IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Minh, Bùi Quang; Schmidt, Heiko A.; Chernomor, Olga; Schrempf, Dominik; Woodhams, Michael D.; Haeseler, Arndt von; Lanfear, Robert

doi:10.1093/molbev/msaa015

Cited by 7,765 publications

(5,965 citation statements)

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“…Concatenation of these loci resulted in an alignment of 1,761,114 bp, with the fraction of gaps/ambiguities varying from 4.04% ( Macaca mulatta ) to 18.37% ( Carlito syrichta ) (Table S3). We then inferred the species tree using both gene tree (as implemented in ASTRAL III, [38] and concatenation (as implemented in IQ-TREE 2; [39]) approaches.…”

Section: Resultsmentioning

confidence: 99%

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Vanderpool

Minh

Lanfear

et al. 2020

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Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

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Section: Resultsmentioning

confidence: 99%

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Vanderpool

Minh

Lanfear

et al. 2020

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“…Phylogenetic reconstruction of the vertebrate ACE2 species tree . The multiple sequence alignment of 410 ACE2 orthologous protein sequences from mammals, birds, fishes, reptiles and amphibians was used to generate a gene tree using the maximum likelihood method of reconstruction, as implemented in IQTREE (80) . The best fit model of sequence evolution was determined using ModelFinder (81) and…”

Section: Methodsmentioning

confidence: 99%

“…To calculate likelihood-derived dN/dS rates (⍵), CODEML utilises both a species tree and a codon alignment. The species tree for all 64 taxa was calculated using IQTREE (80) and the inferred best-fit model of sequence evolution (JTT+F+R4). This gene topology was generally in agreement with the 410 taxa tree, however bats were now sister taxa to Perissodactyla.…”

Section: Methodsmentioning

confidence: 99%

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

Damas¹,

Hughes

Keough³

et al. 2020

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The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low . Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.

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“…Finally, we reconstructed phylogenies using a recently-developed non-reversible substitution model that captures asymmetries in the exchange rates between amino acids 57 to investigate the position of Undinarchaeota relative to the root of the archaeal tree ( Figure 1c, Supplementary Figures 10,11,19,22,24,25,36 and 39, Supplementary Table 6 ). This method does not rely on an outgroup and therefore avoids potential LBA artifacts associated with the use of distantly related bacterial sequences to root the archaeal tree 27 .…”

Section: Resultsmentioning

confidence: 99%

“…These analyses were performed on the 127 and 364 taxa set using the full alignments and the recoded alignments in which 20% or 40% of the most heterogeneous sites were removed. Trees were generated with an updated version of IQ-TREE v2 57 (while all previously mentioned phylogenies were generated with IQ-TREE v1) 50 . The single partition models were run with the following settings: -mset LG -bb 1000 -alrt 1000 -m MFP+MERGE, followed by --model-joint NONREV --min-freq 0.001 -nparam 10 -optfromgiven - bb 1000 -alrt 1000.…”

Section: Methodsmentioning

confidence: 99%

Undinarchaeota illuminate the evolution of DPANN archaea

Dombrowski

Williams

Sun

et al. 2020

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14 15 #corresponding author. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: anja.spang@nioz.nl. Phone16 number: +31 (0)222 369 526 17 18 19Several recent studies have revealed the presence of a thus far uncharacterized archaeal lineage 77 referred to the Uncultivated Archaeal Phylum 2 (UAP2) 13,40,41 , which seems to affiliate with DPANN 78 archaea and thus may be key in resolving long-standing debates regarding archaeal phylogeny and the 79 evolution of DPANN. In this study, we have used a metagenomics approach to obtain additional genomes 80 of members of the so far uncharacterized UAP2 and provide first insights into their metabolic repertoire 81 and lifestyle. Furthermore, we implemented comprehensive and careful phylogenomic techniques aimed 82 at ameliorating phylogenetic artifacts, shedding new light onto the evolutionary origin and phylogenetic 83 placement of the various DPANN lineages including UAP2 in an updated archaeal phylogeny. 84 Results and Discussion 85A thus far uncharacterized putative archaeal phylum-level lineage in metagenome read archives 86The generation of a large diversity of metagenome-assembled genomes (MAGs) representing 87 archaeal and bacterial lineages across the tree of life has led to the definition of the tentative archaeal 88 UAP2 phylum 41 . Considering our lack of insights into the biology of members of this lineage as well as its 89suggested key position in the archaeal tree, we aimed at obtaining a broader genomic representation of 90 the UAP2. In particular, we screened publicly available metagenomes using ribosomal protein sequences 91 of the previously reconstructed UAP2 MAGs and assembled and binned UAP2-positive samples yielding 92 six additional MAGs belonging to the UAP2 lineage (Table 1, Supplementary Tables 1-2, see Methods for 93 details). Four of the newly assembled MAGs were recovered from metagenomes of a groundwater aquifer 94 located adjacent to the Colorado River 42 , while the two others as well as six previously reconstructed 95MAGs, derived from metagenomes of marine waters in the Atlantic 41,43 and Indian Oceans 44 as well as the 96Mediterranean Sea 45 (Supplementary Table 2). UAP2 representatives were detected in samples from 97 various depths in the water column (85-5000 m), fluctuating oxygen conditions (anoxic to oxic) and 98 temperatures (sampling sites had temperatures from 18 up to 106°C) (Supplementary Figure 1, 99

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Cited by 7,765 publications

References 50 publications

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

Undinarchaeota illuminate the evolution of DPANN archaea

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