1
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Forni G, Mantovani B, Mikheyev AS, Luchetti A. Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction. Genome Biol Evol 2024; 16:evae073. [PMID: 38573594 DOI: 10.1093/gbe/evae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 03/06/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (i) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (ii) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected-and more pleiotropic-genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.
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Affiliation(s)
- Giobbe Forni
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Barbara Mantovani
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, 2600 Canberra, ACT, Australia
| | - Andrea Luchetti
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, Bologna, Italy
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2
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Seneci L, Mikheyev AS. Sodium Channel β Subunits-An Additional Element in Animal Tetrodotoxin Resistance? Int J Mol Sci 2024; 25:1478. [PMID: 38338757 PMCID: PMC10855141 DOI: 10.3390/ijms25031478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024] Open
Abstract
Tetrodotoxin (TTX) is a neurotoxic molecule used by many animals for defense and/or predation, as well as an important biomedical tool. Its ubiquity as a defensive agent has led to repeated independent evolution of tetrodotoxin resistance in animals. TTX binds to voltage-gated sodium channels (VGSC) consisting of α and β subunits. Virtually all studies investigating the mechanisms behind TTX resistance have focused on the α subunit of voltage-gated sodium channels, where tetrodotoxin binds. However, the possibility of β subunits also contributing to tetrodotoxin resistance was never explored, though these subunits act in concert. In this study, we present preliminary evidence suggesting a potential role of β subunits in the evolution of TTX resistance. We gathered mRNA sequences for all β subunit types found in vertebrates across 12 species (three TTX-resistant and nine TTX-sensitive) and tested for signatures of positive selection with a maximum likelihood approach. Our results revealed several sites experiencing positive selection in TTX-resistant taxa, though none were exclusive to those species in subunit β1, which forms a complex with the main physiological target of TTX (VGSC Nav1.4). While experimental data validating these findings would be necessary, this work suggests that deeper investigation into β subunits as potential players in tetrodotoxin resistance may be worthwhile.
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Affiliation(s)
- Lorenzo Seneci
- Adaptive Biotoxicology Lab, School of the Environment, The University of Queensland, St Lucia, QLD 4067, Australia;
| | - Alexander S. Mikheyev
- Evolutionary Genomics Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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3
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Hasegawa N, Techer MA, Adjlane N, Al-Hissnawi MS, Antúnez K, Beaurepaire A, Christmon K, Delatte H, Dukku UH, Eliash N, El-Niweiri MAA, Esnault O, Evans JD, Haddad NJ, Locke B, Muñoz I, Noël G, Panziera D, Roberts JMK, De la Rúa P, Shebl MA, Stanimirovic Z, Rasmussen DA, Mikheyev AS. Evolutionarily diverse origins of deformed wing viruses in western honey bees. Proc Natl Acad Sci U S A 2023; 120:e2301258120. [PMID: 37339224 DOI: 10.1073/pnas.2301258120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023] Open
Abstract
Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, having switched hosts from the eastern to western honey bees (Apis cerana to Apis mellifera). They provide an opportunity to explore how novel transmission routes shape disease epidemiology. As the principal driver of the spread of deformed wing viruses (mainly DWV-A and DWV-B), varroa infestation has also driven global honey bee health declines. The more virulent DWV-B strain has been replacing the original DWV-A strain in many regions over the past two decades. Yet, how these viruses originated and spread remains poorly understood. Here, we use a phylogeographic analysis based on whole-genome data to reconstruct the origins and demography of DWV spread. We found that, rather than reemerging in western honey bees after varroa switched hosts, as suggested by previous work, DWV-A most likely originated in East Asia and spread in the mid-20th century. It also showed a massive population size expansion following the varroa host switch. By contrast, DWV-B was most likely acquired more recently from a source outside East Asia and appears absent from the original varroa host. These results highlight the dynamic nature of viral adaptation, whereby a vector's host switch can give rise to competing and increasingly virulent disease pandemics. The evolutionary novelty and rapid global spread of these host-virus interactions, together with observed spillover into other species, illustrate how increasing globalization poses urgent threats to biodiversity and food security.
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Affiliation(s)
- Nonno Hasegawa
- Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Maeva A Techer
- Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
- Department of Entomology, Texas A&M University, College Station, TX 77483
- Behavioral Plasticity Research Institute, NSF-BII, College Station, TX 77483
| | - Noureddine Adjlane
- Department of Agronomy, Faculty of Science, University M'hamed Bougara, Boumerdes 35000, Algeria
| | | | - Karina Antúnez
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, 11600 Montevideo, Uruguay
| | - Alexis Beaurepaire
- Swiss Bee Research Center, Agroscope, 3003 Bern, Switzerland
- Institute of Bee Health, University of Bern, 3003 Bern, Switzerland
| | - Krisztina Christmon
- United States Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705
| | - Helene Delatte
- Centre de coopération internationale en recherche agronomique pour le développement, UMR Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, F-97410 Saint-Pierre, La Réunion, France
| | - Usman H Dukku
- Department of Biological Sciences, Abubakar Tafawa Balewa University, Bauchi 740211, Nigeria
| | - Nurit Eliash
- Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
- Shamir Research Institute, Haifa University, Haifa 3498838, Israel
| | - Mogbel A A El-Niweiri
- Department of Bee Research, Environment, Natural Resources and Desertification Research Institute, National Centre for Research, Khartoum, Sudan
| | - Olivier Esnault
- Groupement de Défense Sanitaire, Réunion, La plaine des Cafres 97418, La Réunion, France
| | - Jay D Evans
- United States Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705
| | - Nizar J Haddad
- Bee Research Department, National Agricultural Research Center, 19381 Baqa', Jordan
| | - Barbara Locke
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Irene Muñoz
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - Grégoire Noël
- Functional and Evolutionary Entomology, TERRA, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Delphine Panziera
- Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Pilar De la Rúa
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - Mohamed A Shebl
- Department of Plant Protection, Faculty of Agriculture, Suez Canal University, 41522 Ismailia, Egypt
| | - Zoran Stanimirovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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4
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Chapman NC, Colin T, Cook J, da Silva CRB, Gloag R, Hogendoorn K, Howard SR, Remnant EJ, Roberts JMK, Tierney SM, Wilson RS, Mikheyev AS. The final frontier: ecological and evolutionary dynamics of a global parasite invasion. Biol Lett 2023; 19:20220589. [PMID: 37222245 PMCID: PMC10207324 DOI: 10.1098/rsbl.2022.0589] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Studying rapid biological changes accompanying the introduction of alien organisms into native ecosystems can provide insights into fundamental ecological and evolutionary theory. While powerful, this quasi-experimental approach is difficult to implement because the timing of invasions and their consequences are hard to predict, meaning that baseline pre-invasion data are often missing. Exceptionally, the eventual arrival of Varroa destructor (hereafter Varroa) in Australia has been predicted for decades. Varroa is a major driver of honeybee declines worldwide, particularly as vectors of diverse RNA viruses. The detection of Varroa in 2022 at over a hundred sites poses a risk of further spread across the continent. At the same time, careful study of Varroa's spread, if it does become established, can provide a wealth of information that can fill knowledge gaps about its effects worldwide. This includes how Varroa affects honeybee populations and pollination. Even more generally, Varroa invasion can serve as a model for evolution, virology and ecological interactions between the parasite, the host and other organisms.
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Affiliation(s)
- Nadine C. Chapman
- School of Life and Environmental Sciences, Behaviour, Ecology and Evolution Lab, The University of Sydney, NSW 2006, Australia
| | - Théotime Colin
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - James Cook
- Hawkesbury Institute for the Environment, Western Sydney University, NSW 2753, Australia
| | - Carmen R. B. da Silva
- School of Biological Sciences, Faculty of Science, Monash University, Clayton Victoria 3800, Australia
| | - Ros Gloag
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Katja Hogendoorn
- School of Agriculture, The University of Adelaide, Food and Wine, Adelaide SA 5005, Australia
| | - Scarlett R. Howard
- Hawkesbury Institute for the Environment, Western Sydney University, NSW 2753, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, Behaviour, Ecology and Evolution Lab, The University of Sydney, NSW 2006, Australia
| | - John M. K. Roberts
- Commonwealth Scientific & Industrial Research Organisation, Canberra 2601, ACT, Australia
| | - Simon M. Tierney
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, USA
| | - Rachele S. Wilson
- School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander S. Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT 26000, Australia
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5
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Abstract
BACKGROUND Vector-borne viral diseases threaten human and wildlife worldwide. Vectors are often viewed as a passive syringe injecting the virus. However, to survive, replicate and spread, viruses must manipulate vector biology. While most vector-borne viral research focuses on vectors transmitting a single virus, in reality, vectors often carry diverse viruses. Yet how viruses affect the vectors remains poorly understood. Here, we focused on the varroa mite (Varroa destructor), an emergent parasite that can carry over 20 honey bee viruses, and has been responsible for colony collapses worldwide, as well as changes in global viral populations. Co-evolution of the varroa and the viral community makes it possible to investigate whether viruses affect vector gene expression and whether these interactions affect viral epidemiology. RESULTS Using a large set of available varroa transcriptomes, we identified how abundances of individual viruses affect the vector's transcriptional network. We found no evidence of competition between viruses, but rather that some virus abundances are positively correlated. Furthermore, viruses that are found together interact with the vector's gene co-expression modules in similar ways, suggesting that interactions with the vector affect viral epidemiology. We experimentally validated this observation by silencing candidate genes using RNAi and found that the reduction in varroa gene expression was accompanied by a change in viral load. CONCLUSIONS Combined, the meta-transcriptomic analysis and experimental results shed light on the mechanism by which viruses interact with each other and with their vector to shape the disease course.
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Affiliation(s)
- Nurit Eliash
- grid.18098.380000 0004 1937 0562Shamir Research Institute, University of Haifa, Katzrin, Israel ,grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Okinawa, 904-0495 Japan
| | - Miyuki Suenaga
- grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Okinawa, 904-0495 Japan
| | - Alexander S. Mikheyev
- grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Okinawa, 904-0495 Japan ,grid.1001.00000 0001 2180 7477Australian National University, Canberra, ACT, 2600 Australia
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6
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Kowallik V, Das A, Mikheyev AS. Experimental inheritance of antibiotic acquired dysbiosis affects host phenotypes across generations. Front Microbiol 2022; 13:1030771. [PMID: 36532456 PMCID: PMC9751584 DOI: 10.3389/fmicb.2022.1030771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/24/2022] [Indexed: 04/12/2024] Open
Abstract
Microbiomes can enhance the health, fitness and even evolutionary potential of their hosts. Many organisms propagate favorable microbiomes fully or partially via vertical transmission. In the long term, such co-propagation can lead to the evolution of specialized microbiomes and functional interdependencies with the host. However, microbiomes are vulnerable to environmental stressors, particularly anthropogenic disturbance such as antibiotics, resulting in dysbiosis. In cases where microbiome transmission occurs, a disrupted microbiome may then become a contagious pathology causing harm to the host across generations. We tested this hypothesis using the specialized socially transmitted gut microbiome of honey bees as a model system. By experimentally passaging tetracycline-treated microbiomes across worker 'generations' we found that an environmentally acquired dysbiotic phenotype is heritable. As expected, the antibiotic treatment disrupted the microbiome, eliminating several common and functionally important taxa and strains. When transmitted, the dysbiotic microbiome harmed the host in subsequent generations. Particularly, naïve bees receiving antibiotic-altered microbiomes died at higher rates when challenged with further antibiotic stress. Bees with inherited dysbiotic microbiomes showed alterations in gene expression linked to metabolism and immunity, among other pathways, suggesting effects on host physiology. These results indicate that there is a possibility that sublethal exposure to chemical stressors, such as antibiotics, may cause long-lasting changes to functional host-microbiome relationships, possibly weakening the host's progeny in the face of future ecological challenges. Future studies under natural conditions would be important to examine the extent to which negative microbiome-mediated phenotypes could indeed be heritable and what role this may play in the ongoing loss of biodiversity.
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Affiliation(s)
- Vienna Kowallik
- Okinawa Institute of Science and Technology, Tancha Onna-son, Okinawa, Japan
| | - Ashutosh Das
- Australian National University, Canberra, ACT, Australia
- Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Alexander S. Mikheyev
- Okinawa Institute of Science and Technology, Tancha Onna-son, Okinawa, Japan
- Australian National University, Canberra, ACT, Australia
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7
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Forni G, Mikheyev AS, Luchetti A, Mantovani B. Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis. Zoological Lett 2022; 8:14. [PMID: 36435814 PMCID: PMC9701443 DOI: 10.1186/s40851-022-00197-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of reproductive novelties. Here we identify gonads-biased genes in two Bacillus automictic stick-insects and compare their expression profile and sequence evolution with a bisexual congeneric species. The two parthenogens restore ploidy through different cytological mechanisms: in Bacillus atticus, nuclei derived from the first meiotic division fuse to restore a diploid egg nucleus, while in Bacillus rossius, diploidization occurs in some cells of the haploid blastula through anaphase restitution. Parthenogens' gonads transcriptional program is found to be largely assembled from genes that were already present before the establishment of automixis. The three species transcriptional profiles largely reflect their phyletic relationships, yet we identify a shared core of genes with gonad-biased patterns of expression in parthenogens which are either male gonads-biased in the sexual species or are not differentially expressed there. At the sequence level, just a handful of gonads-biased genes were inferred to have undergone instances of positive selection exclusively in the parthenogen species. This work is the first to explore the molecular underpinnings of automixis in a comparative framework: it delineates how reproductive novelties can be sustained by genes whose origin precedes the establishment of the novelty itself and shows that different meiotic mechanisms of reproduction can be associated with a shared molecular ground plan.
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Affiliation(s)
- Giobbe Forni
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
- Dip. Scienze Agrarie e Ambientali, University of Milano, Milano, Italy
| | - Alexander S Mikheyev
- Australian National University, ACT, Canberra, 2600, Australia
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Andrea Luchetti
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy.
| | - Barbara Mantovani
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
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8
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Tong C, Avilés L, Rayor LS, Mikheyev AS, Linksvayer TA. Genomic signatures of recent convergent transitions to social life in spiders. Nat Commun 2022; 13:6967. [PMID: 36414623 PMCID: PMC9681848 DOI: 10.1038/s41467-022-34446-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Leticia Avilés
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Linda S Rayor
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander S Mikheyev
- Evolutionary Genomics Group, Research School of Biology, Australian National University, Canberra, 0200, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
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9
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Tunstrom K, Wheat CW, Parmesan C, Singer MC, Mikheyev AS. A genome for Edith's checkerspot butterfly: an insect with complex host-adaptive suites and rapid evolutionary responses to environmental changes. Genome Biol Evol 2022; 14:6649524. [PMID: 35876165 PMCID: PMC9348621 DOI: 10.1093/gbe/evac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 11/15/2022] Open
Abstract
Insects have been key players in the assessments of biodiversity impacts of anthropogenically driven environmental change, including the evolutionary and ecological impacts of climate change. Populations of Edith’s Checkerspot Butterfly (Euphydryas editha) adapt rapidly to diverse environmental conditions, with numerous high-impact studies documenting these dynamics over several decades. However, studies of the underlying genetic bases of these responses have been hampered by missing genomic resources, limiting the ability to connect genomic responses to environmental change. Using a combination of Oxford Nanopore long reads, haplotype merging, HiC scaffolding followed by Illumina polishing, we generated a highly contiguous and complete assembly (contigs n = 142, N50 = 21.2 Mb, total length = 607.8 Mb; BUSCOs n = 5,286, single copy complete = 97.8%, duplicated = 0.9%, fragmented = 0.3%, missing = 1.0%). A total of 98% of the assembled genome was placed into 31 chromosomes, which displayed large-scale synteny with other well-characterized lepidopteran genomes. The E. editha genome, annotation, and functional descriptions now fill a missing gap for one of the leading field-based ecological model systems in North America.
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Affiliation(s)
- Kalle Tunstrom
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Camille Parmesan
- Station d'Écologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200 Moulis, France.,Biological and Marine Sciences, University of Plymouth, Plymouth, U.K.,Department of Geological Sciences, University of Texas at Austin, U.S.A
| | - Michael C Singer
- Station d'Écologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200 Moulis, France.,Biological and Marine Sciences, University of Plymouth, Plymouth, U.K
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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10
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Techer MA, Roberts JMK, Cartwright RA, Mikheyev AS. The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range. Mol Ecol 2022; 31:1358-1374. [PMID: 34882860 PMCID: PMC11105409 DOI: 10.1111/mec.16322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022]
Abstract
Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real-time, and their demographic parameters remain poorly understood. As a result, fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored how host switches occur in independent host shifts by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni). Both switched to the western honey bee (Apis mellifera) after being brought into contact with their ancestral host (Apis cerana), ~70 and ~12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 63 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found multiple previously undiscovered mitochondrial lineages on the novel host, along with the genetic equivalent of tens of individuals that were involved in the initial host switch. Despite being greatly reduced, some gene flow remains between mites adapted to different hosts. Our findings suggest that while reproductive isolation may facilitate the fixation of traits beneficial for exploiting the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.
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Affiliation(s)
- Maeva A Techer
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - John M K Roberts
- Commonwealth Scientific & Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, Japan
- Australian National University, Canberra, Australian Capital Territory, Australia
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11
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Diaz Arenas C, Ardaševa A, Miller J, Mikheyev AS, Yokobayashi Y. Ribozyme Mutagenic Evolution: Mechanisms of Survival. ORIGINS LIFE EVOL B 2022; 51:321-339. [PMID: 34994918 DOI: 10.1007/s11084-021-09617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
Primeval populations replicating at high error rates required a mechanism to overcome the accumulation of mutations and information deterioration. Known strategies to overcome mutation pressures include RNA processivity, epistasis, selection, and quasispecies. We investigated the mechanism by which small molecular ribozyme populations can survive under high error rates by propagating several lineages under different mutagen concentrations. We found that every population that evolved without mutagen went extinct, while those subjected to mutagenic evolution survived. To understand how they survived, we characterized the evolved genotypic diversity, the formation of genotype-genotype interaction networks, the fitness of the most common mutants for each enzymatic step, and changes in population size along the course of evolution. We found that the elevated mutation rate was necessary for the populations to survive in the novel environment, in which all the steps of the metabolism worked to promote the survival of even less catalytically efficient ligases. Besides, an increase in population size and the mutational coupling of genotypes in close-knit networks, which helped maintain or recover lost genotypes making their disappearance transient, prevented Muller's ratchet and extinction.
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Affiliation(s)
- Carolina Diaz Arenas
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan. .,Yale University, New Haven, CT, USA.
| | - Aleksandra Ardaševa
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Jonathan Miller
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan.,Evolutionary Genomics Lab, Research School of Biology, Australian National University, Canberra, Australia
| | - Yohei Yokobayashi
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan
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12
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Barua A, Koludarov I, Mikheyev AS. Co-option of the same ancestral gene family gave rise to mammalian and reptilian toxins. BMC Biol 2021; 19:268. [PMID: 34949191 PMCID: PMC8705180 DOI: 10.1186/s12915-021-01191-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2021] [Indexed: 12/03/2022] Open
Abstract
Background Evolution can occur with surprising predictability when organisms face similar ecological challenges. For most traits, it is difficult to ascertain whether this occurs due to constraints imposed by the number of possible phenotypic solutions or because of parallel responses by shared genetic and regulatory architecture. Exceptionally, oral venoms are a tractable model of trait evolution, being largely composed of proteinaceous toxins that have evolved in many tetrapods, ranging from reptiles to mammals. Given the diversity of venomous lineages, they are believed to have evolved convergently, even though biochemically similar toxins occur in all taxa. Results Here, we investigate whether ancestral genes harbouring similar biochemical activity may have primed venom evolution, focusing on the origins of kallikrein-like serine proteases that form the core of most vertebrate oral venoms. Using syntenic relationships between genes flanking known toxins, we traced the origin of kallikreins to a single locus containing one or more nearby paralogous kallikrein-like clusters. Additionally, phylogenetic analysis of vertebrate serine proteases revealed that kallikrein-like toxins in mammals and reptiles are genetically distinct from non-toxin ones. Conclusions Given the shared regulatory and genetic machinery, these findings suggest that tetrapod venoms evolved by co-option of proteins that were likely already present in saliva. We term such genes ‘toxipotent’—in the case of salivary kallikreins they already had potent vasodilatory activity that was weaponized by venomous lineages. Furthermore, the ubiquitous distribution of kallikreins across vertebrates suggests that the evolution of envenomation may be more common than previously recognized, blurring the line between venomous and non-venomous animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01191-1.
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Affiliation(s)
- Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Ivan Koludarov
- Animal Venomics Group, Justus Leibig University, Giessen, Germany
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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13
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Cicconardi F, Krapf P, D'Annessa I, Gamisch A, Wagner HC, Nguyen AD, Economo EP, Mikheyev AS, Guénard B, Grabherr R, Andesner P, Wolfgang A, Di Marino D, Steiner FM, Schlick-Steiner BC. Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations. Mol Biol Evol 2021; 37:2211-2227. [PMID: 32181804 PMCID: PMC7403626 DOI: 10.1093/molbev/msaa076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesized two parallel patterns would occur in a genome adapting to an extreme habitat: 1) strong positive selection on genes related to adaptation and 2) a relaxation of previous purifying selection. We tested this hypothesis by sequencing the high-elevation specialist Tetramorium alpestre and four other phylogenetically related species. In support of our hypothesis, we recorded a strong shift of selective forces in T. alpestre, in particular a stronger magnitude of diversifying and relaxed selection when compared with all other ants. We further disentangled candidate molecular adaptations in both gene expression and protein-coding sequence that were identified by our genome-wide analyses. In particular, we demonstrate that T. alpestre has 1) a higher level of expression for stv and other heat-shock proteins in chill-shock tests and 2) enzymatic enhancement of Hex-T1, a rate-limiting regulatory enzyme that controls the entry of glucose into the glycolytic pathway. Together, our analyses highlight the adaptive molecular changes that support colonization of high-altitude environments.
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Affiliation(s)
| | - Patrick Krapf
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Ilda D'Annessa
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", CNR (SCITEC-CNR), Milan, Italy
| | - Alexander Gamisch
- Department of Ecology, University of Innsbruck, Innsbruck, Austria.,Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Herbert C Wagner
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andrew D Nguyen
- Department of Entomology and Nematology, University of Florida, Gainesville, FL
| | - Evan P Economo
- Biodiversity & Biocomplexity Unit, Okinawa Institute of Science & Technology, Onna, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science & Technology, Onna, Japan
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Reingard Grabherr
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Philipp Andesner
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Daniele Di Marino
- Department of Life and Environmental Sciences - New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
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14
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Abstract
From cells in tissue, to bird flocks, to human crowds, living systems display a stunning variety of collective behaviors. Yet quantifying such phenomena first requires tracking a significant fraction of the group members in natural conditions, a substantial and ongoing challenge. We present a comprehensive, computational method for tracking an entire colony of the honey bee Apis mellifera using high-resolution video on a natural honeycomb background. We adapt a convolutional neural network (CNN) segmentation architecture to automatically identify bee and brood cell positions, body orientations and within-cell states. We achieve high accuracy (~10% body width error in position, ~10° error in orientation, and true positive rate > 90%) and demonstrate months-long monitoring of sociometric colony fluctuations. These fluctuations include ~24 h cycles in the counted detections, negative correlation between bee and brood, and nightly enhancement of bees inside comb cells. We combine detected positions with visual features of organism-centered images to track individuals over time and through challenging occluding events, recovering ~79% of bee trajectories from five observation hives over 5 min timespans. The trajectories reveal important individual behaviors, including waggle dances and crawling inside comb cells. Our results provide opportunities for the quantitative study of collective bee behavior and for advancing tracking techniques of crowded systems.
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Affiliation(s)
- Katarzyna Bozek
- Biological Physics Theory Unit, OIST Graduate University, Okinawa, Japan.
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| | - Laetitia Hebert
- Biological Physics Theory Unit, OIST Graduate University, Okinawa, Japan
| | - Yoann Portugal
- Biological Physics Theory Unit, OIST Graduate University, Okinawa, Japan
- Ecology and Evolution Unit, OIST Graduate University, Okinawa, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, OIST Graduate University, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australia
| | - Greg J Stephens
- Biological Physics Theory Unit, OIST Graduate University, Okinawa, Japan
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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15
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Booher DB, Gibson JC, Liu C, Longino JT, Fisher BL, Janda M, Narula N, Toulkeridou E, Mikheyev AS, Suarez AV, Economo EP. Functional innovation promotes diversification of form in the evolution of an ultrafast trap-jaw mechanism in ants. PLoS Biol 2021; 19:e3001031. [PMID: 33651798 PMCID: PMC7924744 DOI: 10.1371/journal.pbio.3001031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/28/2021] [Indexed: 12/16/2022] Open
Abstract
Evolutionary innovations underlie the rise of diversity and complexity-the 2 long-term trends in the history of life. How does natural selection redesign multiple interacting parts to achieve a new emergent function? We investigated the evolution of a biomechanical innovation, the latch-spring mechanism of trap-jaw ants, to address 2 outstanding evolutionary problems: how form and function change in a system during the evolution of new complex traits, and whether such innovations and the diversity they beget are repeatable in time and space. Using a new phylogenetic reconstruction of 470 species, and X-ray microtomography and high-speed videography of representative taxa, we found the trap-jaw mechanism evolved independently 7 to 10 times in a single ant genus (Strumigenys), resulting in the repeated evolution of diverse forms on different continents. The trap mechanism facilitates a 6 to 7 order of magnitude greater mandible acceleration relative to simpler ancestors, currently the fastest recorded acceleration of a resettable animal movement. We found that most morphological diversification occurred after evolution of latch-spring mechanisms, which evolved via minor realignments of mouthpart structures. This finding, whereby incremental changes in form lead to a change of function, followed by large morphological reorganization around the new function, provides a model for understanding the evolution of complex biomechanical traits, as well as insights into why such innovations often happen repeatedly.
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Affiliation(s)
- Douglas B. Booher
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
- Department of Ecology and Evolution, University of California-Los Angeles, Los Angeles, California, United States of America
- Field Museum of Natural History, Chicago, Illinois, United States of America
- Georgia Museum of Natural History, Athens, Georgia, United States of America
- Beckman Institute for Advanced Science and Technology, Department of Entomology, and Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, United States of America
| | - Joshua C. Gibson
- Beckman Institute for Advanced Science and Technology, Department of Entomology, and Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, United States of America
| | - Cong Liu
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - John T. Longino
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Brian L. Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, California, United States of America
| | - Milan Janda
- National Laboratory for Ecological Analysis and Synthesis (LANASE), ENES, UNAM, Morelia, Mexico
- Biology Centre of Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Nitish Narula
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Evropi Toulkeridou
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
- Evolutionary Genomics Research group, Australian National University, Canberra, Australia
| | - Andrew V. Suarez
- Beckman Institute for Advanced Science and Technology, Department of Entomology, and Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, United States of America
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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16
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Cotoras DD, Suenaga M, Mikheyev AS. Intraspecific niche partition without speciation: individual level web polymorphism within a single island spider population. Proc Biol Sci 2021; 288:20203138. [PMID: 33593195 PMCID: PMC7934906 DOI: 10.1098/rspb.2020.3138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Early in the process of adaptive radiation, allopatric disruption of gene flow followed by ecological specialization is key for speciation; but, do adaptive radiations occur on small islands without internal geographical barriers? Island populations sometimes harbour polymorphism in ecological specializations, but its significance remains unclear. On one hand, morphs may correspond to ‘cryptic’ species. Alternatively, they could result from population, developmental or behavioural plasticity. The spider Wendilgarda galapagensis (Araneae, Theridiosomatidae) is endemic to the small Isla del Coco and unique in spinning three different web types, each corresponding to a different microhabitat. We tested whether this variation is associated with ‘cryptic’ species or intraspecific behavioural plasticity. Despite analysing 36 803 loci across 142 individuals, we found no relationship between web type and population structure, which was only weakly geographically differentiated. The same pattern holds when looking within a sampling site or considering only Fst outliers. In line with genetic data, translocation experiments showed that web architecture is plastic within an individual. However, not all transitions between web types are equally probable, indicating the existence of individual preferences. Our data supports the idea that diversification on small islands might occur mainly at the behavioural level producing an intraspecific niche partition without speciation.
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Affiliation(s)
- Darko D Cotoras
- Entomology Department, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA.,Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Tancha 1919-1, Onna-son, Okinawa 904-0495 Japan
| | - Miyuki Suenaga
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Tancha 1919-1, Onna-son, Okinawa 904-0495 Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Tancha 1919-1, Onna-son, Okinawa 904-0495 Japan.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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17
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Hasegawa N, Techer M, Mikheyev AS. A toolkit for studying Varroa genomics and transcriptomics: preservation, extraction, and sequencing library preparation. BMC Genomics 2021; 22:54. [PMID: 33446105 PMCID: PMC7809802 DOI: 10.1186/s12864-020-07363-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/30/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The honey bee parasite, Varroa destructor, is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act as the proximal cause of colony collapses. Nevertheless, until recently, studies of Varroa have been limited by the paucity of genomic tools. Lab- and field-based methods exploiting such methods are still nascent. This study developed a set of methods for preserving Varroa DNA and RNA from the field to the lab and processing them into sequencing libraries. We performed preservation experiments in which Varroa mites were immersed in TRIzol, RNAlater, and absolute ethanol for preservation periods up to 21 days post-treatment to assess DNA and RNA integrity. RESULTS For both DNA and RNA, mites preserved in TRIzol and RNAlater at room temperature degraded within 10 days post-treatment. Mites preserved in ethanol at room temperature and 4 °C remained intact through 21 days. Varroa mite DNA and RNA libraries were created and sequenced for ethanol preserved samples, 15 and 21 days post-treatment. All DNA sequences mapped to the V. destructor genome at above 95% on average, while RNA sequences mapped to V. destructor, but also sometimes to high levels of the deformed-wing virus and to various organisms. CONCLUSIONS Ethanolic preservation of field-collected mites is inexpensive and simple, and allows them to be shipped and processed successfully in the lab for a wide variety of sequencing applications. It appears to preserve RNA from both Varroa and at least some of the viruses it vectors.
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Affiliation(s)
- Nonno Hasegawa
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan.
| | - Maeva Techer
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan.
- Australian National University, 2600, Canberra, ACT, Australia.
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18
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Wepfer PH, Nakajima Y, Sutthacheep M, Radice VZ, Richards Z, Ang P, Terraneo T, Sudek M, Fujimura A, Toonen RJ, Mikheyev AS, Economo EP, Mitarai S. Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Mol Phylogenet Evol 2020; 151:106905. [DOI: 10.1016/j.ympev.2020.106905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
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19
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Fischer G, Friedman NR, Huang JP, Narula N, Knowles LL, Fisher BL, Mikheyev AS, Economo EP. Socially Parasitic Ants Evolve a Mosaic of Host-Matching and Parasitic Morphological Traits. Curr Biol 2020; 30:3639-3646.e4. [DOI: 10.1016/j.cub.2020.06.078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 03/18/2020] [Accepted: 06/23/2020] [Indexed: 11/27/2022]
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20
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Arora J, Mars Brisbin MA, Mikheyev AS. Effects of microbial evolution dominate those of experimental host-mediated indirect selection. PeerJ 2020; 8:e9350. [PMID: 32676220 PMCID: PMC7334978 DOI: 10.7717/peerj.9350] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/23/2020] [Indexed: 12/31/2022] Open
Abstract
Microbes ubiquitously inhabit animals and plants, often affecting their host's phenotype. As a result, even in a constant genetic background, the host's phenotype may evolve through indirect selection on the microbiome. 'Microbiome engineering' offers a promising novel approach for attaining desired host traits but has been attempted only a few times. Building on the known role of the microbiome on development in fruit flies, we attempted to evolve earlier-eclosing flies by selecting on microbes in the growth media. We carried out parallel evolution experiments in no- and high-sugar diets by transferring media associated with fast-developing fly lines over the course of four selection cycles. In each cycle, we used sterile eggs from the same inbred population, and assayed mean fly eclosion times. Ultimately, flies eclosed seven to twelve hours earlier, depending on the diet, but microbiome engineering had no effect relative to a random-selection control treatment. 16S rRNA gene sequencing showed that the microbiome did evolve, particularly in the no sugar diet, with an increase in Shannon diversity over time. Thus, while microbiome evolution did affect host eclosion times, these effects were incidental. Instead, any experimentally enforced selection effects were swamped by uncontrolled microbial evolution, likely resulting in its adaptation to the media. These results imply that selection on host phenotypes must be strong enough to overcome other selection pressures simultaneously operating on the microbiome. The independent evolutionary trajectories of the host and the microbiome may limit the extent to which indirect selection on the microbiome can ultimately affect host phenotype. Random-selection lines accounting for independent microbial evolution are essential for experimental microbiome engineering studies.
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Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | | | - Alexander S. Mikheyev
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- Research School of Biology, Australian National University, Acton, ACT, Australia
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21
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Liu C, Sarnat EM, Friedman NR, Hita Garcia F, Darwell C, Booher D, Kubota Y, Mikheyev AS, Economo EP. Colonize, radiate, decline: Unraveling the dynamics of island community assembly with Fijian trap-jaw ants. Evolution 2020; 74:1082-1097. [PMID: 32342495 PMCID: PMC7384189 DOI: 10.1111/evo.13983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 04/09/2020] [Indexed: 01/17/2023]
Abstract
The study of island community assembly has been fertile ground for developing and testing theoretical ideas in ecology and evolution. The ecoevolutionary trajectory of lineages after colonization has been a particular interest, as this is a key component of understanding community assembly. In this system, existing ideas, such as the taxon cycle, posit that lineages pass through a regular sequence of ecoevolutionary changes after colonization, with lineages shifting toward reduced dispersal ability, increased ecological specialization, and declines in abundance. However, these predictions have historically been difficult to test. Here, we integrate phylogenomics, population genomics, and X-ray microtomography/3D morphometrics, to test hypotheses for whether the ecomorphological diversity of trap-jaw ants (Strumigenys) in the Fijian archipelago is assembled primarily through colonization or postcolonization radiation, and whether species show ecological shifts toward niche specialization, toward upland habitats, and decline in abundance after colonization. We infer that most Fijian endemic Strumigenys evolved in situ from a single colonization and have diversified to fill a large fraction of global morphospace occupied by the genus. Within this adaptive radiation, lineages trend to different degrees toward high elevation, reduced dispersal ability, and demographic decline, and we find no evidence of repeated colonization that displaces the initial radiation. Overall these results are only partially consistent with taxon cycle and associated ideas, while highlighting the potential role of priority effects in assembling island communities.
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Affiliation(s)
- Cong Liu
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
| | - Eli M. Sarnat
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
- Antwork Consulting LLCDavisCalifornia95616
| | - Nicholas R. Friedman
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
| | - Francisco Hita Garcia
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
| | - Clive Darwell
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
| | - Douglas Booher
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
- Field Museum of Natural HistoryChicagoIllinois60605
- Department of entomologyUniversity of IllinoisUrbanaIllinois61801
- Georgia Museum of Natural HistoryAthensGeorgia30602
| | - Yasuhiro Kubota
- Faculty of ScienceUniversity of the RyukyusNishiharaOkinawaJapan
| | - Alexander S. Mikheyev
- Ecology and Evolution UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
- Evolutionary Genomics Research GroupAustralian National UniversityCanberraAustralia
| | - Evan P. Economo
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate University, OnnaOkinawa904‐0495Japan
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22
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Barua A, Mikheyev AS. Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates. Proc Biol Sci 2020; 287:20200613. [PMID: 32345154 PMCID: PMC7282918 DOI: 10.1098/rspb.2020.0613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Key innovations provide ecological opportunity by enabling access to new resources, colonization of new environments, and are associated with adaptive radiation. The most well-known pattern associated with adaptive radiation is an early burst of phenotypic diversification. Venoms facilitate prey capture and are widely believed to be key innovations leading to adaptive radiation. However, few studies have estimated their evolutionary rate dynamics. Here, we test for patterns of adaptive evolution in venom gene expression data from 52 venomous snake species. By identifying shifts in tempo and mode of evolution along with models of phenotypic evolution, we show that snake venom exhibits the macroevolutionary dynamics expected of key innovations. Namely, all toxin families undergo shifts in their rates of evolution, likely in response to changes in adaptive optima. Furthermore, we show that rapid-pulsed evolution modelled as a Lévy process better fits snake venom evolution than conventional early burst or Ornstein-Uhlenbeck models. While our results support the idea of snake venom being a key innovation, the innovation of venom chemistry lacks clear mechanisms that would lead to reproductive isolation and thus adaptive radiation. Therefore, the extent to which venom directly influences the diversification process is still a matter of contention.
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Affiliation(s)
- Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan
- Evolutionary genomics group, Australian National University, Canberra ACT 0200, Australia
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23
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Emborski C, Mikheyev AS. Ancestral diet transgenerationally influences offspring in a parent-of-origin and sex-specific manner. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180181. [PMID: 30966955 PMCID: PMC6365861 DOI: 10.1098/rstb.2018.0181] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parent-of-origin effects, whereby specific phenotypes are differentially inherited paternally or maternally, provide useful clues to better understand transgenerational effect transmission. Ancestral diet influences offspring phenotypes, including body composition and fitness. However, the specific role that mothers and fathers play in the transmission of altered phenotypes to male and female offspring remains unclear. We investigated the influence of the parent-of-origin's diet on adult progeny phenotypes and reproductive output for three generations in fruit flies (Drosophila melanogaster). Males and females reared on a control diet were exposed to the control diet or one of two altered (no- or high-) sugar treatment diets for a single generation. Flies from one of the two altered diet treatments were then mated to control flies in a full-factorial design to produce F1 offspring and kept on control media for each following generation. We found parent-of-origin (triglyceride) and non-parent-of-origin (sugar) body composition effects, which were transgenerational and sex-specific. Additionally, we observed a negative correlation between intergenerational maternal reproductive output and triglyceride levels, suggesting that ancestral diet may affect fitness. This work demonstrates that ancestral diet can transmit altered phenotypes in a parent-of-origin and sex-specific manner and highlights that mechanisms regulating such transmission have been greatly overlooked. This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
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Affiliation(s)
- Carmen Emborski
- 1 The Institute of Environmental and Human Health, Texas Tech University , Lubbock, TX 79416 , USA.,2 Okinawa Institute of Science and Technology , 1919-1 Tancha, Onna, Kunigami District, Okinawa Prefecture 904-0495 , Japan
| | - Alexander S Mikheyev
- 2 Okinawa Institute of Science and Technology , 1919-1 Tancha, Onna, Kunigami District, Okinawa Prefecture 904-0495 , Japan.,3 Research School of Biology, Australia National University , 134 Linnaeus Way, Acton, Australian Capital Territory 2601 , Australia
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24
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Abstract
Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantified and mapped to a distinct genomic locus and traced for millions of years. Using a phylogenetic generalized linear mixed model, we analyzed expression data of toxin genes from 52 snake species spanning the 3 venomous snake families and estimated phylogenetic covariance, which acts as a measure of evolutionary constraint. We find that evolution of toxin combinations is not constrained. However, although all combinations are in principle possible, the actual dimensionality of phylomorphic space is low, with envenomation strategies focused around only four major toxin families: metalloproteases, three-finger toxins, serine proteases, and phospholipases A2. Although most extant snakes prioritize either a single or a combination of major toxin families, they are repeatedly recruited and lost. We find that over macroevolutionary timescales, the venom phenotypes were not shaped by phylogenetic constraints, which include important microevolutionary constraints such as epistasis and pleiotropy, but more likely by ecological filtering that permits a small number of optimal solutions. As a result, phenotypic optima were repeatedly attained by distantly related species. These results indicate that venoms evolve by selection on biochemistry of prey envenomation, which permit diversity through parallelism, and impose strong limits, since only a few of the theoretically possible strategies seem to work well and are observed in extant snakes.
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Affiliation(s)
- Agneesh Barua
- Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University, Onna, Japan.,Evolutionary Genomics Research Group, Ecology and Evolution Unit, Australian National University, Canberra, Australia
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25
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Darwell CT, Fischer G, Sarnat EM, Friedman NR, Liu C, Baiao G, Mikheyev AS, Economo EP. Genomic and phenomic analysis of island ant community assembly. Mol Ecol 2020; 29:1611-1627. [PMID: 31820838 DOI: 10.1111/mec.15326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 01/25/2023]
Abstract
Island biodiversity has long fascinated biologists as it typically presents tractable systems for unpicking the eco-evolutionary processes driving community assembly. In general, two recurring themes are of central theoretical interest. First, immigration, diversification, and extinction typically depend on island geographical properties (e.g., area, isolation, and age). Second, predictable ecological and evolutionary trajectories readily occur after colonization, such as the evolution of adaptive trait syndromes, trends toward specialization, adaptive radiation, and eventual ecological decline. Hypotheses such as the taxon cycle draw on several of these themes to posit particular constraints on colonization and subsequent eco-evolutionary dynamics. However, it has been challenging to examine these integrated dynamics with traditional methods. Here, we combine phylogenomics, population genomics and phenomics, to unravel community assembly dynamics among Pheidole (Hymenoptera, Formicidae) ants in the isolated Fijian archipelago. We uphold basic island biogeographic predictions that isolated islands accumulate diversity primarily through in situ evolution rather than dispersal, and population genomic support for taxon cycle predictions that endemic species have decreased dispersal ability and demography relative to regionally widespread taxa. However, rather than trending toward island syndromes, ecomorphological diversification in Fiji was intense, filling much of the genus-level global morphospace. Furthermore, while most endemic species exhibit demographic decline and reduced dispersal, we show that the archipelago is not an evolutionary dead-end. Rather, several endemic species show signatures of population and range expansion, including a successful colonization to the Cook islands. These results shed light on the processes shaping island biotas and refine our understanding of island biogeographic theory.
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Affiliation(s)
- Clive T Darwell
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Georg Fischer
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Eli M Sarnat
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Nicholas R Friedman
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Cong Liu
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Guilherme Baiao
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Research School of Biology, Evolutionary Genomics Research Group, Australian National University, Acton, ACT, Australia
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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26
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Pessoa ADM, Nunes R, de Campos Telles MP, Nishitsuji K, Hisata K, Aird SD, Mikheyev AS, da Silva NJ. The complete mitochondrial genome of the aquatic coralsnake Micrurus surinamensis (Reptilia, Serpentes, Elapidae). Mitochondrial DNA B Resour 2019; 5:233-235. [PMID: 33366501 PMCID: PMC7748874 DOI: 10.1080/23802359.2019.1699460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 11/23/2019] [Indexed: 11/01/2022] Open
Abstract
In this study, we report the first complete mitochondrial genome sequence of the Aquatic Coralsnake Micrurus surinamensis. The mitochondrial genome lengthis 17,375 bp, comprising 13 protein-coding genes, 2 rRNA (12S and 16S) and 22 tRNA, as well as two typical control regions. Phylogenetic analysis based upon 13 protein-coding genes showed clusters based on terrestrial and marine species.
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Affiliation(s)
- Anita de Moura Pessoa
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade Federal de Goiás, Goiânia, Brasil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brasil
| | - Mariana Pires de Campos Telles
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade Federal de Goiás, Goiânia, Brasil
- Laboratório de Genética & Biodiversidade, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brasil
- Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Goiânia, Brasil
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa-ken, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa-ken, Japan
| | - Steven D. Aird
- Division of Faculty Affairs, Okinawa Institute of Science and Technology Graduate University, Okinawa-ken, Japan
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa-ken, Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa-ken, Japan
| | - Nelson Jorge da Silva
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade Federal de Goiás, Goiânia, Brasil
- Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Goiânia, Brasil
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Escola de Ciências Médicas, Biomédica e Farmacêuticas, Pontifícia Universidade Católica de Goiás, Goiânia, Brasil
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27
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Techer MA, Rane RV, Grau ML, Roberts JMK, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS. Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites. Commun Biol 2019; 2:357. [PMID: 31583288 PMCID: PMC6773775 DOI: 10.1038/s42003-019-0606-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/10/2019] [Indexed: 01/28/2023] Open
Abstract
Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species Varroa destructor and Varroa jacobsoni. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.
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Affiliation(s)
- Maeva A. Techer
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
| | - Rahul V. Rane
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601 Australia
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, VIC 3010 Australia
| | - Miguel L. Grau
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
| | - John M. K. Roberts
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601 Australia
| | | | | | | | | | - Alexander S. Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
- Australian National University, Canberra, ACT 2600 Australia
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28
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Jovanovic N, Mikheyev AS. Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO. Nucleic Acids Res 2019; 47:W266-W269. [PMID: 31114886 PMCID: PMC6602505 DOI: 10.1093/nar/gkz356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/11/2019] [Accepted: 05/13/2019] [Indexed: 11/29/2022] Open
Abstract
Traditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as species-specific information or time calibrations are often displayed in separate figures, making the entire picture difficult for readers to grasp. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, were created to overcome such challenges by allowing interactive displays of complex data sets. The new phylogeny.IO web server (https://phylogeny.io) overcomes this issue by allowing users to easily import, annotate, and share interactive phylogenetic trees. It allows a range of static (e.g. such as shapes and colors) and dynamic (e.g. pop-up text and images) annotations. Annotated trees can be saved on the server for subsequent modification or they may be shared as IFrame HTML objects, easily embeddable in any web page. The principal goal of phylogeny.IO is not to produce publication-ready figures, but rather to provide a simple and intuitive annotation interface that allows easy and rapid sharing of figures in blogs, lecture notes, press releases, etc.
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Affiliation(s)
- Nikola Jovanovic
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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29
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Warner MR, Qiu L, Holmes MJ, Mikheyev AS, Linksvayer TA. Convergent eusocial evolution is based on a shared reproductive groundplan plus lineage-specific plastic genes. Nat Commun 2019; 10:2651. [PMID: 31201311 PMCID: PMC6570765 DOI: 10.1038/s41467-019-10546-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Eusociality has convergently evolved multiple times, but the genomic basis of caste-based division of labor and degree to which independent origins of eusociality have utilized common genes remain largely unknown. Here we characterize caste-specific transcriptomic profiles across development and adult body segments from pharaoh ants (Monomorium pharaonis) and honey bees (Apis mellifera), representing two independent origins of eusociality. We identify a substantial shared core of genes upregulated in the abdomens of queen ants and honey bees that also tends to be upregulated in mated female flies, suggesting that these genes are part of a conserved insect reproductive groundplan. Outside of this shared groundplan, few genes are differentially expressed in common. Instead, the majority of the thousands of caste-associated genes are plastically expressed, rapidly evolving, and relatively evolutionarily young. These results emphasize that the recruitment of both highly conserved and lineage-specific genes underlie the convergent evolution of novel traits such as eusociality. Eusocial caste systems have evolved independently multiple times. Here, Warner et al. investigate the amount of shared vs. lineage-specific genes involved in the evolution of caste in pharaoh ants and honey bees by comparing transcriptomes across tissues, developmental stages, and castes.
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Affiliation(s)
| | - Lijun Qiu
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Michael J Holmes
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,School of Life and Environmental Science, University of Sydney, Sydney, 2006, Australia
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,Research School of Biology, Australian National University, Canberra, 0200, Australia
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30
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Smith CC, Weber JN, Mikheyev AS, Roces F, Bollazzi M, Kellner K, Seal JN, Mueller UG. Landscape genomics of an obligate mutualism: Concordant and discordant population structures between the leafcutter ant Atta texana and its two main fungal symbiont types. Mol Ecol 2019; 28:2831-2845. [PMID: 31141257 DOI: 10.1111/mec.15111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/10/2019] [Accepted: 03/11/2019] [Indexed: 12/22/2022]
Abstract
To explore landscape genomics at the range limit of an obligate mutualism, we use genotyping-by-sequencing (ddRADseq) to quantify population structure and the effect of host-symbiont interactions between the northernmost fungus-farming leafcutter ant Atta texana and its two main types of cultivated fungus. Genome-wide differentiation between ants associated with either of the two fungal types is of the same order of magnitude as differentiation associated with temperature and precipitation across the ant's entire range, suggesting that specific ant-fungus genome-genome combinations may have been favoured by selection. For the ant hosts, we found a broad cline of genetic structure across the range, and a reduction of genetic diversity along the axis of range expansion towards the range margin. This population-genetic structure was concordant between the ants and one cultivar type (M-fungi, concordant clines) but discordant for the other cultivar type (T-fungi). Discordance in population-genetic structures between ant hosts and a fungal symbiont is surprising because the ant farmers codisperse with their vertically transmitted fungal symbionts. Discordance implies that (a) the fungi disperse also through between-nest horizontal transfer or other unknown mechanisms, and (b) genetic drift and gene flow can differ in magnitude between each partner and between different ant-fungus combinations. Together, these findings imply that variation in the strength of drift and gene flow experienced by each mutualistic partner affects adaptation to environmental stress at the range margin, and genome-genome interactions between host and symbiont influence adaptive genetic differentiation of the host during range evolution in this obligate mutualism.
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Affiliation(s)
- Chad C Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas
| | - Jesse N Weber
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas.,Department of Biological Sciences, University of Alaska, Anchorage, Alaska
| | | | - Flavio Roces
- Department of Behavioral Physiology and Sociobiology, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Martin Bollazzi
- Section of Entomology, Universidad de la República, Montevideo, Uruguay
| | - Katrin Kellner
- Department of Biology, University of Texas at Tyler, Tyler, Texas
| | - Jon N Seal
- Department of Biology, University of Texas at Tyler, Tyler, Texas
| | - Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas
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31
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 DOI: 10.1101/514356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 05/20/2023] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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32
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 PMCID: PMC6544314 DOI: 10.1371/journal.pgen.1008156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R. Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A. Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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33
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Morandin C, Brendel VP, Sundström L, Helanterä H, Mikheyev AS. Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect. Mol Ecol 2019; 28:1975-1993. [PMID: 30809873 DOI: 10.1111/mec.15062] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 12/14/2022]
Abstract
Social insects provide systems for studying epigenetic regulation of phenotypes, particularly with respect to differentiation of reproductive and worker castes, which typically arise from a common genetic background. The role of gene expression in caste specialization has been extensively studied, but the role of DNA methylation remains controversial. Here, we perform well replicated, integrated analyses of DNA methylation and gene expression in brains of an ant (Formica exsecta) with distinct female castes using traditional approaches (tests of differential methylation) combined with a novel approach (analysis of co-expression and co-methylation networks). We found differences in expression and methylation profiles between workers and queens at different life stages, as well as some overlap between DNA methylation and expression at the functional level. Large portions of the transcriptome and methylome are organized into "modules" of genes, some significantly associated with phenotypic traits of castes and developmental stages. Several gene co-expression modules are preserved in co-methylation networks, consistent with possible regulation of caste-specific gene expression by DNA methylation. Surprisingly, brain co-expression modules were highly preserved when compared with a previous study that examined whole-body co-expression patterns in 16 ant species, suggesting that these modules are evolutionarily conserved and for specific functions in various tissues. Altogether, these results suggest that DNA methylation participates in regulation of caste specialization and age-related physiological changes in social insects.
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Affiliation(s)
- Claire Morandin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Åbo, Finland.,Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, Indiana.,Department of Computer Science, Indiana University, Bloomington, Indiana
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Heikki Helanterä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Ecology and Genetics Research Unit, Faculty of Science, University of Oulu, Oulu, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, Japan.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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34
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Wallberg A, Bunikis I, Pettersson OV, Mosbech MB, Childers AK, Evans JD, Mikheyev AS, Robertson HM, Robinson GE, Webster MT. A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics 2019; 20:275. [PMID: 30961563 PMCID: PMC6454739 DOI: 10.1186/s12864-019-5642-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/24/2019] [Indexed: 01/27/2023] Open
Abstract
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. Electronic supplementary material The online version of this article (10.1186/s12864-019-5642-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mai-Britt Mosbech
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna K Childers
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA.,USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | - Jay D Evans
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | | | - Hugh M Robertson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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35
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Aird SD, Arora J, Barua A, Qiu L, Terada K, Mikheyev AS. Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry. Genome Biol Evol 2018; 9:2640-2649. [PMID: 29048530 PMCID: PMC5737360 DOI: 10.1093/gbe/evx199] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/24/2022] Open
Abstract
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested. Using a combination of de novo genome sequencing, population genomics, transcriptomics, and proteomics, we compare the two modes of evolution in the pitviper, Protobothrops mucrosquamatus. By partitioning selective constraints and adaptive evolution in a McDonald–Kreitman-type framework, we find support for both hypotheses: venom proteins indeed experience both stronger positive selection, and lower selective constraint than other genes in the genome. Furthermore, the strength of selection may be modulated by expression level, with more abundant proteins experiencing weaker selective constraint, leading to the accumulation of more deleterious mutations. These findings show that snake venoms evolve by a combination of adaptive and neutral mechanisms, both of which explain their extraordinarily high rates of molecular evolution. In addition to positive selection, which optimizes efficacy of the venom in the short term, relaxed selective constraints for deleterious mutations can lead to more rapid turnover of individual proteins, and potentially to exploration of a larger venom phenotypic space.
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Affiliation(s)
- Steven D Aird
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Jigyasa Arora
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Lijun Qiu
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Kouki Terada
- Okinawa Prefectural Institute of Health and the Environment, Biology and Ecology Group, Nanjo-shi, Okinawa, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
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36
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Carlson AL, Ishak HD, Kurian J, Mikheyev AS, Gifford I, Mueller UG. Nuclear populations of the multinucleate fungus of leafcutter ants can be dekaryotized and recombined to manipulate growth of nutritive hyphal nodules harvested by the ants. Mycologia 2018; 109:832-846. [PMID: 29300677 DOI: 10.1080/00275514.2017.1400304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We dekaryotized the multinucleate fungus Leucocoprinus gongylophorus, a symbiotic fungus cultivated vegetatively by leafcutter ants as their food. To track genetic changes resulting from dekaryotization (elimination of some nuclei from the multinuclear population), we developed two multiplex microsatellite fingerprinting panels (15 loci total), then characterized the allele profiles of 129 accessions generated by dekaryotization treatment. Genotype profiles of the 129 accessions confirmed allele loss expected by dekaryotization of the multinucleate fungus. We found no evidence for haploid and single-nucleus strains among the 129 accessions. Microscopy of fluorescently stained dekaryotized accessions revealed great variation in nuclei number between cells of the same vegetative mycelium, with cells containing typically between 3 and 15 nuclei/cell (average = 9.4 nuclei/cell; mode = 8). We distinguish four mycelial morphotypes among the dekaryotized accessions; some of these morphotypes had lost the full competence to produce gongylidia (nutritive hyphal-tip swellings consumed by leafcutter ants as food). In mycelial growth confrontations between different gongylidia-incompetent accessions, allele profiles suggest exchange of nuclei between dekaryotized accessions, restoring full gongylidia competence in some of these strains. The restoration of gongylidia competence after genetic exchange between dekaryotized strains suggests the hypothesis that complementary nuclei interact, or nuclear and cytoplasmic factors interact, to promote or enable gongylidia competence.
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Affiliation(s)
- Alexis L Carlson
- a Department of Integrative Biology , University of Texas at Austin , Austin , Texas 78712
| | - Heather D Ishak
- a Department of Integrative Biology , University of Texas at Austin , Austin , Texas 78712
| | - James Kurian
- a Department of Integrative Biology , University of Texas at Austin , Austin , Texas 78712
| | - Alexander S Mikheyev
- b Okinawa Institute of Science and Technology , 1919-1 Tancha, Onna-son, Kunigami , Okinawa 904-2234 , Japan
| | - Isaac Gifford
- a Department of Integrative Biology , University of Texas at Austin , Austin , Texas 78712
| | - Ulrich G Mueller
- a Department of Integrative Biology , University of Texas at Austin , Austin , Texas 78712
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37
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Mueller UG, Ishak HD, Bruschi SM, Smith CC, Herman JJ, Solomon SE, Mikheyev AS, Rabeling C, Scott JJ, Cooper M, Rodrigues A, Ortiz A, Brandão CRF, Lattke JE, Pagnocca FC, Rehner SA, Schultz TR, Vasconcelos HL, Adams RMM, Bollazzi M, Clark RM, Himler AG, LaPolla JS, Leal IR, Johnson RA, Roces F, Sosa-Calvo J, Wirth R, Bacci M. Biogeography of mutualistic fungi cultivated by leafcutter ants. Mol Ecol 2017; 26:6921-6937. [PMID: 29134724 DOI: 10.1111/mec.14431] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/19/2017] [Accepted: 10/04/2017] [Indexed: 01/03/2023]
Abstract
Leafcutter ants propagate co-evolving fungi for food. The nearly 50 species of leafcutter ants (Atta, Acromyrmex) range from Argentina to the United States, with the greatest species diversity in southern South America. We elucidate the biogeography of fungi cultivated by leafcutter ants using DNA sequence and microsatellite-marker analyses of 474 cultivars collected across the leafcutter range. Fungal cultivars belong to two clades (Clade-A and Clade-B). The dominant and widespread Clade-A cultivars form three genotype clusters, with their relative prevalence corresponding to southern South America, northern South America, Central and North America. Admixture between Clade-A populations supports genetic exchange within a single species, Leucocoprinus gongylophorus. Some leafcutter species that cut grass as fungicultural substrate are specialized to cultivate Clade-B fungi, whereas leafcutters preferring dicot plants appear specialized on Clade-A fungi. Cultivar sharing between sympatric leafcutter species occurs frequently such that cultivars of Atta are not distinct from those of Acromyrmex. Leafcutters specialized on Clade-B fungi occur only in South America. Diversity of Clade-A fungi is greatest in South America, but minimal in Central and North America. Maximum cultivar diversity in South America is predicted by the Kusnezov-Fowler hypothesis that leafcutter ants originated in subtropical South America and only dicot-specialized leafcutter ants migrated out of South America, but the cultivar diversity becomes also compatible with a recently proposed hypothesis of a Central American origin by postulating that leafcutter ants acquired novel cultivars many times from other nonleafcutter fungus-growing ants during their migrations from Central America across South America. We evaluate these biogeographic hypotheses in the light of estimated dates for the origins of leafcutter ants and their cultivars.
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Affiliation(s)
- Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Heather D Ishak
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Sofia M Bruschi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Chad C Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jacob J Herman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Scott E Solomon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.,Department of Ecology & Evolutionary Biology, Rice University, Houston, TX, USA
| | - Alexander S Mikheyev
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Okinawa Institute of Science & Technology, Kunigami, Okinawa, Japan
| | - Christian Rabeling
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jarrod J Scott
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael Cooper
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Andre Rodrigues
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Adriana Ortiz
- Universidad Nacional de Colombia, Medellin, Colombia
| | | | - John E Lattke
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil
| | - Fernando C Pagnocca
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Stephen A Rehner
- Mycology and Nematology Genomic Diversity and Biology Laboratory, Beltsville, MD, USA
| | - Ted R Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Rachelle M M Adams
- Department of Evolution, Ecology & Organismal Biology, Museum of Biological Diversity, Columbus, OH, USA
| | - Martin Bollazzi
- Section of Entomology, Universidad de la República, Montevideo, Uruguay
| | - Rebecca M Clark
- Integrative Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Anna G Himler
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Biology, College of Idaho, Caldwell, ID, USA
| | - John S LaPolla
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Biological Sciences, Towson University, Towson, MD, USA
| | - Inara R Leal
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Robert A Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Flavio Roces
- Department of Behavioral Physiology and Sociobiology, Biozentrum, University of Würzburg, Würzburg, Germany
| | | | - Rainer Wirth
- Department of Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Maurício Bacci
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
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38
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Abstract
Kin selection is thought to drive the evolution of cooperation and conflict, but the specific genes and genome-wide patterns shaped by kin selection are unknown. We identified thousands of genes associated with the sterile ant worker caste, the archetype of an altruistic phenotype shaped by kin selection, and then used population and comparative genomic approaches to study patterns of molecular evolution at these genes. Consistent with population genetic theoretical predictions, worker-upregulated genes experienced reduced selection compared with genes upregulated in reproductive castes. Worker-upregulated genes included more taxonomically restricted genes, indicating that the worker caste has recruited more novel genes, yet these genes also experienced reduced selection. Our study identifies a putative genomic signature of kin selection and helps to integrate emerging sociogenomic data with longstanding social evolution theory.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
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39
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Aird SD, da Silva NJ, Qiu L, Villar-Briones A, Saddi VA, Pires de Campos Telles M, Grau ML, Mikheyev AS. Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa. Toxins (Basel) 2017; 9:toxins9060187. [PMID: 28594382 PMCID: PMC5488037 DOI: 10.3390/toxins9060187] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022] Open
Abstract
Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2-6 toxin classes that account for 91-99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A₂ (PLA₂s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA₂s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1-2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6-9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to have arisen in three species by gene duplication and fusion. Four species have transcripts homologous to the nociceptive toxin, (MitTx) α-subunit, but all six species had homologs to the β-subunit. The first non-neurotoxic, non-catalytic elapid phospholipase A₂s are reported. All are probably myonecrotic. Phylogenetic analysis indicates that the six taxa diverged 15-35 million years ago and that they split from their last common ancestor with Old World elapines nearly 55 million years ago. Given their early diversification, many cryptic micrurine taxa are anticipated.
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Affiliation(s)
- Steven D Aird
- Division of Faculty Affairs, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Nelson Jorge da Silva
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás 74605-140, Brazil.
| | - Lijun Qiu
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Alejandro Villar-Briones
- Research Support Division, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Vera Aparecida Saddi
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás 74605-140, Brazil.
- Laboratório de Oncogenética e Radiobiologia da Associação de Combate ao Câncer em Goiás, Universidade Federal de Goiás, Rua 239 no. 52-Setor Universitário, Goiânia, Goiás 74065-070, Brazil.
| | - Mariana Pires de Campos Telles
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás 74605-140, Brazil.
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil.
| | - Miguel L Grau
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
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40
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Morandin C, Mikheyev AS, Pedersen JS, Helanterä H. Evolutionary constraints shape caste-specific gene expression across 15 ant species. Evolution 2017; 71:1273-1284. [PMID: 28262920 DOI: 10.1111/evo.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Jes Søe Pedersen
- Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
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41
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Okada Y, Watanabe Y, Tin MMY, Tsuji K, Mikheyev AS. Social dominance alters nutrition-related gene expression immediately: transcriptomic evidence from a monomorphic queenless ant. Mol Ecol 2017; 26:2922-2938. [DOI: 10.1111/mec.13989] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Yasukazu Okada
- Department of General Systems Studies; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Tokyo Japan
| | - Yutaka Watanabe
- Ecology and Evolution Unit; Okinawa Institute of Science and Technology; 1919-1 Tancha Onna-son Kunigami Okinawa 904-0495 Japan
| | - Mandy M. Y. Tin
- Ecology and Evolution Unit; Okinawa Institute of Science and Technology; 1919-1 Tancha Onna-son Kunigami Okinawa 904-0495 Japan
| | - Kazuki Tsuji
- Department of Subtropical Agro-Environmental Sciences; Faculty of Agriculture; University of the Ryukyus; Nishihara Okinawa 903-0213 Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit; Okinawa Institute of Science and Technology; 1919-1 Tancha Onna-son Kunigami Okinawa 904-0495 Japan
- Research School of Biology; Australian National University; Canberra ACT 0200 Australia
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42
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Yeates DK, Zwick A, Mikheyev AS. Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections. Curr Opin Insect Sci 2016; 18:83-88. [PMID: 27939715 DOI: 10.1016/j.cois.2016.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.
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Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia.
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun 904-0412, Japan
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43
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Aird SD, Villar Briones A, Roy MC, Mikheyev AS. Polyamines as Snake Toxins and Their Probable Pharmacological Functions in Envenomation. Toxins (Basel) 2016; 8:toxins8100279. [PMID: 27681740 PMCID: PMC5086639 DOI: 10.3390/toxins8100279] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/05/2016] [Indexed: 12/19/2022] Open
Abstract
While decades of research have focused on snake venom proteins, far less attention has been paid to small organic venom constituents. Using mostly pooled samples, we surveyed 31 venoms (six elapid, six viperid, and 19 crotalid) for spermine, spermidine, putrescine, and cadaverine. Most venoms contained all four polyamines, although some in essentially trace quantities. Spermine is a potentially significant component of many viperid and crotalid venoms (≤0.16% by mass, or 7.9 µmol/g); however, it is almost completely absent from elapid venoms assayed. All elapid venoms contained larger molar quantities of putrescine and cadaverine than spermine, but still at levels that are likely to be biologically insignificant. As with venom purines, polyamines impact numerous physiological targets in ways that are consistent with the objectives of prey envenomation, prey immobilization via hypotension and paralysis. Most venoms probably do not contain sufficient quantities of polyamines to induce systemic effects in prey; however, local effects seem probable. A review of the pharmacological literature suggests that spermine could contribute to prey hypotension and paralysis by interacting with N-methyl-d-aspartate (NMDA) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, nicotinic and muscarinic acetylcholine receptors, γ-Aminobutyric acid (GABA) receptors, blood platelets, ryanodine receptors, and Ca2+-ATPase. It also blocks many types of cation-permeable channels by interacting with negatively charged amino acid residues in the channel mouths. The site of envenomation probably determines which physiological targets assume the greatest importance; however, venom-induced liberation of endogenous, intracellular stores of polyamines could potentially have systemic implications and may contribute significantly to envenomation sequelae.
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Affiliation(s)
- Steven D Aird
- Division of Faculty Affairs, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Alejandro Villar Briones
- Division of Research Support, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Michael C Roy
- Division of Research Support, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
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44
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Morandin C, Tin MMY, Abril S, Gómez C, Pontieri L, Schiøtt M, Sundstrom L, Tsuji K, Pedersen JS, Helantera H, Mikheyev AS. Erratum to: Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biol 2016; 17:179. [PMID: 27561688 PMCID: PMC4997753 DOI: 10.1186/s13059-016-1048-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 11/26/2022] Open
Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. .,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland.
| | - Mandy M Y Tin
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Sílvia Abril
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Crisanto Gómez
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Luigi Pontieri
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Liselotte Sundstrom
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Kazuki Tsuji
- Department of Subtropical Agro-Environmental Sciences, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Jes Søe Pedersen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Heikki Helantera
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan. .,Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
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45
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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46
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Helmkampf M, Mikheyev AS, Kang Y, Fewell J, Gadau J. Gene expression and variation in social aggression by queens of the harvester ant Pogonomyrmex californicus. Mol Ecol 2016; 25:3716-30. [PMID: 27178446 DOI: 10.1111/mec.13700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/14/2016] [Accepted: 05/02/2016] [Indexed: 02/03/2023]
Abstract
A key requirement for social cooperation is the mitigation and/or social regulation of aggression towards other group members. Populations of the harvester ant Pogonomyrmex californicus show the alternate social phenotypes of queens founding nests alone (haplometrosis) or in groups of unrelated yet cooperative individuals (pleometrosis). Pleometrotic queens display an associated reduction in aggression. To understand the proximate drivers behind this variation, we placed foundresses of the two populations into social environments with queens from the same or the alternate population, and measured their behaviour and head gene expression profiles. A proportion of queens from both populations behaved aggressively, but haplometrotic queens were significantly more likely to perform aggressive acts, and conflict escalated more frequently in pairs of haplometrotic queens. Whole-head RNA sequencing revealed variation in gene expression patterns, with the two populations showing moderate differentiation in overall transcriptional profile, suggesting that genetic differences underlie the two founding strategies. The largest detected difference, however, was associated with aggression, regardless of queen founding type. Several modules of coregulated genes, involved in metabolism, immune system and neuronal function, were found to be upregulated in highly aggressive queens. Conversely, nonaggressive queens exhibited a striking pattern of upregulation in chemosensory genes. Our results highlight that the social phenotypes of cooperative vs. solitary nest founding tap into a set of gene regulatory networks that seem to govern aggression level. We also present a number of highly connected hub genes associated with aggression, providing opportunity to further study the genetic underpinnings of social conflict and tolerance.
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Affiliation(s)
- Martin Helmkampf
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, 904-0495, Japan
| | - Yun Kang
- College of Letters and Sciences, Arizona State University, 7001 E. Williams Field Road, Mesa, AZ, 85212, USA
| | - Jennifer Fewell
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA
| | - Jürgen Gadau
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA
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47
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Reyes-Bermudez A, Villar-Briones A, Ramirez-Portilla C, Hidaka M, Mikheyev AS. Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks. Genome Biol Evol 2016; 8:851-70. [PMID: 26941230 PMCID: PMC4824149 DOI: 10.1093/gbe/evw042] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/20/2022] Open
Abstract
Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic transitions at the base of the eumetazoa, we performed quantitative RNA-seq analysis duringAcropora digitifera's development. We collected embryonic, larval, and adult samples to characterize stage-specific transcription profiles, as well as broad expression patterns. Transcription profiles reconstructed development revealing two main expression clusters. The first cluster grouped blastula and gastrula and the second grouped subsequent developmental time points. Consistently, we observed clear differences in gene expression between early and late developmental transitions, with higher numbers of differentially expressed genes and fold changes around gastrulation. Furthermore, we identified three coexpression clusters that represented discrete gene expression patterns. During early transitions, transcriptional networks seemed to regulate cellular fate and morphogenesis of the larval body. In late transitions, these networks seemed to play important roles preparing planulae for switch in lifestyle and regulation of adult processes. Although developmental progression inA. digitiferais regulated to some extent by differential coexpression of well-defined gene networks, stage-specific transcription profiles appear to be independent entities. While negative regulation of transcription is predominant in early development, cell differentiation was upregulated in larval and adult stages.
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Affiliation(s)
- Alejandro Reyes-Bermudez
- Okinawa Institute of Science and Technology, Okinawa, Japan School of Natural Sciences, Ryukyus University, Okinawa, Japan
| | | | | | - Michio Hidaka
- School of Natural Sciences, Ryukyus University, Okinawa, Japan
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48
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Morandin C, Tin MMY, Abril S, Gómez C, Pontieri L, Schiøtt M, Sundström L, Tsuji K, Pedersen JS, Helanterä H, Mikheyev AS. Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biol 2016; 17:43. [PMID: 26951146 PMCID: PMC4780134 DOI: 10.1186/s13059-016-0902-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species. RESULTS Using queen and worker transcriptomic data from 16 ant species we tested the hypothesis that conserved sets of genes are involved in ant reproductive division of labor. We further hypothesized that such sets of genes should also be involved in the parallel evolution of other key traits. We applied weighted gene co-expression network analysis, which clusters co-expressed genes into modules, whose expression levels can be summarized by their 'eigengenes'. Eigengenes of most modules were correlated with phenotypic differentiation between queens and workers. Furthermore, eigengenes of some modules were correlated with repeated evolution of key phenotypes such as complete worker sterility, the number of queens per colony, and even invasiveness. Finally, connectivity and expression levels of genes within the co-expressed network were strongly associated with the strength of selection. Although caste-associated sets of genes evolve faster than non-caste-associated, we found no evidence for queen- or worker-associated co-expressed genes evolving faster than one another. CONCLUSIONS These results identify conserved functionally important genomic units that likely serve as building blocks of phenotypic innovation, and allow the remarkable breadth of parallel evolution seen in ants, and possibly other eusocial insects as well.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. .,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland.
| | - Mandy M Y Tin
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Sílvia Abril
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Crisanto Gómez
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Luigi Pontieri
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Kazuki Tsuji
- Department of Subtropical Agro-Environmental Sciences, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Jes Søe Pedersen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan. .,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia.
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49
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Abstract
Sex determination mechanisms play a central role in life-history characteristics, affecting mating systems, sex ratios, inbreeding tolerance, etc. Downstream components of sex determination pathways are highly conserved, but upstream components evolve rapidly. Evolutionary dynamics of sex determination remain poorly understood, particularly because mechanisms appear so diverse. Here we investigate the origins and evolution of complementary sex determination (CSD) in ants and bees. The honey bee has a well-characterized CSD locus, containing tandemly arranged homologs of the transformer gene [complementary sex determiner (csd) and feminizer (fem)]. Such tandem paralogs appear frequently in aculeate hymenopteran genomes. However, only comparative genomic, but not functional, data support a broader role for csd/fem in sex determination, and whether species other than the honey bee use this pathway remains controversial. Here we used a backcross to test whether csd/fem acts as a CSD locus in an ant (Vollenhovia emeryi). After sequencing and assembling the genome, we computed a linkage map, and conducted a quantitative trait locus (QTL) analysis of diploid male production using 68 diploid males and 171 workers. We found two QTLs on separate linkage groups (CsdQTL1 and CsdQTL2) that jointly explained 98.0% of the phenotypic variance. CsdQTL1 included two tandem transformer homologs. These data support the prediction that the same CSD mechanism has indeed been conserved for over 100 million years. CsdQTL2 had no similarity to CsdQTL1 and included a 236-kb region with no obvious CSD gene candidates, making it impossible to conclusively characterize it using our data. The sequence of this locus was conserved in at least one other ant genome that diverged >75 million years ago. By applying QTL analysis to ants for the first time, we support the hypothesis that elements of hymenopteran CSD are ancient, but also show that more remains to be learned about the diversity of CSD mechanisms. Whether a developing embryo becomes male or female has significant downstream consequences. Depending on the species, sex can be determined by a wide variety of mechanisms. Sex determination systems can evolve rapidly, but how this occurs, and even how widespread the same mechanism is within a given taxonomic group, remains largely unknown. By experimentally mapping the sex determination architecture in the ant, Vollenhovia emeryi, we found that the well-characterized honey bee sex determination locus originated more than 100 million years ago. However, we also found an additional locus that has no homology to the first. Currently uncharacterized, this locus suggests that different species may use a variety of complementary sex determination mechanisms. Yet, core elements of the complementary sex determination machinery appear to be ancient.
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Affiliation(s)
- Misato O. Miyakawa
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
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50
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Fischer G, Azorsa F, Garcia FH, Mikheyev AS, Economo EP. Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. Zookeys 2015:77-105. [PMID: 26487817 PMCID: PMC4607851 DOI: 10.3897/zookeys.525.6057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 09/17/2015] [Indexed: 11/12/2022] Open
Abstract
Phragmotic or "door head" ants have evolved independently in several ant genera across the world, but in Africa only one case has been documented until now. Carebara elmenteitae (Patrizi) is known from only a single phragmotic major worker collected from sifted leaf-litter near Lake Elmenteita in Kenya, but here the worker castes of two species collected from Kakamega Forest, a small rainforest in Western Kenya, are studied. Phragmotic major workers were previously identified as Carebara elmenteitae and non-phragmotic major and minor workers were assigned to Carebara thoracica (Weber). Using evidence of both morphological and next-generation sequencing analysis, it is shown that phragmotic and non-phragmotic workers of the two different species are actually the same and that neither name - Carebara elmenteitae or Carebara thoracica - correctly applies to them. Instead, this and another closey related species from Ivory Coast are both morphologically different from Carebara elmenteitae, and thus they are described as the new species Carebara phragmotica sp. n. and Carebara lilith sp. n.
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Affiliation(s)
- Georg Fischer
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son 904-0495, Japan
| | - Frank Azorsa
- División de Entomologia, Centro de Ecologia y Biodiversidad, CEBIO. Lima, PERU
| | - Francisco Hita Garcia
- Department of Natural History - Zoology, Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son 904-0495, Japan
| | - Evan P Economo
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son 904-0495, Japan ; Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 830 N University Street, Ann Arbor, MI 48701, USA
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