Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera

Abstract The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

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Recombinant transfer in the basic genome ofEscherichia coli

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510839112 ◽

2015 ◽

Vol 112 (29) ◽

pp. 9070-9075 ◽

Cited By ~ 59

Author(s):

Purushottam D. Dixit ◽

Tin Yau Pang ◽

F. William Studier ◽

Sergei Maslov

Keyword(s):

Common Ancestor ◽

Recipient Cell ◽

Gene Clusters ◽

Selective Advantage ◽

Last Common Ancestor ◽

Genome Sequences ◽

Bacterial Genomes ◽

Basic Genome ◽

Single Base Pair ◽

Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

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Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

10.21203/rs.3.rs-33194/v1 ◽

2020 ◽

Author(s):

Tingting Li ◽

Dongxia Liu ◽

Yadi Yang ◽

Jiali Guo ◽

Yujie Feng ◽

...

Keyword(s):

Phylogenetic Tree ◽

Common Ancestor ◽

Virus Disease ◽

Evolutionary Relationship ◽

Critical Issue ◽

Last Common Ancestor ◽

Genome Sequences ◽

Phylogenetic Tree Analysis ◽

Origin And Evolution ◽

Bat Coronavirus

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

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Bacterial proteins pinpoint a single eukaryotic root

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1420657112 ◽

2015 ◽

Vol 112 (7) ◽

pp. E693-E699 ◽

Cited By ~ 100

Author(s):

Romain Derelle ◽

Guifré Torruella ◽

Vladimír Klimeš ◽

Henner Brinkmann ◽

Eunsoo Kim ◽

...

Keyword(s):

Common Ancestor ◽

Innovative Approach ◽

Phylogenetic Position ◽

Last Common Ancestor ◽

Phylogenetic Distance ◽

Genome Sequences ◽

Bacterial Proteins ◽

Eukaryotic Genes

The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between “Unikonta” and “Bikonta,” with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.

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Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

10.1101/013326 ◽

2014 ◽

Author(s):

Arcady Mushegian

Keyword(s):

Evolutionary Biology ◽

Common Ancestor ◽

Recent Literature ◽

Last Common Ancestor ◽

Gene Repertoire ◽

Ancestral State ◽

Last Universal Common Ancestor ◽

Cellular Life ◽

Universal Common Ancestor ◽

Life On Earth

I review recent literature on the reconstruction of gene repertoire of the Last Universal Common Ancestor of cellular life (LUCA). The form of the phylogenetic record of cellular life on Earth is important to know in order to reconstruct any ancestral state; therefore I also discuss the emerging understanding that this record does not take the form of a tree. I argue that despite this, “tree-thinking” remains an essential component in evolutionary thinking and that “pattern pluralism” in evolutionary biology can be only epistemological, but not ontological.

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Search asymmetries for threatening faces in chimpanzees (Pan troglodytes)

10.31234/osf.io/kc4xj ◽

2021 ◽

Author(s):

Duncan Wilson ◽

Masaki Tomonaga

Keyword(s):

Pan Troglodytes ◽

Search Strategy ◽

Common Ancestor ◽

Brightness Contrast ◽

Configural Processing ◽

Last Common Ancestor ◽

Old World Monkeys ◽

Serial Search ◽

Search Tasks ◽

Efficient Detection

For primates, the ability to efficiently detect threatening faces is highly adaptive, however, it is not clear exactly how faces are detected. This study investigated whether chimpanzees show search asymmetries for conspecific threatening faces featuring scream and bared teeth expressions. Five adult female chimpanzees participated in a series of touchscreen matching-to-sample visual search tasks. In Experiment 1, search advantages for scream versus neutral targets, and scream versus bared teeth targets were found. A serial search strategy indicated greater difficulty in disengaging attention from scream versus neutral distractors. In Experiments 2a and 2b, search advantages for scream versus neutral targets remained when the mouth was darkened, suggesting that the brightness contrast of the mouth was not critical for the efficient detection of scream targets. In Experiments 3a and 3b, search advantages for inverted scream versus neutral targets disappeared, indicating configural processing. Together, exclusion of the brightness contrast of the mouth as a low-level perceptual confound, and evidence of configural processing, suggested the scream faces may have been perceived as threatening. However, the search advantage for scream faces is most likely explained by the presence of teeth, independently of threat. The study provides further support that an attentional bias towards threatening faces is a homologous trait, which can be traced back to at least the last common ancestor of Old-World monkeys and apes.

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Genome sequences reveal divergence times of malaria parasite lineages

Parasitology ◽

10.1017/s0031182010001575 ◽

2010 ◽

Vol 138 (13) ◽

pp. 1737-1749 ◽

Cited By ~ 34

Author(s):

JOANA C. SILVA ◽

AMY EGAN ◽

ROBERT FRIEDMAN ◽

JAMES B. MUNRO ◽

JANE M. CARLTON ◽

...

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Orthologous Gene ◽

The Other ◽

Divergence Times ◽

Last Common Ancestor ◽

Genome Sequences ◽

Malaria Parasites ◽

Human Malaria ◽

History Of

SUMMARYObjectiveThe evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum.MethodsWe present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups.ResultsOur analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys.ConclusionThe results support an ancient association between malaria parasites and their primate hosts, including humans.

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Tracking the genome-wide outcomes of a transposable element burst over decades of amplification

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1716459114 ◽

2017 ◽

Vol 114 (49) ◽

pp. E10550-E10559 ◽

Cited By ~ 20

Author(s):

Lu Lu ◽

Jinfeng Chen ◽

Sofia M. C. Robb ◽

Yutaka Okumoto ◽

Jason E. Stajich ◽

...

Keyword(s):

Transposable Element ◽

Common Ancestor ◽

Success Strategies ◽

Host Recognition ◽

Last Common Ancestor ◽

Virtual Absence ◽

Copy Numbers ◽

Genome Wide ◽

Host Detection ◽

Rapid Amplification

To understand the success strategies of transposable elements (TEs) that attain high copy numbers, we analyzed two pairs of rice (Oryza sativa) strains, EG4/HEG4 and A119/A123, undergoing decades of rapid amplification (bursts) of the class 2 autonomous Ping element and the nonautonomous miniature inverted repeat transposable element (MITE) mPing. Comparative analyses of whole-genome sequences of the two strain pairs validated that each pair has been maintained for decades as inbreds since divergence from their respective last common ancestor. Strains EG4 and HEG4 differ by fewer than 160 SNPs and a total of 264 new mPing insertions. Similarly, strains A119 and A123 exhibited about half as many SNPs (277) as new mPing insertions (518). Examination of all other potentially active TEs in these genomes revealed only a single new insertion out of ∼40,000 loci surveyed. The virtual absence of any new TE insertions in these strains outside the mPing bursts demonstrates that the Ping/mPing family gradually attains high copy numbers by maintaining activity and evading host detection for dozens of generations. Evasion is possible because host recognition of mPing sequences appears to have no impact on initiation or maintenance of the burst. Ping is actively transcribed, and both Ping and mPing can transpose despite methylation of terminal sequences. This finding suggests that an important feature of MITE success is that host recognition does not lead to the silencing of the source of transposase.

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Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

Scientific Reports ◽

10.1038/s41598-020-79160-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evy van Berlo ◽

Alejandra P. Díaz-Loyo ◽

Oscar E. Juárez-Mora ◽

Mariska E. Kret ◽

Jorg J. M. Massen

Keyword(s):

Experimental Evidence ◽

Common Ancestor ◽

Great Apes ◽

Pongo Pygmaeus ◽

Last Common Ancestor ◽

Contagious Yawning ◽

Proximate Mechanism ◽

Social Species ◽

Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

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Germline Transformation of Drosophila virilis With the Transposable Element mariner

Genetics ◽

10.1093/genetics/143.1.365 ◽

1996 ◽

Vol 143 (1) ◽

pp. 365-374 ◽

Cited By ~ 1

Author(s):

Allan R Lohe ◽

Daniel L Hartl

Keyword(s):

Transposable Element ◽

Common Ancestor ◽

Pcr Amplification ◽

Drosophila Virilis ◽

Cell Region ◽

Diverse Species ◽

Drosophila Mauritiana ◽

Characteristic 2 ◽

In Situ Hybridizations

Abstract An important goal in molecular genetics has been to identify a transposable element that might serve as an efficient transformation vector in diverse species of insects. The transposable element mariner occurs naturally in a wide variety of insects. Although virtually all mariner elements are nonfunctional, the Mosl element isolated from Drosophila mauritiana is functional. Mosl was injected into the pole-cell region of embryos of D. virilis, which last shared a common ancestor with D. mauritiana 40 million years ago. Mosl PCR fragments were detected in several pools of DNA from progeny of injected animals, and backcross lines were established. Because Go lines were pooled, possibly only one transformation event was actually obtained, yielding a minimum frequency of 4%. Mosl segregated in a Mendelian fashion, demonstrating chromosomal integration. The copy number increased by spontaneous mobilization. In situ hybridization confirmed multiple polymorphic locations of Mosl. Integration results in a characteristic 2-bp TA duplication. One Mosl element integrated into a tandem array of 370-bp repeats. Some copies may have integrated into heterochromatin, as evidenced by their ability to support PCR amplification despite absence of a signal in Southern and in situ hybridizations.

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