Synthesizing phylogenetic knowledge for ecological research

Beaulieu, Jeremy M.; Ree, Richard H.; Cavender‐Bares, Jeannine; Weiblen, George D.; Donoghue, Michael J.

doi:10.1890/11-0638.1

Cited by 54 publications

(55 citation statements)

References 87 publications

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“…Assumptions of monophyly, based primarily on caecilian taxonomy, are required because a substantial proportion of the included taxa have never been included in any explicit phylogenetic analyses. For the same reason, formal supertree methods are not applicable here and we have essentially produced the tree using ''judicious grafting of clades'' (Beaulieu et al 2012) following Wilkinson et al's (2001) analysis of what assumption underpin this procedure. The tree is logically implied by the combination of relevant phylogenetic results and limited assumptions of monophyly but many clades are poorly resolved because of the uncertainty of the precise relationships the phylogenetically understudied taxa they are assumed to include.…”

Section: Study Samples and Phylogenymentioning

confidence: 99%

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

et al. 2014

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Insights into morphological diversification can be obtained from the ways the species of a clade occupy morphospace. Projecting a phylogeny into morphospace provides estimates of evolutionary trajectories as lineages diversified information that can be used to infer the dynamics of evolutionary processes that produced patterns of morphospace occupation. We present here a large-scale investigation into evolution of morphological variation in the skull of caecilian amphibians, a major clade of vertebrates. Because caecilians are limbless, predominantly fossorial animals, diversification of their skull has occurred within a framework imposed by the functional demands of head-first burrowing. We examined cranial shape in 141 species, over half of known species, using X-ray computed tomography and geometric morphometrics. Mapping an existing phylogeny into the cranial morphospace to estimate the history of morphological change (phylomorphospace), we find a striking pattern: most species occupy distinct clusters in cranial morphospace that closely correspond to the main caecilian clades, and each cluster is separated by unoccupied morphospace. The empty spaces in shape space are unlikely to be caused entirely by extinction or incomplete sampling. The main caecilian clades have different amounts of morphological disparity, but neither clade age nor number of species account for this variation. Cranial shape variation is clearly linked to phyletic divergence, but there is also homoplasy, which is attributed to extrinsic factors associated with head-first digging: features of caecilian crania that have been previously argued to correlate with differential microhabitat use and burrowing ability, such as subterminal and terminal mouths, degree of temporal fenestration (stegokrotaphy/ zygokrotaphy), and eyes covered by bone, have evolved and many combinations occur in modern species. We find evidence of morphological convergence in cranial shape, among species that have eyes covered by bone, resulting in a narrow bullet-shaped head. These results reveal a complex history, including early expansion of morphospace and both divergent and convergent evolution resulting in the diversity we observe today.

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Section: Study Samples and Phylogenymentioning

confidence: 99%

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

et al. 2014

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“…The first tree (Supplement 1) was assembled collaboratively by the Ecophylogenetics working group (EcoPhyWG) at the National Center for Ecological Analysis and Synthesis (Beaulieu et al 2012). This tree was pruned for our yard species and species of Cedar Creek, separately.…”

Section: Phylogenetic Datamentioning

confidence: 99%

Phylogenetic and functional characteristics of household yard floras and their changes along an urbanization gradient

Knapp

Dinsmore

Fissore

et al. 2012

Ecology

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131

124

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Abstract. Urban areas are among the most heavily managed landscapes in the world, yet they harbor a remarkable richness of species. Private yards are common habitats in urban areas and are places where cultivated species manage to escape cultivation and become part of the spontaneous species pool. Yards are novel ecosystems where community assembly is driven by both natural and anthropogenic processes. Phylogenetic diversity and functional traits are increasingly recognized as critical to understanding processes of community assembly. Recent evidence indicates that urban areas may select more closely related plant species from the pool of regionally occurring species than do nonurban areas, and that exotic species are phylogenetically clustered within communities. We tested whether phylogenetic diversity and functional trait composition in privately managed yards change along a gradient of housing density in the Minneapolis-Saint Paul metropolis, Minnesota, USA, in accordance with these predictions. We also identified characteristics of the spontaneous yard flora by comparing its phylogenetic diversity and functional composition with the ''natural-areas'' species pool represented by the flora of nearby Cedar Creek Ecosystem Science Reserve. Along the urbanization gradient, yards had more species per hectare in densely built regions than in lower-density regions, but phylogenetic diversity and functional composition did not change with housing density. In contrast, in comparison to species in natural areas, yard species were more closely related to each other and functionally distinct: They were more often short-lived, self-compatible, and had higher specific leaf area than species of Cedar Creek. The high number of exotic yard species increased the yard flora's phylogenetic relatedness in comparison to species of Cedar Creek, causing a degree of phylogenetic homogenization within yards. The urban environment and homeowners' preferences select for trait attributes and phylogenetic lineages that can colonize and persist in yards. As yard species disperse beyond household boundaries, their functional attributes will affect ecosystem processes in urban environments and beyond, such as accelerating decomposition rates. Limited phylogenetic diversity may reduce the potential of ecosystems to respond to environmental changes. As cities continue to expand globally, understanding the impacts of yard management for biodiversity and ecosystem services becomes increasingly important.

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“…We used Phylomatic to construct a phylogeny of all the species based on the R20080417 megatree (Webb and Donoghue 2005) and branches dated according to Wikstrom et al (2001). This is the most commonly used method to obtain plant phylogenetic trees for ecophylogenetic studies like ours, but other methods are increasingly becoming available (see Sanderson et al 2008, Kress et al 2009, Beaulieu et al 2012. Phylomatic trees are typically not fully resolved at the younger nodes; for our tree many species within genera were not resolved and neither were many genera within families.…”

Section: Constructing Phylogenetic Diversity-area Curvesmentioning

confidence: 99%

Phylogenetic diversity–area curves

Helmus

Ives

2012

Ecology

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Abstract. Phylogenetic diversity-area curves are analogous to species-area curves and quantify the relationship between the phylogenetic diversity of species assemblages and the area over which assemblages are sampled. Here, we developed theoretical expectations of these curves under different ecological and macroevolutionary processes. We first used simulations to generate curves expected under three ecological community assembly processes: species sorting, where species have distinct environmental preferences; random placement, where species have no environmental preference but vary in their prevalence across communities; and limited dispersal, where species have no environmental preference but vary in their ability to disperse. Second, we simulated curves expected across regions (e.g., across oceanic islands) that are derived from colonization among regions, within-region speciation, and extinction. We also computed curves for two data sets, one on forest plots along an elevation gradient and the other on Caribbean island Anolis lizards. Of the three ecological processes, only species sorting produced strong relationships between phylogenetic diversity and area. The forest plot curves matched the species-sorting expectation, but only when phylogenetic repulsion (that caused closely related species to be found in similar habitats but not in the same plots) was also included in the simulation. Strong relationships between regional phylogenetic diversity and area were simulated if species were derived only from within-region speciation; colonizations among regions obscured the pattern. Similarly, larger Caribbean islands had more withinisland speciation and contained more Anolis phylogenetic diversity than smaller islands, but colonizations among islands obscured this relationship. This work furthers our understanding of the processes that govern the phylogenetic diversity of ecological communities and biogeographic regions.

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Synthesizing phylogenetic knowledge for ecological research

Cited by 54 publications

References 87 publications

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

Phylogenetic and functional characteristics of household yard floras and their changes along an urbanization gradient

Phylogenetic diversity–area curves

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