Correlated evolutionary rates across genomic compartments in Annonaceae

Paul H Hoekstra, Jan J Wieringa, Erik Smets, Rita D Brandão, Jenifer de Carvalho Lopes, Roy H J Erkens, Lars W Chatrou

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.

Original languageEnglish
Pages (from-to)63-72
Number of pages10
JournalMolecular Phylogenetics and Evolution
Volume114
DOIs
Publication statusPublished - Sep 2017

Keywords

  • Annonaceae
  • Base Composition
  • Bayes Theorem
  • Chloroplasts
  • DNA, Plant
  • DNA, Ribosomal
  • Evolution, Molecular
  • Genes, Plant
  • Phylogeny
  • Sequence Analysis, DNA
  • Journal Article
  • Substitution rates
  • ARABIDOPSIS-THALIANA
  • Plastid genome
  • SPECIES-RICHNESS
  • Phylogenetics
  • FLOWERING PLANTS
  • NUCLEOTIDE SUBSTITUTION RATES
  • Malmeoideae
  • PHYLOGENETIC ANALYSIS
  • Annonoideae
  • MOLECULAR EVOLUTION
  • BIASED GENE CONVERSION
  • ENDOSYMBIOTIC BACTERIA
  • Nuclear ribosomal DNA
  • GRASS CHLOROPLAST DNA
  • SEQUENCE EVOLUTION

Cite this

Hoekstra, Paul H ; Wieringa, Jan J ; Smets, Erik ; Brandão, Rita D ; Lopes, Jenifer de Carvalho ; Erkens, Roy H J ; Chatrou, Lars W. / Correlated evolutionary rates across genomic compartments in Annonaceae. In: Molecular Phylogenetics and Evolution. 2017 ; Vol. 114. pp. 63-72.
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Correlated evolutionary rates across genomic compartments in Annonaceae. / Hoekstra, Paul H; Wieringa, Jan J; Smets, Erik; Brandão, Rita D; Lopes, Jenifer de Carvalho; Erkens, Roy H J; Chatrou, Lars W.

In: Molecular Phylogenetics and Evolution, Vol. 114, 09.2017, p. 63-72.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Correlated evolutionary rates across genomic compartments in Annonaceae

AU - Hoekstra, Paul H

AU - Wieringa, Jan J

AU - Smets, Erik

AU - Brandão, Rita D

AU - Lopes, Jenifer de Carvalho

AU - Erkens, Roy H J

AU - Chatrou, Lars W

N1 - Copyright © 2017 Elsevier Inc. All rights reserved.

PY - 2017/9

Y1 - 2017/9

N2 - The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.

AB - The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.

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KW - Bayes Theorem

KW - Chloroplasts

KW - DNA, Plant

KW - DNA, Ribosomal

KW - Evolution, Molecular

KW - Genes, Plant

KW - Phylogeny

KW - Sequence Analysis, DNA

KW - Journal Article

KW - Substitution rates

KW - ARABIDOPSIS-THALIANA

KW - Plastid genome

KW - SPECIES-RICHNESS

KW - Phylogenetics

KW - FLOWERING PLANTS

KW - NUCLEOTIDE SUBSTITUTION RATES

KW - Malmeoideae

KW - PHYLOGENETIC ANALYSIS

KW - Annonoideae

KW - MOLECULAR EVOLUTION

KW - BIASED GENE CONVERSION

KW - ENDOSYMBIOTIC BACTERIA

KW - Nuclear ribosomal DNA

KW - GRASS CHLOROPLAST DNA

KW - SEQUENCE EVOLUTION

U2 - 10.1016/j.ympev.2017.05.026

DO - 10.1016/j.ympev.2017.05.026

M3 - Article

C2 - 28578201

VL - 114

SP - 63

EP - 72

JO - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

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