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Hoyal Cuthill JF, Lloyd GT. Measuring homoplasy I: comprehensive measures of maximum and minimum cost under parsimony across discrete cost matrix character types. Cladistics 2024. [PMID: 38924583 DOI: 10.1111/cla.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 06/28/2024] Open
Abstract
Here, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non-additive) symmetric, multistate linear ordered symmetric, multistate non-linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (m), maximum (g) and maximum possible (gmax) character cost for applicable character types. Algorithms for exhaustive calculation of m, g and gmax applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (m) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character g and gmax are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (gmax) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using m, g and gmax, including extra cost (h), consistency index (ci), retention index (ri) or indices based thereon.
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2
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Geng FD, Liu MQ, Zhang XD, Wang LZ, Lei MF. Genomics of hybrid parallel origin in Aquilegia ecalcarata. BMC Ecol Evol 2024; 24:75. [PMID: 38844857 PMCID: PMC11155106 DOI: 10.1186/s12862-024-02266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear. RESULTS In this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata. CONCLUSIONS Our results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.
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Affiliation(s)
- Fang-Dong Geng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Miao-Qing Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xue-Dong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Lu-Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meng-Fan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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3
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Rivas-González I, Schierup MH, Wakeley J, Hobolth A. TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting. PLoS Genet 2024; 20:e1010836. [PMID: 38330138 PMCID: PMC10880969 DOI: 10.1371/journal.pgen.1010836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/21/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.
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Affiliation(s)
| | - Mikkel H. Schierup
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Massachusetts, United States of America
| | - Asger Hobolth
- Department of Mathematics, Aarhus University, Aarhus, Denmark
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de Santis MD. On the nature of evolutionary explanations: a critical appraisal of Walter Bock's approach with a new revised proposal. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2024; 46:3. [PMID: 38190055 PMCID: PMC10774170 DOI: 10.1007/s40656-023-00601-7] [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: 11/08/2022] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
Walter Bock was committed to developing a framework for evolutionary biology. Bock repeatedly discussed how evolutionary explanations should be considered within the realm of Hempel's deductive-nomological model of scientific explanations. Explanation in evolution would then consist of functional and evolutionary explanations, and within the latter, an explanation can be of nomological-deductive and historical narrative explanations. Thus, a complete evolutionary explanation should include, first, a deductive functional analysis, and then proceed through nomological and historical evolutionary explanations. However, I will argue that his views on the deductive proprieties of functional analysis and the deductive-nomological parts of evolution fail because of the nature of evolution, which contains a historical element that the logic of deduction and Hempel's converting law model do not compass. Conversely, Bock's historical approach gives a critical consideration of the historical narrative element of evolutionary explanation, which is fundamental to the methodology of the historical nature of evolutionary theory. Herein, I will expand and discuss a modern view of evolutionary explanations of traits that includes the currentacknowledgement of the differences between experimental and the historical sciences, including the token and type event dichotomy, that mutually illuminate each other in order to give us a well confirmed and coherent hypothesis for evolutionary explanations. Within this framework, I will argue that the duality of evolutionary explanations is related to two components of character evolution: origin, with its evolutionary pathways along with the history, and maintenance, the function (mainly a current function) for the character being selected.
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Affiliation(s)
- Marcelo Domingos de Santis
- Departamento de Entomologia, Museu Nacional, UFRJ, Rio de Janeiro, RJ, Brazil.
- Museum Koenig Bonn, Leibniz-Institut zur Analyse des Bioaffiliationersitatswandels, Adenauerallee 127, 53113, Bonn, Germany.
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5
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Pucker B, Walker‐Hale N, Dzurlic J, Yim WC, Cushman JC, Crum A, Yang Y, Brockington SF. Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme. THE NEW PHYTOLOGIST 2024; 241:471-489. [PMID: 37897060 PMCID: PMC10952170 DOI: 10.1111/nph.19341] [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: 09/11/2022] [Accepted: 09/23/2023] [Indexed: 10/29/2023]
Abstract
In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pigmentation. Utilizing transcriptomic and genomic datasets across 357 species and 31 families, we scrutinize 18 flavonoid pathway genes and six regulatory genes spanning four transitions to betalain pigmentation. We examined evidence for hypotheses of wholesale gene loss, modified gene function, altered gene expression, and degeneration of the MBW (MYB-bHLH-WD40) trasnscription factor complex, within betalain-pigmented lineages. Our analyses reveal that most flavonoid synthesis genes remain conserved in betalain-pigmented lineages, with the notable exception of TT19 orthologs, essential for the final step in anthocyanidin synthesis, which appear to have been repeatedly and entirely lost. Additional late-stage flavonoid pathway genes upstream of TT19 also manifest strikingly reduced expression in betalain-pigmented species. Additionally, we find repeated loss and alteration in the MBW transcription complex essential for canonical anthocyanin synthesis. Consequently, the loss and exclusion of anthocyanins in betalain-pigmented species appear to be orchestrated through several mechanisms: loss of a key enzyme, downregulation of synthesis genes, and degeneration of regulatory complexes. These changes have occurred iteratively in Caryophyllales, often coinciding with evolutionary transitions to betalain pigmentation.
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Affiliation(s)
- Boas Pucker
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICSTU Braunschweig38106BraunschweigGermany
| | | | - Jasmina Dzurlic
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Won C. Yim
- Department of Biochemistry & Molecular BiologyUniversity of NevadaRenoNV89557USA
| | - John C. Cushman
- Department of Biochemistry & Molecular BiologyUniversity of NevadaRenoNV89557USA
| | - Alexandra Crum
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin CitiesSt PaulMN55108USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin CitiesSt PaulMN55108USA
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6
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Rocha DM, Nogueira FM, André T, de Araujo Mariath JE, Vanzela ALL. Evolutionary features of microspore and pollen grain development in Cyperaceae. PLANT REPRODUCTION 2023; 36:333-342. [PMID: 37532894 DOI: 10.1007/s00497-023-00477-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
KEY MESSAGE Asymmetric meiosis leading to the release of pollen grains as pseudomonads is a synapomorphy in Cyperaceae, but differences in microspore development are relevant in the family's evolutionary history. Cyperaceae members present atypical microsporogenesis, in which one meiotic product is functional while the other three degenerate, culminating in pseudomonad pollen formation. Differences during development, such as pseudomonad shape and degenerative microspore positioning, are seen throughout the family, but no phylogenetic interpretation has been made regarding these variances thus far. In this study, we analyzed the early- and late-diverging sedge genera Hypolytrum and Eleocharis, respectively, while comparing them to data available in the literature and conducting an ancestral character reconstruction for pseudomonad traits. Light microscopy results show that pseudomonad development in Hypolytrum is homologous to several other sedge genera, presenting apical degenerative microspores. However, pseudomonads are round and centrally arranged in the anther locule in this case, which consists of a pleisiomorphic trait for the family. The basal positioning of degenerative microspores is restricted to Rhynchospora, consisting of an apomorphic trait for this genus. Despite these differences, ultrastructural analysis of Eleocharis pseudomonad revealed shared features with other genera studied, which include variations in chromatin condensation and cytoplasmic turnover in functional cells. These common features seem related to the different cellular fates seen during microspore development and further corroborate the synapomorphic status of pseudomonads in sedges.
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Affiliation(s)
- Danilo Massuia Rocha
- Laboratório de Citogenética e Diversidade Vegetal (LCDV), Universidade Estadual de Londrina (UEL), Londrina, PR, 86057-970, Brazil.
| | - Fernanda Mayara Nogueira
- Faculdade de Filosofia Ciências e Letras de Ribeirao Preto (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, SP, 14040-901, Brazil
| | - Thiago André
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, 70910-900, Brazil
| | - Jorge Ernesto de Araujo Mariath
- Laboratório de Anatomia Vegetal - LAVeg, Instituto de Biociências, Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal (LCDV), Universidade Estadual de Londrina (UEL), Londrina, PR, 86057-970, Brazil
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7
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Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [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: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
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Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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8
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Cordero GA. Turtle Shell Kinesis Underscores Constraints and Opportunities in the Evolution of the Vertebrate Musculoskeletal System. Integr Org Biol 2023; 5:obad033. [PMID: 37840690 PMCID: PMC10576247 DOI: 10.1093/iob/obad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/04/2023] [Accepted: 09/03/2023] [Indexed: 10/17/2023] Open
Abstract
Species groups that feature traits with a low number of potentially variable (evolvable) character states are more likely to repeatedly evolve similar phenotypes, that is, convergence. To evaluate this phenomenon, this present paper addresses anatomical alterations in turtles that convergently evolved shell kinesis, for example, the movement of shell bones to better shield the head and extremities. Kinesis constitutes a major departure from the evolutionarily conserved shell of modern turtles, yet it has arisen independently at least 8 times. The hallmark signature of kinesis is the presence of shell bone articulations or "hinges," which arise via similar skeletal remodeling processes in species that do not share a recent common ancestor. Still, the internal biomechanical components that power kinesis may differ in such distantly related species. Complex diarthrodial joints and modified muscle connections expand the functional boundaries of the limb girdles and neck in a lineage-specific manner. Some lineages even exhibit mobility of thoracic and sacral vertebrae to facilitate shell closure. Depending on historical contingency and structural correlation, a myriad of anatomical alterations has yielded similar functional outcomes, that is, many-to-one mapping, during the convergent evolution of shell kinesis. The various iterations of this intricate phenotype illustrate the potential for the vertebrate musculoskeletal system to undergo evolutionary change, even when constraints are imposed by the development and structural complexity of a shelled body plan. Based on observations in turtles and comparisons to other vertebrates, a hypothetical framework that implicates functional interactions in the origination of novel musculoskeletal traits is presented.
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Affiliation(s)
- G A Cordero
- Department of Animal Biology, Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, 1740-016 Lisbon, Portugal
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9
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González-Ferreiro M, García-París M, Sainz-Escudero L, López-Estrada EK. Analyses of head and thorax in Eupomphini (Meloidae) suggest that complex behaviors are not associated to changes in general shape. Integr Zool 2023; 18:949-957. [PMID: 36929152 DOI: 10.1111/1749-4877.12708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Our results reject an association between general shape of head and thorax with defensive and courtship behaviors in the studied Eupomphini blister beetles. Instead we found that shape of thorax and head radiated in all directions of the morphospace. We also identified a radical separation between two lineages that could represent future evolutionary constraints for thorax evolution.
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Affiliation(s)
| | | | | | - E Karen López-Estrada
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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10
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Safian D, Ahmed M, van Kruistum H, Furness AI, Reznick DN, Wiegertjes GF, Pollux BJ. Repeated independent origins of the placenta reveal convergent and divergent organ evolution within a single fish family (Poeciliidae). SCIENCE ADVANCES 2023; 9:eadf3915. [PMID: 37611099 PMCID: PMC10446500 DOI: 10.1126/sciadv.adf3915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
An outstanding question in biology is to what extent convergent evolution produces similar, but not necessarily identical, complex phenotypic solutions. The placenta is a complex organ that repeatedly evolved in the livebearing fish family Poeciliidae. Here, we apply comparative approaches to test whether evolution has produced similar or different placental phenotypes in the Poeciliidae and to what extent these phenotypes correlate with convergence at the molecular level. We show the existence of two placental phenotypes characterized by distinctly different anatomical adaptations (divergent evolution). Furthermore, each placental phenotype independently evolved multiple times across the family, providing evidence for repeated convergence. Moreover, our comparative genomic analysis revealed that the genomes of species with different placentas are evolving at a different pace. Last, we show that the two placental phenotypes correlate with two previously described contrasting life-history optima. Our results argue for high evolvability (both divergent and convergent) of the placenta within a group of closely related species in a single family.
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Affiliation(s)
- Diego Safian
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Evolutionary Developmental Biology Laboratory, The Francis Crick Institute, London, UK
| | - Marwa Ahmed
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Henri van Kruistum
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Animal Breeding and Genomics, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrew I. Furness
- U.S. Fish and Wildlife Service, Maryland Fish and Wildlife Conservation Office, Annapolis, MD, USA
| | - David N. Reznick
- Department of Biology, University of California, Riverside, Riverside, CA, USA
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Bart J.A. Pollux
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
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Pereira AG, Kohlsdorf T. Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways. Genet Mol Biol 2023; 46:e20220384. [PMID: 37486083 PMCID: PMC10364090 DOI: 10.1590/1678-4685-gmb-2022-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Repeated phenotypes, often referred to as 'homoplasies' in cladistic analyses, may evolve through changes in developmental processes. Genetic bases of recurrent evolution gained attention and have been studied in the past years using approaches that combine modern analytical phylogenetic tools with the stunning assemblage of new information on developmental mechanisms. In this review, we evaluated the topic under an integrated perspective, revisiting the classical definitions of convergence and parallelism and detailing comparative methods used to evaluate evolution of repeated phenotypes, which include phylogenetic inference, estimates of evolutionary rates and reconstruction of ancestral states. We provide examples to illustrate how a given methodological approach can be used to identify evolutionary patterns and evaluate developmental mechanisms associated with the intermittent expression of a given trait along the phylogeny. Finally, we address why repeated trait loss challenges strict definitions of convergence and parallelism, discussing how changes in developmental pathways might explain the high frequency of repeated trait loss in specific lineages.
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Affiliation(s)
- Anieli Guirro Pereira
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
| | - Tiana Kohlsdorf
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
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12
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Gouvêa DY, Brigandt I. Against unifying homology concepts: Redirecting the debate. J Morphol 2023; 284:e21599. [PMID: 37313763 DOI: 10.1002/jmor.21599] [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: 07/27/2022] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 06/15/2023]
Abstract
The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.
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Affiliation(s)
- Devin Y Gouvêa
- Department of Philosophy, College of the Holy Cross, Worcester, Massachusetts, USA
| | - Ingo Brigandt
- Department of Philosophy, University of Alberta, Edmonton, Canada
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Kimball RT, Braun EL, Liu Y, Zhou L, Goodale E, Zhou W, Robinson SK. Can convergence in mixed-species flocks lead to evolutionary divergence? Evidence for and methods to test this hypothesis. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220112. [PMID: 37066651 PMCID: PMC10107229 DOI: 10.1098/rstb.2022.0112] [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: 07/14/2022] [Accepted: 01/31/2023] [Indexed: 04/18/2023] Open
Abstract
One of the most fundamental goals of modern biology is to achieve a deep understanding of the origin and maintenance of biodiversity. It has been observed that in some mixed-species animal societies, there appears to be a drive towards some degree of phenotypic trait matching, such as similar coloration or patterning. Here we build on these observations and hypothesize that selection in mixed-species animal societies, such as mixed-species bird flocks, may drive diversification, potentially leading to speciation. We review evidence for possible convergent evolution and even outright mimicry in flocks from southwestern China, where we have observed several cases in which species and subspecies differ from their closest relatives in traits that match particular flock types. However, understanding whether this is phenotypic matching driven by convergence, and whether this divergence has promoted biodiversity, requires testing multiple facets of this hypothesis. We propose a series of steps that can be used to tease apart alternative hypotheses to build our understanding of the potential role of convergence in diversification in participants of mixed-species societies. Even if our social convergence/divergence hypothesis is not supported, the testing at each step should help highlight alternative processes that may affect mixed-species flocks, trait evolution and possible convergence. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.
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Affiliation(s)
- Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Liping Zhou
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
| | - Eben Goodale
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, People's Republic of China
| | - Wenyi Zhou
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Scott K. Robinson
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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14
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Mera-Rodríguez D, Jourdan H, Ward PS, Shattuck S, Cover SP, Wilson EO, Rabeling C. Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics. Mol Phylogenet Evol 2023:107825. [PMID: 37244505 DOI: 10.1016/j.ympev.2023.107825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The ants in the genus Myrmecia are a well-suited system for testing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species M. apicalis inhabiting the Pacific Island of New Caledonia, and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of M. apicalis and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species M. apicalis and to reveal the origin and evolution of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a comprehensive molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known Myrmecia species as well as for the sister lineage Nothomyrmecia macrops and selected outgroups. Our time-calibrated phylogeny inferred that: (i) stem Myrmeciinae originated during the Paleocene ∼58 Ma ago; (ii) the current disjunct biogeographic distribution of M. apicalis was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ∼14 Ma ago; (iii) the single social parasite species, M. inquilina, evolved directly from one of the two known host species, M. nigriceps, in sympatry via the intraspecific route of social parasite evolution; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries into the biology, taxonomy, and classification of Myrmeciinae.
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Affiliation(s)
- Daniela Mera-Rodríguez
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany.
| | - Hervé Jourdan
- Institute of Research for Development. Promenade Roger Laroque, Nouméa 98848, New Caledonia
| | - Philip S Ward
- Department of Entomology and Nematology, University of California, Davis, CA 95616, United States of America
| | - Steven Shattuck
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Stefan P Cover
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Edward O Wilson
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Christian Rabeling
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany; Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America.
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15
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Zhou Z, Yi H, Zhou Q, Wang L, Zhu Y, Wang W, Liu Z, Xiong H. Evolution and epidemic success of Mycobacterium tuberculosis in eastern China: evidence from a prospective study. BMC Genomics 2023; 24:241. [PMID: 37147590 PMCID: PMC10161668 DOI: 10.1186/s12864-023-09312-6] [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: 01/10/2023] [Accepted: 04/14/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Lineage distribution of Mycobacterium tuberculosis (Mtb) isolates is strongly associated with geographically distinct human populations, and its transmission can be further impacted by the bacterial genome. However, the epidemic success of Mtb isolates at an individual level was unknown in eastern China. Knowledge regarding the emergence and transmission of Mtb isolates as well as relevant factors may offer a new solution to curb the spread of the disease. Thus, this study aims to reveal the evolution and epidemic success of Mtb isolates in eastern China. RESULTS Of initial 1040 isolates, 997 were retained after removing duplicates and those with insufficient sequencing depth. Of the final samples, 733 (73.52%) were from Zhejiang Province, and 264 (26.48%) were from Shanghai City. Lineage 2 and lineage 4 accounted for 80.44% and 19.56%, with common ancestors dating around 7017 years ago and 6882 years ago, respectively. Sub-lineage L2.2 (80.34%) contributed the majority of total isolates, followed by L4.4 (8.93%) and L4.5 (8.43%). Additionally, 51 (5.12%) isolates were identified to be multidrug-resistant (MDR), of which 21 (29.17%) were pre-extensively drug-resistant (pre-XDR). One clade harboring katG S315T mutation may date back to 65 years ago and subsequently acquired mutations conferring resistance to another five antibiotic drugs. The prevalence of compensatory mutation was the highest in pre-XDR isolates (76.19%), followed by MDR isolates (47.06%) and other drug-resistant isolates (20.60%). Time-scaled haplotypic density analyses suggested comparable success indices between lineage 2 and lineage 4 (P = 0.306), and drug resistance did not significantly promote the transmission of Mtb isolates (P = 0.340). But for pre-XDR isolates, we found a higher success index in those with compensatory mutations (P = 0.025). Mutations under positive selection were found in genes associated with resistance to second-line injectables (whiB6) and drug tolerance (prpR) in both lineage 2 and lineage 4. CONCLUSIONS Our study demonstrates the population expansion of lineage 2 and lineage 4 in eastern China, with comparable transmission capacity, while accumulation of resistance mutations does not necessarily facilitate the success of Mtb isolates. Compensatory mutations usually accompany drug resistance and significantly contribute to the epidemiological transmission of pre-XDR strains. Prospective molecular surveillance is required to further monitor the emergence and spread of pre-XDR/XDR strains in eastern China.
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Affiliation(s)
- Zonglei Zhou
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Huaiming Yi
- Center for Disease Control and Prevention of Changshan County, 324200, Zhejiang, China
| | - Qingrong Zhou
- Center for Disease Control and Prevention of Jiangshan City, 324100, Zhejiang, China
| | - Luqi Wang
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Yue Zhu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Weibing Wang
- School of Public Health, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, 200032, China.
| | - Zhengwe Liu
- Institute of Tuberculosis Control, Zhejiang Provincial Center for Disease Control and Prevention, 310051, Zhejiang, China.
| | - Haiyan Xiong
- School of Public Health, Fudan University, Shanghai, 200032, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, 200032, China
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16
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Braga J, Wood BA, Zimmer VA, Moreno B, Miller C, Thackeray JF, Zipfel B, Grine FE. Hominin fossils from Kromdraai and Drimolen inform Paranthropus robustus craniofacial ontogeny. SCIENCE ADVANCES 2023; 9:eade7165. [PMID: 37134165 PMCID: PMC10156105 DOI: 10.1126/sciadv.ade7165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ontogeny provides critical information about the evolutionary history of early hominin adult morphology. We describe fossils from the southern African sites of Kromdraai and Drimolen that provide insights into early craniofacial development in the Pleistocene robust australopith Paranthropus robustus. We show that while most distinctive robust craniofacial features appear relatively late in ontogeny, a few do not. We also find unexpected evidence of independence in the growth of the premaxillary and maxillary regions. Differential growth results in a proportionately larger and more postero-inferiorly rotated cerebral fossa in P. robustus infants than in the developmentally older Australopithecus africanus juvenile from Taung. The accumulated evidence from these fossils suggests that the iconic SK 54 juvenile calvaria is more likely early Homo than Paranthropus. It is also consistent with the hypothesis that P. robustus is more closely related to Homo than to A. africanus.
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Affiliation(s)
- José Braga
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, Toulouse, France
- Evolutionary Studies Institute, University of the Witwatersrand, Private Bag 3, WITS 2050, Johannesburg, South Africa
| | - Bernard A Wood
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC 20052, USA
| | | | - Benjamin Moreno
- SARL IMA Solutions, 19 rue Jean Mermoz, 31100 Toulouse, France
| | - Catherine Miller
- Department of Anthropology, Dartmouth College, Hanover, NH 03755, USA
| | - John F Thackeray
- Evolutionary Studies Institute, University of the Witwatersrand, Private Bag 3, WITS 2050, Johannesburg, South Africa
| | - Bernhard Zipfel
- Evolutionary Studies Institute, University of the Witwatersrand, Private Bag 3, WITS 2050, Johannesburg, South Africa
| | - Frederick E Grine
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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17
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Patterson EL, Richardson A, Bartlett M. Pushing the boundaries of organ identity: Homology of the grass lemma. AMERICAN JOURNAL OF BOTANY 2023; 110:e16161. [PMID: 37021711 DOI: 10.1002/ajb2.16161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 05/11/2023]
Affiliation(s)
- Erin L Patterson
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Annis Richardson
- Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Madelaine Bartlett
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
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18
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Uluar O, Yahyaoğlu Ö, Başıbüyük HH, Çıplak B. Taxonomy of the rear-edge populations: the case of genus Anterastes (Orthoptera, Tettigoniidae). ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-023-00602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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19
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Salazar-Ciudad I, Cano-Fernández H. Evo-devo beyond development: Generalizing evo-devo to all levels of the phenotypic evolution. Bioessays 2023; 45:e2200205. [PMID: 36739577 DOI: 10.1002/bies.202200205] [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: 10/24/2022] [Revised: 12/25/2022] [Accepted: 01/12/2023] [Indexed: 02/06/2023]
Abstract
A foundational idea of evo-devo is that morphological variation is not isotropic, that is, it does not occur in all directions. Instead, some directions of morphological variation are more likely than others from DNA-level variation and these largely depend on development. We argue that this evo-devo perspective should apply not only to morphology but to evolution at all phenotypic levels. At other phenotypic levels there is no development, but there are processes that can be seen, in analogy to development, as constructing the phenotype (e.g., protein folding, learning for behavior, etc.). We argue that to explain the direction of evolution two types of arguments need to be combined: generative arguments about which phenotypic variation arises in each generation and selective arguments about which of it passes to the next generation. We explain how a full consideration of the two types of arguments improves the explanatory power of evolutionary theory. Also see the video abstract here: https://youtu.be/Egbvma_uaKc.
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Affiliation(s)
- Isaac Salazar-Ciudad
- Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain.,Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hugo Cano-Fernández
- Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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20
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Button DJ, Porro LB, Lautenschlager S, Jones MEH, Barrett PM. Multiple pathways to herbivory underpinned deep divergences in ornithischian evolution. Curr Biol 2023; 33:557-565.e7. [PMID: 36603586 DOI: 10.1016/j.cub.2022.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
The extent to which evolution is deterministic is a key question in biology,1,2,3,4,5,6,7,8,9 with intensive debate on how adaptation6,10,11,12,13 and constraints14,15,16 might canalize solutions to ecological challenges.4,5,6 Alternatively, unique adaptations1,9,17 and phylogenetic contingency1,3,18 may render evolution fundamentally unpredictable.3 Information from the fossil record is critical to this debate,1,2,11 but performance data for extinct taxa are limited.7 This knowledge gap is significant, as general morphology may be a poor predictor of biomechanical performance.17,19,20 High-fiber herbivory originated multiple times within ornithischian dinosaurs,21 making them an ideal clade for investigating evolutionary responses to similar ecological pressures.22 However, previous biomechanical modeling studies on ornithischian crania17,23,24,25 have not compared early-diverging taxa spanning independent acquisitions of herbivory. Here, we perform finite-element analysis on the skull of five early-diverging members of the major ornithischian clades to characterize morphofunctional pathways to herbivory. Results reveal limited functional convergence among ornithischian clades, with each instead achieving comparable performance, in terms of reconstructed patterns and magnitudes of functionally induced stress, through different adaptations of the feeding apparatus. Thyreophorans compensated for plesiomorphic low performance through increased absolute size, heterodontosaurids expanded jaw adductor muscle volume, ornithopods increased jaw system efficiency, and ceratopsians combined these approaches. These distinct solutions to the challenges of herbivory within Ornithischia underpinned the success of this diverse clade. Furthermore, the resolution of multiple solutions to equivalent problems within a single clade through macroevolutionary time demonstrates that phenotypic evolution is not necessarily predictable, instead arising from the interplay of adaptation, innovation, contingency, and constraints.1,2,3,7,8,9,18.
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Affiliation(s)
- David J Button
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Laura B Porro
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6DE, UK
| | - Stephan Lautenschlager
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Marc E H Jones
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paul M Barrett
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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21
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Poore HA, Stuart YE, Rennison DJ, Roesti M, Hendry AP, Bolnick DI, Peichel CL. Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution 2023; 77:110-122. [PMID: 36622692 DOI: 10.1093/evolut/qpac025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 01/10/2023]
Abstract
Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.
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Affiliation(s)
- Hilary A Poore
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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22
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Schlosser G. Rebuilding ships while at sea-Character individuality, homology, and evolutionary innovation. J Morphol 2023; 284:e21522. [PMID: 36282954 PMCID: PMC10100095 DOI: 10.1002/jmor.21522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/15/2022] [Accepted: 10/15/2022] [Indexed: 11/05/2022]
Abstract
How novel traits originate in evolution is still one of the most perplexing questions in Evolutionary Biology. Building on a previous account of evolutionary innovation, I here propose that evolutionary novelties are those individualized characters that are not homologous to any characters in the ancestor. To clarify this definition, I here provide a detailed analysis of the concepts of "character individuality" and "homology" first, before addressing their role for our understanding of evolutionary innovation. I will argue (1) that functional as well as structural considerations are important for character individualization; and (2) that compositional (structural) and positional homology need to be clearly distinguished to properly describe the evolutionary transformations of hierarchically structured characters. My account will therefore integrate functional and structural perspectives and put forward a new multi-level view of character identity and transformation.
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Affiliation(s)
- Gerhard Schlosser
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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23
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Hu J, Barrett RDH. The role of plastic and evolved DNA methylation in parallel adaptation of threespine stickleback (Gasterosteus aculeatus). Mol Ecol 2022; 32:1581-1591. [PMID: 36560898 DOI: 10.1111/mec.16832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Repeated phenotypic patterns among populations undergoing parallel evolution in similar environments provide support for the deterministic role of natural selection. Epigenetic modifications can mediate plastic and evolved phenotypic responses to environmental change and might make important contributions to parallel adaptation. While many studies have explored the genetic basis of repeated phenotypic divergence, the role of epigenetic processes during parallel adaptation remains unclear. The parallel evolution of freshwater ecotypes of threespine stickleback fish (Gasterosteus aculeatus) following colonization of thousands of lakes and streams from the ocean is a classic example of parallel phenotypic and genotypic adaptation. To investigate epigenetic modifications during parallel adaptation of threespine stickleback, we reanalysed three independent data sets that investigated DNA methylation variation between marine and freshwater ecotypes. Although we found widespread methylation differentiation between ecotypes, there was no significant tendency for CpG sites associated with repeated methylation differentiation across studies to be parallel versus nonparallel. To next investigate the role of plastic versus evolved changes in methylation during freshwater adaptation, we explored if CpG sites exhibiting methylation plasticity during salinity change were more likely to also show evolutionary divergence in methylation between ecotypes. The directions of divergence between ecotypes were generally in the opposite direction to those observed for plasticity when ecotypes were challenged with non-native salinity conditions, suggesting that most plastic responses are likely to be maladaptive during colonization of new environments. Finally, we found a greater number of CpG sites showing evolved changes when ancestral marine ecotypes are acclimated to freshwater environments, whereas plastic changes predominate when derived freshwater ecotypes transition back to their ancestral marine environments. These findings provide evidence for an epigenetic contribution to parallel adaptation and demonstrate the contrasting roles of plastic and evolved methylation differences during adaptation to new environments.
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Affiliation(s)
- Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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24
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Riddell EA, Patton JL, Beissinger SR. Thermal adaptation of pelage in desert rodents balances cooling and insulation. Evolution 2022; 76:3001-3013. [PMID: 36221218 PMCID: PMC10091991 DOI: 10.1111/evo.14643] [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: 08/23/2021] [Accepted: 08/15/2022] [Indexed: 01/22/2023]
Abstract
Phenotypic convergence across distantly related taxa can be driven by similar selective pressures from the environment or intrinsic constraints. The roles of these processes on physiological strategies, such as homeothermy, are poorly understood. We studied the evolution of thermal properties of mammalian pelage in a diverse community of rodents inhabiting the Mojave Desert, USA. We used a heat flux device to measure the thermal insulation of museum specimens and determined whether thermal properties were associated with habitat preferences while assessing phylogenetic dependence. Species that prefer arid habitats exhibited lower conductivity and thinner pelage relative to species with other habitat preferences. Despite being thinner, the pelage of arid species exhibited comparable insulation to the pelage of the other species due to its lower conductivity. Thus, arid species have insulative pelage while simultaneously benefitting from thin pelage that promotes convective cooling. We found no evidence of intrinsic constraints or phylogenetic dependence, indicating pelage readily evolves to environmental pressures. Thermoregulatory simulations demonstrated that arid specialists reduced energetic costs required for homeothermy by 14.5% by evolving lower conductivity, providing support for adaptive evolution of pelage. Our study indicates that selection for lower energetic requirements of homeothermy has shaped evolution of pelage thermal properties.
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Affiliation(s)
- Eric A Riddell
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, 94720.,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50010
| | - James L Patton
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, 94720
| | - Steven R Beissinger
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, 94720.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, 94720
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25
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Fan M, Li X, Zhang Y, Wu S, Song Z, Yin H, Liu W, Fan Z, Li J. Floral organ transcriptome in Camellia sasanqua provided insight into stamen petaloid. BMC PLANT BIOLOGY 2022; 22:474. [PMID: 36199021 PMCID: PMC9535933 DOI: 10.1186/s12870-022-03860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The cultivated Camellia sasanqua forms a divergent double flower pattern, and the stamen petaloid is a vital factor in the phenomenon. However, the regulation mechanism remains largely unclear. RESULTS Here, a comprehensive comparative transcriptome analysis of the wild-type, "semi-double", "peony double", and "rose double" was performed. The cluster analysis of global gene expression level showed petal and stamen difficulty separable in double flower. The crucial pathway and genes related to double flower patterns regulation were identified by pairwise comparisons and weighted gene coexpression network (WGCNA). Divergent genes expression, such as AUX1 and AHP, are involved in plant hormone signaling and photosynthesis, and secondary metabolites play an important role. Notably, the diversity of a petal-specific model exhibits a similar molecular signature to the stamen, containing extensin protein and PSBO1, supporting the stamen petaloid point. Moreover, the expansion of class A gene activity influenced the double flower formation, showing that the key function of gene expression was probably demolished. CONCLUSIONS Overall, this work confirmed the ABCE model and provided new insights for elucidating the molecular signature of double formation.
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Affiliation(s)
- Menglong Fan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinlei Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
| | - Ying Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Si Wu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhixin Song
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Weixin Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhengqi Fan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Jiyuan Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
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26
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Trevine VC, Grazziotin FG, Giraudo A, Sallesbery‐Pinchera N, Vianna JA, Zaher H. The systematics of Tachymenini (Serpentes, Dipsadidae): An updated classification based on molecular and morphological evidence. ZOOL SCR 2022. [DOI: 10.1111/zsc.12565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Vivian C. Trevine
- Laboratório de Coleções Zoológicas Instituto Butantan São Paulo Brazil
- Programa de Pós‐Graduação de Zoologia, Insituto de Biociências Universidade de São Paulo São Paulo Brazil
| | | | - Alejandro Giraudo
- Instituto Nacional de Limnología (CONICET – UNL) Ciudad Universitaria Santa Fe Argentina
- Facultad de Humanidades y Ciencias (FHUC – UNL) Ciudad Universitaria Santa Fe Argentina
| | - Nicole Sallesbery‐Pinchera
- Escuela Medicina Veterinaria, Facultad Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Juliana A. Vianna
- Millennium Institute Center for Genome Regulation (CRG), Departamento de Ecosistemas y Medio Ambiente Pontificia Universidad Católica de Chile Santiago Chile
| | - Hussam Zaher
- Laboratório de Herpetologia, Museu de Zoologia da Universidade de São Paulo São Paulo Brazil
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27
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Pereira AG, Grizante MB, Kohlsdorf T. What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda. Proc Biol Sci 2022; 289:20220841. [PMID: 35975445 PMCID: PMC9382212 DOI: 10.1098/rspb.2022.0841] [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: 05/01/2022] [Accepted: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Developmental pathways encompass transcription factors and cis-regulatory elements that interact as transcription factor-regulatory element (TF-RE) units. Independent origins of similar phenotypes likely involve changes in different parts of these units, a hypothesis promisingly tested addressing the evolution of the rib-associated lumbar (RAL) morphotype that characterizes emblematic animals such as snakes and elephants. Previous investigation in these lineages identified a polymorphism in the Homology region 1 [H1] enhancer of the Myogenic factor-5 [Myf5], which interacts with HOX10 proteins to modulate rib development. Here we address the evolution of TF-RE units focusing on independent origins of RAL morphotypes. We compiled an extensive database for H1-Myf5 and HOX10 sequences with two goals: (i) evaluate if the enhancer polymorphism is present in amphibians exhibiting the RAL morphotype and (ii) test a hypothesis of enhanced evolutionary flexibility mediated by TF-RE units, according to which independent origins of the RAL morphotype might involve changes in either component of the interaction unit. We identified the H1-Myf5 polymorphism in lineages that diverged around 340 Ma, including Lissamphibia. Independent origins of the RAL morphotype in Tetrapoda involved sequence variation in either component of the TF-RE unit, confirming that different changes may similarly affect the phenotypic outcome of a given developmental pathway.
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Affiliation(s)
- Anieli G. Pereira
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mariana B. Grizante
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Dante Pazzanese Institute of Cardiology, Sao Paulo, Brazil
| | - Tiana Kohlsdorf
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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28
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Doyle JJ. Cell types as species: Exploring a metaphor. FRONTIERS IN PLANT SCIENCE 2022; 13:868565. [PMID: 36072310 PMCID: PMC9444152 DOI: 10.3389/fpls.2022.868565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/29/2022] [Indexed: 06/05/2023]
Abstract
The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.
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Affiliation(s)
- Jeff J. Doyle
- Section of Plant Biology and Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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29
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Collar DC, Tremaine S, Harrington RC, Beckett HT, Friedman M. Mosaic adaptive peak shifts underlie body shape diversification in pelagiarian fishes (Acanthomorpha: Percomorpha). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac096] [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
Extreme body elongation in fishes is a major evolutionary transformation that extends the boundaries of morphological diversity and alters aspects of function, behaviour and ecology. Prior studies have identified features of the cranial and axial skeleton that characterize elongate fishes, but a lack of detailed reconstructions of anatomical evolution has limited inferences about factors that underlie major shifts in body shape. In this study, we fitted multi-peak adaptive (Ornstein–Uhlenbeck) evolutionary models to species body shape and anatomical dimensions in Pelagiaria, a radiation of open-ocean fishes whose species span a continuum from deep bodied to highly elongate. We inferred an ancestral fusiform adaptive peak that is retained by several major pelagiarian lineages (e.g. Scombridae) and found robust support for multiple transitions to deep-bodied optima (in the families Stromateidae, Bramidae and Caristiidae) and elongate-bodied optima (within Trichiuroidei), including two instances of sequential shifts towards increasingly elongate optima that followed distinct paths of anatomical evolution. Within Trichiuridae, initial increases in head length and the number of vertebrae were followed by changes in head and vertebral shape. Within an elongate-bodied subclade of taxa traditionally identified as ‘gempylids’, changes in head and vertebral shape and in the number of precaudal vertebrae preceded an increase in the number of caudal vertebrae. Altogether, this mosaic of anatomical peak shifts suggests that body shape transformations were associated with differing selective demands and developmental changes.
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Affiliation(s)
- David C Collar
- Department of Organismal and Environmental Biology, Christopher Newport University , Newport News, VA , USA
| | - Samantha Tremaine
- Department of Organismal and Environmental Biology, Christopher Newport University , Newport News, VA , USA
| | - Richard C Harrington
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , USA
| | - Hermione T Beckett
- Department of Earth Sciences, University of Oxford , Oxford , UK
- Department of Biology, King’s High School for Girls , Warwick , UK
| | - Matt Friedman
- Museum of Paleontology, University of Michigan , Ann Arbor, MI , USA
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, MI , USA
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30
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Wang Q, Purrafee Dizaj L, Huang J, Kumar Sarker K, Kevrekidis C, Reichenbacher B, Reza Esmaeili H, Straube N, Moritz T, Li C. Molecular phylogenetics of the Clupeiformes based on exon-capture data and a new classification of the order. Mol Phylogenet Evol 2022; 175:107590. [PMID: 35850406 DOI: 10.1016/j.ympev.2022.107590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/21/2022] [Accepted: 07/12/2022] [Indexed: 10/17/2022]
Abstract
The Clupeiformes, including among others herrings, anchovies, shads and menhadens are ecologically and commercially important, yet their phylogenetic relationships are still controversial. Previous classification of Clupeiformes were based on morphological characters or lack of synapomorphic characters. More recent studies based on molecular data as well as new morphological evidence are keeping challenging their phylogenetic relations and there is still no consensus on many interrelationships within the Clupeiformes. In this study, we collected nuclear sequence data from 4,434 single-copy protein coding loci using a gene-capture method. We obtained a robust phylogeny based on 1,165 filtered loci with less than 30 % missing data. Our major findings include: 1) reconfirmation of monophyly of the Clupeiformes, that is, Denticipitidae is sister to all other clupeiforms; 2) the polyphyletic nature of dussumieriids and early branching of Spratelloididae from all other clupeoids were confirmed using datasets curated for less missing data and more balanced base composition in the respective taxa. The next branching clade is the monophyletic Engraulidae. Pristigasteridae also is monophyletic, but it was nested in the previously defined "Clupeidae". Within Pristigasteridae there is no support for monophyletic Pelloninae. Chirocentrus is close to Dussumieria and not to engraulids. The miniaturized Sundasalanx is placed close to the ehiravine Clupeonella, however, with a relatively deep split. The genus Clupea, is not part of the diverse "Clupeidae", but part of a clade containing additionally Sprattus and Etrumeus. Within the crown group clades, Alosidae and Dorosomatidae are retrieved as sister clades. Based on new fossil calibration points, we found that major lineages of the clupeiforms diverged in the late Cretaceous and early Paleogene. The extinction event at the end of the Cretaceous may have created ecological niches, which could have fueled the diversification of clupeiform fishes. Based on the strong evidence of the present study, we propose an updated classification of Clupeiformes consisting of ten families: Denticipitidae; Spratelloididae; Engraulidae (Engraulinae + Coiliinae); Clupeidae; Chirocentridae; Dussumieriidae; Pristigasteridae; Ehiravidae; Alosidae, Dorosomatidae.
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Affiliation(s)
- Qian Wang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.
| | - Leyli Purrafee Dizaj
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran.
| | - Junman Huang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
| | - Kishor Kumar Sarker
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
| | - Charalampos Kevrekidis
- Ludwig-Maximilians-Universität München, Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Richard-Wagner-Str. 10, 80333 Munich, Germany.
| | - Bettina Reichenbacher
- Ludwig-Maximilians-Universität München, Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Richard-Wagner-Str. 10, 80333 Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Hamid Reza Esmaeili
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran.
| | - Nicolas Straube
- University Museum, Department of Natural History, University of Bergen, Norway.
| | - Timo Moritz
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany; Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059 Rostock, Germany.
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
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31
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González-Miguéns R, Todorov M, Blandenier Q, Duckert C, Porfirio-Sousa AL, Ribeiro GM, Ramos D, Lahr DJG, Buckley D, Lara E. Deconstructing Difflugia: The tangled evolution of lobose testate amoebae shells (Amoebozoa: Arcellinida) illustrates the importance of convergent evolution in protist phylogeny. Mol Phylogenet Evol 2022; 175:107557. [PMID: 35777650 DOI: 10.1016/j.ympev.2022.107557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/17/2022]
Abstract
Protists, the micro-eukaryotes that are neither plants, animals nor fungi build up the greatest part of eukaryotic diversity on Earth. Yet, their evolutionary histories and patterns are still mostly ignored, and their complexity overlooked. Protists are often assumed to keep stable morphologies for long periods of time (morphological stasis). In this work, we test this paradigm taking Arcellinida testate amoebae as a model. We build a taxon-rich phylogeny based on two mitochondrial (COI and NADH) and one nuclear (SSU) gene, and reconstruct morphological evolution among clades. In addition, we prove the existence of mitochondrial mRNA editing for the COI gene. The trees show a lack of conservatism of shell outlines within the main clades, as well as a widespread occurrence of morphological convergences between far-related taxa. Our results refute, therefore, a widespread morphological stasis, which may be an artefact resulting from low taxon coverage. As a corollary, we also revise the groups systematics, notably by emending the large and highly polyphyletic genus Difflugia. These results lead, amongst others, to the erection of a new infraorder Cylindrothecina, as well as two new genera Cylindrifflugia and Golemanskia.
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Affiliation(s)
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Quentin Blandenier
- Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Clément Duckert
- Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | | | - Giulia M Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - Diana Ramos
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, 28014 Madrid, Spain
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - David Buckley
- Department of Biology (Genetics), Universidad Autónoma de Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, 28014 Madrid, Spain.
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32
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Suzuki TK. Phenotypic systems biology for organisms: Concepts, methods and case studies. Biophys Physicobiol 2022; 19:1-17. [PMID: 35749096 PMCID: PMC9159793 DOI: 10.2142/biophysico.bppb-v19.0011] [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] [Received: 10/05/2021] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Design principles of phenotypes in organisms are fundamental issues in physical biology. So far, understanding "systems" of living organisms have been chiefly promoted by understanding the underlying biomolecules such as genes and proteins, and their intra- and inter-relationships and regulations. After a long period of sophistication, biophysics and molecular biology have established a general framework for understanding 'molecular systems' in organisms without regard to species, so that the findings of fly studies can be applied to mouse studies. However, little attention has been paid to exploring "phenotypic systems" in organisms, and thus its general framework remains poorly understood. Here I review concepts, methods, and case studies using butterfly and moth wing patterns to explore phenotypes as systems. First, I present a unifying framework for phenotypic traits as systems, termed multi-component systems. Second, I describe how to define components of phenotypic systems, and also show how to quantify interactions among phenotypic parts. Subsequently, I introduce the concept of the macro-evolutionary process, which illustrates how to generate complex traits. In this point, I also introduce mathematical methods, "phylogenetic comparative methods", which provide stochastic processes along molecular phylogeny as bifurcated paths to quantify trait evolution. Finally, I would like to propose two key concepts, macro-evolutionary pathways and genotype-phenotype loop (GP loop), which must be needed for the next directions. I hope these efforts on phenotypic biology will become one major target in biophysics and create the next generations of textbooks. This review article is an extended version of the Japanese article, Biological Physics in Phenotypic Systems of Living Organisms, published in SEIBUTSU-BUTSURI Vol. 61, p. 31-35 (2021).
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Affiliation(s)
- Takao K. Suzuki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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33
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Abouheif E. My road to the ants: A model clade for eco-evo-devo. Curr Top Dev Biol 2022; 147:231-290. [PMID: 35337451 DOI: 10.1016/bs.ctdb.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter is the story of how I pioneered ants as a system for studying eco-evo-devo, a field that integrates developmental biology with ecology and evolutionary biology. One aim of eco-evo-devo is to understand how the interactions between genes and their environments during development facilitates the origin and evolution of novel phenotypes. In a series of six parts, I review some of the key discoveries from my lab on how novel worker caste systems in ants--soldiers and supersoldiers--originated and evolved. I also discuss some of the ideas that emerged from these discoveries, including the role that polyphenisms, hidden developmental potentials, and rudimentary organs play in facilitating developmental and evolutionary change. As superorganisms, I argue that ants are uniquely positioned to reveal types of variation that are often difficult to observe in nature. In doing so, they have the potential to transform our view of biology and provide new perspectives in medicine, agriculture, and biodiversity conservation. With my story I hope to inspire the next generation of biologists to continue exploring the unknown regions of phenotypic space to solve some of our most pressing societal challenges.
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Affiliation(s)
- Ehab Abouheif
- Department of Biology, McGill University, Montreal, QC, Canada.
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34
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Castellucci F, Luchetti A, Mantovani B. Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera. Sci Rep 2022; 12:4931. [PMID: 35322086 PMCID: PMC8942981 DOI: 10.1038/s41598-022-08873-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae.
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Affiliation(s)
- Filippo Castellucci
- Department of Biological, Geological and Environmental Sciences-University of Bologna, via Selmi 3, 40126, Bologna, Italy.,Zoology Section, Natural History Museum of Denmark-University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences-University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences-University of Bologna, via Selmi 3, 40126, Bologna, Italy
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35
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Marugán‐Lobón J, Nebreda SM, Navalón G, Benson R. Beyond the beak: Brain size and allometry in avian craniofacial evolution. J Anat 2022; 240:197-209. [PMID: 34558058 PMCID: PMC8742972 DOI: 10.1111/joa.13555] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/18/2021] [Accepted: 09/10/2021] [Indexed: 12/01/2022] Open
Abstract
Birds exhibit an enormous variety of beak shapes. Such remarkable variation, however, has distracted research from other important aspects of their skull evolution, the nature of which has been little explored. Key aspects of avian skull variation appear to be qualitatively similar to those of mammals, encompassing variation in the degree of cranial vaulting, cranial base flexure, and the proportions and orientations of the occipital and facial regions. The evolution of these traits has been studied intensively in mammals under the Spatial Packing Hypothesis (SPH), an architectural constraint so-called because the general anatomical organization and development of such skull parts makes them evolve predictably in response to changes in relative brain size. Such SPH predictions account for the different appearances of skull configurations across species, either in having longer or shorter faces, and caudally or ventrally oriented occiputs, respectively. This pattern has been morphometrically and experimentally proven in mammals but has not been examined in birds or other tetrapods, and so its generality remains unknown. We explored the SPH in an interspecific sample of birds using three-dimensional geometric morphometrics. Our results show that the dominant trend of evolutionary variation in the skull of crown-group birds can be predicted by the SPH, involving concomitant changes in the face, the cranial vault and the basicranium, and with striking similarities to craniofacial variation among mammals. Although craniofacial variation is significantly affected by allometry, these allometric effects are independent of the influence of the SPH on skull morphology, as are any effects of volumetric encephalization. Our results, therefore, validate the hypothesis that a general architectural constraint underlies skull homoplasy evolution of cranial morphology among avian clades, and possibly between birds and mammals, but they downplay encephalization and allometry as the only factors involved.
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Affiliation(s)
- Jesús Marugán‐Lobón
- Unidad de PaleontologíaDpto. BiologíaUniversidad Autónoma de MadridMadridSpain
- Dinosaur InstituteNatural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
| | - Sergio M. Nebreda
- Unidad de PaleontologíaDpto. BiologíaUniversidad Autónoma de MadridMadridSpain
| | - Guillermo Navalón
- Unidad de PaleontologíaDpto. BiologíaUniversidad Autónoma de MadridMadridSpain
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
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36
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Das S, Brecko J, Pauwels OSG, Merilä J. Cranial osteology of
Hypoptophis
(Aparallactinae: Atractaspididae: Caenophidia), with a discussion on the evolution of its fossorial adaptations. J Morphol 2022; 283:510-538. [PMID: 35094424 PMCID: PMC9305546 DOI: 10.1002/jmor.21457] [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: 04/17/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI‐00014 University of Helsinki Finland
| | - Jonathan Brecko
- Department of Recent Vertebrates Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, B‐1000 Brussels Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren Belgium
| | - Olivier S. G. Pauwels
- Department of Recent Vertebrates Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, B‐1000 Brussels Belgium
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI‐00014 University of Helsinki Finland
- Division of Ecology and Biodiversity, Faculty of Science The University of Hong Kong, KBSB 3N19 Hong Kong SAR
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37
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Zúñiga-Vega JJ, Aspbury AS, Johnson JB, Pollux BJA. Editorial: Ecology, Evolution, and Behavior of Viviparous Fishes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.832216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Comparative anatomy of the rostrosoma of Solifugae, Pseudoscorpiones and Acari. ZOOMORPHOLOGY 2022. [DOI: 10.1007/s00435-021-00551-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractWe compare the microscopic anatomy of the mouthparts of representative species of Solifugae, Pseudoscorpiones and Parasitiformes (Acari). Specifically, we focus on the epistome, the labrum, the lateral lips (= endites of the pedipalpal coxae) and the musculature of the pharyngeal suction pump. We provide evidence that the labrum is reduced in Solifugae, but present and functional in Pseudoscorpiones and Acari. The epistome constitutes the entire dorsal face of the rostrosoma in Solifugae, but is internalized into the prosoma in Pseudoscorpiones. In Acari, the epistome shows an ancestral morphology, probably close to the ground pattern of chelicerates. The lateral lips of Solifugae contribute to the ventral face of the rostrosoma and the two lips of the mouth opening. In Solifugae, the ventral rostrosoma also includes a sclerite that might derive from a tritosternum. In Pseudoscorpiones, the lateral lips remain independent of the rostrosoma, they interlock ventral to the rostrosoma forming a perioral space. Here, the rostrosoma has an unpaired ventral lip of unresolved morphological origin, which is, however, clearly distinct from the lateral lips of Solifugae. The pharyngeal suction pump differs in all three clades in attachment, number of muscles and origin of muscles. We interpret the data as evidence for independent, parallel evolution of elements of the ground pattern of the (eu)chelicerate mouth parts. Based on the morphological elements of a common euchelicerate ground plan, the rostrosoma evolved independently in the three clades. We reject earlier hypotheses that consider the rostrosoma a character to support a phylogenetic relationship of the three clades.
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39
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Griffing AH, Gamble T, Cohn MJ, Sanger TJ. Convergent developmental patterns underlie the repeated evolution of adhesive toe pads among lizards. Biol J Linn Soc Lond 2022; 135:518-532. [PMID: 35185322 PMCID: PMC8842688 DOI: 10.1093/biolinnean/blab164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/07/2023]
Abstract
How developmental modifications produce key innovations, which subsequently allow for rapid diversification of a clade into new adaptive zones, has received much attention. However, few studies have used a robust comparative framework to investigate the influence of evolutionary and developmental constraints on the origin of key innovations, such as the adhesive toe pad of lizards. Adhesive toe pads evolved independently at least 16 times in lizards, allowing us to examine whether the patterns observed are general evolutionary phenomena or unique, lineage-specific events. We performed a high-resolution comparison of plantar scale development in 14 lizard species in Anolis and geckos, encompassing five independent origins of toe pads (one in Anolis, four in geckos). Despite substantial evolutionary divergence between Anolis and geckos, we find that these clades have undergone similar developmental modifications to generate their adhesive toe pads. Relative to the ancestral plantar scale development, in which scale ridges form synchronously along the digit, both padded geckos and Anolis exhibit scansor formation in a distal-to-proximal direction. Both clades have undergone developmental repatterning and, following their origin, modifications in toe pad morphology occurred through relatively minor developmental modifications, suggesting that developmental constraints governed the diversification of the adhesive toe pad in lizards.
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Affiliation(s)
- Aaron H Griffing
- Department of Biological Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA,Corresponding author. E-mail:
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA,Milwaukee Public Museum, 800 W. Wells St., Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, 2088 Larpenteur Ave. W., St. Paul, MN 55113, USA
| | - Martin J Cohn
- Department of Molecular Genetics and Microbiology, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA,Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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Martínez-Gómez J, Atluri TAM, Rose IJ, Holliday AJ, Strock CF, Lynch JP, Miller WB, Stevenson DW, Specht CD. Developmental Morphology and Anatomy Shed Light on Both Parallel and Convergent Evolution of the Umbellate Inflorescence in Monocots, Underlain by a New Variant of Metatopy. FRONTIERS IN PLANT SCIENCE 2022; 13:873505. [PMID: 35574142 PMCID: PMC9100582 DOI: 10.3389/fpls.2022.873505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 05/22/2023]
Abstract
Inflorescence structure is very diverse and homoplasious, yet the developmental basis of their homoplasy is poorly understood. To gain an understanding of the degree of homology that these diverse structures share, we characterize the developmental morphology and anatomy of various umbellate inflorescences across the monocots and analyzed them in an evolutionary context. To characterize branching order, we characterized the developmental morphology of multiple inflorescences with epi-illumination, and vascular anatomy with Laser Ablation Tomography, a novel high-throughput method to reconstruct three-dimensional vasculature. We used these approaches to analyze the umbellate inflorescences in five instances of presumed homoplasy: in three members of the Amaryllidaceae; in three members of the Asparagaceae, including a putatively derived raceme in Dichelostemma congestum; in Butomus umbellatus (Alismataceae), in Tacca chantrieri (Dioscoreaceae), and in umbellate structure in Fritillaria imperialis (Liliaceae). We compare these with racemes found in three members of the subfamily Scilliioideae (Asparagaceae). We find there are three convergent developmental programs that generate umbellate inflorescences in the monocots, bostryx-derived, cincinnus-derived and raceme-derived. Additionally, among the bostryx-derived umbellate inflorescence, there are three instances of parallel evolution found in the Amaryllidaceae, in two members of Brodiaeoideae (Asparagaceae), and Butomus umbellatus, all of which share the same generative developmental program. We discuss the morphological modifications necessary to generate such complex and condensed structures and use these insights to describe a new variant of metatopy, termed horizontal concaulesence. We contextualize our findings within the broader literature of monocot inflorescence development, with a focus on synthesizing descriptive developmental morphological studies.
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Affiliation(s)
- Jesús Martínez-Gómez
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Jesús Martínez-Gómez,
| | - Tara A. M. Atluri
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Irving Jason Rose
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Aaliyah J. Holliday
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Christopher F. Strock
- Department of Plant Science, Pennsylvania State University, University Park, PA, United States
| | - Jonathan P. Lynch
- Department of Plant Science, Pennsylvania State University, University Park, PA, United States
| | - William B. Miller
- Section of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Chelsea D. Specht
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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41
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Ahmadi E, Zabihi MR, Hosseinzadeh R, Mohamed Khosroshahi L, Noorbakhsh F. SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study. PLoS One 2021; 16:e0260360. [PMID: 34855795 PMCID: PMC8639087 DOI: 10.1371/journal.pone.0260360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/09/2021] [Indexed: 12/28/2022] Open
Abstract
Recent emergence of SARS-CoV-2 and associated COVID-19 pandemic have posed a great challenge for the scientific community. In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with non-coronavirus ssRNA viruses. Comparing the proteins of SARS-CoV-2 with non-coronavirus positive and negative strand ssRNA viruses revealed multiple sequence similarities between SARS-CoV-2 and non-coronaviruses, including similarities between RNA-dependent RNA-polymerases and helicases (two highly-conserved proteins). We also observed similarities between SARS-CoV-2 surface (i.e. spike) protein with paramyxovirus fusion proteins. This similarity was restricted to a segment of spike protein S2 subunit which is involved in cell fusion. We next analyzed spike proteins from SARS-CoV-2 “variants of concern” (VOCs) and “variants of interests” (VOIs) and found that some of these variants show considerably higher spike-fusion similarity with paramyxoviruses. The ‘spike-fusion’ similarity was also observed for some pathogenic coronaviruses other than SARS-CoV-2. Epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that several B cell epitopes as well as T cell and MHC binding epitopes map within the spike-fusion similarity region. These data indicate that there might be a degree of convergent evolution between SARS-CoV-2 and paramyxovirus surface proteins which could be of pathogenic and immunological importance.
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Affiliation(s)
- Ehsan Ahmadi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zabihi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Hosseinzadeh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran
- * E-mail:
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42
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Le Verger K, González Ruiz LR, Billet G. Comparative anatomy and phylogenetic contribution of intracranial osseous canals and cavities in armadillos and glyptodonts (Xenarthra, Cingulata). J Anat 2021; 239:1473-1502. [PMID: 34275130 PMCID: PMC8602025 DOI: 10.1111/joa.13512] [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: 04/25/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022] Open
Abstract
The evolutionary history of the Cingulata, as for many groups, remains a highly debated topic to this day, particularly for one of their most emblematic representatives: the glyptodonts. There is no consensus among morphological and molecular phylogenies regarding their position within Cingulata. As demonstrated by recent works, the study of the internal anatomy constitutes a promising path for enriching morphological matrices for the phylogenetic study of armadillos. However, internal cranial anatomy remains understudied in the Cingulata. Here we explored and compared the anatomy of intracranial osseous canals and cavities in a diverse sample of extant and extinct cingulates, including the earliest well-preserved glyptodont crania. The virtual 3D reconstruction (using X-ray microtomography) of selected canals, that is, the nasolacrimal canal, the palatine canal, the sphenopalatine canal, the canal for the frontal diploic vein, the transverse canal, the orbitotemporal canal, the canal for the capsuloparietal emissary vein and the posttemporal canal, and alveolar cavities related to cranial vascularization, innervation or tooth insertion allowed us to compare the locations, trajectories, and shape of these structures and to discuss their potential interest for cingulate systematics. We tentatively reconstructed evolutionary scenarios for eight selected traits related to these structures in which glyptodonts often showed a close resemblance to pampatheres, to the genus Proeutatus, and/or to chlamyphorines. This latter pattern was partly congruent with recent molecular hypotheses, but more research is needed on these resemblances and on the potential effects of development and allometry on the observed variations. Overall, these comparisons have enabled us to highlight new anatomical variation that may be of great interest to further explore the evolutionary history of cingulates and the origins of glyptodonts on a morphological basis.
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Affiliation(s)
- Kévin Le Verger
- Museum national d’Histoire naturelleCentre de Recherche en Paléontologie – ParisUMR 7207 CR2P MNHN/CNRS/UPMCSorbonne UniversitésParisFrance
| | - Laureano R. González Ruiz
- Laboratorio de Investigaciones en Evolución y Biodiversidad (LIEB‐FCNyCS sede EsquelUNPSJB) y Centro de Investigaciones Esquel de Montaña y Estepa Patagónica (CIEMEP), CONICETUniversidad Nacional de La Patagonia San Juan Bosco (UNPSJB)ChubutArgentina
| | - Guillaume Billet
- Museum national d’Histoire naturelleCentre de Recherche en Paléontologie – ParisUMR 7207 CR2P MNHN/CNRS/UPMCSorbonne UniversitésParisFrance
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43
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Van Damme K, Cornetti L, Fields PD, Ebert D. Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution. Syst Biol 2021; 71:777-787. [PMID: 34850935 PMCID: PMC9203061 DOI: 10.1093/sysbio/syab094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022] Open
Abstract
Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]
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Affiliation(s)
- Kay Van Damme
- Centre for Academic Heritage and Archives & Ghent University Botanical Garden, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Tvärminne Zoological Station (TZS), University of Helsinki, J.A. Palménin tie 260, Hanko, Finland
| | - Luca Cornetti
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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44
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Law CJ. Different evolutionary pathways lead to incomplete convergence of elongate body shapes in carnivoran mammals. Syst Biol 2021; 71:788-796. [PMID: 34791502 DOI: 10.1093/sysbio/syab091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Although convergence is often recognized as a ubiquitous feature across the Tree of Life, whether the underlying traits also exhibit similar evolutionary pathways towards convergent forms puzzles biologists. In carnivoran mammals, "elongate," "slender," and "long" are often used to describe and even to categorize mustelids (martens, polecats, and weasels), herpestids (mongooses), viverrids (civets and genets), and other carnivorans together. But just how similar these carnivorans are and whether there is convergence in the morphological component that contribute to elongation has never been assessed. Here, I found that these qualitatively-described elongate carnivorans exhibited incomplete convergence towards elongate bodies compared to other terrestrial carnivorans. In contrast, the morphological components underlying body shape variation do not exhibit convergence despite evidence that these components are more elongate in elongate carnivorans compared to non-elongate carnivorans. Furthermore, these components also exhibited shorter but different phylogenetic half-lives towards more elongate adaptive peaks, indicating that different selective pressures can create multiple pathways to elongation. Incorporating the fossil record will facilitate further investigation of whether body elongation evolved adaptively or if it is simply a retained ancestral trait.
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Affiliation(s)
- Chris J Law
- Department of Biology, University of Washington, Seattle, WA, 98105; Richard Gilder Graduate School, Department of Mammalogy, and Division of Paleontology, American Museum of Natural History, New York, NY, USA 10024
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45
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Potdar S, Westerman EL. Digest: Recurrence of sexually dimorphic neurological structure in neotropical butterflies . Evolution 2021; 75:3221-3223. [PMID: 34773401 DOI: 10.1111/evo.14401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022]
Abstract
Although many traits can be gained or lost over evolutionary time, it has long been unclear whether complex sensory processing structures, such as brain neuropils, can be regained after having been lost. Morris et al. show that a part of the brain once lost in butterflies, a macro-glomeruli complex (MGC) in the antennal lobe, is prevalent and has diversified in the Ithomiini tribe. This structure is sexually dimorphic in some species. This re-emergence of a complex sensory processing structure is likely driven by ecological factors.
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Affiliation(s)
- Sushant Potdar
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701
| | - Erica L Westerman
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701
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46
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Paluh DJ, Dillard WA, Stanley EL, Fraser GJ, Blackburn DC. Re-evaluating the morphological evidence for the re-evolution of lost mandibular teeth in frogs. Evolution 2021; 75:3203-3213. [PMID: 34674263 PMCID: PMC9299036 DOI: 10.1111/evo.14379] [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] [Received: 07/16/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022]
Abstract
Dollo's law of irreversibility states that once a complex structure is lost, it cannot be regained in the same form. Several putative exceptions to Dollo's law have been identified using phylogenetic comparative methods, but the anatomy and development of these traits are often poorly understood. Gastrotheca guentheri is renowned as the only frog with teeth on the lower jaw. Mandibular teeth were lost in the ancestor of frogs more than 200 million years ago and subsequently regained in G. guentheri. Little is known about the teeth in this species despite being a frequent example of trait “re‐evolution,” leaving open the possibility that it may have mandibular pseudoteeth. We assessed the dental anatomy of G. guentheri using micro‐computed tomography and histology and confirmed the longstanding assumption that true mandibular teeth are present. Remarkably, the mandibular teeth of G. guentheri are nearly identical in gross morphology and development to upper jaw teeth in closely related species. The developmental genetics of tooth formation are unknown in this possibly extinct species. Our results suggest that an ancestral odontogenic pathway has been conserved but suppressed in the lower jaw since the origin of frogs, providing a possible mechanism underlying the re‐evolution of lost mandibular teeth.
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Affiliation(s)
- Daniel J Paluh
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611.,Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Wesley A Dillard
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Edward L Stanley
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611
| | - Gareth J Fraser
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611
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47
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Wertheim JO, Steel M, Sanderson MJ. Accuracy in near-perfect virus phylogenies. Syst Biol 2021; 71:426-438. [PMID: 34398231 PMCID: PMC8385947 DOI: 10.1093/sysbio/syab069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Abstract
Phylogenetic trees from real-world data often include short edges with very few substitutions per site, which can lead to partially resolved trees and poor accuracy. Theory indicates that the number of sites needed to accurately reconstruct a fully resolved tree grows at a rate proportional to the inverse square of the length of the shortest edge. However, when inferred trees are partially resolved due to short edges, “accuracy” should be defined as the rate of discovering false splits (clades on a rooted tree) relative to the actual number found. Thus, accuracy can be high even if short edges are common. Specifically, in a “near-perfect” parameter space in which trees are large, the tree length ξ (the sum of all edge lengths) is small, and rate variation is minimal, the expected false positive rate is less than ξ∕3; the exact value depends on tree shape and sequence length. This expected false positive rate is far below the false negative rate for small ξ and often well below 5% even when some assumptions are relaxed. We show this result analytically for maximum parsimony and explore its extension to maximum likelihood using theory and simulations. For hypothesis testing, we show that measures of split “support” that rely on bootstrap resampling consistently imply weaker support than that implied by the false positive rates in near-perfect trees. The near-perfect parameter space closely fits several empirical studies of human virus diversification during outbreaks and epidemics, including Ebolavirus, Zika virus, and SARS-CoV-2, reflecting low substitution rates relative to high transmission/sampling rates in these viruses.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Mike Steel
- Biomathematics Research Center, School of Mathematics and Statistics, University of Canterbury, Christchurch, 8041, New Zealand
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA
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48
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Tian X, Li X, Yu Q, Zhao H, Liao J. Asymmetric expression patterns of B- and C-class MADS-box genes correspond to the asymmetrically specified androecial identities of Canna indica. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:540-545. [PMID: 33342001 DOI: 10.1111/plb.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Canna indica is a common ornamental plant with asymmetric flowers having colourful petaloid staminodes. The only fertile stamen comprises a one-theca anther and a petaloid appendage and represents the lowest stamen number in the order Zingiberales. The molecular mechanism for the asymmetric androecial petaloidy remains poorly understood. Here, we studied the identity specification in Canna stamen. We observed four types of abnormal flower in terms of androecium identity transformation and analysed the corresponding floral symmetry changes. We further tested the expression patterns of B- and C-class MADS-box genes using in situ hybridization in normal Canna stamen. Homeotic conversions in the androecium were accompanied by floral symmetry changes, and the asymmetric stamen is key in contributing to the floral asymmetry. Both B- and C-class genes exhibited higher expression levels in the anther primordium than in other androecial parts. This asymmetric expression pattern precisely corresponded to the asymmetric identities of the Canna androecium. We identified C. indica as a model species for studying androecial organ identity and floral symmetry synthetically in Zingiberales. We hypothesized that homeotic genes specify floral organ identity in a putative dose-dependent manner. The results add to the current understanding of organ identity-related floral symmetry.
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Affiliation(s)
- X Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - X Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Q Yu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - H Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Xinxing Vocational School of Traditional Chinese Medicine, Xinxing, Guangdong, China
| | - J Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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49
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Collar DC, DiPaolo ECC, Mai SL, Mehta RS. Body shape transformations by alternate anatomical adaptive peak shifts in blenniiform fishes. Evolution 2021; 75:1552-1566. [PMID: 33890296 DOI: 10.1111/evo.14238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 02/24/2021] [Accepted: 04/05/2021] [Indexed: 12/18/2022]
Abstract
Extreme body elongation has occurred repeatedly in the evolutionary history of ray-finned fishes. Lengthening of the anterior-posterior body axis relative to depth and width can involve changes in the cranial skeleton and vertebral column, but to what extent is anatomical evolution determined by selective factors and intrinsic constraints that are shared broadly among closely related lineages? In this study, we fit adaptive (Ornstein-Uhlenbeck) evolutionary models to body shape and its anatomical determinants and identified two instances of extreme elongation by divergent anatomical peak shifts in the Blenniiformes, a radiation of small-bodied substrate-associated marine teleost fishes. Species in the genus Xiphasia (hairtail blennies) evolved toward a peak defined by a highly elongated caudal vertebral region but ancestral cranial and precaudal vertebral morphology. In contrast, a clade that includes the genera Chaenopsis and Lucayablennius (pike and arrow blennies) evolved toward a peak with a long slender skull but ancestral axial skeletal anatomy. Neither set of anatomical peak shifts aligns closely with the major axis of anatomical diversification in other blenniiform fishes. These results provide little evidence that ancestral constraints have affected body shape transformation, and instead suggest that extreme elongation arose with distinct shifts in selective factors and development.
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Affiliation(s)
- David C Collar
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, 23606
| | - Emma C C DiPaolo
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, 23606
| | - Sienna L Mai
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, 23606
| | - Rita S Mehta
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060
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50
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Bonett RM, Ledbetter NM, Hess AJ, Herrboldt MA, Denoël M. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development. Dev Dyn 2021; 251:957-972. [PMID: 33991029 DOI: 10.1002/dvdy.373] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 11/11/2022] Open
Abstract
Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.
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Affiliation(s)
- Ronald M Bonett
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | | | - Alexander J Hess
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Madison A Herrboldt
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and Oceanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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