Gene transfers can date the tree of life

Davín, Adrián; Tannier, Éric; Williams, Tom A.; Boussau, Bastien; Daubin, Vincent; Szöllősi, Gergely J.

doi:10.1038/s41559-018-0525-3

Cited by 59 publications

(68 citation statements)

References 42 publications

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“…With the increasing availability of molecular data, phylogenetic trees generated from different genes are often recognized to have conflicting branching patterns (Maddison 1997;Nichols 2001;Pamilo and Nei 1988). Davin et al (2018) suggested that different genetic markers could yield conflicting estimates of the species phylogeny. In recent years, genome-scale sequence data have become increasingly available in phylogenetic studies for understanding the evolutionary histories of species (Liu et al 2015).…”

Section: Conflicts Between Non-reproductive Genes (F1 and Igs) And Thmentioning

confidence: 99%

Heterothallism and potential hybridization events inferred for twenty-two yellow morel species

Kang

et al. 2020

IMA Fungus

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Mating-type genes are central to sexual reproduction in ascomycete fungi and result in the establishment of reproductive barriers. Together with hybridization, they both play important roles in the evolution of fungi. Recently, potential hybridization events and MAT genes were separately found in the Elata Clade of Morchella. Herein, we characterized the MAT1-1-1 and MAT1-2-1 genes of twenty-two species in the Esculenta Clade, another main group in the genus Morchella, and proved heterothallism to be the predominant mating strategy among the twenty-two species tested. Ascospores of these species were multi-nuclear and had many mitochondrial nucleoids. The number of ascospore nuclei might be positively related with the species distribution range. Phylogenetic analyses of MAT1-1-1, MAT1-2-1, intergenic spacer (IGS), and partial histone acetyltransferase ELP3 (F1) were performed and compared with the species phylogeny framework derived from the ribosomal internal transcribed spacer region (ITS) and translation elongation factor 1-alpha (EF1-a) to evaluate their species delimitation ability and investigate potential hybridization events. Conflicting topologies among these genes genealogies and the species phylogeny were revealed and hybridization events were detected between several species. Different evolutionary patterns were suggested for MAT genes between the Esculenta and the Elata Clades. Complex evolutionary trajectories of MAT1-1-1, MAT1-2-1, F1 and IGS in the Esculenta Clade were highlighted. These findings contribute to a better understanding of the importance of hybridization and gene transfer in Morchella and especially for the appearance of reproductive modes during its evolutionary process.

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Section: Conflicts Between Non-reproductive Genes (F1 and Igs) And Thmentioning

confidence: 99%

Heterothallism and potential hybridization events inferred for twenty-two yellow morel species

Kang

et al. 2020

IMA Fungus

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“…Various attempts in this direction are currently being made but this is clearly a challenging undertaking due to large computational demands of using complex evolutionary models on big datasets. Yet, the further improvement of models of evolution and phylogenetic algorithms (including molecular dating approaches such as recently employed by Wolfe andFournier 2018 andDavín et al 2018) in combination with ever increasing computational resources will certainly help to further refine the tree of life and get a better supported location of the root.…”

Section: An Expanded Microbial Treementioning

confidence: 99%

The Emergence of Life

et al. 2019

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The aim of this article is to provide the reader with an overview of the different possible scenarios for the emergence of life, to critically assess them and, according to the conclusions we reach, to analyze whether similar processes could have been conducive to independent origins of life on the several icy moons of the Solar System. Instead of directly proposing a concrete and unequivocal cradle of life on Earth, we focus on describing the different requirements that are arguably needed for the transition between non-life to life. We Ocean Worlds Edited by 56 Page 2 of 53 E. Camprubí et al.approach this topic from geological, biological, and chemical perspectives with the aim of providing answers in an integrative manner. We reflect upon the most prominent origins hypotheses and assess whether they match the aforementioned abiogenic requirements. Based on the conclusions extracted, we address whether the conditions for abiogenesis are/were met in any of the oceanic icy moons.

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“…For a given set of donor and recipient species, where only the latter has a known fossil record, since the transfer of genetic material must post-date the divergence of the donor lineage, the earliest fossil evidence of the recipient also provides evidence for the minimum age of the donor (dos Reis, 2018). This approach has been used to date divergence times among microbial lineages, most of which lack a substantive fossil record (Davín et al, 2018;Wolfe and Fournier, 2018a;Magnabosco et al, 2018;Gruen et al, 2019). This approach has the potential for constraining parasite evolution, as HGTs have been documented between some hosts and their parasites, including several parasitic plant groups (Molina et al, 2014;Kado and Innan, 2018).…”

Section: Prospects For Understanding the Coevolutionary Dynamics Of Hmentioning

confidence: 99%

The molecular clock as a tool for understanding host-parasite evolution

Warnock¹,

Engelstädter²

2020

Preprint

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The molecular clock in combination with evidence from the geological record can be applied to infer the timing and dynamics of evolutionary events. This has enormous potential to shed light on the complex and often evasive evolution of parasites. Here, we provide an overview of molecular clock methodology and recent advances that increase the potential for the study of host-parasite coevolutionary dynamics, with a focus on Bayesian approaches to divergence time estimation. We highlight the challenges in applying these methods to the study of parasites, including the nature of parasite genomes, the incompleteness of the rock and fossil records, and the complexity of hostparasite interactions. Developments in models of molecular evolution and approaches to deriving temporal constraints from geological evidence will help overcome some of these issues. However, 1 we also describe a case study in which the timescale of host-parasite coevolution cannot easily be inferred using existing methods -that of the alpha-proteobacteria Wolbachia. We conclude by providing a prospective on future methodological developments and data collection that will facilitate in understanding the role of parasitism in deep time. IntroductionA timeline for events throughout geological history is required to address many questions in evolutionary biology, including establishing the sequence of key evolutionary transitions and assessing the role of environmental and evolutionary variables on the evolution of life (Rota-Stabelli et al., 2013;Betts et al., 2018;Morris et al., 2018;Silvestro et al., 2018). Due to the paucity of rocks from different time periods and environments, and the low fossilisation potential of many soft-bodied species, we cannot rely on the fossil record to establish this timeline very precisely (Benton et al., 2009; Parham et al., 2011;Holland, 2016). The genomes of living species provide an alternative source of evidence for inferring the sequence of events in deep time, although in themselves they provide no information about absolute time. Phylogenetic methods that enable us to leverage both sources of evidence simultaneously provide the most promising approach for generating a more precise timeline and a richer view of the past than either record can provide alone (Donoghue and Benton, 2007;Landis, 2017;Álvarez-Carretero et al., 2019).It is estimated that more than half of all living species are parasites (Windsor, 1998;Bass et al., 2015), that is, species that rely on a host organism for survival, at the expense of the other species.The ubiquity of the parasitic lifestyle and the often strong selection pressure imposed by parasites on their hosts (Hughes et al., 2012) indicate that parasites have played an important role in shaping the evolution of life, but the challenge in detecting many parasite species, both now and in the past, suggest that this role is not well understood (Dobson et al., 2008;De Baets and Littlewood, 2015). Estimating the time of origin of parasitism across different groups enables us to answer ...

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Gene transfers can date the tree of life

Cited by 59 publications

References 42 publications

Heterothallism and potential hybridization events inferred for twenty-two yellow morel species

Heterothallism and potential hybridization events inferred for twenty-two yellow morel species

The Emergence of Life

The molecular clock as a tool for understanding host-parasite evolution

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