scholarly journals Phylogenetic dispersion and diversity in regional assemblages of seed plants in China

2019 ◽  
Vol 116 (46) ◽  
pp. 23192-23201 ◽  
Author(s):  
Hong Qian ◽  
Tao Deng ◽  
Yi Jin ◽  
Lingfeng Mao ◽  
Dan Zhao ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Phylogenetic Diversity ◽  
Large Scale ◽  
Environmental Drivers ◽  
Seed Plants ◽  
Niche Conservatism ◽  
Phylogenetic Distance ◽  
Phylogenetic Relatedness ◽  
Phylogenetic Niche Conservatism ◽  
Phylogenetic Dispersion

Species assemble into communities through ecological and evolutionary processes. Phylogenetic niche conservatism—the tendency of species to retain ancestral ecological distributions—is thought to influence which species from a regional species pool can persist in a particular environment. We analyzed data for seed plants in China to test hypotheses about the distribution of species within regional floras. Of 16 environmental variables, actual evapotranspiration, minimum temperature of the coldest month, and annual precipitation most strongly influenced regional species richness, phylogenetic dispersion, and phylogenetic diversity for both gymnosperms (cone-bearing plants) and angiosperms (flowering plants). For most evolutionary clades at, and above, the family level, the relationships between metrics of phylogenetic dispersion (i.e., average phylogenetic distance among species), or phylogenetic diversity, and the 3 environmental variables were consistent with the tropical niche conservatism hypothesis, which predicts closer phylogenetic relatedness and reduced phylogenetic diversity with increasing environmental stress. The slopes of the relationships between phylogenetic relatedness and the 3 environmental drivers identified in this analysis were steeper for primarily tropical clades, implying greater niche conservatism, than for primarily temperate clades. These observations suggest that the distributions of seed plants across large-scale environmental gradients in China are constrained by conserved adaptations to the physical environment, i.e., phylogenetic niche conservatism.

scholarly journals Environmental Drivers of Diversification and Hybridization in Neotropical Butterflies

2021 ◽  
Vol 9 ◽  
Author(s):  
Nicol Rueda-M ◽  
Fabian C. Salgado-Roa ◽  
Carlos H. Gantiva-Q ◽  
Carolina Pardo-Díaz ◽  
Camilo Salazar
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
Distribution Patterns ◽  
Environmental Drivers ◽  
General Distribution ◽  
Ecological Interactions ◽  
Future Studies ◽  
Topographic Complexity ◽  
Geographic Patterns

Studying how the environment shapes current biodiversity patterns in species rich regions is a fundamental issue in biogeography, ecology, and conservation. However, in the Neotropics, the study of the forces driving species distribution and richness, is mostly based on vertebrates and plants. In this study, we used 54,392 georeferenced records for 46 species and 1,012 georeferenced records for 38 interspecific hybrids of the Neotropical Heliconius butterflies to investigate the role of the environment in shaping their distribution and richness, as well as their geographic patterns of phylogenetic diversity and phylogenetic endemism. We also evaluated whether niche similarity promotes hybridization in Heliconius. We found that these insects display five general distribution patterns mostly explained by precipitation and isothermality, and to a lesser extent, by altitude. Interestingly, altitude plays a major role as a predictor of species richness and phylogenetic diversity, while precipitation explains patterns of phylogenetic endemism. We did not find evidence supporting the role of the environment in facilitating hybridization because hybridizing species do not necessarily share the same climatic niche despite some of them having largely overlapping geographic distributions. Overall, we confirmed that, as in other organisms, high annual temperature, a constant supply of water, and spatio-topographic complexity are the main predictors of diversity in Heliconius. However, future studies at large scale need to investigate the effect of microclimate variables and ecological interactions.

scholarly journals Local-Scale Environmental Filtering Shape Plant Taxonomic and Phylogenetic Diversity in the Isolated Amazonian Tepui (Tepequém Table Mountain)

2021 ◽  
Author(s):  
Prímula Campos ◽  
Carlos Ernesto Schaefer ◽  
Vanessa Pontara ◽  
Márcio Xavier ◽  
José Frutuoso Vale Júnior ◽  
...  
Keyword(s):  
Species Richness ◽  
Soil Properties ◽  
Community Assembly ◽  
Altitudinal Gradient ◽  
Phylogenetic Diversity ◽  
Local Scale ◽  
Environmental Drivers ◽  
Phylogenetic Distance ◽  
Phylogenetic Structure ◽  
Table Mountain

Abstract Understanding how environmental drivers induce changes in plant composition and diversity across evolutionary time can provide important insights into the mechanisms of community assembly. We evaluated how taxonomic and phylogenetic diversity and structure of plant communities change along a local-scale edaphic and topographic gradient in the Tepequém table mountain, Brazilian Amazon. We selected three phytophysiognomies along the altitudinal gradient: Open Rupestrian Grassland, Shrubby Rupestrian Grassland, and Forest. We compared community composition and taxonomic and phylogenetic diversity between phytophysiognomies, and we tested regression linear effect models to investigate the effect of altitude and soil properties on taxonomic and phylogenetic diversity. The highest species richness and phylogenetic diversity were found at lower elevation for Forest. Mean pairwise phylogenetic distance, mean nearest taxon phylogenetic distance, and all standardised phylogenetic metrics were significantly lower in Shrubby Rupestrian Grassland. This phytophysiognomy showed phylogenetic clustering. Forest showed a cluster pattern when only terminal nodes are considered and random dispersion to deep phylogenetic nodes. Open Rupestrian Grassland also showed random phylogenetic structure. The regression analyses showed that species richness and different phylogenetic diversity metrics were explained by altitude and soil properties. However, standardised metrics were not explained by these environmental variables. Comprehensive studies including the role of environmental drivers in plant evolutionary history along the altitudinal gradient are necessary for explaining community assembly patterns and provide additional information for conservation planning.

scholarly journals Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments

2020 ◽  
Author(s):  
Guillaume Lentendu ◽  
Micah Dunthorn
Keyword(s):  
Large Scale ◽  
Mutual Exclusion ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Null Models ◽  
Phylogenetic Distance ◽  
Phylogenetic Relatedness ◽  
Network Analyses ◽  
Terrestrial Environments ◽  
Marine Surface

AbstractWe used two large-scale metabarcoding datasets to evaluate phylogenetic signals at global marine and regional terrestrial scales using co-occurrence and co-exclusion networks. Phylogenetic relatedness was estimated using either global pairwise sequence distance or phylogenetic distance and the significance of observed patterns relating networks and phylogenies were evaluated against two null models. In all datasets, we found that phylogenetically close OTUs significantly co-occurred more often, and OTUs with intermediate phylogenetic relatedness co-occurred less often, than expected by chance. Phylogenetically close OTUs co-excluded less often than expected by chance in the marine datasets only. Simultaneous excess of co-occurrences and co-exclusions were observed in the inversion zone between close and intermediate phylogenetic distance classes in marine surface. Similar patterns were observed by using either pairwise sequence or phylogenetic distances, and by using both null models. These results suggest that environmental filtering and dispersal limitation are the preponderant forces driving co-occurrence of protists in both environments, while signal of competitive exclusion was only detected in the marine surface environment. The discrepancy in the co-exclusion pattern is potentially linked to the individual environments: water bodies are more homogeneous while tropical forest soils contain a myriad of nutrient rich micro-environment reducing the strength of mutual exclusion.

Biogeographical patterns and processes in the genus group Scotussae (Acrididae: Melanoplinae): an integrative approach

2020 ◽  
Vol 131 (2) ◽  
pp. 417-433
Author(s):  
María Celeste Scattolini ◽  
Andrés Lira-Noriega ◽  
Viviana Andrea Confalonieri ◽  
Silvia Pietrokovsky ◽  
María Marta Cigliano
Keyword(s):  
Ecological Niche ◽  
Phylogenetic Signal ◽  
Total Evidence ◽  
Integrative Approach ◽  
Niche Conservatism ◽  
Phylogenetic Distance ◽  
Ecological Processes ◽  
Phylogenetic Niche Conservatism ◽  
Patterns And Processes

Abstract A biogeographical study of the genus group Scotussae, a clade of grasshoppers endemic to the subtropical temperate region of the La Plata Basin, South America, was performed within a phylogenetic context to test whether wing reduction reflects evolutionary and ecological processes within the clade. We used an integrative biogeographical approach to determine the role of geohistorical events, geography, ecology and phylogenetic niche conservatism on the distribution and diversification processes of the group. We performed a total evidence phylogenetic analysis and tested the phylogenetic signal of ecological niche traits (niche optimum and niche breadth). We also assessed the degree to which phylogenetic distance is correlated with geographical and ecological niche traits and we used BioGeoBEARS to estimate ancestral ranges. The results provided evidence for phylogenetic niche conservatism as well as a significant association between phylogeny and both geographical and, more strongly, ecological traits. Two main clades were clearly associated with wing development, and evidence points to the evolutionary and ecological processes within these two groups being different. The Brachypterous clade shows evidence that allopatric speciation was the main source of diversification, while for the Macropterous clade sympatric speciation seems more likely.

scholarly journals Co-occurrences of tropical trees in eastern South America: disentangling abiotic and biotic forces

Plant Ecology ◽  
2021 ◽  
Author(s):  
Emma-Liina Marjakangas ◽  
Otso Ovaskainen ◽  
Nerea Abrego ◽  
Vidar Grøtan ◽  
Alexandre A. de Oliveira ◽  
...  
Keyword(s):  
South America ◽  
Tree Species ◽  
Large Scale ◽  
Environmental Filtering ◽  
Limiting Similarity ◽  
Phylogenetic Relatedness ◽  
Biogeographical Regions ◽  
Dependent Processes ◽  
Occurrence Of Species

AbstractSpecies 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.

scholarly journals Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

2021 ◽  
Author(s):  
Lina Kloub ◽  
Sean Gosselin ◽  
Matthew Fullmer ◽  
Joerg Graf ◽  
J Peter Gogarten ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Families ◽  
Microbial Evolution ◽  
Phylogenetic Distance ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
A Genome ◽  
Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

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