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Vela J, Mora P, Montiel EE, Rico-Porras JM, Sanllorente O, Amoasii D, Lorite P, Palomeque T. Exploring horizontal transfer of mariner transposable elements among ants and aphids. Gene 2024; 899:148144. [PMID: 38195050 DOI: 10.1016/j.gene.2024.148144] [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: 07/21/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.
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Affiliation(s)
- Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Eugenia E Montiel
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Olivia Sanllorente
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Daniela Amoasii
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
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Xiang K, Puzakov M, Shi S, Diaby M, Ullah N, Gao B, Song C. Mosquito ( MS), a DD37E Family of Tc1/ Mariner, Displaying a Distinct Evolution Profile from DD37E/ TRT and DD37E/ L18. Genes (Basel) 2023; 14:1379. [PMID: 37510284 PMCID: PMC10379824 DOI: 10.3390/genes14071379] [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: 06/02/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Diverse Tc1/mariner elements with the DD37E signature have been detected. However, their evolutionary relationship and profiles are largely unknown. Using bioinformatics methods, we defined the evolution profile of a Tc1/Mariner family, which harbors the catalytic domain with the DD37E signature, and renamed it DD37E/Mosquito (MS). MS transposons form a separate monophyletic clade in the phylogenetic tree, distinct from the other two groups of elements with the DD37E signature, DD37E/L18 and DD37E/TRT (transposon related to Tc1), and represent a very different taxonomic distribution from that of DD37E/TRT. MS is only detected in invertebrate and is mostly present in Arthropoda, as well as in Cnidaria, Ctenophora, Mollusca, Nematoda, and Platyhelminthes, with a total length of about 1.3 kb, containing an open reading frame (ORF) encoding about 340 amino acids transposases, with a conserved DD37E catalytic domain. The terminal inverted repeat (TIR) lengths range from 19 bp to 203 bp, and the target site duplication (TSD) is TA. We also identified few occurrences of MS horizontal transfers (HT) across lineages of diptera. In this paper, the distribution characteristics, structural characteristics, phylogenetic evolution, and horizontal transfer of the MS family are fully analyzed, which is conducive to supplementing and improving the Tc1/Mariner superfamily and excavating active transposons.
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Affiliation(s)
- Kuilin Xiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Mikhail Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Lenninsky Ave, 38, Moscow 119991, Russia
| | - Shasha Shi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Mohamed Diaby
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Numan Ullah
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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Puzakov MV, Puzakova LV. Prevalence, Diversity, and Evolution of L18 (DD37E) Transposons in the Genomes of Cnidarians. Mol Biol 2022. [DOI: 10.1134/s0026893322030104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Multiple heterochromatin diversification events in the genome of fungus-farming ants: insights from repetitive sequences. Chromosoma 2022; 131:59-75. [PMID: 35325297 DOI: 10.1007/s00412-022-00770-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 11/03/2022]
Abstract
A substantial portion of the eukaryotic genome includes repetitive DNA, which is important for its stability, regulation, and architecture. Fungus-farming ant genomes show remarkable structural rearrangement rates that were necessary for the establishment of their agriculture-based lifestyle, highlighting the relevance of this peculiar group in understanding the repetitive portion of ant genome. Chromosomal banding studies are in accordance with genomic data because they show that repetitive heterochromatic sequences of basal and derivative Attina species are GC-rich, an uncommon trait in Formicidae. To understand the evolutionary dynamics of heterochromatin in Attina, we compared GC-rich heterochromatin patterns between the Paleoattina and Neoattina clades of this subtribe. To this end, we hybridized the Mrel-C0t probe (highly and moderately repetitive DNA) obtained from Mycetomoellerius relictus, Neoattina with GC-rich heterochromatin, in karyotypes of Paleoattina and Neoattina species. Additionally, we mapped the repetitive sequences (GA)15 and (TTAGG)6 in species of the two clades to investigate their organization and evolutionary patterns in the genome of Attina. The Mrel-C0t probe marked the heterochromatin in M. relictus, in other Mycetomoellerius spp., and in species of Mycetarotes, Cyphomyrmex, and Sericomyrmex (Neoattina). In Mycetomoellerius urichii, only pericentromeric heterochromatin was marked with Mrel-C0t. No marking was observed in Paleoattina species or in Atta and Acromyrmex (Neoattina). These results indicated that different evolutionary events led to heterochromatin differentiation in Attina. The most likely hypothesis is that GC-rich heterochromatin arose in the common ancestor of the two clades and accumulated various changes throughout evolution. The sequences (GA)15 and (TTAGG)6 located in euchromatin and telomeres, respectively, showed more homogeneous results among the species.
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Aphids and Ants, Mutualistic Species, Share a Mariner Element with an Unusual Location on Aphid Chromosomes. Genes (Basel) 2021; 12:genes12121966. [PMID: 34946915 PMCID: PMC8701394 DOI: 10.3390/genes12121966] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022] Open
Abstract
Aphids (Hemiptera, Aphididae) are small phytophagous insects. The aim of this study was to determine if the mariner elements found in the ant genomes are also present in Aphis fabae and Aphis hederae genomes and the possible existence of horizontal transfer events. Aphids maintain a relationship of mutualism with the ants. The close contact between these insects could favour horizontal transfer events of transposable elements. Myrmar mariner element isolated from Myrmica ruginodis and Tapinoma ibericum ants have also been found in the two Aphis species: A. fabae and A. hederae (Afabmar-Mr and Ahedmar-Mr elements). Besides, Afabmar-Mr could be an active transposon. Myrmar-like elements are also present in other insect species as well as in one Crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the existence of horizontal transfer. Most aphids have 2n = 8 with a XX-X0 sex determination system. Their complicated life cycle is mostly parthenogenetic with sexual individuals only in autumn. The production of X0 males, originated by XX females which produce only spermatozoa with one X chromosome, must necessarily occur through specialized cytogenetic and molecular mechanisms which are not entirely known. In both aphid species, the mariner elements are located on all chromosomes, including the X chromosomes. However, on the two X chromosomes, no positive signals are detected in their small DAPI-negative telomere regions. The rDNA sites are located, as in the majority of Aphids species, on one of the telomere regions of each X chromosome. The hybridization patterns obtained by double FISH demonstrate that Afabmar-Mr and Ahedmar-Mr elements do not hybridize at the rDNA sites of their host species. Possible causes for the absence of these transposons in the rDNA genes are discussed, probably related with the X chromosome biology.
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Zidi M, Denis F, Klai K, Chénais B, Caruso A, Djebbi S, Mezghani M, Casse N. Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae). G3 (BETHESDA, MD.) 2021; 11:jkab287. [PMID: 34849769 PMCID: PMC8664452 DOI: 10.1093/g3journal/jkab287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022]
Abstract
The whitefly, Bemisia tabaci is a hemipteran pest of vegetable crops vectoring a broad category of viruses. Currently, this insect pest showed a high adaptability and resistance to almost all the chemical compounds commonly used for its control. In many cases, transposable elements (TEs) contributed to the evolution of host genomic plasticity. This study focuses on the annotation of Mariner-like elements (MLEs) and their derived Miniature Inverted repeat Transposable Elements (MITEs) in the genome of B. tabaci. Two full-length MLEs belonging to mauritiana and irritans subfamilies were detected and named Btmar1.1 and Btmar2.1, respectively. Additionally, 548 defective MLE sequences clustering mainly into 19 different Mariner lineages of mauritiana and irritans subfamilies were identified. Each subfamily showed a significant variation in MLE copy number and size. Furthermore, 71 MITEs were identified as MLEs derivatives that could be mobilized via the potentially active transposases encoded by Btmar 1.1 and Btmar2.1. The vast majority of sequences detected in the whitefly genome present unusual terminal inverted repeats (TIRs) of up to 400 bp in length. However, some exceptions are sequences without TIRs. This feature of the MLEs and their derived MITEs in B. tabaci genome that distinguishes them from all the other MLEs so far described in insects, which have TIRs size ranging from 20 to 40 bp. Overall, our study provides an overview of MLEs, especially those with large TIRs, and their related MITEs, as well as diversity of their families, which will provide a better understanding of the evolution and adaptation of the whitefly genome.
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Affiliation(s)
- Marwa Zidi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Françoise Denis
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
- Laboratoire BOREA MNHN, CNRS FRE 2030, SU, IRD 207, UCN, UA, 75231 Paris, France
| | - Khouloud Klai
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Benoît Chénais
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Aurore Caruso
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Salma Djebbi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Nathalie Casse
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
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Ben Amara W, Djebbi S, Ben Lazhar-Ajroud W, Naccache C, Mezghani MK. Insights on mauritiana-like Elements Diversity in Mayetiola destructor and M. hordei (Diptera: Cecidomyiidae). Genome 2021; 65:165-181. [PMID: 34780303 DOI: 10.1139/gen-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mariner-like elements (MLEs) are class II transposons belonging to the Tc1-mariner family, that have successfully invaded many insect genomes. In the current study, the availability of the Hessian fly Mayetiola destructor genome has enabled us to perform in silico analysis of MLEs using as query the previously described mariner element (Desmar1) belonging to mauritiana subfamily. Eighteen mauritiana-like elements were detected and were clustered into three main groups named Desmar1-like, MauCons1 and MauCons2. Subsequently, in vitro analysis was carried out to investigate mauritiana-like elements in M. destructor as well as in Mayetiola hordei using primers designed from TIRs of the previously identified MLEs. PCR amplifications were successful and a total of 12 and 17 mauritiana-like elements were discovered in M. destructor and M. hordei, respectively. Sequence analyses of mauritiana-like elements obtained in silico and in vitro have showed that MauCons1 and MauCons2 elements share low similarity with Desmar1 ranging from 50% to 55% suggesting different groups under mauritiana subfamily have invaded the genomes of M. destructor and M. hordei. These groups are likely inherited by vertical transmission that subsequently underwent different evolutionary histories. This work describes new mauritiana-like elements in M. destructor that are distinct from the previouslydiscovered Desmar1 and provides the first evidence of MLEs belonging to mauritiana subfamily in M. hordei.
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Affiliation(s)
- Wiem Ben Amara
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
| | - Salma Djebbi
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
| | - Wafa Ben Lazhar-Ajroud
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
| | | | - Maha Khemakhem Mezghani
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
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Wang S, Diaby M, Puzakov M, Ullah N, Wang Y, Danley P, Chen C, Wang X, Gao B, Song C. Divergent evolution profiles of DD37D and DD39D families of Tc1/mariner transposons in eukaryotes. Mol Phylogenet Evol 2021; 161:107143. [PMID: 33713798 DOI: 10.1016/j.ympev.2021.107143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 11/29/2022]
Abstract
DNA transposons play a significant role in shaping the size and structure of eukaryotic genomes. The Tc1/mariner transposons are the most diverse and widely distributed superfamily of DNA transposons and the structure and distribution of several Tc1/mariner families, such as DD35E/TR, DD36E/IC, DD37E/TRT, and DD41D/VS, have been well studied. Nonetheless, a greater understanding of the structure and diversity of Tc1/mariner transposons will provide insight into the evolutionary history of eukaryotic genomes. Here, we conducted further analysis of DD37D/maT and DD39D (named Guest, GT), which were identified by the specific catalytic domains DD37D and DD39D. Most transposons of the maT family have a total length of approximately 1.3 kb and harbor a single open reading frame encoding a ~ 346 amino acid (range 302-398 aa) transposase protein, flanked by short terminal inverted repeats (TIRs) (13-48 base pairs, bp). In contrast, GTs transposons were longer (2.0-5.8 kb), encoded a transposase protein of ~400 aa (range 140-592 aa), and were flanked by short TIRs (19-41 bp). Several conserved motifs, including two helix-turn-helix (HTH) motifs, a GRPR (GRKR) motif, a nuclear localization sequence, and a DDD domain, were also identified in maT and GT transposases. Phylogenetic analyses of the DDD domain showed that the maT and GT families each belong to a monophyletic clade and appear to be closely related to DD41D/VS and DD34D/mariner. In addition, maTs are mainly distributed in invertebrates (144 species), whereas GTs are mainly distributed in land plants through a small number of GTs are present in Chromista and animals. Sequence identity and phylogenetic analysis revealed that horizontal transfer (HT) events of maT and GT might occur between kingdoms and phyla of eukaryotes; however, pairwise distance comparisons between host genes and transposons indicated that HT events involving maTs might be less frequent between invertebrate species and HT events involving GTs may be less frequent between land plant species. Overall, the DD37D/maT and DD39D/GT families display significantly different distribution and tend to be identified in more ancient evolutionary families. The discovery of intact transposases, perfect TIRs, and target site duplications (TSD) of maTs and GTs illustrates that the DD37D/maT and DD39D/GT families may be active. Together, these findings improve our understanding of the diversity of Tc1/mariner transposons and their impact on eukaryotic genome evolution.
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Affiliation(s)
- Saisai Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Mikhail Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia
| | - Numan Ullah
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Patrick Danley
- University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Friedman DA, Johnson BR, Linksvayer TA. Distributed physiology and the molecular basis of social life in eusocial insects. Horm Behav 2020; 122:104757. [PMID: 32305342 DOI: 10.1016/j.yhbeh.2020.104757] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
The traditional focus of physiological and functional genomic research is on molecular processes that play out within a single multicellular organism. In the colonial (eusocial) insects such as ants, bees, and termites, molecular and behavioral responses of interacting nestmates are tightly linked, and key physiological processes are regulated at the scale of the colony. Such colony-level physiological processes regulate nestmate physiology in a distributed fashion, through various social communication mechanisms. As a result of physiological decentralization over evolutionary time, organismal mechanisms, for example related to pheromone detection, hormone signaling, and neural signaling pathways, are deployed in novel contexts to influence nestmate and colony traits. Here we explore how functional genomic, physiological, and behavioral studies can benefit from considering the traits of eusocial insects in this light. We highlight functional genomic work exploring how nestmate-level and colony-level traits arise and are influenced by interactions among physiologically-specialized nestmates of various developmental stages. We also consider similarities and differences between nestmate-level (organismal) and colony-level (superorganismal) physiological processes, and make specific hypotheses regarding the physiology of eusocial taxa. Integrating theoretical models of distributed systems with empirical functional genomics approaches will be useful in addressing fundamental questions related to the evolution of eusociality and collective behavior in natural systems.
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Affiliation(s)
- D A Friedman
- University of California, Davis, Department of Entomology, Davis, CA 95616, United States of America.
| | - B R Johnson
- University of California, Davis, Department of Entomology, Davis, CA 95616, United States of America
| | - T A Linksvayer
- University of Pennsylvania, Department of Biology, Pennsylvania, PA 19104, United States of America
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