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1. Biomes as evolutionary arenas: Convergence and conservatism in the trans‐continental succulent biome

   https://doi.org/10.1111/geb.13089  

   Ringelberg, Jens J. ; Zimmermann, Niklaus E. ; Weeks, Andrea ; Lavin, Matt ; Hughes, Colin E. ; Moles, ed., Angela ( March 2020 , Global Ecology and Biogeography)

   Historically, biomes have been defined based on their structurally and functionally similar vegetation, but there is debate about whether these similarities are superficial, and about how biomes are defined and mapped. We propose that combined assessment of evolutionary convergence of plant functional traits and phylogenetic biome conservatism provides a useful approach for characterizing biomes. We focus on the little‐known succulent biome, a trans‐continentally distributed assemblage of succulent‐rich, drought‐deciduous, fire‐free forest, thicket and scrub vegetation as a useful exemplar biome to gain insights into these questions.

   Global lowland (sub)tropics.

   Present.

   Angiosperms.

   We use a model ensemble approach to model the distribution of 884 species of stem succulents, a plant functional group representing a striking example of evolutionary convergence. Using this model, phylogenies, and species occurrence data, we quantify phylogenetic succulent biome conservatism for 10 non‐succulent trans‐continental plant clades including prominent elements of the succulent biome, representing over 800 species.

   The geographical and climatic distributions of stem succulents provide an objective and quantitative proxy for mapping the distribution of the succulent biome. High fractions of succulent biome occupancy across continents suggest all 10 non‐succulent study clades are phylogenetically conserved within the succulent biome.

   The trans‐continental succulent and savanna biomes both show evolutionary convergence in key biome‐related plant functional traits. However, in contrast to the savanna biome, which was apparently assembled via repeated local recruitment of lineages via biome shifts from adjacent biomes within continents, the succulent biome forms a coherent trans‐continental evolutionary arena for drought‐adapted tropical biome conserved lineages. Recognizing the important functional differences between the succulent‐rich, grass‐poor, fire‐free succulent biome and the grass‐dominated, succulent‐poor, fire‐prone savanna biome, and defining them as distinct seasonally dry tropical biomes, occupying essentially non‐overlapping distributions, provides critical insights into tropical biodiversity and the extent of biome stasis versus biome shifting.

    

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2. The interaction of phylogeny and community structure: Linking the community composition and trait evolution of clades

   https://doi.org/10.1111/geb.12938  

   Pearse, William D. ; Legendre, Pierre ; Peres‐Neto, Pedro R. ; Davies, T. Jonathan ; Baselga, ed., Andres ( July 2019 , Global Ecology and Biogeography)

   Community phylogenetic studies use information about the evolutionary relationships of species to understand the ecological processes of community assembly. A central premise of the field is that the evolution of species maps onto ecological patterns, and phylogeny reveals something more than species traits alone about the ecological mechanisms structuring communities, such as environmental filtering, competition, and facilitation. We argue, therefore, that there is a need for better understanding and modelling of the interaction of phylogeny with species traits and community composition.

   We outline a new approach that identifies clades that are ecophylogenetically clustered or overdispersed and assesses whether those clades have different rates of trait evolution. Ecophylogenetic theory would predict that the traits of clustered or overdispersed clades might have evolved differently, in terms of either tempo (fast or slow) or mode (e.g., under constraint or neutrally). We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between the ecological co‐occurrence patterns of a species and its evolutionary history.

   Using an empirical dataset of mammals from around the world, we identify two clades of rodents whose species tend not to co‐occur in the same local assemblages (are phylogenetically overdispersed) and find independent evidence of slower rates of body mass evolution in these clades. Our approach, which assumes nothing about the mode of species trait evolution but instead seeks to explain it using ecological information, presents a new way to examine ecophylogenetic structure.

    

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3. Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

   https://doi.org/10.1002/ece3.8649  

   Pardo‐De la Hoz, Carlos J. ; Medeiros, Ian D. ; Gibert, Jean P. ; Chagnon, Pierre‐Luc ; Magain, Nicolas ; Miadlikowska, Jolanta ; Lutzoni, François ( March 2022 , Ecology and Evolution)

   Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package athttps://github.com/cjpardodelahoz/pss.

    

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4. Time for speciation and niche conservatism explain the latitudinal diversity gradient in clupeiform fishes

   https://doi.org/10.1111/jbi.14465  

   Egan, Joshua P. ; Bloom, Devin D. ; Simons, Andrew M. ( November 2022 , Journal of Biogeography)

   The latitudinal diversity gradient of increasing species richness from poles to equator is one of the most striking and pervasive spatial patterns of biodiversity. Climate appears to have been key to the formation of the latitudinal diversity gradient, but the processes through which climate shaped species richness remain unclear. We tested predictions of the time for speciation, carrying capacity and diversification rate latitudinal diversity gradient hypotheses in a trans‐marine/freshwater clade of fishes.

   Global in marine and freshwater environments.

   Clupeiformes (anchovies, herrings, sardines and relatives).

   We tested predictions of latitudinal diversity gradient hypotheses using a molecular phylogeny, species distribution data and phylogenetic comparative approaches. To test the time for speciation hypothesis, we conducted ancestral state reconstructions to infer the ages of temperate, subtropical and tropical lineages and frequency of evolutionary transitions between climates. We tested the carry capacity hypothesis by characterizing changes in net diversification rates through time. To test the diversification rate hypothesis, we qualitatively compared the diversification rates of temperate, subtropical and tropical lineages and conducted statistical tests for associations between latitude and diversification rates.

   We identified four transitions to temperate climates and two transitions out of temperate climates. We found no differences in diversification rates among temperate and tropical clupeiforms. Net diversification rates remained positive in crown Clupeiformes since their origin ~150 Ma in both tropical and temperate lineages. Climate niche characters exhibited strong phylogenetic signal. All temperate clupeiform lineages arose <50 Ma, after the Early Eocene Climatic Optimum.

   Our results support the time for speciation hypothesis, which proposes that climate niche conservatism and fluctuations in the extent of temperate climates limited the time for species to accumulate in temperate climates, resulting in the latitudinal diversity gradient. We found no support for the carrying capacity or diversification rate hypotheses.

    

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5. Mammals on mountainsides revisited: Trait‐based tests of assembly reveal the importance of abiotic filters

   https://doi.org/10.1111/jbi.14099  

   Kohli, Brooks A. ; Stevens, Richard D. ; Rickart, Eric A. ; Rowe, Rebecca J. ( March 2021 , Journal of Biogeography)

   Mountains provide uniquely informative systems for examining how biodiversity is distributed and identifying the causes of those patterns. Elevational patterns of species richness are well‐documented for many taxa but comparatively few studies have investigated patterns in multiple dimensions of biodiversity along mountainsides, which can reveal the underlying processes at play. Here, we use trait‐based diversity patterns to determine the role of abiotic filters and competition in the assembly of communities of small mammals across elevation and evaluate the surrogacy of taxonomic, functional, and phylogenetic dimensions of diversity.

   Great Basin ecoregion, western North America.

   Rodents and shrews.

   The elevational distributions of 34 species were determined from comprehensive field surveys conducted in three arid, temperate mountain ranges. Elevation–diversity relationships and community assembly processes were inferred from phylogenetic (PD) and functional diversity (FD) patterns of mean pairwise and mean nearest‐neighbor distances while accounting for differences in species richness. FD indices were calculated separately for traits related to either abiotic filtering (β‐niche traits) or biotic interactions (α‐niche traits) to test explicit predictions of the role of each across elevation.

   Trait‐based tests of processes indicated that abiotic filtering tied to a strong aridity gradient drives the assembly of both low‐ and high‐elevation communities. Support for competition was not consistent with theoretical expectations under the stress‐dominance hypothesis, species interactions‐abiotic stress hypothesis, or guild assembly rule. Mid‐elevation peaks in species richness contrasted with overall FD and PD, which generally increased with elevation. PD and total FD were correlated on two of three mountains.

   The functional diversity of small mammal communities in these arid, temperate mountains is most consistent with abiotic filters, whereas support for competition is weak. Decomposing FD into traits related to separate assembly processes and examining ecoregional variation in diversity were critical for uncovering the generality of mechanisms. Divergent patterns among dimensions revealed species richness to be a poor surrogate for PD and FD across elevation and reflect the effect of biogeographic and evolutionary history. This first analysis of elevational multidimensional diversity gradients for temperate mammals provides a versatile framework for future comparative studies.

    

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