ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

Aberer, Andre J.; Kobert, Kassian; Stamatakis, Alexandros

doi:10.1093/molbev/msu236

Cited by 407 publications

(321 citation statements)

References 16 publications

(18 reference statements)

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“…Efficient, highly parallelised algorithms for analysing genomic-scale data do not yet simultaneously infer topology and divergence dates, although some can accommodate morphological data in (undated) simultaneous analyses [68]. Genomic datasets are thus typically analysed stepwise, with topology inferred first, then fixed and time-scaled by node dating [2,3,10].…”

Section: Reviewmentioning

confidence: 99%

Morphological Phylogenetics in the Genomic Age

2015

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Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.

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Section: Reviewmentioning

confidence: 99%

Morphological Phylogenetics in the Genomic Age

2015

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“…We used EXABAYES v. 1.4.1 [52] for Bayesian analysis of the concatenated data matrix, with the GTR þ G model and the same three partition schemes employed in RAxML. Each EXABAYES analysis included two independent runs, each having four coupled chains, and each run was performed for 500 000 generations, sampling every 100 generations.…”

Section: (D) Phylogenetic Analysesmentioning

confidence: 99%

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Ward

Branstetter

2017

Proc. R. Soc. B.

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Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach—ultraconserved element sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants ( Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex / Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.

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“…The resulting RaxML bootstrap tree was analysed with RogueNaRok (Aberer et al 2013). The Bayesian inference was performed with ExaBayes 1.5 (Aberer et al 2014) using the GTR substitution model. Four independent runs with each four Monte Carlo Markov Chains were run for 1,000,000 generations during which convergence, with a standard deviation of split frequencies <2%, had been reached.…”

Section: Methodsmentioning

confidence: 99%

Stolonifera from shallow waters in the north-western Pacific: a description of a new genus and two new species within the Arulidae (Anthozoa, Octocorallia)

Lau¹,

Stokvis²,

Ofwegen³

et al. 2018

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A new genus and two new species of stoloniferous octocorals (Alcyonacea) within the family Arulidae are described based on specimens collected from Okinawa (Japan), Palau and Dongsha Atoll (Taiwan). Hanagen. n. is erected within Arulidae. Hanahanagasasp. n. is characterised by large spindle-like table-radiates and Hanahanatabasp. n. is characterised by having ornamented rods. The distinction of these new taxa is also supported by molecular phylogenetic analyses. The support values resulting from maximum likelihood and Bayesian inference analyses for the genus Hana and new species H.hanagasa and H.hanataba are 82/1.0, 97/1.0 and 61/0.98, respectively. Hanahanagasasp. n. and Hanahanatabasp. n. are the first arulid records for Okinawa, Palau, and Dongsha Atoll, and represent species of the second genus within the family Arulidae.

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ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

Cited by 407 publications

References 16 publications

Morphological Phylogenetics in the Genomic Age

Morphological Phylogenetics in the Genomic Age

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Stolonifera from shallow waters in the north-western Pacific: a description of a new genus and two new species within the Arulidae (Anthozoa, Octocorallia)

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