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Záveská E, Šída O, Leong-Škorničková J, Chumová Z, Trávníček P, Newman MF, Poulsen AD, Böhmová A, Chudáčková H, Fér T. Testing the large genome constraint hypothesis in tropical rhizomatous herbs: life strategies, plant traits and habitat preferences in gingers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1223-1238. [PMID: 37991980 DOI: 10.1111/tpj.16559] [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: 02/08/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Plant species with large genomes tend to be excluded from climatically more extreme environments with a shorter growing season. Species that occupy such environments are assumed to be under natural selection for more rapid growth and smaller genome size (GS). However, evidence for this is available only for temperate organisms. Here, we study the evolution of GS in two subfamilies of the tropical family Zingiberaceae to find out whether species with larger genomes are confined to environments where the vegetative season is longer. We tested our hypothesis on 337 ginger species from regions with contrasting climates by correlating their GS with an array of plant traits and environmental variables. We revealed 16-fold variation in GS which was tightly related to shoot seasonality. Negative correlations of GS with latitude, temperature and precipitation emerged in the subfamily Zingiberoidae, demonstrating that species with larger GS are excluded from areas with a shorter growing season. In the subfamily Alpinioideae, GS turned out to be correlated with the type of stem and light requirements and its members cope with seasonality mainly by adaptation to shady and moist habitats. The Ornstein-Uhlenbeck models suggested that evolution in regions with humid climates favoured larger GS than in drier regions. Our results indicate that climate seasonality exerts an upper constraint on GS not only in temperate regions but also in the tropics, unless species with large genomes find alternative ways to escape from that constraint.
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Affiliation(s)
- E Záveská
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - O Šída
- Department of Botany, National Museum in Prague, Prague, Czech Republic
| | - J Leong-Škorničková
- The Herbarium, Singapore Botanic Gardens, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Z Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - P Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - M F Newman
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - A D Poulsen
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - A Böhmová
- Department of Botany, National Museum in Prague, Prague, Czech Republic
- Department of Botany, Charles University, Prague, Czech Republic
| | - H Chudáčková
- Department of Botany, Charles University, Prague, Czech Republic
| | - T Fér
- Department of Botany, Charles University, Prague, Czech Republic
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2
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Saha A, Bellucci A, Fratini S, Cannicci S, Ciofi C, Iannucci A. Ecological factors and parity mode correlate with genome size variation in squamate reptiles. BMC Ecol Evol 2023; 23:69. [PMID: 38053023 PMCID: PMC10696768 DOI: 10.1186/s12862-023-02180-4] [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: 05/16/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, the second most species-rich order of vertebrates, there are currently no studies investigating drivers of genome size variability. We run a series of phylogenetic generalized least-squares models on 227 species of squamates to test for possible relationships between genome size and ecological factors including latitudinal distribution, bioclimatic variables and microhabitat use. We also tested whether genome size variation can be associated with parity mode, a highly variable life history trait in this order of reptiles. RESULTS The best-fitting model showed that the interaction between microhabitat use and parity mode mainly accounted for genome size variation. Larger genome sizes were found in live-bearing species that live in rock/sand ecosystems and in egg-laying arboreal taxa. On the other hand, smaller genomes were found in fossorial live-bearing species. CONCLUSIONS Environmental factors and species parity mode appear to be among the main parameters explaining genome size variation in squamates. Our results suggest that genome size may favour adaptation of some species to certain environments or could otherwise result from the interaction between environmental factors and parity mode. Integration of genome size and genome sequencing data could help understand the role of differential genome content in the evolutionary process of genome size variation in squamates.
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Affiliation(s)
- Anik Saha
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Arianna Bellucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
- National Biodiversity Future Center, 90133, Palermo, Italy.
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3
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Zhang M, Qiu X. Genetic basis of genome size variation of wheat. Funct Integr Genomics 2023; 23:285. [PMID: 37648783 DOI: 10.1007/s10142-023-01194-x] [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: 06/15/2023] [Revised: 07/22/2023] [Accepted: 07/29/2023] [Indexed: 09/01/2023]
Abstract
Research on various species has revealed a connection between genome size variation and the physiological and ecological characteristics of the species, suggesting that it could be a crucial factor influencing a species' adaptability to different environments. Wheat, being one of the world's three primary grains, holds significance in this regard. Investigating the genome size of wheat and analyzing the genetic factors contributing to its variation could offer valuable insights for enhancing wheat agronomic traits. This project has developed a conservative site ratio calculation approach to determine the size of the wheat genome. Additionally, it employs flow cytometry and k-mer distribution analysis to validate this method. Furthermore, the researchers use re-sequencing data to investigate the impact of environmental selection pressure and transposon dynamics on the variation in the size of the wheat genome. The findings from this study demonstrate a strong relationship between the size of the wheat genome and several environmental factors. These results serve as a valuable reference for understanding the development of variation in the size of the hetero-hexaploid wheat genome. Moreover, they contribute to advancing fundamental research on the genetic mechanisms underlying wheat characteristics. Additionally, the study paves the way for exploring new research directions in wheat breeding, which holds promise for future advancements in this field.
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Affiliation(s)
- Ming Zhang
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuebing Qiu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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4
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [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: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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5
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Zuo B, Nneji LM, Sun YB. Comparative genomics reveals insights into anuran genome size evolution. BMC Genomics 2023; 24:379. [PMID: 37415107 DOI: 10.1186/s12864-023-09499-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. RESULTS Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. CONCLUSIONS Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
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Affiliation(s)
- Bin Zuo
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Yan-Bo Sun
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650091, China.
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6
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Mueller RL, Cressler CE, Schwartz RS, Chong RA, Butler M. Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development. Integr Org Biol 2023; 5:obad015. [PMID: 37143961 PMCID: PMC10153748 DOI: 10.1093/iob/obad015] [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: 09/02/2022] [Revised: 02/25/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023] Open
Abstract
Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lungfish in having the largest vertebrate genomes-3 to 40 times that of humans-as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.
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Affiliation(s)
| | - C E Cressler
- School of Biological Sciences, University of Nebraska Lincoln, Lincoln, NE 68588, USA
| | - R S Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - R A Chong
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
| | - M Butler
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
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7
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Santos FB, Del-Bem LE. The Evolution of tRNA Copy Number and Repertoire in Cellular Life. Genes (Basel) 2022; 14:27. [PMID: 36672768 PMCID: PMC9858662 DOI: 10.3390/genes14010027] [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: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, in contrast to what is observed for protein-coding genes that stop expanding between ~20,000 and ~35,000 loci per haploid genome in eukaryotes, regardless of genome size. Our analyses indicate that after the bacteria/archaea split, the tRNA gene pool experienced the evolution of increased anticodon diversity in the archaeal lineage, along with a tRNA gene size increase and mature tRNA size decrease. The evolution and diversification of eukaryotes from archaeal ancestors involved further expansion of the tRNA anticodon repertoire, additional increase in tRNA gene size and decrease in mature tRNA length, along with an explosion of the tRNA gene copy number that emerged coupled with accelerated genome size expansion. Our findings support the notion that macroscopic eukaryotes with a high diversity of cell types, such as land plants and vertebrates, independently evolved a high diversity of tRNA anticodons along with high gene redundancy caused by the expansion of the tRNA copy number. The results presented here suggest that the evolution of tRNA genes played important roles in the early split between bacteria and archaea, and in eukaryogenesis and the later emergence of complex eukaryotes, with potential implications in protein translation and gene regulation through tRNA-derived RNA fragments.
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Affiliation(s)
- Fenícia Brito Santos
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
| | - Luiz-Eduardo Del-Bem
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
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8
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Pincheira‐Donoso D, Harvey LP, Johnson JV, Hudson D, Finn C, Goodyear LEB, Guirguis J, Hyland EM, Hodgson DJ. Genome size does not influence extinction risk in the world's amphibians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lilly P. Harvey
- School of Science and Technology Nottingham Trent University Nottingham UK
| | - Jack V. Johnson
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave Hudson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Catherine Finn
- School of Biological Sciences Queen's University Belfast Belfast UK
| | | | - Jacinta Guirguis
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Edel M. Hyland
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave J. Hodgson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
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9
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Ji Y, Feng S, Wu L, Fang Q, Brüniche-Olsen A, DeWoody JA, Cheng Y, Zhang D, Hao Y, Song G, Qu Y, Suh A, Zhang G, Hackett SJ, Lei F. Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds. SCIENCE ADVANCES 2022; 8:eabo0099. [PMID: 36044583 PMCID: PMC9432842 DOI: 10.1126/sciadv.abo0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific variation of orthologous microsatellite length, transposable element (TE) length, and deletion length and how these genomic attributes affect genome sizes. In nonpasserines, we found that generation time is correlated to both orthologous microsatellite length and TE length, and body mass is negatively correlated to DNA deletions. These patterns are less pronounced in passerines. In all species, we found that DNA deletions relate to genome size similarly as TE length, suggesting a role of body mass dynamics in genome evolution. Our results indicate that generation time and body mass shape the evolution of genomic attributes in neoavian birds.
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Affiliation(s)
- Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
- Evolutionary and Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Anna Brüniche-Olsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - J. Andrew DeWoody
- Departments of Forestry and Natural Resources and Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Alexander Suh
- School of Biological Sciences, Organism and Environment, University of East Anglia, NR4 7TU, Norwich, UK
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala SE-752 36, Sweden
| | - Guojie Zhang
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
- Evolutionary and Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Women’s Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou, 310006, China
| | - Shannon J. Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
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10
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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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11
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Iannucci A, Saha A, Cannicci S, Bellucci A, Cheng CLY, Ng KH, Fratini S. Ecological, physiological and life-history traits correlate with genome sizes in decapod crustaceans. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930888] [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] Open
Abstract
Crustaceans are characterized by some of the most variable genome sizes among animals. Significant relationships between genome size and specific eco-physiological and morphological features have been described in many crustacean taxa, such as Amphipoda, Ostracoda, Cladocera, and Copepoda. A consistent pattern of genome size variation is yet to be found, however, in one of the most specious order of crustaceans, the Decapoda. We investigated how genome size is related to selected eco-physiological and life-history traits in species belonging to this order. We analyzed the respiratory, excretory, and developmental adaptations of 179 decapod species inhabiting shallow marine, deep marine, freshwater, intertidal, and terrestrial habitats. Our results show that the genome size is significantly larger in decapods that have a direct development. Moreover, in Anomura, Astacidea, and Brachyura we found larger genome sizes in species (i) living in freshwater habitats, (ii) using gills as a strictly water-breathing organs, and (iii) presenting a direct development. While species that (i) live in shallow waters, and intertidal and terrestrial habitats, (ii) have some degrees of air-breathing adaptations, namely gills that can exchange oxygen with air if wet or branchiostegal lungs, and (iii) possess an indirect or extended development are characterized by significantly smaller genomes. Our analyses show that developmental complexity affects genome size in decapods, and that multiple eco-physiological and life-history traits correlate with genome size in Anomura, Astacidea, and Brachyura.
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12
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Hultgren KM, Chak STC, Bjelajac J, Macdonald KS. Correlated evolution of larval development, egg size and genome size across two genera of snapping shrimp. J Evol Biol 2021; 34:1827-1839. [PMID: 34626036 DOI: 10.1111/jeb.13945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 01/21/2023]
Abstract
Across plants and animals, genome size is often correlated with life-history traits: large genomes are correlated with larger seeds, slower development, larger body size and slower cell division. Among decapod crustaceans, caridean shrimps are among the most variable both in terms of genome size variation and life-history characteristics such as larval development mode and egg size, but the extent to which these traits are associated in a phylogenetic context is largely unknown. In this study, we examine correlations among egg size, larval development and genome size in two different genera of snapping shrimp, Alpheus and Synalpheus, using phylogenetically informed analyses. In both Alpheus and Synalpheus, egg size is strongly linked to larval development mode: species with abbreviated development had significantly larger eggs than species with extended larval development. We produced the first comprehensive dataset of genome size in Alpheus (n = 37 species) and demonstrated that genome size was strongly and positively correlated with egg size in both Alpheus and Synalpheus. Correlated trait evolution analyses showed that in Alpheus, changes in genome size were clearly dependent on egg size. In Synalpheus, evolutionary path analyses suggest that changes in development mode (from extended to abbreviated) drove increases in egg volume; larger eggs, in turn, resulted in larger genomes. These data suggest that variation in reproductive traits may underpin the high degree of variation in genome size seen in a wide variety of caridean shrimp groups more generally.
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Affiliation(s)
| | - Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA.,Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, New York, USA
| | - Jeremy Bjelajac
- Department of Biology, Seattle University, Seattle, Washington, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
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13
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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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14
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Johnson BB, Searle JB, Sparks JP. Genome size influences adaptive plasticity of water loss, but not metabolic rates, in lungless salamanders. J Exp Biol 2021; 224:237790. [PMID: 33914029 DOI: 10.1242/jeb.242196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/09/2021] [Indexed: 12/14/2022]
Abstract
Many expressions of phenotype, such as physiological performance, integrate multiple underlying traits to function. Linking component traits to adaptive physiology thus gives insight into mechanisms of selection acting on performance. Genome size (C-value) is a trait that influences physiology in multiple taxa by exerting a nucleotypic effect, constraining cell size and cellular physiology such that whole-organism mass-specific metabolism is reduced with increasing C-value. We tested for this mechanism of C-value function acting in lungless salamanders, plus an unexplored potential mechanism of C-value effects constraining water transport across the body surface to influence cutaneous water loss rates. We found no evidence for a nucleotypic effect on metabolic rates, but we demonstrate a relationship between C-value and water loss physiology. Under warmer experimental conditions, C-value was inversely correlated with water loss and positively correlated with resistance to water loss, which demonstrated adaptive plasticity at higher temperatures. We hypothesize that this pattern results from differences in cell size constraining diffusion and evaporation of water from the skin under warm conditions when cutaneous perfusion is reduced. Testing this hypothesis may confirm a previously unappreciated adaptive role for C-value variation in this group, and reveals the possibility that genome size influences physiological exchange across transport barriers more broadly.
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Affiliation(s)
- Benjamin B Johnson
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY14853, USA
| | - Jeremy B Searle
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY14853, USA
| | - Jed P Sparks
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY14853, USA
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15
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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16
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Miller KE, Brownlee C, Heald R. The power of amphibians to elucidate mechanisms of size control and scaling. Exp Cell Res 2020; 392:112036. [PMID: 32343955 PMCID: PMC7246146 DOI: 10.1016/j.yexcr.2020.112036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 01/26/2023]
Abstract
Size is a fundamental feature of biology that affects physiology at all levels, from the organism to organs and tissues to cells and subcellular structures. How size is determined at these different levels, and how biological structures scale to fit together and function properly are important open questions. Historically, amphibian systems have been extremely valuable to describe scaling phenomena, as they occupy some of the extremes in biological size and are amenable to manipulations that alter genome and cell size. More recently, the application of biochemical, biophysical, and embryological techniques to amphibians has provided insight into the molecular mechanisms underlying scaling of subcellular structures to cell size, as well as how perturbation of normal size scaling impacts other aspects of cell and organism physiology.
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Affiliation(s)
- Kelly E Miller
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA
| | - Christopher Brownlee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794-8651, USA.
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA.
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17
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Choi IY, Kwon EC, Kim NS. The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy. Genes Genomics 2020; 42:699-714. [DOI: 10.1007/s13258-020-00941-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
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18
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Canapa A, Biscotti MA, Barucca M, Carducci F, Carotti E, Olmo E. Shedding light upon the complex net of genome size, genome composition and environment in chordates. EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1747558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- A. Canapa
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - M. A. Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - M. Barucca
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - F. Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - E. Carotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - E. Olmo
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
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19
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Bonett RM, Hess AJ, Ledbetter NM. Facultative Transitions Have Trouble Committing, But Stable Life Cycles Predict Salamander Genome Size Evolution. Evol Biol 2020. [DOI: 10.1007/s11692-020-09497-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Lertzman-Lepofsky G, Mooers AØ, Greenberg DA. Ecological constraints associated with genome size across salamander lineages. Proc Biol Sci 2019; 286:20191780. [PMID: 31530144 DOI: 10.1098/rspb.2019.1780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Salamanders have some of the largest, and most variable, genome sizes among the vertebrates. Larger genomes have been associated with larger cell sizes, lower metabolic rates, and longer embryonic and larval durations in many different taxonomic groups. These life-history traits are often important for dictating fitness under different environmental conditions, suggesting that a species' genome size may have the potential to constrain its ecological distribution. We test how genome size varies with the ephemerality of larval habitat across the salamanders, predicting that species with larger genomes will be constrained to more permanent habitats that permit slower development, while species with smaller genomes will be more broadly distributed across the gradient of habitat ephemerality. We found that salamanders with larger genomes are almost exclusively associated with permanent aquatic habitats. In addition, the evolutionary transition rate between permanent and ephemeral larval habitats is much higher in salamander lineages with smaller genome sizes. These patterns suggest that genome size may act as an evolutionary constraint on the ecological habitats of salamanders, restricting those species with large genomes and slower development to habitats with permanent sources of water.
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Affiliation(s)
- Gavia Lertzman-Lepofsky
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Arne Ø Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Dan A Greenberg
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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