scholarly journals Distribution and Community Assembly of Trees Along an Andean Elevational Gradient

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 326
Author(s):  
Samantha J. Worthy ◽  
Rosa A. Jiménez Paz ◽  
Álvaro J. Pérez ◽  
Alex Reynolds ◽  
Jennifer Cruse-Sanders ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Phylogenetic Analyses ◽  
Elevation Gradient ◽  
Elevational Gradient ◽  
Pairwise Distance ◽  
Phylogenetic Structure ◽  
Tree Ferns ◽  
Fern Species ◽  
Standardized Effect Sizes ◽  
Angiosperm Species

Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440–3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon–Weaver diversity, Simpson’s Dominance, Simpson’s Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations.

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.

scholarly journals For common community phylogenetic analyses, go ahead and use synthesis phylogenies

2018 ◽  
Author(s):  
Daijiang Li ◽  
Lauren Trotta ◽  
Hannah E. Marx ◽  
Julie M. Allen ◽  
Miao Sun ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Gene Sequence ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Pairwise Distance ◽  
Highly Correlated ◽  
Gene Sequence Data

AbstractShould we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

scholarly journals Avoiding potential biases in ses.PD estimations with the Picante software package

2019 ◽  
Author(s):  
Rafael Molina-Venegas
Keyword(s):  
Species Richness ◽  
Software Package ◽  
Phylogenetic Diversity ◽  
Phylogenetic Analyses ◽  
R Package ◽  
List Type ◽  
Routine Procedure ◽  
Phylogenetic Structure ◽  
Simulation Exercise ◽  
Simple Simulation

AbstractFaith’s phylogenetic diversity (PD) is one of the most widespread used indices of phylogenetic structure in the eco-phylogenetic literature. The metric became notably popular with the publication of the function pd as part of the Picante R package, which is nowadays a reference software for phylogenetic analyses.Because PD is not statistically independent of species richness, the routine procedure is to standardize the observed PD values for unequal richness across samples. The function ses.pd, which is also implemented in the Picante R package, is the reference function to conduct such standardization.Unfortunately, I have detected an anomaly in the function that may result in biased estimations of standardized PD values, particularly in communities with low species richness (i.e. less than four species) and unbalanced phylogenies.I conduct a simple simulation exercise to illustrate the issue and propose two alternative and easy to implement solutions to go around the problem.

scholarly journals Family Legacy: Depicting Diversity-Elevation Relationships of Tropical Tree Communities

2022 ◽  
Author(s):  
Vitor de Andrade Kamimura ◽  
Gabriel Mendes Marcusso ◽  
Gabriel Pavan Sabino ◽  
Marco Antonio Assis ◽  
Carlos Alfredo Joly ◽  
...  
Keyword(s):  
Elevational Gradient ◽  
Species Selection ◽  
Southeastern Brazil ◽  
Tropical Rainforests ◽  
Ecological Processes ◽  
Phylogenetic Structure ◽  
Diversity Pattern ◽  
Tree Communities ◽  
Fern Species ◽  
Unimodal Pattern

Abstract Unveiling the ecological processes driving diversity and its relationship to the environment remains a central goal in ecological studies. Here, we investigated the elevation effect on plant diversity patterns of tropical rainforests, using beta-, phylogenetic and alpha diversities. To do so, we compiled a forest dataset with 22,236 trees (DBH ≥ 4.8 cm) from 17 plots of 1 ha each along an elevational gradient (0 – 1,200 m a.s.l) in the Atlantic Forest of Southeastern Brazil. We found high phylogenetic and species rates of turnover – beta-diversity - along the elevational gradient. Alpha phylodiversity showed a monotonic decrease with increasing elevation, including or not fern species (a distantly related clade usually ignored in tropical ecology studies), while the phylogenetic structure was highly affected by the inclusion of fern trees. Species diversity showed a unimodal pattern for the whole community, and different patterns for the richest families. The diversity pattern of the whole community emerges from differences among species distribution of the richest families, while phylogenetic diversity seems to be gradually filtered by elevation. At intermediate elevations, higher species diversification within families might have led to different strategies and cooccurrence in tropical rainforests. We also showed that intricate effects of elevation in species assemblages can be better assessed using both ecological and evolutionary approaches, stressing the importance of species selection in diversity analyzes. Finally, we demonstrate that elevation has different effects on the species distributions of the richest families and warn that these differences should be considered in conservation planning.

Functional evenness of bird communities varies along the elevational gradient in Europe: Conservation implications

2019 ◽  
Author(s):  
Federico Morelli ◽  
Yanina
Keyword(s):  
Species Richness ◽  
Elevation Gradient ◽  
Bird Species ◽  
Elevational Gradient ◽  
Negative Association ◽  
Bird Communities ◽  
Breeding Bird ◽  
Bird Species Richness ◽  
Large Spatial Scale ◽  
Functional Evenness

ContextThe negative association between elevation and species richness is a well-recognized pattern in macro-ecology. ObjectivesThe aim of this study was to investigate changes in functional evenness of breeding bird communities along an elevation gradient in Europe. MethodsUsing the bird data from the EBCC Atlas of European Breeding Birds we estimated an index of functional evenness which can be assumed as a measure of the potential resilience of communities.ResultsOur findings confirm the existence of a negative association between elevation and bird species richness in all European eco regions. However, we also explored a novel aspect of this relationship, important for conservation: Our findings provide evidence at large spatial scale of a negative association between the functional evenness (potential community resilience) and elevation, independent of the eco region. We also found that the Natura2000 protected areas covers the territory most in need of protection, those characterized by bird communities with low potential resilience, in hilly and mountainous areas.ConclusionsThese results draw attention to European areas occupied by bird communities characterized by a potential lower capacity to respond to strong ecological changes, and, therefore, potentially more exposed to risks for conservation.

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 Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

scholarly journals Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae

2021 ◽  
Author(s):  
Julien Guglielmini ◽  
Melanie Hennart ◽  
Edgar Badell ◽  
Julie Toubiana ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Corynebacterium Diphtheriae ◽  
Phylogenetic Structure ◽  
Genomic Epidemiology ◽  
Short Timescale ◽  
Genomic Taxonomy ◽  
Sporadic Cases ◽  
Small Clusters ◽  
Genome Scale ◽  
Analytical Approaches

Background Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. Methods We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST genes diversity among 602 isolates from sporadic clinical cases, small clusters or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. Results The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii . We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold, and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed short timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500 cgMLST mismatches threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible at https://bigsdb.pasteur.fr/diphtheria . Conclusions Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae . The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies into the ecology, evolution and virulence heterogeneity among C. diphtheriae sublineages.

scholarly journals Fenestelloid clades of the Cucurbitariaceae

2020 ◽  
Vol 44 (1) ◽  
pp. 1-40
Author(s):  
W.M. Jaklitsch ◽  
H. Voglmayr
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Lsu Rdna ◽  
Phylogenetic Structure ◽  
Protein Coding ◽  
Molecular Phylogenetic ◽  
Type Studies ◽  
Asexual Morphs ◽  
One New Species

Fresh collections and their ascospore and conidial isolates backed up by type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-, complete ITS, partial LSU rDNA, rpb2, tef1 and tub2 sequences were used to evaluate the boundaries and species composition of Fenestella and related genera of the Cucurbitariaceae. Eight species, of which five are new, are recognised in Fenestella s.str., 13 in Parafenestella with eight new species and two in the new genus Synfenestella with one new species. Cucurbitaria crataegi is combined in Fenestella, C. sorbi in Synfenestella, Fenestella faberi and Thyridium salicis in Parafenestella. Cucurbitaria subcaespitosa is distinct from C. sorbi and combined in Neocucurbitaria. Fenestella minor is a synonym of Valsa tetratrupha, which is combined in Parafenestella. Cucurbitaria marchica is synonymous with Parafenestella salicis, Fenestella bavarica with S. sorbi, F. macrospora with F. media, and P. mackenziei is synonymous with P. faberi, and the latter is lectotypified. Cucurbitaria sorbi, C. subcaespitosa and Fenestella macrospora are lecto- and epitypified, Cucurbitaria crataegi, Fenestella media, F. minor and Valsa tetratrupha are epitypified in order to stabilise the names in their phylogenetic positions. A neotype is proposed for Thyridium salicis. A determinative key to species is given. Asexual morphs of fenestelloid fungi are phoma-like and do not differ from those of other representatives of the Cucurbitariaceae. The phylogenetic structure of the fenestelloid clades is complex and can only be resolved at the species level by protein-coding genes, such as rpb2, tef1 and tub2. All fungal species studied here occur, as far as has been possible to determine, on members of Diaporthales, most frequently on asexual and sexual morphs of Cytospora.

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