Evolutionary Biology

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Review Ecology

Rewriting results sections in the language of evidence

Stefanie Muff, Erlend B. Nilsen, Robert B. O'Hara, Chloe R. Nater

Summary: Despite criticism, the black-or-white null-hypothesis significance testing with an arbitrary P-value cutoff remains the standard way to report scientific findings. However, a lack of knowledge about suitable alternatives hampers progress. This study suggests using a language of evidence as a simpler and more intuitive alternative, which allows for a more nuanced approach in communicating scientific findings.

TRENDS IN ECOLOGY & EVOLUTION (2022)

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Review Ecology

Addressing context dependence in ecology

Jane A. Catford, John R. U. Wilson, Petr Pysek, Philip E. Hulme, Richard P. Duncan

Summary: Context dependence is a key factor in explaining diverse outcomes in ecology, and it arises when the conditions under which a relationship is observed change. It can lead to contradictory conclusions and limit the transferability of research findings. Through examples from biological invasions, two types of context dependence, mechanistic and apparent, are identified.

TRENDS IN ECOLOGY & EVOLUTION (2022)

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Article Biochemistry & Molecular Biology

TimeTree 5: An Expanded Resource for Species Divergence Times

Sudhir Kumar, Michael Suleski, Jack M. Craig, Adrienne E. Kasprowicz, Maxwell Sanderford, Michael Li, Glen Stecher, S. Blair Hedges

Summary: The fifth edition of the TimeTree of Life resource (TToL5) synthesizes published molecular timetrees to make evolutionary knowledge easily accessible. It contains divergence time information on 137,306 species, an increase of 41% from the previous edition. The web interface is now ADA-compliant and mobile-friendly.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

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Article Ecology

Climatic and soil factors explain the two-dimensional spectrum of global plant trait variation

Julia S. Joswig, Christian Wirth, Meredith C. Schuman, Jens Kattge, Bjorn Reu, Ian J. Wright, Sebastian D. Sippel, Nadja Rueger, Ronny Richter, Michael E. Schaepman, Peter M. van Bodegom, J. H. C. Cornelissen, Sandra Diaz, Wesley N. Hattingh, Koen Kramer, Frederic Lens, Ulo Niinemets, Peter B. Reich, Markus Reichstein, Christine Roemermann, Franziska Schrodt, Madhur Anand, Michael Bahn, Chaeho Byun, Giandiego Campetella, Bruno E. L. Cerabolini, Joseph M. Craine, Andres Gonzalez-Melo, Alvaro G. Gutierrez, Tianhua He, Pedro Higuchi, Herve Jactel, Nathan J. B. Kraft, Vanessa Minden, Vladimir Onipchenko, Josep Penuelas, Valerio D. Pillar, Enio Sosinski, Nadejda A. Soudzilovskaia, Evan Weiher, Miguel D. Mahecha

Summary: The study reveals that variation in plant size is mainly influenced by latitudinal gradients in water or energy limitation, while variation in leaf economics traits is primarily influenced by climate, soil fertility, and their interactions. These findings help improve predictions and understanding of biodiversity patterns and the impacts of climate change on biogeochemical cycles.

NATURE ECOLOGY & EVOLUTION (2022)

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Article Plant Sciences

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

Janaina Gomes-da-Silva, Fabiana L. R. Filardi, Maria Regina Barbosa, Jose Fernando A. Baumgratz, Carlos E. M. Bicudo, Taciana B. Cavalcanti, Marcus A. N. Coelho, Andrea F. Costa, Denise P. Costa, Eduardo Couto Dalcin, Paulo Labiak, Haroldo C. Lima, Lucia G. Lohmann, Leonor C. Maia, Vidal F. Mansano, Mariangela Menezes, Marli P. Morim, Carlos Wallace N. Moura, Eimear Nic Lughadha, Denilson F. Peralta, Jefferson Prado, Nadia Roque, Joao Renato Stehmann, Lana S. Sylvestre, Larissa Trierveiler-Pereira, Bruno M. T. Walter, Geraldo Zimbrao, Rafaela C. Forzza

Summary: The shortage of reliable taxonomic data hinders biodiversity research, but recent studies on algae, plants, and fungi in Brazil have demonstrated the country's species richness and endemism. Scientific collaboration has proven to be powerful in achieving ambitious goals.

TAXON (2022)

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Article Evolutionary Biology

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

William J. Baker, Paul Bailey, Vanessa Barber, Abigail Barker, Sidonie Bellot, David Bishop, Laura R. Botigue, Grace Brewer, Tom Carruthers, James J. Clarkson, Jeffrey Cook, Robyn S. Cowan, Steven Dodsworth, Niroshini Epitawalage, Elaine Francoso, Berta Gallego, Matthew G. Johnson, Jan T. Kim, Kevin Leempoel, Olivier Maurin, Catherine Mcginnie, Lisa Pokorny, Shyamali Roy, Malcolm Stone, Eduardo Toledo, Norman J. Wickett, Alexandre R. Zuntini, Wolf L. Eiserhardt, Paul J. Kersey, Ilia J. Leitch, Felix Forest

Summary: The tree of life is a fundamental roadmap for understanding the evolution and characteristics of life on Earth, but there is still much that is unknown. High-throughput sequencing is expected to deepen our understanding of evolutionary relationships. A comprehensive phylogenomic platform has been established to explore the angiosperm tree of life, including open tools and data.

SYSTEMATIC BIOLOGY (2022)

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Editorial Material Ecology

The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, Jose A. Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklos Balint

Summary: Progress in genome sequencing has enabled the generation of large-scale reference genomes, representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, allowing comprehensive analyses in population and functional genomics, and are expected to revolutionize conservation genomics.

TRENDS IN ECOLOGY & EVOLUTION (2022)

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Article Evolutionary Biology

Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination

Spyros Lytras, Joseph Hughes, Darren Martin, Phillip Swanepoel, Arne de Klerk, Rentia Lourens, Sergei L. Kosakovsky Pond, Wei Xia, Xiaowei Jiang, David L. Robertson

Summary: The study suggests that horseshoe bats in southern China and Southeast Asia are likely the reservoir species for the proximal animal ancestor of SARS-CoV-2. The research also reveals recent geographic movement and cocirculation of these viruses' ancestors. However, a direct proximal ancestor to SARS-CoV-2 has not been sampled yet, highlighting the need for more wildlife sampling to determine the exact origins, intermediate species involved in transmission, and the diversity of related sarbecoviruses that pose a high risk for future spillovers.

GENOME BIOLOGY AND EVOLUTION (2022)

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Article Ecology

An earlier start of the thermal growing season enhances tree growth in cold humid areas but not in dry areas

Shan Gao, Eryuan Liang, Ruishun Liu, Flurin Babst, J. Julio Camarero, Yongshuo H. Fl, Shilong Piao, Sergio Rossi, Miaogen Shen, Tao Wang, Josep Penuelas

Summary: The study demonstrates that an earlier onset of the thermal growing season significantly affects tree growth in regions outside the temperate zone, especially in cold humid areas. While previous research has explored the connection between temperature and leaf phenology, the impact of phenological changes on tree growth remains less understood. The findings suggest that climate-driven changes in wood phenology may have implications for the carbon sequestration capacity of temperate forest ecosystems.

NATURE ECOLOGY & EVOLUTION (2022)

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Article Ecology

Seed germination and vigor: ensuring crop sustainability in a changing climate

Reagan C. Reed, Kent J. Bradford, Imtiyaz Khanday

Summary: Maintaining a steady food supply for the increasing world population will require high-yielding crop plants that can thrive under changing conditions. Seed vigor plays a crucial role in the successful establishment of plants, and climate change, including warming trends and temperature variability, can affect seed germination and growth.

HEREDITY (2022)

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Review Ecology

Freshwater salinisation: a research agenda for a saltier world

David Cunillera-Montcusi, Meryem Beklioglu, Miguel Canedo-Arguelles, Erik Jeppesen, Robert Ptacnik, Cihelio A. Amorim, Shelley E. Arnott, Stella A. Berger, Sandra Brucet, Hilary A. Dugan, Miriam Gerhard, Zsofia Horvath, Silke Langenheder, Jens C. Nejstgaard, Marko Reinikainen, Maren Striebel, Pablo Urrutia-Cordero, Csaba F. Vad, Egor Zadereev, Miguel Matias

Summary: The salinisation of freshwater ecosystems is a significant threat, affecting biodiversity and human societies. Understanding its ecological and evolutionary consequences is still a challenge, with various research gaps identified. Focusing on global- and landscape-scale processes, functional approaches, genetic and molecular levels, and ecoevolutionary dynamics can help predict the impacts of freshwater salinisation.

TRENDS IN ECOLOGY & EVOLUTION (2022)

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Article Ecology

Enhanced habitat loss of the Himalayan endemic flora driven by warming-forced upslope tree expansion

Xiaoyi Wang, Tao Wang, Jinfeng Xu, Zehao Shen, Yongping Yang, Anping Chen, Shaopeng Wang, Eryuan Liang, Shilong Piao

Summary: The realized range limit of trees in the Himalaya varies due to temperature and anthropogenic factors. While trees have reached their thermal treeline in the eastern region, they are absent in the western and central regions. Predictions indicate that trees will migrate upslope by the end of the twenty-first century, leading to a loss of habitats for the endemic flora.

NATURE ECOLOGY & EVOLUTION (2022)

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Article Evolutionary Biology

Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution

Massimo Amicone, Vitor Borges, Maria Joao Alves, Joana Isidro, Libia Ze-Ze, Silvia Duarte, Luis Vieira, Raquel Guiomar, Joao Paulo Gomes, Isabel Gordo

Summary: By conducting experimental evolution with two strains of SARS-CoV-2 in Vero cells, researchers estimated a high rate of mutation accumulation, particularly in the strain carrying the D614G mutation.

EVOLUTION MEDICINE AND PUBLIC HEALTH (2022)

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Article Ecology

Colonial history and global economics distort our understanding of deep-time biodiversity

Nussaibah B. Raja, Emma M. Dunne, Aviwe Matiwane, Tasnuva Ming Khan, Paulina S. Naetscher, Aline M. Ghilardi, Devapriya Chattopadhyay

Summary: The biases in fossil sampling records not only reflect geological and spatial aspects, but are also influenced by the historical legacy of colonialism and socio-economic factors. Researchers in high- or upper-middle-income countries hold a monopoly over paleontological knowledge production by contributing to 97% of fossil data, leading to biased spatial sampling across the globe and disenfranchisement of researchers in lower-income countries.

NATURE ECOLOGY & EVOLUTION (2022)

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Article Ecology

Integrating remote sensing with ecology and evolution to advance biodiversity conservation

Jeannine Cavender-Bares, Fabian D. Schneider, Maria Joao Santos, Amanda Armstrong, Ana Carnaval, Kyla M. Dahlin, Lola Fatoyinbo, George C. Hurtt, David Schimel, Philip A. Townsend, Susan L. Ustin, Zhihui Wang, Adam M. Wilson

Summary: This Perspective discusses the importance of integrating remote sensing with field-based ecology and evolution to fully understand and preserve Earth's biodiversity. The inclusive integration of data collected through different methods can benefit conservation efforts and advance biodiversity science.

NATURE ECOLOGY & EVOLUTION (2022)

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Article Evolutionary Biology

A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science

Rudolf Meier, Bonnie B. Blaimer, Eliana Buenaventura, Emily Hartop, Thomas Rintelen, Amrita Srivathsan, Darren Yeo

Summary: Halting biodiversity decline is crucial but hindered by taxonomic impediments, including undescribed and superficially described species. A recent study attempted to address the issue by using COI barcode clusters for braconid wasps in Costa Rica, but the accuracy of the descriptions is questionable.

CLADISTICS (2022)

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Article Biochemistry & Molecular Biology

CPGView: A package for visualizing detailed chloroplast genome structures

Shengyu Liu, Yang Ni, Jingling Li, Xinyi Zhang, Heyu Yang, Haimei Chen, Chang Liu

Summary: CPGView is a software package that can draw distribution maps of chloroplast genomes and identify annotation errors. It can draw maps of genes, variable sites, and repetitive sequences, adjust exon-intron boundary positions, and plot the structure of specific genes. The software has shown high accuracy and reliability in testing and will become an important tool for studying chloroplast genome structure.

MOLECULAR ECOLOGY RESOURCES (2023)

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Article Biochemistry & Molecular Biology

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Bjoern Gruening, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, Maciej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio de Oliveira, Sergei L. Kosakovsky Pond

Summary: This study found 13 rare mutations among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene, which may impact important regions and functions of the S-gene. The mutations were predicted to decrease the fitness of the virus they occurred in prior to the emergence of Omicron. The study also suggests that the mutations in each cluster interact cooperatively to alter the function of Spike. Understanding how these complex and highly adaptive mutation constellations were assembled in the Omicron S-gene, and why they went undetected in the early stages, is crucial.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

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Article Ecology

Phylotype diversity within soil fungal functional groups drives ecosystem stability

Shengen Liu, Pablo Garcia-Palacios, Leho Tedersoo, Emilio Guirado, Marcel G. A. van der Heijden, Cameron Wagg, Dima Chen, Qingkui Wang, Juntao Wang, Brajesh K. Singh, Manuel Delgado-Baquerizo

Summary: The diversity of soil fungi plays a critical role in ensuring stable plant production and buffering against extreme climate events in global terrestrial ecosystems.

NATURE ECOLOGY & EVOLUTION (2022)

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Article Biochemistry & Molecular Biology

Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Francois Keck, Rosetta C. Blackman, Raphael Bossart, Jeanine Brantschen, Marjorie Couton, Samuel Hurlemann, Dominik Kirschner, Nadine Locher, Heng Zhang, Florian Altermatt

Summary: DNA metabarcoding provides consistent richness estimates with traditional methods for aquatic community assessment, particularly in fish. However, there are pronounced differences between DNA metabarcoding and traditional methods for plankton, microphytobenthos, and macroinvertebrates, with DNA metabarcoding missing some taxa but also detecting otherwise overlooked diversity.

MOLECULAR ECOLOGY (2022)

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