Explore the vast range of titles available.

Comparison is fundamental to evolutionary anthropology. When scientists study chimpanzee cognition, for example, they compare chimp performance on cognitive tasks to the performance of human children on the same tasks. And when new fossils are found, such as those of the tiny humans of Flores, scientists compare these remains to other fossils and contemporary humans. Comparison provides a way to draw general inferences about the evolution of traits and therefore has long been the cornerstone of efforts to understand biological and cultural diversity. Individual studies of fossilized remains, living species, or human populations are the essential units of analysis in a comparative study; bringing these elements into a broader comparative framework allows the puzzle pieces to fall into place, creating a means of testing adaptive hypotheses and generating new ones. With this book, Charles L. Nunn intends to ensure that evolutionary anthropologists and organismal biologists have the tools to realize the potential of comparative research. Nunn provides a wide-ranging investigation of the comparative foundations of evolutionary anthropology in past and present research, including studies of animal behavior, biodiversity, linguistic evolution, allometry, and cross-cultural variation. He also points the way to the future, exploring the new phylogeny-based comparative approaches and offering a how-to manual for scientists who wish to incorporate these new methods into their research.

Altitude, as a key environmental factor, shapes the spatial patterns of species diversity, phylogenetic diversity, and community phylogenetic structure. Studying grassland diversity and phylogenetic structure along altitudinal gradients helps clarify how altitude-driven environmental changes influence community assembly, and reveal vertical patterns in community formation. This study examines grasslands at 1300–2500 m elevation in the Two-River Source Forest Area, Altai Mountains, Xinjiang. Six elevation gradients (200 m intervals) were surveyed with 90 grassland quadrats, documenting community characteristics and environmental data. The study analyzes the patterns of species composition, diversity, and phylogeny across different elevation gradients and explores their relationships with key environmental factors. The results indicate that the grassland species composition is dominated by species from the Poaceae, Rosaceae, and Asteraceae families, with Poa annua (annual bluegrass) being the dominant species within Poaceae. The species diversity along the elevation gradient exhibits a bimodal trend, with an initial increase, followed by a decrease, another increase, and finally a decline as the elevation rises. In contrast, phylogenetic diversity shows a unimodal pattern, characterized by an initial increase followed by a decline with increasing elevation. Although the phylogenetic structure did not exhibit a significant trend of transitioning from divergence to clustering along the altitudinal gradient, the overall phylogenetic pattern of grassland communities tended toward clustering. Further analysis reveals significant correlations between species diversity and environmental factors such as temperature, precipitation, forest cover, and soil moisture. However, no environmental factors were found to have a significant correlation with the phylogenetic indices.

Periodic climatic oscillations and species dispersal during the postglacial period are two important causes of plant assemblage and distribution on the Qinghai‐Tibet Plateau (QTP). To improve our understanding of the bio‐geological histories of shrub communities on the QTP, we tested two hypotheses. First, the intensity of climatic oscillations played a filtering role during community structuring. Second, species dispersal during the postglacial period contributed to the recovery of species and phylogenetic diversity and the emergence of phylogenetic overdispersion. To test these hypotheses, we investigated and compared the shrub communities in the alpine and desert habitats of the northeastern QTP. Notably, we observed higher levels of species and phylogenetic diversity in the alpine habitat than in the desert habitat, leading to phylogenetic overdispersion in the alpine shrub communities versus phylogenetic clustering in the desert shrub communities. This phylogenetic overdispersion increased with greater climate anomalies. These results suggest that (a) although climate anomalies strongly affect shrub communities, these phenomena do not act as a filter for shrub community structuring, and (b) species dispersal increases phylogenetic diversity and overdispersion in a community. Moreover, our investigation of the phylogenetic community composition revealed a larger number of plant clades in the alpine shrub communities than in the desert shrub communities, which provided insights into plant clade‐level differences in the phylogenetic structures of alpine and desert shrub communities in the northeastern QTP. In this manuscript, we studied the phylogenetic community composition of shrub in the northeastern Qinghai‐Tibetan Plateau and found that existing significant difference in phylogenetic community composition of shrub communities from different habitats (desert and alpine), which interpreted phylogenetic community structure from perspective of phylogenetic community composition, enhanced our knowledge of shrub, and helped us to obtain further interpretation for present‐day community structure from historical processes.

Summary One of the most pervasive concepts in the study of community assembly is the metaphor of the environmental filter, which refers to abiotic factors that prevent the establishment or persistence of species in a particular location. The metaphor has its origins in the study of community change during succession and in plant community dynamics, although it has gained considerable attention recently as part of a surge of interest in functional trait and phylogenetic‐based approaches to the study of communities. While the filtering metaphor has clear utility in some circumstances, it has been challenging to reconcile the environmental filtering concept with recent developments in ecological theory related to species coexistence. These advances suggest that the evidence used in many studies to assess environmental filtering is insufficient to distinguish filtering from the outcome of biotic interactions. We re‐examine the environmental filtering metaphor from the perspective of coexistence theory. In an effort to move the discussion forward, we present a simple framework for considering the role of the environment in shaping community membership, review the literature to document the evidence typically used in environmental filtering studies and highlight research challenges to address in coming years. The current usage of the environmental filtering term in empirical studies likely overstates the role abiotic tolerances play in shaping community structure. We recommend that the term ‘environmental filtering’ only be used to refer to cases where the abiotic environment prevents establishment or persistence in the absence of biotic interactions, although only 15% of the studies in our review presented such evidence. Finally, we urge community ecologists to consider additional mechanisms aside from environmental filtering by which the abiotic environment can shape community pattern. Lay Summary

1. The subdiscipline of ‘community phylogenetics’ is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co-occurring species within a community is commonly used as a proxy to identify which community assembly processes may have structured a particular community: phylogenetic clustering as a proxy for abiotic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition.2. We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii)trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) communities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylogenetic dispersion is driven predominantly by local and present-day processes.3. Moreover, technical sophistication of the phylogenetic-patterns-as-proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes.4. Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macroevolutionary diversification of habitat lineage-pools (i.e. phylogenetic-patterns-as-result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage-pools and how it affects present-day species coexistence in local communities (i.e. phylogeneticpatterns- as-cause approach).5. We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage-pool, for example through competition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage-pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition.

This book presents a history of microbial evolutionary biology from the 19th century to the present. It follows the research of molecular evolutionists who explore the origins of the genetic system and the primary life forms: three domains and multiple kingdoms, created by mechanisms very unlike those considered by Darwin and his followers.

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.

The study of community assembly processes currently involves (a) long-standing questions about the relative importance of environmental filtering vs. niche partitioning in a wide range of ecosystems, and (b) more recent questions about methodology. The rapidly growing field of community phylogenetics has generated debate about the choice between functional traits and phylogenetic relationships for understanding species similarities, and has raised additional questions about the contribution of experimental vs. observational approaches to understanding evolutionary constraints on community assembly. In this study, we use traits, a phylogeny, and field surveys to identify the forces structuring communities of herbivorous marine amphipods and isopods living in adjacent seagrass and macroalgae. In addition, we compare our field results to a recently published mesocosm experiment that tested the effects of both trait and phylogenetic diversity on coexistence using the same species and system. With respect to community assembly processes, we found that environmental filtering was the dominant process in macroalgae habitats, that niche partitioning was the dominant process in seagrass habitats, and that the strength of these assembly mechanisms varied with seasonal fluctuations in environmental conditions and resource availability. These patterns are indicated by both phylogenetic relationships and trait distances, but the type of resources being partitioned in seagrass habitats can only be deciphered using trait data. Species coexisting in seagrass in the field differed not in their feeding niche but in traits related to microhabitat use, providing novel evidence of the relative importance of competition for food vs. habitat in structuring communities of phytophagous invertebrates. With respect to methodology, the results for seagrass habitats conflict with those obtained in mesocosms, where feeding trait diversity did promote coexistence and phylogenetic diversity had no effect. This contrast arises because a greater range of traits (some of which have much stronger phylogenetic signal than feeding traits) contribute to community assembly in the field. This highlights a mismatch between the processes that drive community assembly in the field and the processes we isolated in experimental tests, and illustrates that using phylogeny as a single proxy in both contexts may impede the synthesis of observational and experimental results.

1. It is now commonplace in community ecology to assess patterns of phylogenetic or functional diversity in order to inform our understanding of the assembly mechanisms that structure communities. While both phylogenetic and functional approaches have been used in conceptually similar ways, it is not clear if they both in fact reveal similar community diversity patterns or support similar inferences. We review studies that use both measures to determine the degree to which they support congruent patterns and inferences about communities. 2. We performed a literature review with 188 analyses from 79 published papers that compared some facet of phylogenetic (PD) and functional diversity (FD) in community ecology. These studies generally report four main cases in which phylogenetic and functional information are used together in community analyses, to determine if: (a) there were phylogenetic signals in the measured traits in communities; (b) PD and FD were correlated with one another; (c) standardized PD and FD measures similarly revealed patterns of community over- or under-dispersion; and (d) PD and FD were both related to other explanatory variables (e.g. elevation) similarly. 3. We found that the vast majority of studies found both strong phylogenetic signals in their traits and positive correlations of PD and FD measures across sites. However, and surprisingly, we found substantial incongruencies for the other tests. Phylogenetic and functional dispersion patterns were congruent only about half the time. Specifically, when communities were phylogenetically over-dispersed, these same communities were more likely to be functionally under-dispersed. Similarly, we found that phylogenetic and functional relationships with independent predictors were incongruent in about half of the analyses. 4. Synthesis. Phylogenetic signal tests and PD-FD correlations appear to strongly support the congruence between traits and phylogeny. It is surprising that strong phylogenetic signals appeared so ubiquitous given that ecological studies often analyse phylogenetically incomplete sets of species that have undergone ecological sorting. Despite the largely congruent findings based on phylogenetic signal tests and PD-FD correlations, we found substantial incongruencies when researchers assessed either dispersion patterns or relationships with independent predictors. We discuss a number of potential ecological, evolutionary and methodological reasons for these incongruencies. Phylogenetic and functional information might reflect species ecological differences unequally with phylogenies better reflecting multivariate conserved elements of ecological similarity, and single traits better able to capture recent divergence, and both elements influence ecological patterns.

Summary Hundreds of experiments have now manipulated species richness (SR) of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity (PD) among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than SR because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. Here, we reanalyse data from 16 experiments that have manipulated plant SR in grassland ecosystems and examined the impact on above‐ground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the PD of plants impacts average community biomass production as well as the stability of community biomass production through time. Using four complementary analyses, we show that, after statistically controlling for variation in SR, PD (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for SR, PD was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. In contrast to the non‐significant relationships between PD, biomass and stability, our analyses show that SR per se tends to increase the mean biomass production of plant communities, after controlling for PD. The relationship between SR and temporal variation in community biomass was either positive, non‐significant or negative depending on which analysis was used. However, the increases in community biomass with SR, independently of PD, always led to increased stability. These results suggest that PD is no better as a predictor of ecosystem functioning than SR. Synthesis. Our study on grasslands offers a cautionary tale when trying to relate PD to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of SR as a way to maintain productive and stable communities under changing environmental conditions. Lay Summary