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Messeder JVS, Carlo TA, Zhang G, Tovar JD, Arana C, Huang J, Huang CH, Ma H. A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L. THE NEW PHYTOLOGIST 2024; 243:765-780. [PMID: 38798267 DOI: 10.1111/nph.19849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships. We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size. Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits. We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.
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Affiliation(s)
- João Vitor S Messeder
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Graduate Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tomás A Carlo
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Graduate Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Guojin Zhang
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Juan David Tovar
- Programa de Pós-Graduação em Botânica, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, 69060-001, Brazil
| | - César Arana
- Museo de Historia Natural and Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, 15072, Peru
| | - Jie Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia University, Hohhot, 010000, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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2
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Leong JV, Mezzomo P, Kozel P, Volfová T, de Lima Ferreira P, Seifert CL, Butterill PT, Freiberga I, Michálek J, Matos-Maraví P, Weinhold A, Engström MT, Salminen JP, Segar ST, Sedio BE, Volf M. Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European Salix. Oecologia 2024:10.1007/s00442-024-05569-0. [PMID: 38829402 DOI: 10.1007/s00442-024-05569-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
Plants employ diverse anti-herbivore defences that can covary to form syndromes consisting of multiple traits. Such syndromes are hypothesized to impact herbivores more than individual defences. We studied 16 species of lowland willows occurring in central Europe and explored if their chemical and physical traits form detectable syndromes. We tested for phylogenetic trends in the syndromes and explored whether three herbivore guilds (i.e., generalist leaf-chewers, specialist leaf-chewers, and gallers) are affected more by the detected syndromes or individual traits. The recovered syndromes showed low phylogenetic signal and were mainly defined by investment in concentration, richness, or uniqueness of structurally related phenolic metabolites. Resource acquisition traits or inducible volatile organic compounds exhibited a limited correlation with the syndromes. Individual traits composing the syndromes showed various correlations to the assemblages of herbivores from the three studied guilds. In turn, we found some support for the hypothesis that defence syndromes are composed of traits that provide defence against various herbivores. However, individual traits rather than trait syndromes explained more variation for all studied herbivore assemblages. The detected negative correlations between various phenolics suggest that investment trade-offs may occur primarily among plant metabolites with shared metabolic pathways that may compete for their precursors. Moreover, several traits characterizing the recovered syndromes play additional roles in willows other than defence from herbivory. Taken together, our findings suggest that the detected syndromes did not solely evolve as an anti-herbivore defence.
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Affiliation(s)
- Jing V Leong
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic.
| | - Priscila Mezzomo
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Petr Kozel
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Tereza Volfová
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Paola de Lima Ferreira
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Carlo L Seifert
- Department of Forest Nature Conservation, Faculty of Forest Sciences and Forest Ecology, Georg-August-University of Göttingen, Göttingen, Germany
| | - Phillip T Butterill
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Inga Freiberga
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Jan Michálek
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Institute of Microbiology, Centre Algatech Czech Academy of Sciences, Trebon, Czech Republic
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Marica T Engström
- Bioanalytical Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Juha-Pekka Salminen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, Turku, Finland
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, United Kingdom
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
- Smithsonian Tropical Research Institute, Ancón, Panama
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
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3
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Yuan ML, Westeen EP. Decoupled evolution of ventral and dorsal scales in agamid lizards: ventral keels are associated with arboreality. Biol Lett 2024; 20:20240171. [PMID: 38955224 DOI: 10.1098/rsbl.2024.0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Arboreality has evolved in all major vertebrate lineages and is often associated with morphological adaptations and increased diversification concomitant with accessing novel niche space. In squamate reptiles, foot, claw, and tail morphology are well-studied adaptations shown to be associated with transitions to arboreality. Here, we examined a less well understood trait-the keeled scale-in relation to microhabitat, climate, and diversification dynamics across a diverse lizard radiation, Agamidae. We found that the ancestral agamid had keeled dorsal but not ventral scales; further, dorsal and ventral keels are evolutionarily decoupled. Ventral keeled scales evolved repeatedly in association with arboreality and may be advantageous in reducing wear or by promoting interlocking when climbing. We did not find an association between keeled scales and diversification, suggesting keels do not allow finer-scale microhabitat partitioning observed in other arboreal-associated traits. We additionally found a relationship between keeled ventral scales and precipitation in terrestrial species where we posit that the keels may function to reduce scale degradation. Our results suggest that keeled ventral scales facilitated transitions to arboreality across agamid lizards, and highlight a need for future studies that explore their biomechanical function in relation to microhabitat and climate.
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Affiliation(s)
- Michael L Yuan
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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Zhang C, Ji L, Li Z, Lucas JR, Feng J, Sun C, Jiang T. Resting posture drives the evolution of agonistic displays in bats. Evolution 2024; 78:964-970. [PMID: 38305496 DOI: 10.1093/evolut/qpae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
Agonistic displays are one of the most diverse social behaviors that have important functions in animal's life history. However, their origin and driving factors have largely been unexplored. Here, we evaluated agonistic displays of 71 bat species across 10 families and classified these displays into two categories: (a) boxing displays where a bat attacks its opponent with its wrist and thumb and (b) pushing displays where a bat uses its head or body to hit a rival. We estimated the strength of the phylogenetic signal of the agonistic displays, revealed their origin, and tested the potential evolutionary relationships between agonistic behaviors and body size or resting posture (free hanging vs. contact hanging where the bat is in contact with some surface). We found that agonistic displays were phylogenetically conserved and that boxing displays are the ancestral state. Moreover, we found that bats with a free-hanging resting posture were more likely to exhibit boxing displays than pushing displays. In addition, bats with longer forearms do not have a higher propensity for boxing displays. This study expands our limited knowledge of the evolution of agonistic displays and highlights the importance of resting posture as a driving force in the diversity of agonistic displays.
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Affiliation(s)
- Chunmian Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Ligen Ji
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Ziji Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Jeffrey R Lucas
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Congnan Sun
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
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5
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Yurtseven A, Buyanova S, Agrawal AA, Bochkareva OO, Kalinina OV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiol 2023; 23:404. [PMID: 38124060 PMCID: PMC10731705 DOI: 10.1186/s12866-023-03147-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. RESULTS In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models' performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. CONCLUSIONS Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.
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Affiliation(s)
- Alper Yurtseven
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany.
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany.
| | - Sofia Buyanova
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
| | - Amay Ajaykumar Agrawal
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
| | - Olga O Bochkareva
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Djerassiplatz 1 A, Wien, 1030, Austria
| | - Olga V Kalinina
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
- Faculty of Medicine, Saarland University, Homburg, 66421, Saarland, Germany
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6
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Redlich R, Kowalczyk A, Tene M, Sestili HH, Foley K, Saputra E, Clark N, Chikina M, Meyer WK, Pfenning A. RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570425. [PMID: 38106136 PMCID: PMC10723433 DOI: 10.1101/2023.12.06.570425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many of these methods, including our evolutionary rates based method, RERconverge, lack the capability of analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion to RERconverge that associates shifts in evolutionary rates with the convergent evolution of multi-categorical traits. The categorical RERconverge expansion includes methods for performing categorical ancestral state reconstruction, statistical tests for associating relative evolutionary rates with categorical variables, and a new method for performing phylogenetic permulations on multi-categorical traits. In addition to demonstrating our new method on a three-category diet phenotype, we compare its performance to naive pairwise binary RERconverge analyses and two existing methods for comparative genomic analyses of categorical traits: phylogenetic simulations and a phylogenetic signal based method. We also present a diagnostic analysis of the new permulations approach demonstrating how the method scales with the number of species and the number of categories included in the analysis. Our results show that our new categorical method outperforms phylogenetic simulations at identifying genes and enriched pathways significantly associated with the diet phenotype and that the new ancestral reconstruction drives an improvement in our ability to capture diet-related enriched pathways. Our categorical permulations were able to account for non-uniform null distributions and correct for non-independence in gene rank during pathway enrichment analysis. The categorical expansion to RERconverge will provide a strong foundation for applying the comparative method to categorical traits on larger data sets with more species and more complex trait evolution.
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Jesser KJ, Trueba G, Konstantinidis KT, Levy K. Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador. Gut Microbes 2023; 15:2281010. [PMID: 37992406 PMCID: PMC10730187 DOI: 10.1080/19490976.2023.2281010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.
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Affiliation(s)
- Kelsey J Jesser
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
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Herrando-Moraira S, Roquet C, Calleja JA, Chen YS, Fujikawa K, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, Mandel JR, Mehregan I, Sáez L, Sennikov AN, Susanna A, Vilatersana R, Xu LS. Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae). Mol Phylogenet Evol 2023; 189:107928. [PMID: 37714444 DOI: 10.1016/j.ympev.2023.107928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Juan-Antonio Calleja
- Departament of Biology (Botany), Faculty of Sciences, Research Centre on Biodiversity and Global Change (CIBC-UAM), 28049 Madrid, Spain
| | - You-Sheng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kazumi Fujikawa
- Kochi Prefectural Makino Botanical Garden, 4200-6, Godaisan, Kochi 781-8125, Japan
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Jian-Quan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Llorenç Sáez
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Alexander N Sennikov
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Lian-Sheng Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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9
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Meng Y, Davison J, Clarke JT, Zobel M, Gerz M, Moora M, Öpik M, Bueno CG. Environmental modulation of plant mycorrhizal traits in the global flora. Ecol Lett 2023; 26:1862-1876. [PMID: 37766496 DOI: 10.1111/ele.14309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023]
Abstract
Mycorrhizal symbioses are known to strongly influence plant performance, structure plant communities and shape ecosystem dynamics. Plant mycorrhizal traits, such as those characterising mycorrhizal type (arbuscular (AM), ecto-, ericoid or orchid mycorrhiza) and status (obligately (OM), facultatively (FM) or non-mycorrhizal) offer valuable insight into plant belowground functionality. Here, we compile available plant mycorrhizal trait information and global occurrence data (∼ 100 million records) for 11,770 vascular plant species. Using a plant phylogenetic mega-tree and high-resolution climatic and edaphic data layers, we assess phylogenetic and environmental correlates of plant mycorrhizal traits. We find that plant mycorrhizal type is more phylogenetically conserved than plant mycorrhizal status, while environmental variables (both climatic and edaphic; notably soil texture) explain more variation in mycorrhizal status, especially FM. The previously underestimated role of environmental conditions has far-reaching implications for our understanding of ecosystem functioning under changing climatic and soil conditions.
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Affiliation(s)
- Yiming Meng
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - John T Clarke
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Pyrenean Institute of Ecology, IPE-CSIC, Jaca, Spain
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10
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Rothstein AP, Jesser KJ, Feistel DJ, Konstantinidis KT, Trueba G, Levy K. Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105476. [PMID: 37392822 PMCID: PMC10599324 DOI: 10.1016/j.meegid.2023.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/11/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.
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Affiliation(s)
- Andrew P. Rothstein
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kelsey J. Jesser
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Dorian J. Feistel
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
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11
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Cerrito P, Burkart JM. Human Amygdala Volumetric Patterns Convergently Evolved in Cooperatively Breeding and Domesticated Species. HUMAN NATURE (HAWTHORNE, N.Y.) 2023; 34:501-511. [PMID: 37735331 PMCID: PMC10543585 DOI: 10.1007/s12110-023-09461-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/10/2023] [Indexed: 09/23/2023]
Abstract
The amygdala is a hub in brain networks that supports social life and fear processing. Compared with other apes, humans have a relatively larger lateral nucleus of the amygdala, which is consistent with both the self-domestication and the cooperative breeding hypotheses of human evolution. Here, we take a comparative approach to the evolutionary origin of the relatively larger lateral amygdala nucleus in humans. We carry out phylogenetic analysis on a sample of 17 mammalian species for which we acquired single amygdala nuclei volumetric data. Our results indicate that there has been convergent evolution toward larger lateral amygdala nuclei in both domesticated and cooperatively breeding mammals. These results suggest that changes in processing fearful stimuli to reduce fear-induced aggression, which are necessary for domesticated and cooperatively breeding species alike, tap into the same neurobiological proximate mechanism. However, humans show changes not only in processing fearful stimuli but also in proactive prosociality. Since cooperative breeding, but not domestication, is also associated with increased proactive prosociality, a prominent role of the former during human evolution is more parsimonious, whereas self-domestication may have been involved as an additional stepping stone.
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Affiliation(s)
- Paola Cerrito
- Collegium Helveticum, ETH Zürich, Schmelzbergstrasse 25, Zürich, 8092, Switzerland.
- Department of Evolutionary Anthropology, University of Zurich, Zürich, Switzerland.
| | - Judith M Burkart
- Department of Evolutionary Anthropology, University of Zurich, Zürich, Switzerland
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zurich, Zürich, Switzerland
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12
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Gônet J, Laurin M, Hutchinson JR. Evolution of posture in amniotes-Diving into the trabecular architecture of the femoral head. J Evol Biol 2023; 36:1150-1165. [PMID: 37363887 DOI: 10.1111/jeb.14187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/29/2023] [Accepted: 04/16/2023] [Indexed: 06/28/2023]
Abstract
Extant amniotes show remarkable postural diversity. Broadly speaking, limbs with erect (strongly adducted, more vertically oriented) posture are found in mammals that are particularly heavy (graviportal) or show good running skills (cursorial), while crouched (highly flexed) limbs are found in taxa with more generalized locomotion. In Reptilia, crocodylians have a "semi-erect" (somewhat adducted) posture, birds have more crouched limbs and lepidosaurs have sprawling (well-abducted) limbs. Both synapsids and reptiles underwent a postural transition from sprawling to more erect limbs during the Mesozoic Era. In Reptilia, this postural change is prominent among archosauriforms in the Triassic Period. However, limb posture in many key Triassic taxa remains poorly known. In Synapsida, the chronology of this transition is less clear, and competing hypotheses exist. On land, the limb bones are subject to various stresses related to body support that partly shape their external and internal morphology. Indeed, bone trabeculae (lattice-like bony struts that form the spongy bone tissue) tend to orient themselves along lines of force. Here, we study the link between femoral posture and the femoral trabecular architecture using phylogenetic generalized least squares. We show that microanatomical parameters measured on bone cubes extracted from the femoral head of a sample of amniote femora depend strongly on body mass, but not on femoral posture or lifestyle. We reconstruct ancestral states of femoral posture and various microanatomical parameters to study the "sprawling-to-erect" transition in reptiles and synapsids, and obtain conflicting results. We tentatively infer femoral posture in several hypothetical ancestors using phylogenetic flexible discriminant analysis from maximum likelihood estimates of the microanatomical parameters. In general, the trabecular network of the femoral head is not a good indicator of femoral posture. However, ancestral state reconstruction methods hold great promise for advancing our understanding of the evolution of posture in amniotes.
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Affiliation(s)
- Jordan Gônet
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
| | - Michel Laurin
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
| | - John R Hutchinson
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hatfield, UK
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13
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Herting J, Schönenberger J, Sauquet H. Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales and angiosperms. AMERICAN JOURNAL OF BOTANY 2023; 110:e16213. [PMID: 37459475 DOI: 10.1002/ajb2.16213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Recent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors. METHODS Here, we compiled a data set of 33 floral characters scored for 414 species of Ericales sampled from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal-rates Markov model for each character. We estimated rates of morphological evolution for Ericales and for a separate angiosperm-wide data set of 19 characters and 792 species, creating "rate profiles" for Ericales, angiosperms, and major angiosperm subclades. We compared morphological rates among flower modules within each data set separately and between data sets, and we compared rates among angiosperm subclades using the angiosperm data set. RESULTS The androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve more slowly in both Ericales and angiosperms. Both high and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm-wide floral data set reveal that this pattern appears to be conserved across most major angiosperm clades. CONCLUSIONS Elevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.
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Affiliation(s)
- Julian Herting
- National Herbarium of New South Wales, Botanic Gardens Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Hervé Sauquet
- National Herbarium of New South Wales, Botanic Gardens Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, NSW 2052, Australia
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14
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Silva L, Mendes T, Ramos L, Zhang G, Antunes A. Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature. J Genet Genomics 2023; 50:600-610. [PMID: 36935037 DOI: 10.1016/j.jgg.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023]
Abstract
Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/interspecific interactions. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution, and diversification, especially in the most basal groups. Here, we conduct an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2-583 genes). While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated with expansions in the ORs gene families sensitive to airborne molecules. Additionally, we verify that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. Finally, we identify 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs.
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Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Tito Mendes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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15
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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16
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Jantzen JR, Laliberté E, Carteron A, Beauchamp-Rioux R, Blanchard F, Crofts AL, Girard A, Hacker PW, Pardo J, Schweiger AK, Demers-Thibeault S, Coops NC, Kalacska M, Vellend M, Bruneau A. Evolutionary history explains foliar spectral differences between arbuscular and ectomycorrhizal plant species. THE NEW PHYTOLOGIST 2023; 238:2651-2667. [PMID: 36960543 DOI: 10.1111/nph.18902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Leaf spectra are integrated foliar phenotypes that capture a range of traits and can provide insight into ecological processes. Leaf traits, and therefore leaf spectra, may reflect belowground processes such as mycorrhizal associations. However, evidence for the relationship between leaf traits and mycorrhizal association is mixed, and few studies account for shared evolutionary history. We conduct partial least squares discriminant analysis to assess the ability of spectra to predict mycorrhizal type. We model the evolution of leaf spectra for 92 vascular plant species and use phylogenetic comparative methods to assess differences in spectral properties between arbuscular mycorrhizal and ectomycorrhizal plant species. Partial least squares discriminant analysis classified spectra by mycorrhizal type with 90% (arbuscular) and 85% (ectomycorrhizal) accuracy. Univariate models of principal components identified multiple spectral optima corresponding with mycorrhizal type due to the close relationship between mycorrhizal type and phylogeny. Importantly, we found that spectra of arbuscular mycorrhizal and ectomycorrhizal species do not statistically differ from each other after accounting for phylogeny. While mycorrhizal type can be predicted from spectra, enabling the use of spectra to identify belowground traits using remote sensing, this is due to evolutionary history and not because of fundamental differences in leaf spectra due to mycorrhizal type.
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Affiliation(s)
- Johanna R Jantzen
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Etienne Laliberté
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Rosalie Beauchamp-Rioux
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Florence Blanchard
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Anna L Crofts
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2X9, Canada
| | - Alizée Girard
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Paul W Hacker
- Department of Forest Resources Management, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Juliana Pardo
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Anna K Schweiger
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
- Department of Geography, Remote Sensing Laboratories, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Sabrina Demers-Thibeault
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Nicholas C Coops
- Department of Forest Resources Management, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Margaret Kalacska
- Department of Geography, McGill University, Montréal, QC, H3A 0B9, Canada
| | - Mark Vellend
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2X9, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
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17
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Ramírez MJ, Wolff JO, Jäger P, Pavlek M, Pérez‐González A, Magalhaes I, Michalik P. Geometric regularity in webs of non-orb-weaving spiders. Ecol Evol 2023; 13:e9839. [PMID: 36937056 PMCID: PMC10019946 DOI: 10.1002/ece3.9839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 03/18/2023] Open
Abstract
Geometric regularity of spider webs has been intensively studied in orb-weaving spiders, although it is not exclusive of orb weavers. Here, we document the geometrically regular, repetitive elements in the webs of the non-orb-weaving groups Leptonetidae and Telemidae for the first time. Similar to orb weavers, we found areas with regularly spaced parallel lines in the webs of Calileptoneta helferi, Sulcia sp., and cf. Pinelema sp. Furthermore, we provide a detailed account of the regular webs of Ochyrocera (Ochyroceratidae). The sections of the web with regularly disposed parallel lines are built as U-shaped modules reminiscent of orb webs. It has been suggested that the regularly spaced parallel lines in the webs of Ochyroceratidae and Psilodercidae may be produced in a single sweep of their posterior lateral spinnerets, which have regularly spaced aciniform gland spigots, perhaps involving expansion of the spinnerets. To test this hypothesis, we compared the spacing between parallel lines with the spacing between spigots, searched for expansible membranes in the spinnerets, and examined the junctions of regularly spaced lines. The distance between parallel lines was 10-20 times the distance between spigots, and we found no expansible membranes, and the intersection of parallel lines are cemented, which opposes the single sweep hypothesis. Furthermore, we found cues of viscid silk in the parallel lines of the psilodercid Althepus and broadened piriform gland spigots that may be responsible of its production. Finally, we evaluated the presence or absence of geometrically regular web elements across the spider tree of life. We found reports of regular webs in 31 spider families, including 20 families that are not orb weavers and hypothesize that the two basic aspects of regularity (parallel lines spaced at regular intervals, and radial lines spaced at regular angles) probably appeared many times in the evolution of spiders.
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Affiliation(s)
- Martín J. Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - Jonas O. Wolff
- Zoological Institute and MuseumUniversity of GreifswaldGreifswaldGermany
| | - Peter Jäger
- Arachnology, Senckenberg Research InstituteFrankfurt am MainGermany
| | - Martina Pavlek
- Ruđer Bošković InstituteZagrebCroatia
- Croatian Biospeleological SocietyZagrebCroatia
| | - Abel Pérez‐González
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - Ivan Magalhaes
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - Peter Michalik
- Zoological Institute and MuseumUniversity of GreifswaldGreifswaldGermany
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18
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Gônet J, Bardin J, Girondot M, Hutchinson JR, Laurin M. Locomotor and postural diversity among reptiles viewed through the prism of femoral microanatomy: Palaeobiological implications for some Permian and Mesozoic taxa. J Anat 2023; 242:891-916. [PMID: 36807199 PMCID: PMC10093171 DOI: 10.1111/joa.13833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/28/2022] [Accepted: 01/13/2023] [Indexed: 02/20/2023] Open
Abstract
The water-to-land transition by the first tetrapod vertebrates represents a key stage in their evolution. Selection pressures exerted by this new environment on animals led to the emergence of new locomotor and postural strategies that favoured access to different ecological niches and contributed to their evolutionary success. Today, amniotes show great locomotor and postural diversity, particularly among Reptilia, whose extant representatives include parasagittally locomoting erect and crouched bipeds (birds), sub-parasagittal 'semi-erect' quadrupeds (crocodylians) and sprawling quadrupeds (squamates and turtles). But the different steps leading to such diversity remain enigmatic and the type of locomotion adopted by many extinct species raises questions. This is notably the case of certain Triassic taxa such as Euparkeria and Marasuchus. The exploration of the bone microanatomy in reptiles could help to overcome these uncertainties. Indeed, this locomotor and postural diversity is accompanied by great microanatomical disparity. On land, the bones of the appendicular skeleton support the weight of the body and are subject to multiple constraints that partly shape their external and internal morphology. Here we show how microanatomical parameters measured in cross-section, such as bone compactness or the position of the medullocortical transition, can be related to locomotion. We hypothesised that this could be due to variations in cortical thickness. Using statistical methods that take phylogeny into account (phylogenetic flexible discriminant analyses), we develop different models of locomotion from a sample of femur cross-sections from 51 reptile species. We use these models to infer locomotion and posture in 7 extinct reptile taxa for which they remain debated or not fully clear. Our models produced reliable inferences for taxa that preceded and followed the quadruped/biped and sprawling/erect transitions, notably within the Captorhinidae and Dinosauria. For taxa contemporary with these transitions, such as Terrestrisuchus and Marasuchus, the inferences are more questionable. We use linear models to investigate the effect of body mass and functional ecology on our inference models. We show that body mass seems to significantly impact our model predictions in most cases, unlike the functional ecology. Finally, we illustrate how taphonomic processes can impact certain microanatomical parameters, especially the eccentricity of the section, while addressing some other potential limitations of our methods. Our study provides insight into the evolution of enigmatic locomotion in various early reptiles. Our models and methods could be used by palaeontologists to infer the locomotion and posture in other extinct reptile taxa, especially when considered in combination with other lines of evidence.
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Affiliation(s)
- Jordan Gônet
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
| | - Jérémie Bardin
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
| | - Marc Girondot
- Laboratoire écologie, systématique et évolution, UMR 8079, AgroParisTech, Université Paris-Saclay, Centre national de la recherche scientifique, Orsay, France
| | - John R Hutchinson
- Structure and Motion Laboratory, Royal Veterinary College, Department of Comparative Biomedical Sciences, Hatfield, UK
| | - Michel Laurin
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
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19
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Gônet J, Bardin J, Girondot M, Hutchinson JR, Laurin M. Unravelling the postural diversity of mammals: Contribution of humeral cross-sections to palaeobiological inferences. J MAMM EVOL 2023. [DOI: 10.1007/s10914-023-09652-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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20
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Chen C, Ruhfel BR, Li J, Wang Z, Zhang L, Zhang L, Mao X, Wang J, He D, Luo Y, Hu Q, Duan Y, Xu X, Xi Z, Liu J. Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36749624 DOI: 10.1111/jipb.13464] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.
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Affiliation(s)
- Chunlin Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Brad R Ruhfel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zefu Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Dashan He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yue Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yuanwen Duan
- Institute Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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21
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Bartlett A, Padfield D, Lear L, Bendall R, Vos M. A comprehensive list of bacterial pathogens infecting humans. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748702 DOI: 10.1099/mic.0.001269] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There exists an enormous diversity of bacteria capable of human infection, but no up-to-date, publicly accessible list is available. Combining a pragmatic definition of pathogenicity with an extensive search strategy, we report 1513 bacterial pathogens known to infect humans described pre-2021. Of these, 73 % were regarded as established (have infected at least three persons in three or more references) and 27 % as putative (fewer than three known cases). Pathogen species belong to 10 phyla and 24 classes scattered throughout the bacterial phylogeny. We show that new human pathogens are discovered at a rapid rate. Finally, we discuss how our results could be expanded to a database, which could provide a useful resource for microbiologists. Our list is freely available and archived on GitHub and Zenodo and we have provided walkthroughs to facilitate access and use.
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Affiliation(s)
- Abigail Bartlett
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, UK
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, UK
| | - Luke Lear
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, UK
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22
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Data collected by citizen scientists reveal the role of climate and phylogeny on the frequency of shelter types used by frogs across the Americas. ZOOLOGY 2022; 155:126052. [PMID: 36152596 DOI: 10.1016/j.zool.2022.126052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 01/25/2023]
Abstract
Shelters are microhabitats where animals rest and hide. These microhabitats can be used from short daily periods to long-term estivation or hibernation. Environmental conditions and the phenotypical characteristics of the animal drive habitat selection in relation to shelters. Based on this, climate regions and phylogeny are expected to affect the use of different shelter types. Although shelters are yet to be described for most anuran species, a variety of microhabitats have already been reported as shelter-sites, including dense vegetation, rock crevices, and holes in the ground. In this study, we evaluated photos of frogs for sheltering behaviour from 29 countries in the Americas deposited on the popular citizen-science platform, iNaturalist. We compared the frequency of use of different shelter types identified on the photos among different climate regions and anuran families, also testing possible phylogenetic signals. We identified 11,133 photographs of 378 frog species showing individuals hiding in shelters or in a resting position. We classified observations into 10 shelter types, with live vegetation (24.7 %) being the most commonly recorded natural shelter, followed by hole in the ground (11.4 %) and tree trunk (11.1 %). The use of different shelter types varied between arid and humid climates, and also among different anuran families. We found strong phylogenetic signal for three shelter types (hole in the ground, live vegetation, and water) and the differences in shelter use among taxa suggest a relation with body characteristics. Approximately 47 % of observations of threatened and near threatened species were in hole in the ground, while artificial habitat represented only 3.6 % of the observations in this group. The daily pattern of shelter use corroborated the nocturnal activity of most species. Our findings also expanded the description of shelter sites for 330 species that had no published information on this behaviour. This study contributes to our current knowledge about animal behaviour and highlights the use of citizen science as an effective approach to understand the natural history of amphibians at a large scale.
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23
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Melle Säve‐Söderbergh
- Science Division Swedish Food Agency Uppsala Sweden
- Institute of Environmental Medicine, Karolinska Institutet Stockholm Sweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public Health Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
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24
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Cabral H, Cacciali P, Santana DJ. Evolution of the rostral scale and mimicry in the genus Xenodon Boie, 1826 (Serpentes: Dipsadidae: Xenodontinae). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Snakes are a stimulating life form from an evolutionary perspective. Despite the basic morphological body shape (limbless, with a tubular body), these vertebrates are extremely diverse. The Neotropical region is one of the most diverse regions for snakes in the world, with >650 known species. Within this great diversity, the genus Xenodon includes 12 species with interesting adaptations to terrestrial and semi-fossorial habitats. Members of this genus are mostly diurnal and terrestrial, feed mainly on anurans and exhibit Batesian mimicry of venomous snakes of the genera Bothrops or Micrurus. Here, through phylogenetic analysis and ancestral state estimation, we explore the evolution of the rostral scale and mimicry within the genus Xenodon. Our results suggest that the ancestral lineage of Xenodon had a rounded rostral scale and exhibited Bothrops mimicry. The evolution of the rostral scale in Xenodon might be related to abiotic factors, as an adaptation for open and forested habitats, and mimicry is likely to be related to biotic factors, as a defensive strategy resembling those of venomous snakes.
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Affiliation(s)
- Hugo Cabral
- Programa de Pós-Graduação em Biologia Animal, Universidade Estadual Paulista , São José do Rio Preto, SP , Brazil
- Instituto de Investigación Biológica del Paraguay , Del Escudo 1607, Asunción , Paraguay
- Asociación Guyra Paraguay , Avenida Coronel Carlos Bóveda, Parque Asunción Verde, Viñas Cué , Paraguay
| | - Pier Cacciali
- Instituto de Investigación Biológica del Paraguay , Del Escudo 1607, Asunción , Paraguay
- Asociación Guyra Paraguay , Avenida Coronel Carlos Bóveda, Parque Asunción Verde, Viñas Cué , Paraguay
| | - Diego José Santana
- Mapinguari Lab, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul , 79002-970, Campo Grande, MS , Brazil
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25
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Ashokan A, Leong-Škorničková J, Suksathan P, Newman M, Kress WJ, Gowda V. Floral evolution and pollinator diversification in Hedychium: Revisiting Darwin's predictions using an integrative taxonomic approach. AMERICAN JOURNAL OF BOTANY 2022; 109:1410-1427. [PMID: 35862825 DOI: 10.1002/ajb2.16039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/08/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Hedychium J. Koenig (Zingiberaceae) is endemic to the Indo-Malayan Realm and is known for its colorful and fragrant flowers. Historically, two different pollination syndromes characterize Hedychium: diurnal or bird pollination, and nocturnal or moth pollination. In this study, we aim to understand the evolution of nocturnal and diurnal flowers, and to test its putative association with lineage diversification in Hedychium. METHODS A molecular tree of Hedychium was used as a scaffold upon which we estimated ancestral character states, phylogenetic signals, and correlations for certain categorical and continuous floral traits. Furthermore, we used phylomorphospace and trait-dependent diversification rate estimation analyses to understand phenotypic evolution and associated lineage diversification in Hedychium. RESULTS Although floral color and size lacked any association with specific pollinators, white or pale flowers were most common in the early branching clades when compared to bright-colored flowers, which were more widely represented in the most-derived clade IV. Five categorical and two continuous characters were identified to have informative evolutionary patterns, which also emphasized that ecology may have played a critical role in the diversification of Hedychium. CONCLUSIONS From our phylogenetic analyses and ecological observations, we conclude that specializations in pollinator interactions are rare in the hyperdiverse clade IV, thus challenging the role of both moth-specialization and bird-specialization as central factors in the diversification of Hedychium. However, our results also suggest that clade III (predominantly island clade) may show specializations, and future studies should investigate ecological and pollinator interactions, along with inclusion of new traits such as floral fragrance and anthesis time.
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Affiliation(s)
- Ajith Ashokan
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, 462066, India
| | - Jana Leong-Škorničková
- Research & Conservation branch, Singapore Botanic Gardens, 1 Cluny Road, 259569, Singapore
| | - Piyakaset Suksathan
- Herbarium (QBG), Queen Sirikit Botanic Garden, P. O. Box 7, Mae Rim, Chiang Mai, 50180, Thailand
| | - Mark Newman
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, Scotland, United Kingdom
| | - W John Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P. O. Box 37012, Washington, DC, 20013-7012, United States
| | - Vinita Gowda
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, 462066, India
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26
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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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Tam J, Lagisz M, Cornwell W, Nakagawa S. Quantifying research interests in 7,521 mammalian species with h-index: a case study. Gigascience 2022; 11:6665406. [PMID: 35962776 PMCID: PMC9375528 DOI: 10.1093/gigascience/giac074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Taxonomic bias is a known issue within the field of biology, causing scientific knowledge to be unevenly distributed across species. However, a systematic quantification of the research interest that the scientific community has allocated to individual species remains a big data problem. Scalable approaches are needed to integrate biodiversity data sets and bibliometric methods across large numbers of species. The outputs of these analyses are important for identifying understudied species and directing future research to fill these gaps. FINDINGS In this study, we used the species h-index to quantity the research interest in 7,521 species of mammals. We tested factors potentially driving species h-index, by using a Bayesian phylogenetic generalized linear mixed model (GLMM). We found that a third of the mammals had a species h-index of zero, while a select few had inflated research interest. Further, mammals with higher species h-index had larger body masses; were found in temperate latitudes; had their humans uses documented, including domestication; and were in lower-risk International Union for Conservation of Nature Red List categories. These results surprisingly suggested that critically endangered mammals are understudied. A higher interest in domesticated species suggested that human use is a major driver and focus in mammalian scientific literature. CONCLUSIONS Our study has demonstrated a scalable workflow and systematically identified understudied species of mammals, as well as identified the likely drivers of this taxonomic bias in the literature. This case study can become a benchmark for future research that asks similar biological and meta-research questions for other taxa.
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Affiliation(s)
- Jessica Tam
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Will Cornwell
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
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28
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Meseguer AS, Carrillo R, Graham SW, Sanmartín I. Macroevolutionary dynamics in the transition of angiosperms to aquatic environments. THE NEW PHYTOLOGIST 2022; 235:344-355. [PMID: 35292979 PMCID: PMC9320795 DOI: 10.1111/nph.18100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Angiosperm lineages in aquatic environments are characterized by high structural and functional diversity, and wide distributions. A long-standing evolutionary riddle is what processes have caused the relatively low diversity of aquatic angiosperms compared to their terrestrial relatives. We use diversification and ancestral reconstruction models with a comprehensive > 10 000 genus angiosperm phylogeny to elucidate the macroevolutionary dynamics associated with transitions of terrestrial plants to water. Our study reveals that net diversification rates are significantly lower in aquatic than in terrestrial angiosperms due to lower speciation and higher extinction. Shifts from land to water started early in angiosperm evolution, but most events were concentrated during the last c. 25 million years. Reversals to a terrestrial habitat started only 40 million years ago, but occurred at much higher rates. Within aquatic angiosperms, the estimated pattern is one of gradual accumulation of lineages, and relatively low and constant diversification rates throughout the Cenozoic. Low diversification rates, together with infrequent water transitions, account for the low diversity of aquatic angiosperms today. The stressful conditions and small global surface of the aquatic habitat available for angiosperms are hypothesized to explain this pattern.
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Affiliation(s)
| | - Rubén Carrillo
- Real Jardín Botánico de Madrid (RJB)CSIC28014MadridSpain
| | - Sean W. Graham
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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29
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Bertolet BL, Louden SI, Jones SE. Microbial community composition, and not
pH
, influences lake sediment function. Ecosphere 2022. [DOI: 10.1002/ecs2.4091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Brittni L. Bertolet
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana USA
| | - Sydney I. Louden
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana USA
| | - Stuart E. Jones
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana USA
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30
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Wilson JD, Mongiardino Koch N, Ramírez MJ. Chronogram or phylogram for ancestral state estimation? Model‐fit statistics indicate the branch lengths underlying a binary character’s evolution. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeremy D. Wilson
- Biodiversity and Geosciences Program, Queensland Museum South Brisbane, Queensland 4101 Australia
- Museo Argentino de Ciencias Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Angel Gallardo 470, C1405DJR Buenos Aires Argentina
| | - Nicolás Mongiardino Koch
- Department of Earth & Planetary Sciences Yale University 210 Whitney Avenue, New Haven, CT 06511 USA
- Scripps Institution of Oceanography University of California San Diego, 8750 Biological Grade, La Jolla, CA 92037 USA
| | - Martín J. Ramírez
- Museo Argentino de Ciencias Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Angel Gallardo 470, C1405DJR Buenos Aires Argentina
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31
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Resident birds are more behaviourally plastic than migrants. Sci Rep 2022; 12:5743. [PMID: 35388121 PMCID: PMC8986783 DOI: 10.1038/s41598-022-09834-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/29/2022] [Indexed: 11/08/2022] Open
Abstract
Species subjected to more variable environments should have greater phenotypic plasticity than those that are more restricted to specific habitat types leading to the expectation that migratory birds should be relatively more plastic than resident birds. We tested this comparatively by studying variation in flight initiation distance (FID), a well-studied antipredator behaviour. We predicted that variation in FID would be greater for migratory species because they encountered a variety of locations during their lives and therefore had less predictable assessments of risk compared to more sedentary species. Contrary to our prediction, we found that non-migratory species (sedentary) had greater variation in FID than migratory ones. Migratory and partially migratory birds had greater average FIDs than sedentary birds, suggesting that they were generally more wary. These results suggest that the predictability associated with not migrating permits more nuanced risk assessment which was seen in the greater variation in FID of sedentary bird species.
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32
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Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes.. [PMID: 36238714 PMCID: PMC9558438 DOI: 10.1101/2022.03.30.486478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.
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Porto DS, Dahdul WM, Lapp H, Balhoff JP, Vision TJ, Mabee PM, Uyeda J. Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies. Syst Biol 2022; 71:1290-1306. [PMID: 35285502 PMCID: PMC9558846 DOI: 10.1093/sysbio/syac022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 02/09/2022] [Accepted: 03/05/2022] [Indexed: 11/18/2022] Open
Abstract
Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent “parts”, but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies—structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.]
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Affiliation(s)
- Diego S Porto
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Wasila M Dahdul
- UCI Libraries,University of California, Irvine, Irvine, CA 92623, USA
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
- Battelle, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061, USA
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A milk-sharing economy allows placental mammals to overcome their metabolic limits. Proc Natl Acad Sci U S A 2022; 119:e2114674119. [PMID: 35238685 PMCID: PMC8915790 DOI: 10.1073/pnas.2114674119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we demonstrate that a naturally evolving behavior (allonursing) has greater effect on reproductive power (mass per unit of time) and output (litter mass at birth) than does artificial selection (domestication). Additionally, we demonstrate the importance of resource optimization afforded by sociality (rather than resource abundance per se) in shaping a species’ life history profile and its ability to overcome its own physiological constraints. Maternal resource availability and metabolism have a strong limiting effect on reproductive output. Allomaternal care and domestication increase the energy available to the mother and should correlate with an increase in reproductive output. Here, we take a comparative approach to understand how this increase is accomplished (e.g., litter mass, reproductive frequency, etc.) and the strength of the effect among different forms of external energetic supplementation. We find that domestication and all forms of allocare correlate with increased fertility. All forms of provisioning correlate with larger litters without compromising offspring size. The greatest increase we observe in reproductive power is in species that practice allonursing. Our results suggest that the ultimate factor limiting reproductive output in placental mammals is maternal metabolic power rather than resource availability.
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Pinna CS, Vilbert M, Borensztajn S, Daney de Marcillac W, Piron-Prunier F, Pomerantz A, Patel NH, Berthier S, Andraud C, Gomez D, Elias M. Mimicry can drive convergence in structural and light transmission features of transparent wings in Lepidoptera. eLife 2021; 10:e69080. [PMID: 34930525 PMCID: PMC8691843 DOI: 10.7554/elife.69080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 11/19/2021] [Indexed: 01/30/2023] Open
Abstract
Müllerian mimicry is a positive interspecific interaction, whereby co-occurring defended prey species share a common aposematic signal. In Lepidoptera, aposematic species typically harbour conspicuous opaque wing colour patterns with convergent optical properties among co-mimetic species. Surprisingly, some aposematic mimetic species have partially transparent wings, raising the questions of whether optical properties of transparent patches are also convergent, and of how transparency is achieved. Here, we conducted a comparative study of wing optics, micro and nanostructures in neotropical mimetic clearwing Lepidoptera, using spectrophotometry and microscopy imaging. We show that transparency, as perceived by predators, is convergent among co-mimics in some mimicry rings. Underlying micro- and nanostructures are also sometimes convergent despite a large structural diversity. We reveal that while transparency is primarily produced by microstructure modifications, nanostructures largely influence light transmission, potentially enabling additional fine-tuning in transmission properties. This study shows that transparency might not only enable camouflage but can also be part of aposematic signals.
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Affiliation(s)
- Charline Sophie Pinna
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, EPHE, Université des AntillesParisFrance
| | - Maëlle Vilbert
- Centre de Recherche sur la Conservation (CRC), CNRS, MNHN, Ministère de la CultureParisFrance
| | - Stephan Borensztajn
- Institut de Physique du Globe de Paris (IPGP), Université de Paris, CNRSParisFrance
| | | | - Florence Piron-Prunier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, EPHE, Université des AntillesParisFrance
| | - Aaron Pomerantz
- Marine Biological LaboratoryWoods HoleUnited States
- Department Integrative Biology, University of California BerkeleyBerkeleyUnited States
| | | | - Serge Berthier
- Institut des NanoSciences de Paris (INSP), Sorbonne Université, CNRSParisFrance
| | - Christine Andraud
- Centre de Recherche sur la Conservation (CRC), CNRS, MNHN, Ministère de la CultureParisFrance
| | - Doris Gomez
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, Univ MontpellierMontpellierFrance
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, EPHE, Université des AntillesParisFrance
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Hernández‐Agüero JA, Ruiz‐Tapiador I, Cayuela L. What feeds on
Quercus ilex
L.? A biogeographical approach to studying trophic interactions in a Mediterranean keystone species. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | | | - Luis Cayuela
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Madrid Spain
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Abstract
Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs. IMPORTANCE Considering the enormous variety of LBDs at sensor proteins, an important question resides in establishing the forces that have driven their evolution and selection. We present here the first clear demonstration that environmental factors play an important role in the selection and evolution of LBDs. We were able to demonstrate the existence of LBD families that are highly enriched in plant-associated bacteria but show a wide phylogenetic spread. These findings offer a number of research opportunities in the field of single transduction, such as the exploration of similar relationships in chemoreceptors of bacteria with a different lifestyle, like those inhabiting or infecting the human intestine. Similarly, our results raise the question whether similar LBD types might be shared by members of different sensor protein families. Lastly, we provide a comprehensive catalogue of CRs classified by their LBD region that includes a large number of putative new LBD types.
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Verster KI, Tarnopol RL, Akalu SM, Whiteman NK. Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes. Genome Biol Evol 2021; 13:6358723. [PMID: 34450656 PMCID: PMC8455502 DOI: 10.1093/gbe/evab202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 12/26/2022] Open
Abstract
A growing body of evidence has underscored the role of horizontal gene transfer (HGT) in animal evolution. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the pea aphid Acyrthosiphon pisum secondary endosymbiont (APSE) phages to drosophilid and aphid nuclear genomes. Here, we report cdtB in the nuclear genome of the gall-forming "swede midge" Contarinia nasturtii (Diptera: Cecidomyiidae) via HGT. We searched all available gall midge genome sequences for evidence of APSE-to-insect HGT events and found five toxin genes (aip56, cdtB, lysozyme, rhs, and sltxB) transferred horizontally to cecidomyiid nuclear genomes. Surprisingly, phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor lineage of the toxin gene to cecidomyiids. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for animal HGT, which suggested that microbe-to-insect HGT was more likely between taxa that share environments than those from different environments. Many of the toxins we found in midge genomes target eukaryotic cells, and catalytic residues important for toxin function are conserved in insect copies. This class of horizontally transferred, eukaryotic cell-targeting genes is potentially important in insect adaptation.
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Affiliation(s)
- Kirsten I Verster
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Rebecca L Tarnopol
- Department of Plant & Microbial Biology, University of California, Berkeley, California, USA
| | - Saron M Akalu
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, California, USA,Department of Molecular and Cell Biology, University of California, Berkeley, California, USA,Corresponding author: E-mail:
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Abstract
Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas)9 transactivating CRISPR RNAs (tracrRNAs) form distinct structures essential for target recognition and cleavage and dictate exchangeability between orthologous proteins. As noncoding RNAs that are often apart from the CRISPR array, their identification can be arduous. In this article, a new bioinformatic method for the detection of Cas9 tracrRNAs is presented. The approach utilizes a covariance model based on both sequence homology and predicted secondary structure to locate tracrRNAs. This method predicts a tracrRNA for 98% of CRISPR-Cas9 systems identified by us. To ensure accuracy, we also benchmark our approach against biochemically vetted tracrRNAs finding false-positive and false-negative rates of 5.5% and 7.1%, respectively. Finally, the association between Cas9 amino acid sequence-based phylogeny and tracrRNA secondary structure is evaluated, revealing strong evidence that secondary structure is evolutionarily conserved among Cas9 lineages. Altogether, our findings provide insight into Cas9 tracrRNA evolution and efforts to characterize the tracrRNA of Cas9 systems.
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Affiliation(s)
- Shane K. Dooley
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA; Johnston, Iowa, USA
| | - Erica K. Baken
- Department of Science, Chatham University, Pittsburgh, Pennsylvania, USA; Johnston, Iowa, USA
| | - Walter N. Moss
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA; and Johnston, Iowa, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA; Johnston, Iowa, USA
| | - Joshua K. Young
- Department of Molecular Engineering, Corteva AgriscienceJohnston, , Johnston, Iowa, USA
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40
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Tunes P, Camargo MGG, Guimarães E. Floral UV Features of Plant Species From a Neotropical Savanna. FRONTIERS IN PLANT SCIENCE 2021; 12:618028. [PMID: 34025689 PMCID: PMC8137824 DOI: 10.3389/fpls.2021.618028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Despite the wide interest in flower colours, only after the end of the nineteenth-century studies started to comprise floral UV reflection, which is invisible to humans but visible to the major groups of pollinators. Many flowers and inflorescences display colour patterns, an important signal for pollinators, promoted by the presence of at least two different colours within flowers or inflorescences, including colours in the UV waveband. For Neotropical savanna plant species, we characterised floral UV features using UV-photography and reflectance measurements. We tested (i) whether floral UV features were constrained by their shared ancestry, (ii) whether floral UV features were associated with pollinators, and (iii) whether floral UV features were associated with floral traits mediating these interactions, including floral resource, type of attraction unit and presence/absence of non-UV colour patterns. Of 80 plant species, ca. 70% were UV-patternless, most of them UV-absorbing. Approximately 30% presented one of three types of UV-patterns: bullseye, contrasting corolla markings oriented toward floral resources or contrasting reproductive structures, which were all considered as floral guides. Floral UV features were phylogenetically constrained and were associated with pollinators, floral resources and attraction unit, but not with non-UV colour patterns. UV-patternless flowers were associated with most of the pollination systems, while UV-patterned flowers were mainly associated with bee-pollination. UV-absorbing flowers comprised the only category with hawkmoth- and butterfly-pollinated flowers, and a high percentage of hummingbird-pollinated species. Nocturnal pollinated species were also commonly UV-absorbing, except for one UV-reflecting bat-pollinated species and one beetle-pollinated species with UV-reflecting stigmas. All types of floral UV features were associated with nectar; however, flowers with contrasting reproductive structures were mainly associated with pollen. There was an association between UV-absorbing species and the presence of inflorescences and intermediate attraction units. Our results evince that phylogenetic relatedness can constraint floral UV features' diversification, but combinations of evolutionary and ecological processes may be expected in this scenario.
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Affiliation(s)
- Priscila Tunes
- Laboratory of Ecology and Evolution of Plant-Animal Interactions, Postgraduate Program in Biological Sciences (Botany), Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | | | - Elza Guimarães
- Laboratory of Ecology and Evolution of Plant-Animal Interactions, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
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41
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Tseng ZJ. Rethinking the use of finite element simulations in comparative biomechanics research. PeerJ 2021; 9:e11178. [PMID: 33868821 PMCID: PMC8035905 DOI: 10.7717/peerj.11178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 12/04/2022] Open
Abstract
In the past 15 years, the finite element (FE) method has become a ubiquitous tool in the repertoire of evolutionary biologists. The method is used to estimate and compare biomechanical performance implicated as selective factors in the evolution of morphological structures. A feature common to many comparative studies using 3D FE simulations is small taxonomic sample sizes. The time-consuming nature of FE model construction is considered a main limiting factor in taxonomic breadth of comparative FE analyses. Using a composite FE model dataset, I show that the combination of small taxonomic sample sizes and comparative FE data in analyses of evolutionary associations of biomechanical performance to feeding ecology generates artificially elevated correlations. Such biases introduce false positives into interpretations of clade-level trends. Considering this potential pitfall, recommendations are provided to consider the ways FE analyses are best used to address both taxon-specific and clade-level evolutionary questions.
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Affiliation(s)
- Z Jack Tseng
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA, USA
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42
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Motyka M, Kusy D, Masek M, Bocek M, Li Y, Bilkova R, Kapitán J, Yagi T, Bocak L. Conspicuousness, phylogenetic structure, and origins of Müllerian mimicry in 4000 lycid beetles from all zoogeographic regions. Sci Rep 2021; 11:5961. [PMID: 33727670 PMCID: PMC7971032 DOI: 10.1038/s41598-021-85567-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
Biologists have reported on the chemical defences and the phenetic similarity of net-winged beetles (Coleoptera: Lycidae) and their co-mimics. Nevertheless, our knowledge has remained fragmental, and the evolution of mimetic patterns has not been studied in the phylogenetic context. We illustrate the general appearance of ~ 600 lycid species and ~ 200 co-mimics and their distribution. Further, we assemble the phylogeny using the transcriptomic backbone and ~ 570 species. Using phylogenetic information, we closely scrutinise the relationships among aposematically coloured species, the worldwide diversity, and the distribution of aposematic patterns. The emitted visual signals differ in conspicuousness. The uniform coloured dorsum is ancestral and was followed by the evolution of bicoloured forms. The mottled patterns, i.e. fasciate, striate, punctate, and reticulate, originated later in the course of evolution. The highest number of sympatrically occurring patterns was recovered in New Guinea and the Andean mountain ecosystems (the areas of the highest abundance), and in continental South East Asia (an area of moderate abundance but high in phylogenetic diversity). Consequently, a large number of co-existing aposematic patterns in a single region and/or locality is the rule, in contrast with the theoretical prediction, and predators do not face a simple model-like choice but cope with complex mimetic communities. Lycids display an ancestral aposematic signal even though they sympatrically occur with differently coloured unprofitable relatives. We show that the highly conspicuous patterns evolve within communities predominantly formed by less conspicuous Müllerian mimics and, and often only a single species displays a novel pattern. Our work is a forerunner to the detailed research into the aposematic signalling of net-winged beetles.
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Affiliation(s)
- Michal Motyka
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Dominik Kusy
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Michal Masek
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Matej Bocek
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Yun Li
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - R. Bilkova
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Josef Kapitán
- grid.10979.360000 0001 1245 3953Department of Optics, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Takashi Yagi
- grid.261455.10000 0001 0676 0594Department of Biological Sciences, Graduate School of Science, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8570 Japan
| | - Ladislav Bocak
- grid.10979.360000 0001 1245 3953Laboratory of Diversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
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Wang J, Xu G, Chen W, Ma Y, Qi W, Zhang C, Cui X. Impacts of growth form and phylogenetic relatedness on seed germination: A large-scale analysis of a subtropical regional flora. Ecol Evol 2021; 11:1280-1293. [PMID: 33598130 PMCID: PMC7863672 DOI: 10.1002/ece3.7132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022] Open
Abstract
Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25°C; daily alternating 25/15°C for each 12 hr). Germination was low with a skewed distribution (mean = 38.9% at 25°C, and 43.3% at 25/15°C). One fifth of the species had low (<10%) and slow (4-30 days) germination, and only a few (8%) species had a high (>80%) and rapid (1.2-6.6 days) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.
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Affiliation(s)
- JuHong Wang
- College of Food Technology and Life ScienceHanshan Normal UniversityChaozhouChina
| | - GeXi Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Wen Chen
- College of Geography and Tourism ManagementHanshan Normal UniversityChaozhouChina
| | - YanBo Ma
- College of Mathematics and StatisticsHanshan Normal UniversityChaozhouChina
| | - Wei Qi
- State Key Laboratory of Grassland AgroecosystemsSchool of Life SciencesLanzhou UniversityLanzhouChina
| | - ChunHui Zhang
- State Key Laboratory of Plateau Ecology and AgricultureQinghai UniversityXiningChina
| | - XianLiang Cui
- College of Biology and ChemistryPuer UniversityPuerChina
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44
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Epstein B, Tiffin P. Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes. Proc Biol Sci 2021; 288:20201804. [PMID: 33402066 DOI: 10.1098/rspb.2020.1804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.
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Affiliation(s)
- Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA
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45
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Assessing the Diversity of the Form of Age-Specific Changes in Adult Mortality from Captive Mammalian Populations. DIVERSITY 2020. [DOI: 10.3390/d12090354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Actuarial senescence (i.e., the age-specific increase in mortality rate) is pervasive across mammalian species, but our current understanding of the diversity of forms that actuarial senescence displays across species remains limited. Although several mathematical models have been proposed to model actuarial senescence, there is still no consensus on which model to use, especially when comparing mortality patterns among species. To fill this knowledge gap, we fitted and compared different forms of increase using models commonly used in senescence studies (i.e., Gompertz, Weibull, and logistic) across 61 species of mammalian captive populations using the Bayesian Survival Trajectory Analysis (BaSTA) approach. For as much as 79% of the species, a Gompertz increase of mortality with age was the most parsimonious model that satisfactorily described the shape of age-specific mortality changes in adults. This highlights that the form of the increase in mortality is mostly consistent across mammalian species and follows the Gompertz rule with some rare exceptions. The implications of that result are twofold. First, the Gompertz rate of mortality increase should be used in cross-species comparative analyses of mammals, as already done in some studies. Second, although the Gompertz model accurately describes actuarial senescence in most mammals, there are notable exceptions, and the factors causing this deviation from an exponential mortality increase during the adult stage warrant further investigation.
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García-Girón J, Heino J, Baastrup-Spohr L, Bove CP, Clayton J, de Winton M, Feldmann T, Fernández-Aláez M, Ecke F, Grillas P, Hoyer MV, Kolada A, Kosten S, Lukács BA, Mjelde M, Mormul RP, Rhazi L, Rhazi M, Sass L, Xu J, Alahuhta J. Global patterns and determinants of lake macrophyte taxonomic, functional and phylogenetic beta diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 723:138021. [PMID: 32213415 DOI: 10.1016/j.scitotenv.2020.138021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
Documenting the patterns of biological diversity on Earth has always been a central challenge in macroecology and biogeography. However, for the diverse group of freshwater plants, such research program is still in its infancy. Here, we examined global variation in taxonomic, functional and phylogenetic beta diversity patterns of lake macrophytes using regional data from six continents. A data set of ca. 480 lake macrophyte community observations, together with climatic, geographical and environmental variables, was compiled across 16 regions worldwide. We (a) built the very first phylogeny comprising most freshwater plant lineages; (b) exploited a wide array of functional traits that are important to macrophyte autoecology or that relate to lake ecosystem functioning; (c) assessed if different large-scale beta diversity patterns show a clear latitudinal gradient from the equator to the poles using null models; and (d) employed evolutionary and regression models to first identify the degree to which the studied functional traits show a phylogenetic signal, and then to estimate community-environment relationships at multiple spatial scales. Our results supported the notion that ecological niches evolved independently of phylogeny in macrophyte lineages worldwide. We also showed that taxonomic and phylogenetic beta diversity followed the typical global trend with higher diversity in the tropics. In addition, we were able to confirm that species, multi-trait and lineage compositions were first and foremost structured by climatic conditions at relatively broad spatial scales. Perhaps more importantly, we showed that large-scale processes along latitudinal and elevational gradients have left a strong footprint in the current diversity patterns and community-environment relationships in lake macrophytes. Overall, our results stress the need for an integrative approach to macroecology, biogeography and conservation biology, combining multiple diversity facets at different spatial scales.
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Affiliation(s)
- Jorge García-Girón
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
| | - Jani Heino
- Finnish Environment Institute, Freshwater Centre, P.O. Box 413, 90014 Oulu, Finland.
| | - Lars Baastrup-Spohr
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, 2100 København Ø, Denmark.
| | - Claudia P Bove
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, RJ 20940-040, Brazil
| | - John Clayton
- National Institute of Water and Atmospheric Research Limited, P.O. Box 11115, Hamilton, New Zealand.
| | - Mary de Winton
- National Institute of Water and Atmospheric Research Limited, P.O. Box 11115, Hamilton, New Zealand.
| | - Tõnu Feldmann
- Centre for Limnology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 61117 Rannu, Tartumaa, Estonia.
| | | | - Frauke Ecke
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), P.O. Box 7050, 750 07 Uppsala, Sweden; Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences (SLU), 901 83 Umeå, Sweden.
| | - Patrick Grillas
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, Le Sambuc, 13200 Arles, France.
| | - Mark V Hoyer
- Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, Institute of Food and Agricultural Services, University of Florida, 7922 NW 71st Street, Gainesville, FL 32609, USA.
| | - Agnieszka Kolada
- Department of Freshwater Protection, Institute of Environmental Protection-National Research Institute, Krucza 5/11D, 00-548 Warsaw, Poland.
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, the Netherlands.
| | - Balázs A Lukács
- Department of Tisza River Research, MTA Centre for Ecological Research, DRI, Bem tér 18/C, Debrecen 4026, Hungary.
| | - Marit Mjelde
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, 0349 Oslo, Norway.
| | - Roger P Mormul
- Department of Biology, Research Group in Limnology, Ichthyology and Aquaculture-Nupélia, State University of Maringá, Av. Colombo 5790, Bloco H90, CEP-87020-900 Mringá, PR, Brazil
| | - Laila Rhazi
- Research Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, 4 avenue Ibn Battouta, B.P. 1014 RP, Rabat, Morocco
| | - Mouhssine Rhazi
- Faculty of Science and Technology, Department of Biology, Moulay Ismail University, PB 509, Boutalamine, Errachidia, Morocco
| | - Laura Sass
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA.
| | - Jun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China.
| | - Janne Alahuhta
- Finnish Environment Institute, Freshwater Centre, P.O. Box 413, 90014 Oulu, Finland; Geography Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
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47
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Field J, Gonzalez-Voyer A, Boulton RA. The evolution of parental care strategies in subsocial wasps. Behav Ecol Sociobiol 2020. [DOI: 10.1007/s00265-020-02853-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
Insect parental care strategies are particularly diverse, and prolonged association between parents and offspring may be a key precursor to the evolution of complex social traits. Macroevolutionary patterns remain obscure, however, due to the few rigorous phylogenetic analyses. The subsocial sphecid wasps are a useful group in which to study parental care because of the diverse range of strategies they exhibit. These strategies range from placing a single prey item in a pre-existing cavity to mass provisioning a pre-built nest, through to complex progressive provisioning where a female feeds larvae in different nests simultaneously as they grow. We show that this diversity stems from multiple independent transitions between states. The strategies we focus on were previously thought of in terms of a stepping-stone model in which complexity increases during evolution, ending with progressive provisioning which is a likely precursor to eusociality. We find that evolution has not always followed this model: reverse transitions are common, and the ancestral state is the most flexible rather than the simplest strategy. Progressive provisioning has evolved several times independently, but transitions away from it appear rare. We discuss the possibility that ancestral plasticity has played a role in the evolution of extended parental care.
Significance statement
Parental care behaviour leads to prolonged associations between parents and offspring, which is thought to drive the evolution of social living. Despite the importance of insect parental care for shaping the evolution of sociality, relatively few studies have attempted to reconstruct how different strategies evolve in the insects. In this study, we use phylogenetic methods to reconstruct the evolution of the diverse parental care strategies exhibited by the subsocial digger wasps (Sphecidae). Contrary to expectations, we show that parental care in this group has not increased in complexity over evolutionary time. We find that the ancestral state is not the simplest, but may be the most flexible strategy. We suggest that this flexible ancestral strategy may have allowed rapid response to changing environmental conditions which might explain the diversity in parental care strategies that we see in the digger wasps today.
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48
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Deline B, Thompson JR, Smith NS, Zamora S, Rahman IA, Sheffield SL, Ausich WI, Kammer TW, Sumrall CD. Evolution and Development at the Origin of a Phylum. Curr Biol 2020; 30:1672-1679.e3. [PMID: 32197083 DOI: 10.1016/j.cub.2020.02.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/24/2020] [Accepted: 02/18/2020] [Indexed: 01/07/2023]
Abstract
Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible, enabling continued evolutionary innovation throughout the clades' history.
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Affiliation(s)
- Bradley Deline
- Department of Geoscience, University of West Georgia, Carrollton, GA 30118, USA.
| | - Jeffrey R Thompson
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Nicholas S Smith
- Department of Geoscience, University of West Georgia, Carrollton, GA 30118, USA; Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Samuel Zamora
- Instituto Geológico y Minero de España, 50006 Zaragoza, Spain; Grupo Aragosaurus-IUCA, Área de Paleontología, Facultad de Ciencias, Universidad de Zaragoza, 50006 Zaragoza, Spain
| | - Imran A Rahman
- Oxford University Museum of Natural History, Oxford OX1 3PW, UK
| | - Sarah L Sheffield
- School of Geosciences, University of South Florida, Tampa, FL 33620, USA
| | - William I Ausich
- School of Earth Sciences, Ohio State University, Columbus, OH 43210, USA
| | - Thomas W Kammer
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506, USA
| | - Colin D Sumrall
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA
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49
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Borges R, Fonseca J, Gomes C, Johnson WE, O'Brien SJ, Zhang G, Gilbert MTP, Jarvis ED, Antunes A. Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype. Genome Biol Evol 2020; 11:2244-2255. [PMID: 31386143 PMCID: PMC6735850 DOI: 10.1093/gbe/evz111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2019] [Indexed: 01/04/2023] Open
Abstract
Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from other birds include: 1) shifts in frontal orientation to improve binocularity, 2) rod-dominated retina, and 3) enlarged corneas and lenses. Some of these features parallel mammalian eye patterns, which are hypothesized to have initially evolved in nocturnal environments. Here, we used an integrative approach combining phylogenomics and functional phenotypes of 211 eye-development genes across 48 avian genomes representing most avian orders, including the stem lineage of the scotopic-adapted barn owl. Overall, we identified 25 eye-development genes that coevolved under intensified or relaxed selection in the retina, lens, cornea, and optic nerves of the barn owl. The agtpbp1 gene, which is associated with the survival of photoreceptor populations, was pseudogenized in the barn owl genome. Our results further revealed that barn owl retinal genes responsible for the maintenance, proliferation, and differentiation of photoreceptors experienced an evolutionary relaxation. Signatures of relaxed selection were also observed in the lens and cornea morphology-associated genes, suggesting that adaptive evolution in these structures was essentially structural. Four eye-development genes (ephb1, phactr4, prph2, and rs1) evolved in positive association with the orbit convergence in birds and under relaxed selection in the barn owl lineage, likely contributing to an increased reliance on binocular vision in the barn owl. Moreover, we found evidence of coevolutionary interactions among genes that are expressed in the retina, lens, and optic nerve, suggesting synergetic adaptive events. Our study disentangles the genomic changes governing the binocularity and low-light perception adaptations of barn owls to nocturnal environments while revealing the molecular mechanisms contributing to the shift from the typical avian photopic vision to the more-novel scotopic-adapted eye.
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Affiliation(s)
- Rui Borges
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - João Fonseca
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia.,Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, Maryland
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark.,China National GeneBank, BGI-Shenzen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, Rockefeller University.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Portugal
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