Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

Bromham, Lindell; Hua, Xia; Lanfear, Robert; Cowman, Peter F.

doi:10.1086/680052

Cited by 97 publications

(107 citation statements)

References 112 publications

(140 reference statements)

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“…Therefore, our results provide a line of evidence toward higher rates of molecular evolution associated with the evolution of myrmecophily in lycaenids, but also of diversification as found in other systems (Bromham et al, 2015). We found a higher rate of molecular evolution in the nuclear markers, but not in the mitochondrial one studied here.…”

Section: Discussionsupporting

confidence: 79%

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High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids

et al. 2017

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Understanding the variations in the rate of molecular evolution among lineages may provide clues on the processes that molded extant biodiversity. Here, we report the high rate of molecular evolution in Lycaenidae and Riodinidae compared to other families of butterflies (Papilionoidea). We assembled a phylogeny of butterflies using eight molecular markers and comprising 4,891 species. We found that the rate of molecular evolution is higher in Lycaenidae and Riodinidae compared to the other families, but only the nuclear protein coding sequence Wingless showed a marked difference, while Elongation factor 1-alpha showed a more moderate difference. In contrast, Cytochrome Oxidase subunit 1 showed no difference between Lyacenidae and Riodinidae, and other butterflies. In parallel, we calculated the rates of diversification in all subfamilies of the Papilionoidea using the method-of-moments estimator for stem-group ages, which does not require a fully solved phylogeny for the target clades. We found that the Lycaeninae lineage, from the Lycaenidae family had the highest rate of diversification among all lineages. Among the life-history traits that could explain differences in molecular evolution and diversification rate, lycaenids display mutualistic or antagonistic interactions with ants, a higher level of host plant specialization and reduced dispersal abilities compared to other butterfly families. Since the current study is limited by a unique contrast, the relationship with traits cannot be evaluated statistically. Future studies should measure myrmecophily and dispersal abilities quantitatively across a more detailed phylogeny of lycaenids to test for an association between shifts in the strength of mutualism, rates of molecular evolution and the diversification of lineages.

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Section: Discussionsupporting

confidence: 79%

“…For instance, Bromham et al (2015) proposed that species traits contribute to lineage-specific differences in the mutation rate, increasing the rate of molecular evolution, fostering among-populations divergence and diversification. Moreover, strong selection during phases of high diversification (e.g.…”

Section: Introductionmentioning

confidence: 99%

High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids

et al. 2017

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“…It is of great interested to understand why the dN and dS substitution rates are co-accelerated in Cupressoideae plastomes. Substitutions at dS sites are evolutionarily neutral and largely dependent on mutation rates (Kimura 1983), whereas those at dN sites might be affected by multiple mechanisms, including mutation rates, population size, and selection pressure (Bromham et al 2015). In the plastomes of Cupressoideae, the co-accelerated substitution rates at both dN and dS sites are likely being affected by mutation rates.…”

Section: Discussionmentioning

confidence: 99%

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)

Chaw

et al. 2017

Genome Biology and Evolution

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The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae. Our PCR and read mapping analyses together suggested the existence of isomeric plastomes in eight of the ten sequenced Cupressoideae species. The isomeric plastomes were also detected in 176 individuals from nine wild populations of four Cupressoideae species. Within Calocedrus macrolepis, we discovered a new type of isomeric plastomes that was likely derived from homologous recombination mediated by an 11-bp repeat. We conclude that isomeric plastomes are commonly present in Cupressoideae, thereby contributing to increased plastomic complexity.

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“…The sequences were verified to be free of stop codons or gaps of 1-2 base pairs. We chose an equal number of species from each sister clade within a terrestrialfreshwater pair, in a phylogenetically dispersed fashion (Robinson et al 1998), to reduce node density effects (Hugall and Lee 2007;Bromham et al 2015). Molecular rates for the clades of interest were often estimated within the context of a larger tree having multiple sister clades, and the number of clade pairs was maximized such that the connections through branches among differing pairings were not overlapping, thus maintaining phylogenetic independence of sister lineages.…”

Section: Collection Of Datamentioning

confidence: 99%

“…Future studies may incorporate multivariate analysis (e.g., Bromham et al 2015) to reduce noise in trends of molecular evolution linked to individual characteristics of lineages.…”

Section: Parallels Between Aquatic Habitat and Other Biological And Ementioning

confidence: 99%

Rates and patterns of molecular evolution in freshwater versus terrestrial insects

Mitterboeck

Adamowicz

2016

Genome

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Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group. While ratios of nonsynonymous-to-synonymous substitutions across available loci were higher in terrestrial than freshwater-associated taxa in 26 of 42 lineage pairs, a stronger trend was observed (20 of 31, p binomial = 0.15, p Wilcoxon = 0.017) when examining only terrestrial-aquatic pairs including fully aquatic taxa. We did not observe any widespread changes at particular amino acid sites in COI associated with habitat shifts, although there may be general differences in selection regime linked to habitat.Key words: molecular evolution, habitat transition, relative rates, Insecta, DNA barcoding.Résumé : À plusieurs reprises, des groupes d'insectes ont alterné entre des habitats terrestres et aquatiques, tant pour les stades immatures qu'adultes. Les auteurs explorent les taux d'évolution moléculaire chez 42 paires de clades d'insectes apparentés terrestres et aquatiques à l'aide de données publiques de séquences codantes au sein des ordres Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera et Neuroptera. De plus, les auteurs ont vérifié s'il y avait eu évolution moléculaire convergente associée à l'habitat au sein du gène codant pour la sous-unité I de la cytochrome c oxydase (COI) de manière générale et à l'endroit d'un acide aminé particulier qui a été rapporté comme faisant l'objet d'une convergence liée à l'habitat au sein d'un groupe de scarabées aquatiques. Bien que les ratios de substitutions non-synonymes à synonymes étaient plus élevés, au sein des locus disponibles, chez les taxons terrestres que chez les taxons aquatiques pour 26 des 42 paires comparées, une tendance plus marquée a été observée (20 de 31, p binomial = 0,15, p Wilcoxon = 0,017) lorsque les paires terrestres/ aquatiques n'incluaient que des taxons pleinement aquatiques. Les auteurs n'ont pas observé de changements importants à des acides aminés particuliers au sein de la COI qui étaient associés à des changements d'habitat, bien qu'il puisse y avoir des différences générales dans le régime de sélection qui soient associées à l'habitat. [Traduit par la Rédaction] Mots-clés : évolution moléculaire, transition d'habitat, taux relatifs, insectes, codage à barres de l'ADN.

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Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

Cited by 97 publications

References 112 publications

High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids

High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)

Rates and patterns of molecular evolution in freshwater versus terrestrial insects

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