Lesley Gibson ◽  
Keith L. McDougall
Keyword(s):  
Management Practices ◽  
Phytophthora Cinnamomi ◽  
Species Abundance ◽  
Ecological Communities ◽  
Complete Control ◽  
Natural Systems ◽  
Limited Effectiveness ◽  
Federal Initiatives ◽  
Serious Disease ◽  
Made In

Phytophthora cinnamomi continues to cause devastating disease in Australian native vegetation and consequently the disease is listed by the Federal Government as a process that is threatening Australia’s biodiversity. Although several advances have been made in our understanding of how this soil-borne pathogen interacts with plants and of how we may tackle it in natural systems, our ability to control the disease is limited. The pathogen occurs widely across Australia but the severity of its impact is most evident within ecological communities of the south-west and south-east of the country. A regional impact summary for all states and territories shows the pathogen to be the cause of serious disease in numerous species, a significant number of which are rare and threatened. Many genera of endemic taxa have a high proportion of susceptible species including the iconic genera Banksia, Epacris and Xanthorrhoea. Long-term studies in Victoria have shown limited but probably unsustainable recovery of susceptible vegetation, given current management practices. Management of the disease in conservation reserves is reliant on hygiene, the use of chemicals and restriction of access, and has had only limited effectiveness and not provided complete control. The deleterious impacts of the disease on faunal habitat are reasonably well documented and demonstrate loss of individual animal species and changes in population structure and species abundance. Few plant species are known to be resistant to P. cinnamomi; however, investigations over several years have discovered the mechanisms by which some plants are able to survive infection, including the activation of defence-related genes and signalling pathways, the reinforcement of cell walls and accumulation of toxic metabolites. Manipulation of resistance and resistance-related mechanisms may provide avenues for protection against disease in otherwise susceptible species. Despite the advances made in Phytophthora research in Australia during the past 40 years, there is still much to be done to give land managers the resources to combat this disease. Recent State and Federal initiatives offer the prospect of a growing and broader awareness of the disease and its associated impacts. However, awareness must be translated into action as time is running out for the large number of susceptible, and potentially susceptible, species within vulnerable Australian ecological communities.

scholarly journals Species richness, phylogenetic diversity and phylogenetic structure patterns of exotic and native plants along an elevational gradient in the Himalaya

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kumar Manish
Keyword(s):  
Species Richness ◽  
Exotic Species ◽  
Native Species ◽  
Phylogenetic Diversity ◽  
Elevational Gradient ◽  
Species Assemblages ◽  
Native Plant ◽  
Phylogenetic Structure ◽  
Phylogenetic Overdispersion ◽  
The Himalaya

Abstract Background So far, macroecological studies in the Himalaya have mostly concentrated on spatial variation of overall species richness along the elevational gradient. Very few studies have attempted to document the difference in elevational richness patterns of native and exotic species. In this study, this knowledge gap is addressed by integrating data on phylogeny and elevational distribution of species to identify the variation in species richness, phylogenetic diversity and phylogenetic structure of exotic and native plant species along an elevational gradient in the Himalaya. Results Species distribution patterns for exotic and native species differed; exotics tended to show maximum species richness at low elevations while natives tended to predominate at mid-elevations. Native species assemblages showed higher phylogenetic diversity than the exotic species assemblages over the entire elevational gradient in the Himalaya. In terms of phylogenetic structure, exotic species assemblages showed majorly phylogenetic clustering while native species assemblages were characterized by phylogenetic overdispersion over the entire gradient. Conclusions The findings of this study indicate that areas with high native species richness and phylogenetic diversity are less receptive to exotic species and vice versa in the Himalaya. Species assemblages with high native phylogenetic overdispersion are less receptive to exotic species than the phylogenetically clustered assemblages. Different ecological processes (ecological filtering in case of exotics and resource and niche competition in case of natives) may govern the distribution of exotic and native species along the elevational gradient in the Himalaya.

Sign in / Sign up

Export Citation Format

Share Document