TimeTree 5: An Expanded Resource for Species Divergence Times

Kumar, Sudhir; Suleski, Michael; Craig, Jack M.; Kasprowicz, Adrienne; Sanderford, Maxwell; Li, Michael; Stecher, Glen; Hedges, S. Blair

doi:10.1093/molbev/msac174

Cited by 672 publications

(535 citation statements)

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“…That was made by the method of maximum likelihood implemented in the “ fastAnc ” function of the phytools R package (Revell 2012). Then we mapped the estimated ancestral states ( fastAnc function) on the phylogeny obtained from the Time Tree of Life database (Kumar et al 2022) using ggplot2 (Sievert 2016).…”

Section: Methodsmentioning

confidence: 99%

“…We also provide annotation information, including raw output files from InterProScan for each species, as well as parsed data for all distinct annotation databases members of InterProScan. Finally, we also gathered a newick file containing a species tree for 142 species gathered from the TimeTree web tool (Kumar et al 2022). The initial tree produced by this tool was enriched by including species from closely related taxa as placeholders for the original species.…”

Section: Obtention Of High-quality Non-redundant Annotated Proteomes ...mentioning

confidence: 99%

“…All authors declare no conflict of interest for this publication taxonomic diversity of the plant genome databases used to build ARCADE. B) Species tree for 142 species found in ARCADE (extracted from the TimeTree web tool (Kumar et al 2022) as described in "Methods". Species abbreviations are as follows: Acer yangbiense (Aya), Akebia trifoliata (Atr), Amaranthus hypochondriacus (Ahy), Amborella trichopoda (Ati), Ananas comosus (Aco), Andreaea rupestris (Aru), Anthoceros angustus (Aan), Arabidopsis halleri (Aha), Arabidopsis thaliana (Ath), Arabis nemorensis (Ane), Ascarina rubricaulis (Arb), Asparagus officinalis (Aof), Asplenium platyneuron (Apl), Aulacom-nium heterostichum (Ahe), Azolla filiculoides (Afi), Beta vulgaris subsp.…”

Section: Conflict Of Interestmentioning

confidence: 99%

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Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants

Menezes

Almeida

Del-Bem

et al. 2022

Preprint

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The abundance of plant genomic information caused by the decrease of sequencing costs contrasts with the lack of databases that integrate genome annotation, taxonomy and phenotypes to produce statistically sound, biologically meaningful knowledge. Here we present ARCADE (ARChaeplastida Annotation DatabasE), a database of 171 high-quality archaeplastidian non-redundant proteomes gathered from six primary genomic databases, together with proteome quality metrics and a growing number of associated metadata. As a case study to demonstrate the usefulness of ARCADE, we used it to investigate the expansion and contraction of protein domains associated with the evolution of genome size (hereafter GS). GS varies greatly among land plants and the synthesis of large genomes can be costly to cells. Although GS has been studied extensively for decades, the molecular mechanisms involved in the adaptations of plants to the increase in GS are still poorly understood. We used the annotation and phylogenetic information available in ARCADE, together with estimated GS values available for 83 land plant species, to search for associations between the abundance of protein domain families in these species and GS variation through phylogenetic-aware methods. Additionally, we estimated the GS for the ancestral nodes of the extant land plant species. GS seems to be decreasing along the course of evolution, except for a few branches that might have undergone independent GS increases. We found 7 Pfam correlated with the variation in GS in land plants, mainly related to nucleotide metabolism, DNA repair and genome organization. We found larger genomes to have a greater frequency of the Histone 2A superfamily, responsible for diverse functions, including the nucleosome formation and silencing of transposable elements. These molecular functions we found correlated to GS variation suggests they may be associated with preserving genome stability in larger genomes, and might indicate the evolution of mechanisms to cope with the variation in GS in land plants. ARCADE is available at https://osf.io/2fkvh/.

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Section: Methodsmentioning

confidence: 99%

Section: Obtention Of High-quality Non-redundant Annotated Proteomes ...mentioning

confidence: 99%

Section: Conflict Of Interestmentioning

confidence: 99%

See 1 more Smart Citation

Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants

Menezes

Almeida

Del-Bem

et al. 2022

Preprint

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“…Evolutionary time scale analysis. Evolutionary lineage of the order Hymenoptera, family Formicidae and the subfamily Formicinae were constructed in TimeTree (Kumar et al, 2022). The TimeTree is a public knowledge base on the evolution of life.…”

Section: Quantitative Genetic Analysismentioning

confidence: 99%

Caste-specific quantitative genetics and phylogenetic signal analysis revealed the morphological adaptation of Asian weaver ant, Oecophylla smaragdina (Hymenoptera, Formicidae)

Anand

Mahima

Vardhanan

2022

J. Insect Biodivers. Syst

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Insect caste development and their morphological divergence are not yet studied well, especially in ants. However, the role of developmental and genetic integration in evolution is contentious. In our study, we tried to reveal the quantitative genetics selection responses, phylogenetic signal, and evolutionary origin of weaver ant female castes (queen, major and minor). The widening and lengthening of the head region, as well as the welldeveloped mandibular process, are the major heritable characteristics found in the major worker ants. We hypothesized that these conserved and heritable characteristics may help the major worker ants for defense, foraging purposes and other nest-building function aspects. However, in the case of minor worker, small heads and the reduced mandibular process are the more heritable characteristics. Compared to worker ants, in queen, the highly heritable and conserved morphological character is well-developed thoracic regions and large-sized abdomen. It is interesting to note that there is no detectable phylogenetic signal across the female cast of the Asian weaver ants, which suggests that the caste development and morphological divergence are environmentally modulated not evolutionary conserved. From this study, we concluded that caste-specific morphological shape and size are highly conserved traits and these traits are modulated by their niche preferences.

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“…While past work has focused on Drosophila , the predominance of maternal inheritance of mitochondria in eukaryotes allows for a taxonomically diverse investigation of the generality of mother’s curse. Here we test predictions of the MCH using the splash-pool copepod Tigriopus californicus , an arthropod that shares a common ancestor with Drosophila around 409.3 – 536.6 million years ago[45]. We used a genetic panel of mitonuclear hybrids to assay both fertility and longevity.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial effects on fertility and longevity in Tigriopus californicus contradict predictions of the mother’s curse hypothesis

Watson

Flanagan

Pascar

et al. 2022

Preprint

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SUMMARYStrict maternal inheritance of mitochondria favors the evolutionary accumulation of sex-biased fitness effects, as mitochondrial evolution occurs exclusively in female lineages. The “mother’s curse” hypothesis proposes that male-harming mutations should accumulate in mitochondrial genomes when they have neutral or beneficial effects on female fitness. Rigorous empirical tests have largely focused on Drosophila, where support for the predictions of mother’s curse has been mixed. We investigated the impact of mother’s curse mutations in Tigriopus californicus, a minute crustacean. Using nonrecombinant backcrosses, we introgressed four divergent mitochondrial haplotypes into two nuclear backgrounds and recorded measures of fertility and longevity. We found that the phenotypic effects of mitochondrial mutations were context-dependent, being influenced by the nuclear-background in which they were expressed, as well as the sex of the individual and rearing temperature. Mitochondrial haplotype effects were greater for fertility than longevity, and temperature effects were greater for longevity. However, in opposition to mother’s curse expectations, females had a higher level of mitochondrial genetic variance than males for both fertility and longevity, and there was no evidence for mitochondrial mutations favoring female performance at the cost of male performance. These results indicate that selection has not resulted in the accumulation of male mutation load in Tigriopus californicus.

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TimeTree 5: An Expanded Resource for Species Divergence Times

Cited by 672 publications

References 15 publications

Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants

Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants

Caste-specific quantitative genetics and phylogenetic signal analysis revealed the morphological adaptation of Asian weaver ant, Oecophylla smaragdina (Hymenoptera, Formicidae)

Mitochondrial effects on fertility and longevity in Tigriopus californicus contradict predictions of the mother’s curse hypothesis

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