Emerging patterns in the comparative analysis of phylogenetic community structure

Vamosi, Steven M.; Heard, Stephen B.; Vamosi, Jana C.; Webb, Campbell O.

doi:10.1111/j.1365-294x.2008.04001.x

Cited by 554 publications

(792 citation statements)

References 104 publications

(272 reference statements)

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“…In the past decade, there has been a push to integrate phylogeny into community ecology, and a number of recent studies have evaluated whether the phylogenetic relatedness of co-occurring species can be used to understand mechanisms of community assembly (see reviews by Cavender-Bares et al 2009, Vamosi et al 2009, Lebrija-Trejos et al 2014). These studies have primarily used one of two analytical approaches.…”

Section: Accepted Ar Ticlementioning

confidence: 99%

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

et al. 2017

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Interactions among neighbors influence the structure of communities of sessile organisms. Closely related species tend to share habitat and resource requirements and to interact with the same mutualists and natural enemies so that the strength of interspecific interactions tends to decrease with evolutionary divergence time. Nevertheless, the degree to which such phylogenetically related ecological interactions structure plant communities remains unclear. Using data from five large mapped forest plots combined with a DNA barcode mega‐phylogeny, we employed an individual‐based approach to assess the collective effects of focal tree size on neighborhood phylogenetic relatedness. Abundance‐weighted average divergence time for all neighbors (ADT_all) and for heterospecific neighbors only (ADT_hetero) were calculated for each individual of canopy tree species. Within local neighborhoods, we found phylogenetic composition changed with focal tree size. Specifically, significant increases in ADT_all with focal tree size were evident at all sites. In contrast, there was no significant change in ADT_hetero with tree size in four of the five sites for both sapling‐sized and all neighbors, even at the smallest neighbourhood scale (0–5 m), suggesting a limited role for phylogeny‐dependent interactions. However, there were inverse relationships between focal tree size and the proportion of heterospecific neighbors belonging to closely related species at some sites, providing evidence for negative phylogenetic density dependence. Overall, our results indicate that negative interaction with conspecifics had a much greater impact on neighborhood assemblages than interactions among closely related species and could contribute to community structure and diversity maintenance in different forest communities.

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Section: Accepted Ar Ticlementioning

confidence: 99%

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

et al. 2017

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“…Vamosi et al [5] note that the difficulty of demarcating a community has contributed to a limited selection of case studies in community phylogenetics, dominated by plant communities or communities with discretely bounded habitats. This bias must be addressed if we are to understand what general principles may (or may not) underpin the assembly and structure of ecological communities.…”

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confidence: 99%

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

Emerson

Cicconardi

Fanciulli

et al. 2011

Phil. Trans. R. Soc. B

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There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.

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“…The variation in these core genes, which are present in all bacteria, has been extensively exploited for the investigation of taxonomic relationships 12 , including defining and identifying species 13,14 , and forms the basis of many metagenomic community studies 15 . For these applications, 16S rRNA gene sequences provide an inordinate quantity of information in relation to their small size, and they were seminal in establishing that 'prokaryotes' are not a monophyletic group, but contain two of the three domains of life: Bacteria and Archaea 12 .…”

Section: Pre-wgs Cataloguing Of Diversitymentioning

confidence: 99%

MLST revisited: the gene-by-gene approach to bacterial genomics

et al. 2013

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Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.Advances in nucleotide-sequencing technology have provided unparalleled access to the enormous genetic diversity that has accumulated in the bacterial domain during 3.5-4 billion years of evolution 1 . Numerous sets of whole-genome sequencing (WGS) data for bacterial isolates (BOX 1) are available 2 , and metagenomic studies using these technologies continue to reveal further, seemingly boundless, diversity in bacterial communities 3 . Faced with this plethora of information, microbiologists must develop structured means of describing this diversity and of linking phenotype and genotype, thereby facilitating an improved understanding of the microbiological world. Given that we have precise information on the function of only a very small proportion of bacterial genes, and no knowledge at all about most, this is a formidable, if extremely exciting, challenge.Here, we focus primarily on pathogenic bacteria, although the concepts discussed are applicable more widely to all bacteria and archaea. Bacterial pathogens played a crucial part in the development of experimental microbiology and remain the most intensively studied prokaryotes more than 100 years later 4 . Pathogens have emerged across the diversity of the bacterial -but, interestingly, not the archaeal -domain on many occasions and are both polyphyletic and highly diverse. Thus, although pathogens represent only a tiny subset of the bacterial world, the challenges faced by the clinical microbiology laboratory are representative of those faced by microbiology as a whole.Taxonomic and functional analyses are based on the observations that diversity among bacteria is not continuous and that distinct, stable types with particular properties exist 5 . These founding principles of microbiology 6 have been upheld by much subsequent research, but the study of such clusters remains largely descriptive, and the evolutionary mechanisms that led to cluster emergence and persistence remain incompletely understood 7,8 . Structuring is also evident within bacterial genomes, as diversity is unevenly distributed among genes Pre-WGS cataloguing of diversityA major advance in defining bacterial diversity was the proposal, by the late Carl Woese and colleagues, of a universal and 'natural' -that is, genealogical -classification system based on small-su...

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Emerging patterns in the comparative analysis of phylogenetic community structure

Cited by 554 publications

References 104 publications

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

MLST revisited: the gene-by-gene approach to bacterial genomics

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