Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies by Josefin Stiller, Guojie Zhang

“…Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. …”
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Senescence: why and where selection gradients might not decline with age by Roper, M, Capdevila, P, Salguero-Gomez, R

“…Patterns of ageing across the tree of life are much more diverse than previously thought. …”

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean by Young Ho Lee, Linelle Abueg, Jin-Koo Kim, Young Wook Kim, Olivier Fedrigo, Jennifer Balacco, Giulio Formenti, Kerstin Howe, Alan Tracey, Jonathan Wood, Françoise Thibaud-Nissen, Bo Hye Nam, Eun Soo No, Hye Ran Kim, Chul Lee, Erich D. Jarvis, Heebal Kim

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Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems by Shivakumara Manu, Govindhaswamy Umapathy

“…We also quantified the compositional changes using Bray-Curtis dissimilarity and showed that extracellular eDNA can resolve the broad-scale spatiotemporal variation of biodiversity across the tree of life. These results demonstrate that PCR-free deep sequencing of extracellular eDNA is an effective approach for taxonomic diversity assessment across the tree of life in large ecosystems. …”
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Improved species assignments across the entire Anopheles genus using targeted sequencing by Marilou Boddé, Marilou Boddé, Marilou Boddé, Alex Makunin, Fiona Teltscher, Jewelna Akorli, Nana Efua Andoh, Nana Efua Andoh, Amy Bei, Victor Chaumeau, Victor Chaumeau, Ife Desamours, Uwem F. Ekpo, Nicodem J. Govella, Jonathan Kayondo, Kevin Kobylinski, Elhadji Malick Ngom, El Hadji Amadou Niang, Fredros Okumu, Olaitan O. Omitola, Alongkot Ponlawat, Malala Nirina Rakotomanga, Mialy Tatamo Rasolonjatovoniaina, Diego Ayala, Diego Ayala, Mara Lawniczak

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The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon by Bourne Philip E, Valas Ruben E

“…<p>Abstract</p> <p>Background</p> <p>The tree of life is usually rooted between archaea and bacteria. …”
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A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain [version 1; peer review: 2 approved] by Ying Sims, Shane A. McCarthy, Damon-Lee B. Pointon, Jonathan MD Wood, James W. Torrance, Harriet Johnson, Ksenia Krasheninnikova, Haynes Heaton, Joanna Collins, Alan Tracey, Marcela Uliano Da Silva, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Mara Lawniczak, Tibebu Habtewold, Mgeni Mohamed Tambwe, Martin Wagah, Nikolai Windbichler, Sarah Moore, Sarah E. Pelan, George Christophides

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KARAKTERISTIK AGROFORESTRI TREES ALONG BORDER PADA VARIASI LUAS LAHAN MILIK DI DESA NGLANGGERAN KECAMATAN PATUK KABUPATEN GUNUNG KIDUL by , HENY ENDRASARI, , Dr. Priyono Suryanto, S.Hut., M.P.

“…Af TAB 2 has 11 constituent types of stands, with the dominant type of mahogany with IVI value of 119% at the level of the tree of life and 115% IVI pole at the level of living and the highest Lbds in shown by plant mahogany with 5,13 m2/ha with the highest potential in Af TAB 2 is 368,12 m3/ha . …”

Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation by Yu, Xilin, Le, Thien, Christensen, Sarah A., Molloy, Erin K., Warnow, Tandy

“…Abstract One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. …”
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A chromosomal reference genome sequence for the malaria mosquito, Anopheles maculipalpis, Giles, 1902 [version 1; peer review: 2 approved] by Shane A. McCarthy, Damon-Lee B. Pointon, Ying Sims, James W. Torrance, Marcela Uliano-Silva, Martin G. Wagah, Diego Ayala, Jonathan M. D. Wood, Joanna C. Collins, Harriet F. Johnson, Ksenia Krasheninnikova, Mara K. N. Lawniczak, Haynes Heaton, Alan Tracey, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Boris K. Makanga, Lemonde B. A. Bouafou, Sarah E. Pelan, Nil Rahola

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A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain [version 2; peer review: 2 approved] by Ying Sims, Shane A. McCarthy, Damon-Lee B. Pointon, Jonathan MD Wood, James W. Torrance, Harriet Johnson, Ksenia Krasheninnikova, Haynes Heaton, Joanna Collins, Alan Tracey, Mara Lawniczak, Marcela Uliano Da Silva, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Mara K.N. Lawniczak, Tibebu Habtewold, Mgeni Mohamed Tambwe, Martin Wagah, Nikolai Windbichler, Sarah Moore, Sarah E. Pelan, George Christophides

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Bioinformatics for biologists / by Pevzner, Pavel 310329, Shamir, Ron 410488

“…Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. …”

Textbook of Phylogenetics / by Krieger, Joshua, author 648873

“…In biological systematics as a whole, phylogenetic analyzes have become essential in researching the evolutionary tree of life. Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. …”
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OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. by Jacob L Steenwyk, Dayna C Goltz, Thomas J Buida, Yuanning Li, Xing-Xing Shen, Antonis Rokas

“…Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole-genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.…”
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Phylogenomics and the rise of the angiosperms by Zuntini, AR, Carruthers, T, Maurin, O, Bailey, PC, Leempoel, K, Brewer, GE, Epitawalage, N, Françoso, E, Gallego-Paramo, B, McGinnie, C, Negrão, R, Roy, SR, Simpson, L, Toledo Romero, E, Barber, VMA, Botigué, L, Clarkson, JJ, Cowan, RS, Dodsworth, S, Johnson, MG, Kim, JT, Pokorny, L, Wickett, NJ, Antar, GM, Antonelli, A

“…So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3, 4. …”

Comparative analysis of stalked and acorn barnacle adhesive proteomes by Janna N. Schultzhaus, William Judson Hervey, Chris R. Taitt, Chris R. So, Dagmar H. Leary, Kathryn J. Wahl, Christopher M. Spillmann

“…Barnacle adhesive is primarily composed of proteins, but knowledge of how the adhesive proteome varies across the tree of life is unknown due to a lack of genomic information. …”
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The public goods hypothesis for the evolution of life on Earth by Bapteste Eric, Pisani Davide, McInerney James O, O'Connell Mary J

“…We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.</p>…”
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The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758) [version 1; peer review: 2 approved, 2 approved with reservations] by Eerik Aunin, Victoria McKenna, Graeme Oatley, Sarah Lemer, Isabelle Ailish Clayton-Lucey, Ruiqi Li, Jose Victor Lopez, Jingchun Li, Elizabeth Sinclair, Camilla Santos, Noah Gettle, Haoyu Niu, Michael Paulini, Rebecca O’Brien

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Microbial diversity of a Brazilian coastal region influenced by an upwelling system and anthropogenic activity. by Juliano C Cury, Fabio V Araujo, Sergio A Coelho-Souza, Raquel S Peixoto, Joana A L Oliveira, Henrique F Santos, Alberto M R Dávila, Alexandre S Rosado

“…<h4>Methodology/principal findings</h4>We carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil). …”
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A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism by James P. Bernot, Geoffrey A. Boxshall, Keith A. Crandall

“…A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. …”
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