Phylogenetic and non-phylogenetic patterns in the richness, frequency and composition of links in a herbivore-parasitoid interaction network
Frazer SinclairChang‐Ti TangRichard I. BaileyGyörgy CsókaGeorge MelikaJames A. NichollsJ. L. Nieves‐AldreyAlexander ReissY. Miles ZhangAlbert B. PhillimoreKarsten SchönroggeGraham N. Stone
0
Citation
140
Reference
10
Related Paper
Abstract:
Revealing processes that structure species interactions is central to understanding community assembly and dynamics. Species interact via their phenotypes, but identifying and quantifying the traits that structure species-specific interactions (links) can be challenging. Where these traits show phylogenetic signal, however, link properties may be predictable using models that incorporate phylogenies in place of trait data. We analysed variation in link richness, frequency, and species identity in a multi-site dataset of interactions between oak cynipid galls and parasitoid natural enemies, using a Bayesian mixed modelling framework allowing concurrent fitting of phylogenetic effects of both trophic levels. In both link incidence (presence/absence) and link frequency datasets, we identified strong signatures of cophylogeny (related parasitoids attack related host galls) alongside patterns independent of either phylogeny. Our results are robust to simulations of substantially reduced sample completeness, and are consistent with the structuring of trophic interactions by a combination of phylogenetically conserved and convergently evolving traits in both trophic levels. We discuss our results in light of phenotypic traits thought to structure gall-parasitoid interactions and consider wider applications of this approach, including inference of underlying community assembly processes and prediction of economically important trophic interactions.Keywords:
Phylogenetic diversity
Should 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, was 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.
Community
Cite
Citations (96)
Understanding variation of species richness along latitudinal gradients, with more species toward the tropics, represents a challenge for ecologists. Species richness also varies according to the available area, with more species in larger regions, with area and latitude posited as major drivers of richness variations. However, species richness does not fully capture the evolutionary history behind those patterns. Phylogenetic diversity can provide insights on the role of time and evolutionary drivers of environmental gradients. We analyzed here the latitudinal gradient of endemic snakes from the Atlantic Forest of South America, a megadiverse and highly threatened portion of the Neotropics. We assessed the effect of area and average clade age on species richness and phylogenetic diversity, testing whether species richness and phylogenetic diversity increase with area availability and in lower latitudes. We found that area can predict species richness, but not phylogenetic diversity. Brazilian southeastern mountain ranges include larger patches of Atlantic Forest and the highest richness levels, but generally harboring snakes from relatively recent clades (neoendemics). There is a negative relationship between species richness and average clade age along the latitudinal gradient, with older clades found mainly in northern portions, increasing phylogenetic diversity at lower latitudes. Different dimensions of diversity, species richness and phylogenetic diversity, are thus affected in different ways by area and time for speciation in the Atlantic Forest, and this may be a trend in highly diverse tropical regions.
Phylogenetic diversity
Gamma diversity
Cite
Citations (0)
Cite
Citations (6)
Both native and non-native taxa richness patterns are useful for evaluating areas of greatest conservation concern. To determine those patterns, we analyzed fish and macroinvertebrate taxa richness data obtained at 3475 sites collected by the USEPA's National Rivers and Streams Assessment. We also determined which natural and anthropogenic variables best explained patterns in regional richness. Macroinvertebrate and fish richness increased with the number of sites sampled per region. Therefore, we determined residual taxa richness from the deviation of observed richness from predicted richness given the number of sites per region. Regional richness markedly exceeded average site richness for both macroinvertebrates and fish. Predictors of macroinvertebrate-genus and fish-species residual-regional richness differed. Air temperature was an important predictor in both cases but was positive for fish and negative for macroinvertebrates. Both natural and land use variables were significant predictors of regional richness. This study is the first to determine mean site and regional richness of both fish and aquatic macroinvertebrates across the conterminous USA, and the key anthropogenic drivers of regional richness. Thus, it offers important insights into regional USA biodiversity hotspots.
Cite
Citations (10)
Abstract Should 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.
Phylogenetic diversity
Trait
Phylogenetic comparative methods
Tree (set theory)
Cite
Citations (3)
Jaccard index
Independence
Cite
Citations (1)
Understanding variation of species richness along latitudinal gradients, with more species toward the tropics, represents a challenge for ecologists. Species richness also varies according to the available area, with more species in larger regions, with area and latitude posited as major drivers of richness variations. However, species richness does not fully capture the evolutionary history behind those patterns. Phylogenetic diversity can provide insights on the role of time and evolutionary drivers of environmental gradients. We analyzed here the latitudinal gradient of endemic snakes from the Atlantic Forest of South America, a megadiverse and highly threatened portion of the Neotropics. We assessed the effect of area and average clade age on species richness and phylogenetic diversity, testing whether species richness and phylogenetic diversity increase with area availability and in lower latitudes. We found that area can predict species richness, but not phylogenetic diversity. Brazilian southeastern mountain ranges include larger patches of Atlantic Forest and the highest richness levels, but generally harboring snakes from relatively recent clades (neoendemics). There is a negative relationship between species richness and average clade age along the latitudinal gradient, with older clades found mainly in northern portions, increasing phylogenetic diversity at lower latitudes. Different dimensions of diversity, species richness and phylogenetic diversity, are thus affected in different ways by area and time for speciation in the Atlantic Forest, and this may be a trend in highly diverse tropical regions.
Phylogenetic diversity
Gamma diversity
Cite
Citations (0)
What are the local community consequences of changes in regional species richness and composition? To answer this question we followed the assembly of microarthropod communities in defaunated areas of moss, embedded in a larger moss "region." Regions were created by combining moss from spatially distinct sites, resulting in regional species pools that differed in both microarthropod richness and composition, but not area. Regional effects were less important than seasonality for local richness. Initial differences in regional richness had no direct effect on local species richness at any time along a successional gradient of 0.5-16 months. The structure of the regional pool affected both local richness and local composition, but these effects were seasonally dependent. Local species richness differed substantially between dates along the successional gradient and continued to increase 16 months after assembly began. To the best of our knowledge, this is the first critical test of saturation theory that experimentally manipulates regional richness. Further, our results failed to support the most important mechanisms proposed to explain the local richness-regional richness relationship. The results demonstrate that complicated interactions between assembly time, seasonality, and regional species pools contribute to structuring local species richness and composition in this community.
Cite
Citations (43)
Summary Urbanization is increasing faster than ever, contributing to a global extinction crisis. Recently, scientists have debated whether species richness on local and regional scales is mostly declining, but long‐term changes in phylogenetic richness and divergence were largely disregarded. Space‐for‐time approaches revealed that plant phylogenetic divergence is lower in urban than in non‐urban areas. However, such approaches cannot fully disentangle the relative importance of the biotic processes that drive temporal changes in diversity. Using a unique European urban flora covering 320 years in seven time steps, combined with a comprehensive plant phylogeny, we examined (i) how species richness changed with urbanization over time; (ii) whether trends in phylogenetic richness and divergence parallel trends in species richness; and (iii) whether species extirpation or immigration is driving these changes. We found that over time urban species richness increased, but phylogenetic richness and divergence decreased. Extirpations of phylogenetically distinct native species and immigrations of phylogenetically common native and non‐native species caused a non‐random loss of phylogenetic diversity. Our analyses suggest that if future extirpations and immigrations continue to follow the patterns observed over history, this loss will continue. Synthesis and applications . Measures to protect phylogenetic diversity should combine the protection of threatened habitats and their species with the maintenance of habitats that mitigate heat and safeguard evolutionary history. Urban planners should consider a phylogenetically diverse set of species when designing green spaces.
Phylogenetic diversity
Extinction (optical mineralogy)
Cite
Citations (55)