Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity

Barrera‐Redondo, Josué; Ramírez‐Barahona, Santiago; Eguiarte, Luis E.

doi:10.1111/evo.13475

Cited by 11 publications

(10 citation statements)

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“…We estimated that the split between the two major clades of tree ferns occurred around 164 Ma (range 110.8-192.5 Ma), although older (206-176 Ma, Schuettpelz and Pryer, 2009;Testo andSundue, 2016, respectively) andyounger (72-162 Ma, Rothfels et al, 2015;Qi et al, 2018, respectively) ages have been suggested. With a comprehensive sampling of 150 taxa in Cyatheales, Barrera-Redondo et al (2018) estimated the stem age of Cyatheaceae, by far the largest family in the order, to be around 160 Ma, which is similar to both nuclear (157 Ma, Qi et al, 2018) and plastid (174-168 Ma, Schuettpelz and Pryer, 2009;Testo and Sundue, 2016, respectively) studies, but differs considerably from our estimate of 108.6 Ma (range 102.4-170.5 Ma). In our supplemental analysis including the S. lepifera transcriptome and additional fossil calibrations (see Section "Materials and Methods" and Supplementary Figure 6), we recovered a stem age of Cyatheaeceae at 121.1 Ma (range 119.8-124.6 Ma), which is still younger than previous estimates.…”

Section: Cyathealesmentioning

confidence: 99%

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

et al. 2022

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Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.

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Section: Cyathealesmentioning

confidence: 99%

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

et al. 2022

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“…2005 ; Machado et al. 2016 ; Barrera-Redondo et al. 2018 ), but our study is among the first to show clear evidence for an effect of latitude on rates of mutation accumulation.…”

Section: Discussionmentioning

confidence: 50%

Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus

Koufopanou

Lomas

Pronina

et al. 2020

Genome Biology and Evolution

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This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyse the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.

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“…I used GenBank's plant database (last updated June 28, 2020) by querying for 'Cyatheales' sequences longer than 400 bp, with a minimum sequence identity of 0.2, and a minimum coverage of 0.65. I complemented the resulting alignments with sequence data retrieved from NCBI's PopSet database (PopSet numbers: 1722035357, 1722034779, 1722034120) and from previously published data 55 ; I incorporated sequences for additional taxa using Clustal2.0 59 and AliView 60 and identified and eliminated species synonyms. The final molecular dataset consisted of DNA sequences for 442 species of Cyatheales (60% of the total diversity) with a total length of 15,249 bp for ten chloroplast regions (protein coding regions: rbcL, atpB, atpA, SQD1, and matK; intergenic spacers: atpB-rbcL, rbcL-accD, trnL-trnF, trnG-trnR, and rps3-rpl16) (Supplementary data 2); the per-site missing information I estimated a maximum likelihood phylogeny with RAxML v.8 61 , using the GTRCAT model, automatic bootstrap replicates (autoMRE), and substitution parameters estimated for each marker independently.…”

Section: Methodsmentioning

confidence: 99%

Laurasian legacies in the Gondwanan tree fern order Cyatheales

Ramírez‐Barahona

2023

Preprint

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Present-day geographic and phylogentic patterns often reflect the Gondwana-Laurasia separation and subsequent history of continental drift. However, some lineages show non-overlapping fossil distributions relative to extant species and in some cases extant Gondwanan lineages have Laurasian extinct relatives. Here, I combined distribution data for 101 fossils and 442 extant species of tree ferns (Cyatheales) to reconstruct their biogeographic history over the last 220 million years. The time calibrated tree showed most tree ferns families originating during the Jurassic and the onset of crown group diversification beginning during the Cretaceous; a major shift in diversification rates occurred in the largest tree fern family (Cyatheaceae) that comprises ~90% of extant diversity in the group. Biogeographical reconstructions based on extant distributions alone supported a Gondwanan origin for the group; the most probable ancestral range encompassed Australasia and South America. Alternatively, incorporating fossil distribution data into reconstructions showed a Laurasian origin and a most probable ancestral range in Eurasia. These results evince the Laurasian legacies of the Cyatheales spanning the Triassic-Cretaceous, which otherwise remain hidden from biogeographic inferences. These results show that extant-only biogeographic analyses are limited when fossils distribution are more wide spread than in the present-day, highlighting the need to directly incorporate fossils into biogeographical analyses and improve the reliability of ancestral geographic range estimation.

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Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity

Cited by 11 publications

References 71 publications

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus

Laurasian legacies in the Gondwanan tree fern order Cyatheales

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