From cacti to carnivores

Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph F. Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximilian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & 1 others Stephen A. Smith

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Premise of the Study: The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods: We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. Key Results: Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. Conclusions: Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.

Original languageEnglish (US)
Pages (from-to)446-462
Number of pages17
JournalAmerican journal of botany
Volume105
Issue number3
DOIs
StatePublished - Mar 1 2018

Fingerprint

Cactaceae
Caryophyllales
cactus
carnivore
homology
Transcriptome
carnivores
transcriptome
sampling
gene
Genes
Cluster Analysis
phylogeny
genes
phylogenetics
Phylogeny
methodology
History
Genome
genome

Keywords

  • Agdestidaceae
  • Amaranthaceae
  • Caryophyllales
  • coalescent
  • gene-tree conflict
  • homology
  • phylogenomics
  • phylotranscriptomic
  • supermatrix

PubMed: MeSH publication types

  • Evaluation Studies
  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

From cacti to carnivores : Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. / Walker, Joseph F.; Yang, Ya; Feng, Tao; Timoneda, Alfonso; Mikenas, Jessica; Hutchison, Vera; Edwards, Caroline; Wang, Ning; Ahluwalia, Sonia; Olivieri, Julia; Walker-Hale, Nathanael; Majure, Lucas C.; Puente, Raúl; Kadereit, Gudrun; Lauterbach, Maximilian; Eggli, Urs; Flores-Olvera, Hilda; Ochoterena, Helga; Brockington, Samuel F.; Moore, Michael J.; Smith, Stephen A.

In: American journal of botany, Vol. 105, No. 3, 01.03.2018, p. 446-462.

Research output: Contribution to journalArticle

Walker, JF, Yang, Y, Feng, T, Timoneda, A, Mikenas, J, Hutchison, V, Edwards, C, Wang, N, Ahluwalia, S, Olivieri, J, Walker-Hale, N, Majure, LC, Puente, R, Kadereit, G, Lauterbach, M, Eggli, U, Flores-Olvera, H, Ochoterena, H, Brockington, SF, Moore, MJ & Smith, SA 2018, 'From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales', American journal of botany, vol. 105, no. 3, pp. 446-462. https://doi.org/10.1002/ajb2.1069
Walker, Joseph F. ; Yang, Ya ; Feng, Tao ; Timoneda, Alfonso ; Mikenas, Jessica ; Hutchison, Vera ; Edwards, Caroline ; Wang, Ning ; Ahluwalia, Sonia ; Olivieri, Julia ; Walker-Hale, Nathanael ; Majure, Lucas C. ; Puente, Raúl ; Kadereit, Gudrun ; Lauterbach, Maximilian ; Eggli, Urs ; Flores-Olvera, Hilda ; Ochoterena, Helga ; Brockington, Samuel F. ; Moore, Michael J. ; Smith, Stephen A. / From cacti to carnivores : Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. In: American journal of botany. 2018 ; Vol. 105, No. 3. pp. 446-462.
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abstract = "Premise of the Study: The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods: We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. Key Results: Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. Conclusions: Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.",
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