Article
Multidisciplinary Sciences
Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farre, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Harris A. Tewin
Summary: Decrypting the rearrangements that drive mammalian chromosome evolution is crucial for understanding speciation, adaptation, and disease susceptibility. By computationally reconstructing ancestral karyotypes and syntenic relationships, the study reveals the chromosome structure and evolutionary history of the mammalian ancestors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Lucas C. Wheeler, Michael J. Harms
Summary: The study suggests that ancestral proteins may have been less specific than modern proteins, but when interactions with random peptide targets are considered, the picture becomes more complex. It demonstrates that altered biological specificity does not necessarily indicate altered intrinsic specificity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Letter
Biochemistry & Molecular Biology
Roberto Del Amparo, Miguel Arenas
Summary: Selecting the best-fitting substitution model is recommended for accurately reconstructing ancestral sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Zoology
Mariana Neves Moura, Danon Clemes Cardoso, Maykon Passos Cristiano
Summary: The study estimated genome sizes of 99 ant species, with the mean GS of Formicidae being 0.38 pg and an AT/GC ratio of 62.40/37.60. Phylogenetic reconstruction indicated significant differences in GS between subfamilies sampled. The evolution of GS in Formicidae was suggested to occur through loss and accumulation of non-coding regions, mainly transposable elements, and occasionally by whole genome duplication.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Biochemical Research Methods
Milos Musil, Rayyan Tariq Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jiri Damborsky, David Bednar
Summary: Researchers are increasingly interested in improving the stability of proteins, and ancestral sequence reconstruction has been proven to be an effective method for designing stable proteins. FireProt(ASR) offers a fully automated workflow to help users obtain ancestral sequences based on just a sequence query.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Federico Scossa, Alisdair R. Fernie
Summary: Ancestral proteins were more promiscuous than modern ones, with specificity often evolving after gene duplication; some modern proteins are found to have evolved de novo from ancestors lacking those functions; new interactions evolved from just a few mutations, suggesting acquisition of new functions is not difficult but often lost to subsequent mutations.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Rosario Valenti, Jagoda Jablonska, Dan S. Tawfik
Summary: The study identifies the ancestors of early SODs and their metal specificity, providing new insights into how the predicted Last Common Universal Ancestor dealt with the decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.
Article
Biochemistry & Molecular Biology
Louise Laursen, Jelena Calyseva, Toby J. Gibson, Per Jemth
Summary: DLG plays a key role in controlling the structure and function of the postsynaptic density, with the PDZ3:CRIPT interaction maintaining high affinity in most animal phyla but low affinity in nematodes and insects, raising questions about the physiological function of this interaction in these animal groups. This study demonstrates how a well-established protein interaction involved in cellular scaffolding in bilaterians can undergo dynamic evolution, potentially leading to loss of function.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Sarah Z. Dungan, Belinda S. W. Chang
Summary: This study reconstructs and experiments on the light-activation metrics of rhodopsin pigments in the eyes of cetaceans, revealing significant changes in their visual system during the evolution from terrestrial to aquatic environments. The findings show a blue-shift in the spectral sensitivity of cetaceans' vision and an increased decay rate of light-activated rhodopsin. These transitions may be related to cetaceans' adaptation to deep-diving underwater environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Letter
Biodiversity Conservation
Michal Berec, Irena Setlikova
Summary: A recent proposal to increase species protection by maximizing the overlap of the IUCN Red List and CITES Appendices may be unnecessary or counterproductive, as these lists are based on different protection rules and objectives.
ECOLOGICAL INDICATORS
(2021)
Review
Biochemistry & Molecular Biology
Raine E. S. Thomson, Saskya E. Carrera-Pacheco, Elizabeth M. J. Gillam
Summary: The engineering of proteins to improve stability is important for various applications. Structural information is needed for rational design approaches, while bioinspired methods based on phylogenetic analyses show promise when structures are unavailable. This review provides an overview of factors important for successful inference of thermostable proteins using ancestral sequence reconstruction.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Callum R. Nicoll, Marta Massari, Marco W. Fraaije, Maria Laura Mascotti, Andrea Mattevi
Summary: Ancestral sequence reconstruction (ASR) is a powerful technique for understanding protein sequence changes across evolution and how they give rise to different phenotypes. It has been particularly useful in revealing common molecular factors governing enzyme function. This article highlights the strength of ASR in uncovering catalytic mechanisms and emerging phenotypes for various proteins, as well as its potential applications in biotechnology.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sebastian Ploch, Julia Kruse, Young-Joon Choi, Hjalmar Thiel, Marco Thines
Summary: The study shows that a clade of Peronospora species infecting members of the Ranunculales originated in Papaveraceae, with subsequent host jumps to Berberidaceae, Euphorbiaceae, and Ranunculaceae. Radiation to a variety of hosts took place within Ranunculaceae, followed by a new host jump to Caryophyllaceae. This highlights the importance of host jumping and subsequent radiation in driving the diversification of Peronospora.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Clement Pichot, Anis Djari, Joseph Tran, Marion Verdenaud, William Marande, Cecile Huneau, Veronique Gautier, David Latrasse, Sandrine Arribat, Vivien Sommard, Christelle Troadec, Charles Poncet, Mohammed Bendahmane, Judit Szecsi, Catherine Dogimont, Jerome Salse, Moussa Benhamed, Mohamed Zouine, Adnane Boualem, Abdelhafid Bendahmane
Summary: This study provides insights into the diversity and evolution of melon, and offers comprehensive genomic resources for further research.
Editorial Material
Multidisciplinary Sciences
Xi-guang Zhang, Brian R. Pratt
Summary: This article presents Tian et al.'s claim about Cambrian yunnanozoan animals being stem vertebrates based on their observation of microfibrillar tissue in the branchial arches. However, an alternative view suggests that the observed "microfibrils" are more likely modern organic contamination.
Article
Plant Sciences
Stefan D. Loefstrand, Charlotte M. Taylor, Sylvain G. Razafimandimbison, Catarina Rydin
Summary: This study is the first broad-scale phylogenetic study of Faramea, revealing poorly understood infrageneric relationships and species boundaries in the genus. Some Faramea lineages appear to be geographically isolated, with several clades containing solely specimens collected in the Atlantic Forest biomes.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Plant Sciences
Gildas Gateble, David Bruy, Guillaume Lannuzel, Jerome Munzinger
Summary: Two names of Ilex L. were published for New Caledonia at the end of the 19th century. The placement of Ilex neocaledonica Maxim. under Ilex sebertii Pancher has been confirmed, with both names lectotypified. The single New Caledonian endemic species shows morphological variability and is found on both ultramafic and nonultramafic substrates on mainland Grande Terre.
Article
Plant Sciences
Gregoire Blanchard, Thomas Ibanez, Francois Munoz, David Bruy, Christelle Hely, Jerome Munzinger, Philippe Birnbaum
Summary: In the context of global change, this study analyzed the ecological processes driving forest recovery in fire-modified landscapes by studying changes in functional and phylogenetic composition over 8 years. Environmental filtering and light limitation were found to be major drivers of community assembly, with faster changes at the forest edge compared to the interior. The study highlighted deterministic assembly processes in tropical forest post-fire succession, with fire and drought driving environmental filtering during early succession.
PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS
(2021)
Article
Plant Sciences
J. Christopher Havran, Stephan Nylinder, Ulf Swenson
Summary: The Planchonella species in Hawaii are divided into two clades based on fruit color, purple for P. sandwicensis and yellow for P. spathulata, with the former being more adapted to wetter forests and higher altitudes, while the latter prefers lower elevations in mesic to dry forests. Both species exhibit large morphological variation and can occur sympatrically.
Article
Plant Sciences
Neit Snow, John W. Dawson, Jerome Munzinger, Martin W. Caltmander
Summary: Ongoing taxonomic studies on Eugenia L. in New Caledonia have identified several taxonomic and nomenclatural issues that require clarification. This study proposes a new synonym and new names for certain species, as well as designates lectotypes and a neotype for several taxa.
Article
Plant Sciences
Jerome Munzinger, Gordon McPherson, Stacey Meyer, Chrissen Gemmill
Summary: In this study, the distinction between Adenodaphne and Litsea, two genera endemic to New Caledonia, is questioned based on morphological similarity. Through extensive research, including molecular analysis and examination of specimens, it is concluded that Adenodaphne should be recognized within Litsea. Moreover, the phylogenetic analysis suggests a rare long-distance dispersal event from New Caledonia to New Zealand in the evolution of the endemic Litsea species.
Article
Ecology
Guillaume Lannuzel, Lea Pouget, David Bruy, Vanessa Hequet, Shankar Meyer, Jerome Munzinger, Gildas Gateble
Summary: Conservation efforts in biodiversity hotspots are hindered by a lack of knowledge, but computerized data and expert examination can help increase understanding and promote conservation measures.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Geology
Emma R. Locatelli, Derek E. G. Briggs, Andrew Leslie, Jerome Munzinger, Philippe Grandcolas, Porter P. Lowry, David J. Cantrill, Pierre Maurizot, Dominique Cluzel, Nicolas Folcher, Romain Garrouste, Andre Nel
Summary: A Neogene hematite-goethite concretionary 'ironstone' horizon in the Massif du Sud of New Caledonia contains abundant fossil dicotyledonous angiosperm leaves. The leaves are preserved mainly in goethite, replicating the morphology and anatomy of the leaf tissues, and are preserved in multiple ways.
Article
Plant Sciences
Ulf Swenson, Stephan Nylinder, Alicia Marticorena, Mats Thulin, Brendan Lepschi
Summary: Pouteria splendens is the only native species of Sapotaceae in Chile. Through Bayesian inference and molecular clock analysis, its closest relative was identified as Van-royena from Australia, and the age of the disjunction between Australasia and South America was estimated. Based on morphological features and evolutionary relationships, the reinstatement of Gayella genus and the protection of this species are recommended.
Article
Plant Sciences
David Bruy, Guillaume Lannuzel, Gildas Gateble, Jerome Munzinger
Summary: New Caledonia is a tropical archipelago facing significant biodiversity conservation challenges. The knowledge of its flora is limited, and its ecosystems are being increasingly degraded, particularly by mining activity. Therefore, there is an urgent need to identify and protect the most threatened species according to IUCN criteria.
Article
Plant Sciences
Igor V. V. Bartish, Salome Bonnefoi, Abdelkader Ainouche, Helge Bruelheide, Mark Bartish, Andreas Prinzing
Summary: Plant lineages differ in species richness globally, regionally, and locally. Whole-genome characteristics (WGCs) such as chromosome number and ploidy level may explain these differences through speciation or extinction. This study investigates the relationships between WGCs and species richness in a regional flora and local plant communities.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Ulf Swenson, Brendan Lepschi, Porter P. Lowry II, Mario Henrique Terra-Araujo, Karin Santos, Stephan Nylinder, Anderson Alves-Araujo
Summary: Classifications of the pantropical plant family Sapotaceae have historically recognized between 125 and 53 genera based on morphology. However, molecular data have shown that the broad concepts of the genera Chrysophyllum and Pouteria are untenable, and several new genera have been proposed. A recent study tested this classification using expanded sampling and supported the proposed changes.
Article
Plant Sciences
Elizabeth M. Joyce, Marc S. Appelhans, Sven Buerki, Martin Cheek, Jurriaan M. de Vos, Jose R. Pirani, Alexandre R. Zuntini, Julien B. Bachelier, Michael J. Bayly, Martin W. Callmander, Marcelo F. Devecchi, Susan K. Pell, Milton Groppo, Porter P. Lowry, John Mitchell, Carolina M. Siniscalchi, Jerome Munzinger, Harvey K. Orel, Caroline M. Pannell, Lars Nauheimer, Herve Sauquet, Andrea Weeks, Alexandra N. Muellner-Riehl, Ilia J. Leitch, Olivier Maurin, Felix Forest, Katharina Nargar, Kevin R. Thiele, William J. Baker, Darren M. Crayn
Summary: This study generated the most densely sampled phylogenetic trees of Sapindales to date, providing key insights into the family and subfamily relationships within the order. The study revealed that all families were monophyletic and identified two core family clades dividing the order. The research also highlighted the importance of factors such as ancient gene duplication events in understanding the evolutionary history of these families.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Jerome Munzinger, David M. Johnson, Richard M. K. Saunders
Summary: A new species of Goniothalamus from New Caledonia is described in this article. It is one of the three endemic species from the archipelago. The new species was collected over 150 years ago, but its study was not done until recently. Molecular phylogeny analysis shows that the New Caledonian taxa are related and belong to the same clade, but they can be distinguished by their morphology. The new species is assessed as Vulnerable based on IUCN Red List criteria by the New Caledonian Red List Authority.
Article
Ecology
Eva Larsen, Niklas Wikstrom, Anbar Khodabandeh, Catarina Rydin
Summary: Merlin's grass is an ancient genus of isoetalean wood-producing lycopsids. This study reveals the unexpected discovery of a poorly known species, Isoetes wormaldii, which is sister to the remaining family. The evolutionary and biogeographical history of Isoetes is complex and not easily explained.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)