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Papachristos K, Sayadi A, Arnqvist G. Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles. Genome Biol Evol 2024; 16:evae143. [PMID: 38941482 PMCID: PMC11251426 DOI: 10.1093/gbe/evae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/10/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024] Open
Abstract
Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (ω) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall ω values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with ω values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.
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Affiliation(s)
| | - Ahmed Sayadi
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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2
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Degueldre F, Aron S. Long-term sperm storage in eusocial Hymenoptera. Biol Rev Camb Philos Soc 2023; 98:567-583. [PMID: 36397639 DOI: 10.1111/brv.12919] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/21/2022]
Abstract
In internally fertilizing species, sperm transfer is not always immediately followed by egg fertilization, and female sperm storage (FSS) may occur. FSS is a phenomenon in which females store sperm in a specialized organ for periods lasting from a few hours to several years, depending on the species. Eusocial hymenopterans (ants, social bees, and social wasps) hold the record for FSS duration. In these species, mating takes place during a single nuptial flight that occurs early in adult life for both sexes; they never mate again. Males die quickly after copulation but survive posthumously as sperm stored in their mates' spermathecae. Reproductive females, also known as queens, have a much longer life expectancy, up to 20 years in some species. Here, we review what is currently known about the molecular adaptations underlying the remarkable FSS capacities in eusocial hymenopterans. Because sperm quality is crucial to the reproductive success of both sexes, we also discuss the mechanisms involved in sperm storage and preservation in the male seminal vesicles prior to ejaculation. Finally, we propose future research directions that should broaden our understanding of this unique biological phenomenon.
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Affiliation(s)
- Félicien Degueldre
- Evolutionary Biology and Ecology, CP 160/12, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Serge Aron
- Evolutionary Biology and Ecology, CP 160/12, Université Libre de Bruxelles, B-1050, Brussels, Belgium
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3
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Xochipiltecatl D, Cordero C, Baixeras J. The Functional Morphology of the Bursa Copulatrix of a Butterfly That Does Not Digest Spermatophores ( Leptophobiaaripa, Pieridae). INSECTS 2022; 13:714. [PMID: 36005339 PMCID: PMC9409082 DOI: 10.3390/insects13080714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The bursa copulatrix of female Lepidoptera is a complex organ where crucial male-female reproductive interactions occur during and after copulation. The bursa copulatrix receives, stores, and digests the spermatophore and other substances transferred by the male during copulation, and is involved in changes in female receptivity, ovogenesis, and oviposition. Although females of the butterfly Leptophobia aripa do not digest the spermatophore, they possess a prominent signum. Since, in general, the function of the signum is considered to be the piercing or tearing of the spermatophore to initiate its digestion, its presence in L. aripa poses a conundrum. We undertook a microscopic study of the different components of the bursa copulatrix (ductus bursae and corpus bursae) and found structural differences that we interpreted in functional terms. We provide a detailed description of the signum and present experimental data regarding its effect on the spermatophore. Our observations led us to propose a novel hypothesis regarding the function of the signum.
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Affiliation(s)
- David Xochipiltecatl
- Posgrado en Ciencias Biológicas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
| | - Carlos Cordero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
| | - Joaquín Baixeras
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Paterna, 6980 Valencia, Spain
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4
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Agudelo J, Toro M, Ramírez-Sánchez LF, Barrientos LM, Alfonso-Parra C, Avila FW. Putative Degradation of Non-Stored Sperm in the Female Reproductive Tract of the Dengue Vector Mosquito Aedes aegypti. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.816556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In insect vectors of disease, male and female molecules that mediate reproductive processes are promising targets to suppress fertility of these populations. One process, the storage of sperm in the female reproductive tract, is essential for optimal fertility in all organisms examined to date. In the dengue vector mosquito Aedes aegypti, female sperm storage has not been fully characterized, a requirement to identify sex-specific molecules that mediate this process. Aedes aegypti males deposit the ejaculate into the bursa of the female reproductive tract, and sperm enter the spermathecae—the long-term storage sites—quickly after insemination. However, the proportion of sperm received during mating that are stored in the spermathecae is unclear, and the fate of non-stored sperm unknown. We quantified sperm storage in two Ae. aegypti strains, mated in all combinations, and in two contexts (mass mated and when mating was observed) at 1-, 3- and 5-days post-mating. Sperm quantity in the spermathecae was similar at all timepoints; most females stored ~400 sperm on average. Sperm that did not enter the spermathecae remained in the bursa, where they declined in number and became more fragile to mechanical manipulation at each timepoint. Further, sperm viability in the bursa fell from 91.6% shortly after mating to 12.2% 24 h later. One day after insemination, ~50% of sperm detected in the female reproductive tract was stored in the spermathecae. When we quantified sperm storage in females mated to males that transferred reduced ejaculate quantities (but still able to induce optimal fertility in their mates), sperm detected in the spermathecae similarly declined; females stored ~50% of the sperm received even as sperm quantities transferred at mating declined. Our results suggest that sperm storage in Ae. aegypti females is influenced by ejaculate volume, and that sperm that do not enter the spermathecae remain in the bursa, where they appear to degrade. The consistent presence of sperm in the bursa, even when males transferred low sperm quantities, suggests that the putative degradation of bursa sperm may play a role in Ae. aegypti female fertility, potentially identifying a novel process in this important vector species.
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5
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Propagation of seminal toxins through binary expression gene drives could suppress populations. Sci Rep 2022; 12:6332. [PMID: 35428855 PMCID: PMC9012762 DOI: 10.1038/s41598-022-10327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this restriction may be relaxed by using a double gene drive design to spread a split binary expression system. One drive carries a dominant lethal/toxic effector alone and the other a transactivator factor, without which the effector will not act. Only after the drives reach sufficiently high frequencies would individuals have the chance to inherit both system components and the effector be expressed. We explore through mathematical modeling the potential of this design to spread dominant lethal/toxic alleles and suppress populations. We show that this system could be implemented to spread engineered seminal proteins designed to kill females, making it highly effective against polyandrous populations.
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6
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Hurtado J, Almeida FC, Belliard SA, Revale S, Hasson E. Research gaps and new insights in the evolution of Drosophila seminal fluid proteins. INSECT MOLECULAR BIOLOGY 2022; 31:139-158. [PMID: 34747062 DOI: 10.1111/imb.12746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/20/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
While the striking effects of seminal fluid proteins (SFPs) on females are fairly conserved among Diptera, most SFPs lack detectable homologues among the SFP repertoires of phylogenetically distant species. How such a rapidly changing proteome conserves functions across taxa is a fascinating question. However, this and other pivotal aspects of SFPs' evolution remain elusive because discoveries on these proteins have been mainly restricted to the model Drosophila melanogaster. Here, we provide an overview of the current knowledge on the inter-specific divergence of the SFP repertoire in Drosophila and compile the increasing amount of relevant genomic information from multiple species. Capitalizing on the accumulated knowledge in D. melanogaster, we present novel sets of high-confidence SFP candidates and transcription factors presumptively involved in regulating the expression of SFPs. We also address open questions by performing comparative genomic analyses that failed to support the existence of many conserved SFPs shared by most dipterans and indicated that gene co-option is the most frequent mechanism accounting for the origin of Drosophila SFP-coding genes. We hope our update establishes a starting point to integrate further data and thus widen the understanding of the intricate evolution of these proteins.
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Affiliation(s)
- Juan Hurtado
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CABA, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Francisca Cunha Almeida
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CABA, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Silvina Anahí Belliard
- Laboratorio de Insectos de Importancia Agronómica, IGEAF (INTA), GV-IABIMO (CONICET), Buenos Aires, Argentina
| | - Santiago Revale
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Esteban Hasson
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CABA, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
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7
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Xochipiltecatl D, Baixeras J, Cordero CR. Atypical functioning of female genitalia explains monandry in a butterfly. PeerJ 2021; 9:e12499. [PMID: 34900425 PMCID: PMC8614189 DOI: 10.7717/peerj.12499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/26/2021] [Indexed: 11/20/2022] Open
Abstract
Monandrous species are rare in nature, especially in animals where males transfer nutrients to females in the ejaculate. The proximate mechanisms responsible for monandry are poorly studied. In butterflies and moths, the male transfers a nutritious spermatophore into the corpus bursae (CB) of the female. The CB is a multifunctional organ that digests the spermatophore and has partial control of the post-mating sexual receptivity of the female. The spermatophore distends the CB and the post-mating sexual receptivity of the female is inversely proportional to the degree of distension. The CB of many butterfly species has a muscular sheath whose contractions mechanically contribute to digest the spermatophore. As the contents of the CB are absorbed, the degree of distension decreases and the female recovers receptivity. We studied the monandrous butterfly Leptophobia aripa (Boisduval, 1836) (Pieridae) and found that females do not digest the spermatophores. We investigated the structure of the CB and found that a muscular sheath is absent, indicating that in this butterfly females lack the necessary "apparatus" for the mechanical digestion of the spermatophore. We propose that female monandry in this species is result of its incapability to mechanically digest the spermatophore, which results in a constant degree of CB distension after mating and, thus, in the maintenance of the sexually unreceptive state of females. Hypotheses on the evolution of this mechanism are discussed.
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Affiliation(s)
- David Xochipiltecatl
- Posgrado en Ciencias Biológicas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Joaquín Baixeras
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna, Valencia, Spain
| | - Carlos R Cordero
- Departamento de Ecología Evolutiva, Universidad Nacional Autónoma de México, Mexico City, México
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8
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Shen Y, Lu JB, Chen YZ, Moussian B, Zhang CX. A lateral oviduct secreted protein plays a vital role for egg movement through the female reproductive tract in the brown planthopper. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 132:103555. [PMID: 33639242 DOI: 10.1016/j.ibmb.2021.103555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/10/2020] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
The oviduct serves as a delivery tube for mature eggs ovulated from ovaries to egg-laying sites. Oviduct secreted components play important roles in ovulation and fertilization in mammals, however, no oviduct secreted protein has been characterized in an insect to date. Here, we identified a gene highly expressed in the lateral oviduct of the adult females in the brown planthopper (BPH), Nilaparvata lugens, the most destructive rice insect pest. Western blotting and immunofluorescence analyses revealed that the gene encodes a protein that is specifically expressed in the lateral oviduct as a component of the gel-like material secreted by the oviduct epithelial cells into the lumen of the swollen part of the lateral oviducts. The protein was tentatively named N. lugens oviduct secreted protein (Nlodsp). RNA interference (RNAi) against NlOdsp transcripts caused a failure of the lateral oviducts to deliver oocytes to the common oviduct that was, by consequence, plugged by 1-2 oocytes. Moreover, although oocytes in the Nlodsp-deficient ovariole were not released to the oviduct, they continued to develop, finally resulting in the presence of several matured oocytes in an ovariole. These defects evidently declined female fecundity. Together, our results demonstrate that NlOdsp plays an essential role in egg transport through the oviduct during ovulation. This work deepens our understanding of insect reproductive system and provides a potential target gene for RNAi-based insect pest control.
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Affiliation(s)
- Yan Shen
- Institute of Insect Science, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yuan-Zhi Chen
- Institute of Insect Science, Zhejiang University, Hangzhou, 310058, China
| | - Bernard Moussian
- Université Côte d'Azur, CNRS, Inserm, Institute of Biology Valrose, Parc Valrose, 06108, Nice, CEDEX 2, France
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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9
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McDonough-Goldstein CE, Borziak K, Pitnick S, Dorus S. Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes. G3 (BETHESDA, MD.) 2021; 11:jkab020. [PMID: 33890615 PMCID: PMC8063083 DOI: 10.1093/g3journal/jkab020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022]
Abstract
Sexual reproduction in internally fertilizing species requires complex coordination between female and male reproductive systems and among the diverse tissues of the female reproductive tract (FRT). Here, we report a comprehensive, tissue-specific investigation of Drosophila melanogaster FRT gene expression before and after mating. We identified expression profiles that distinguished each tissue, including major differences between tissues with glandular or primarily nonglandular epithelium. All tissues were enriched for distinct sets of genes possessing secretion signals that exhibited accelerated evolution, as might be expected for genes participating in molecular interactions between the sexes within the FRT extracellular environment. Despite robust transcriptional differences between tissues, postmating responses were dominated by coordinated transient changes indicative of an integrated systems-level functional response. This comprehensive characterization of gene expression throughout the FRT identifies putative female contributions to postcopulatory events critical to reproduction and potentially reproductive isolation, as well as the putative targets of sexual selection and conflict.
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Affiliation(s)
| | - Kirill Borziak
- Center for Reproductive Evolution, Biology Department, Syracuse University, Syracuse, NY, USA
| | - Scott Pitnick
- Center for Reproductive Evolution, Biology Department, Syracuse University, Syracuse, NY, USA
| | - Steve Dorus
- Center for Reproductive Evolution, Biology Department, Syracuse University, Syracuse, NY, USA
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10
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Gregoriou ME, Reczko M, Kakani EG, Tsoumani KT, Mathiopoulos KD. Decoding the Reproductive System of the Olive Fruit Fly, Bactrocera oleae. Genes (Basel) 2021; 12:355. [PMID: 33670896 PMCID: PMC7997189 DOI: 10.3390/genes12030355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
In most diploid organisms, mating is a prerequisite for reproduction and, thus, critical to the maintenance of their population and the perpetuation of the species. Besides the importance of understanding the fundamentals of reproduction, targeting the reproductive success of a pest insect is also a promising method for its control, as a possible manipulation of the reproductive system could affect its destructive activity. Here, we used an integrated approach for the elucidation of the reproductive system and mating procedures of the olive fruit fly, Bactrocera oleae. Initially, we performed a RNAseq analysis in reproductive tissues of virgin and mated insects. A comparison of the transcriptomes resulted in the identification of genes that are differentially expressed after mating. Functional annotation of the genes showed an alteration in the metabolic, catalytic, and cellular processes after mating. Moreover, a functional analysis through RNAi silencing of two differentially expressed genes, yellow-g and troponin C, resulted in a significantly reduced oviposition rate. This study provided a foundation for future investigations into the olive fruit fly's reproductive biology to the development of new exploitable tools for its control.
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Affiliation(s)
- Maria-Eleni Gregoriou
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; (M.-E.G.); (K.T.T.)
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Centre “Alexander Fleming”, 16672 Vari, Greece;
| | - Evdoxia G. Kakani
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Building 1, Room 103, Boston, MA 02115, USA;
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Konstantina T. Tsoumani
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; (M.-E.G.); (K.T.T.)
| | - Kostas D. Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; (M.-E.G.); (K.T.T.)
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11
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Cridland JM, Majane AC, Sheehy HK, Begun DJ. Polymorphism and Divergence of Novel Gene Expression Patterns in Drosophila melanogaster. Genetics 2020; 216:79-93. [PMID: 32737121 PMCID: PMC7463294 DOI: 10.1534/genetics.120.303515] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Transcriptomes may evolve by multiple mechanisms, including the evolution of novel genes, the evolution of transcript abundance, and the evolution of cell, tissue, or organ expression patterns. Here, we focus on the last of these mechanisms in an investigation of tissue and organ shifts in gene expression in Drosophila melanogaster. In contrast to most investigations of expression evolution, we seek to provide a framework for understanding the mechanisms of novel expression patterns on a short population genetic timescale. To do so, we generated population samples of D. melanogaster transcriptomes from five tissues: accessory gland, testis, larval salivary gland, female head, and first-instar larva. We combined these data with comparable data from two outgroups to characterize gains and losses of expression, both polymorphic and fixed, in D. melanogaster We observed a large number of gain- or loss-of-expression phenotypes, most of which were polymorphic within D. melanogaster Several polymorphic, novel expression phenotypes were strongly influenced by segregating cis-acting variants. In support of previous literature on the evolution of novelties functioning in male reproduction, we observed many more novel expression phenotypes in the testis and accessory gland than in other tissues. Additionally, genes showing novel expression phenotypes tend to exhibit greater tissue-specific expression. Finally, in addition to qualitatively novel expression phenotypes, we identified genes exhibiting major quantitative expression divergence in the D. melanogaster lineage.
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Affiliation(s)
- Julie M Cridland
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Alex C Majane
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Hayley K Sheehy
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David J Begun
- Department of Evolution and Ecology, University of California, Davis, California 95616
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12
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McCullough EL, McDonough CE, Pitnick S, Dorus S. Quantitative proteomics reveals rapid divergence in the postmating response of female reproductive tracts among sibling species. Proc Biol Sci 2020; 287:20201030. [PMID: 32576111 DOI: 10.1098/rspb.2020.1030] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fertility depends, in part, on interactions between male and female reproductive proteins inside the female reproductive tract (FRT) that mediate postmating changes in female behaviour, morphology, and physiology. Coevolution between interacting proteins within species may drive reproductive incompatibilities between species, yet the mechanisms underlying postmating-prezygotic (PMPZ) isolating barriers remain poorly resolved. Here, we used quantitative proteomics in sibling Drosophila species to investigate the molecular composition of the FRT environment and its role in mediating species-specific postmating responses. We found that (i) FRT proteomes in D. simulans and D. mauritiana virgin females express unique combinations of secreted proteins and are enriched for distinct functional categories, (ii) mating induces substantial changes to the FRT proteome in D. mauritiana but not in D. simulans, and (iii) the D. simulans FRT proteome exhibits limited postmating changes irrespective of whether females mate with conspecific or heterospecific males, suggesting an active female role in mediating reproductive interactions. Comparisons with similar data in the closely related outgroup species D. melanogaster suggest that divergence is concentrated on the D. simulans lineage. Our study suggests that divergence in the FRT extracellular environment and postmating response contribute to previously described patterns of PMPZ isolation and the maintenance of species boundaries.
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Affiliation(s)
- Erin L McCullough
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Caitlin E McDonough
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY 13244, USA
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13
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Plakke MS, Walker JL, Lombardo JB, Goetz BJ, Pacella GN, Durrant JD, Clark NL, Morehouse NI. Characterization of Female Reproductive Proteases in a Butterfly from Functional and Evolutionary Perspectives. Physiol Biochem Zool 2019; 92:579-590. [DOI: 10.1086/705722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Sirot LK. On the evolutionary origins of insect seminal fluid proteins. Gen Comp Endocrinol 2019; 278:104-111. [PMID: 30682344 DOI: 10.1016/j.ygcen.2019.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 02/06/2023]
Abstract
In most cases, proteins affect the phenotype of the individual in which they are produced. However, in some cases, proteins have evolved in such a way that they are able to influence the phenotype of another individual of the same or of a different species ("influential proteins"). Examples of interspecific influential proteins include venom proteins and proteins produced by parasites that influence their hosts' physiology or behavior. Examples of intraspecific influential proteins include those produced by both mothers and fetuses that mitigate maternal resource allocation and proteins transferred to females in the seminal fluid during mating that change female physiology and behavior. Although there has been much interest in the functions and evolutionary dynamics of these influential proteins, less is known about the origin of these proteins. Where does the DNA that encodes the proteins that can impact another individual's phenotype come from and how do the proteins acquire their influential abilities? In this mini-review, I use insect seminal fluid proteins as a case study to consider the origin of intraspecific influential proteins. The existing data suggest that influential insect seminal fluid proteins arise both through co-option of existing genes (both single copy genes and gene duplicates) and de novo evolution. Other mechanisms for the origin of new insect seminal fluid proteins (e.g., retrotransoposition and horizontal gene transfer) are plausible but have not yet been demonstrated. Additional gaps in our understanding of the origin of insect seminal fluid proteins include an understanding of the cis-regulatory elements that designate expression in the male reproductive tract and of the evolutionary steps by which individual proteins come to depend on other seminal fluid proteins for their activity within the mated female.
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Affiliation(s)
- Laura King Sirot
- Department of Biology, The College of Wooster, Wooster, OH 44691, United States.
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15
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Romson J, Jacksén J, Emmer Å. An automated system for CE-MALDI and on-target digestion under a fluorocarbon lid applied on spermatophore proteins from Pieris napi. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1104:228-233. [DOI: 10.1016/j.jchromb.2018.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/18/2018] [Accepted: 11/15/2018] [Indexed: 01/27/2023]
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16
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Nallu S, Hill JA, Don K, Sahagun C, Zhang W, Meslin C, Snell-Rood E, Clark NL, Morehouse NI, Bergelson J, Wheat CW, Kronforst MR. The molecular genetic basis of herbivory between butterflies and their host plants. Nat Ecol Evol 2018; 2:1418-1427. [PMID: 30076351 PMCID: PMC6149523 DOI: 10.1038/s41559-018-0629-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 07/02/2018] [Indexed: 12/30/2022]
Abstract
Interactions between herbivorous insects and their host-plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defenses and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host-plants. Parallel genome-wide association studies in the Cabbage White butterfly, Pieris rapae, and its host-plant, Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, yet a core set of highly conserved genes in butterflies as well as their host-plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of nature’s most diverse taxa, butterflies and flowering plants.
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Affiliation(s)
- Sumitha Nallu
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Jason A Hill
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Kristine Don
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Carlos Sahagun
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Wei Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.,Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, and School of Life Sciences, Peking University, Beijing, China
| | - Camille Meslin
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Institut National de la Recherche Agronomique (INRA), Institute of Ecology and Environmental Sciences of Paris (IEES-Paris), Versailles , France
| | - Emilie Snell-Rood
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Nathan L Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathan I Morehouse
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Marcus R Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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17
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Meslin C, Cherwin TS, Plakke MS, Hill J, Small BS, Goetz BJ, Wheat CW, Morehouse NI, Clark NL. Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection. Proc Natl Acad Sci U S A 2017; 114:E5406-E5413. [PMID: 28630352 PMCID: PMC5502654 DOI: 10.1073/pnas.1707680114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Male ejaculates are often structurally complex, and this complexity is likely to influence key reproductive interactions between males and females. However, despite its potential evolutionary significance, the molecular underpinnings of ejaculate structural complexity have received little empirical attention. To address this knowledge gap, we sought to understand the biochemical and functional properties of the structurally complex ejaculates of Pieris rapae butterflies. Males in this species produce large ejaculates called spermatophores composed of an outer envelope, an inner matrix, and a bolus of sperm. Females are thought to benefit from the nutrition contained in the soluble inner matrix through increases in longevity and fecundity. However, the indigestible outer envelope of the spermatophore delays female remating, allowing males to monopolize paternity for longer. Here, we show that these two nonsperm-containing spermatophore regions, the inner matrix and the outer envelope, differ in their protein composition and functional properties. We also reveal how these divergent protein mixtures are separately stored in the male reproductive tract and sequentially transferred to the female reproductive tract during spermatophore assembly. Intriguingly, we discovered large quantities of female-derived proteases in both spermatophore regions shortly after mating, which may contribute to spermatophore digestion and hence, female control over remating rate. Finally, we report evidence of past selection on these spermatophore proteins and female proteases, indicating a complex evolutionary history. Our findings illustrate how structural complexity of ejaculates may allow functionally and/or spatially associated suites of proteins to respond rapidly to divergent selective pressures, such as sexual conflict or reproductive cooperation.
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Affiliation(s)
- Camille Meslin
- Institut National de la Recherche Agronomique (INRA), Institute of Ecology and Environmental Sciences of Paris (IEES-Paris), 78026 Versailles Cedex, France
| | - Tamara S Cherwin
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Melissa S Plakke
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Brandon S Small
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260
| | - Breanna J Goetz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Nathan I Morehouse
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260;
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221
| | - Nathan L Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260;
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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18
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Sikkink KL, Kobiela ME, Snell-Rood EC. Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. BMC Genomics 2017; 18:412. [PMID: 28549454 PMCID: PMC5446745 DOI: 10.1186/s12864-017-3787-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 12/30/2022] Open
Abstract
Background Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades. Results First, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population. Conclusions Taken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and loss of genetic variants rather than de novo gain of adaptive alleles. The present research develops genomic resources to pave the way for future studies using cabbage whites as a model contributing to our understanding of adaptation to agricultural environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3787-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kristin L Sikkink
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA.
| | - Megan E Kobiela
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
| | - Emilie C Snell-Rood
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
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19
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Al-Wathiqui N, Fallon TR, South A, Weng JK, Lewis SM. Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection. Sci Rep 2016; 6:38556. [PMID: 28004739 PMCID: PMC5177949 DOI: 10.1038/srep38556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/09/2016] [Indexed: 11/23/2022] Open
Abstract
Postcopulatory sexual selection is recognized as a key driver of reproductive trait evolution, including the machinery required to produce endogenous nuptial gifts. Despite the importance of such gifts, the molecular composition of the non-gametic components of male ejaculates and their interactions with female reproductive tracts remain poorly understood. During mating, male Photinus fireflies transfer to females a spermatophore gift manufactured by multiple reproductive glands. Here we combined transcriptomics of both male and female reproductive glands with proteomics and metabolomics to better understand the synthesis, composition and fate of the spermatophore in the common Eastern firefly, Photinus pyralis. Our transcriptome of male glands revealed up-regulation of proteases that may enhance male fertilization success and activate female immune response. Using bottom-up proteomics we identified 208 functionally annotated proteins that males transfer to the female in their spermatophore. Targeted metabolomic analysis also provided the first evidence that Photinus nuptial gifts contain lucibufagin, a firefly defensive toxin. The reproductive tracts of female fireflies showed increased gene expression for several proteases that may be involved in egg production. This study offers new insights into the molecular composition of male spermatophores, and extends our understanding of how nuptial gifts may mediate postcopulatory interactions between the sexes.
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Affiliation(s)
| | - Timothy R Fallon
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Adam South
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sara M Lewis
- Department of Biology, Tufts University, Medford, MA, 02155, USA
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20
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Hashimoto K, Sugawara H, Hayashi F. Sclerotised spines in the female bursa associated with male's spermatophore production in cantharidin-producing false blister beetles. JOURNAL OF INSECT PHYSIOLOGY 2016; 93-94:18-27. [PMID: 27498144 DOI: 10.1016/j.jinsphys.2016.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 07/22/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
Cantharidin is a defence chemical synthesised in only two beetle families Meloidae and Oedemeridae. In Meloidae, cantharidin is used as a defence chemical in eggs. However, in Oedemeridae the function of cantharidin remains unclear. Based on morphological comparison of female internal reproductive organs in 39 species of Oedemeridae, we found that some species have sclerotised spines in the bursa copulatrix (bursal spines), while others have no such spines. Molecular phylogenetic trees inferred from mitochondrial 16S and nuclear 28S rRNA gene sequences suggested multiple evolutionary origins of bursal spines from an ancestor without spines. In the species which lacked spines, males transferred small amounts of ejaculates to females; however, in species with spines, males transferred large spermatophores. Deposited spermatophores gradually disappeared in the bursa, probably owing to absorption. To compare the amounts of cantharidin in eggs laid by species with and without bursal spines, we constructed a new bioassay system using the small beetle Mecynotarsus tenuipes from the family Anthicidae. M. tenuipes individuals were attracted to droplets of cantharidin/acetone solution, and the level of attraction increased with cantharidin concentration. This bioassay demonstrated that the eggs of Nacerdes caudata and N. katoi, both of which species have conspicuous bursal spines, contain more cantharidin than the eggs of N. waterhousei, which lacks spines. In the former species, males transfer large spermatophores to the female, and spermatophores are eventually broken down and digested within the female's spiny bursa. Thus, females with bursal spines may be able to provide more cantharidin to their eggs.
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Affiliation(s)
- Kosei Hashimoto
- Department of Biology, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo 192-0397, Japan.
| | - Hirotaka Sugawara
- Department of Biology, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo 192-0397, Japan
| | - Fumio Hayashi
- Department of Biology, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo 192-0397, Japan
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21
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Al-Wathiqui N, Dopman EB, Lewis SM. Postmating transcriptional changes in the female reproductive tract of the European corn borer moth. INSECT MOLECULAR BIOLOGY 2016; 25:629-645. [PMID: 27329655 DOI: 10.1111/imb.12249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Mating triggers a cascade of physiological and behavioural responses in females that persist after copulation. In insects, seminal fluid proteins contained within male ejaculates are known to initiate some responses, but our understanding of how females mediate these reactions remains limited. Few studies have examined postmating transcriptional changes within ejaculate-receiving organs within females or how these changes might depend on the identity of the male. Furthermore, whereas males of many insects transfer packaged ejaculates, transcriptional dynamics have mainly been examined in dipterans, in which males transfer a free ejaculate. To identify genes that may be important in mediating female physiological responses in a spermatophore-producing species, we sequenced the transcriptomes of the ejaculate-receiving organs and examined postmating gene expression within and between pheromone strains of the European corn borer (ECB) moth, Ostrinia nubilalis. After within-strain mating, significant differential expression of 978 transcripts occurred in the female bursa or its associated bursal gland, including peptidases, transmembrane transporters, and hormone processing genes; such genes may potentially play a role in postmating male-female interactions. We also identified 14 transcripts from the bursal gland that were differentially expressed after females mated with cross-strain males, representing candidates for previously observed postmating reproductive isolation between ECB strains.
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Affiliation(s)
- N Al-Wathiqui
- Department of Biology, Tufts University, Medford, MA, USA
| | - E B Dopman
- Department of Biology, Tufts University, Medford, MA, USA
| | - S M Lewis
- Department of Biology, Tufts University, Medford, MA, USA
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22
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Plakke MS, Deutsch AB, Meslin C, Clark NL, Morehouse NI. Dynamic digestive physiology of a female reproductive organ in a polyandrous butterfly. ACTA ACUST UNITED AC 2016; 218:1548-55. [PMID: 25994634 DOI: 10.1242/jeb.118323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Reproductive traits experience high levels of selection because of their direct ties to fitness, often resulting in rapid adaptive evolution. Much of the work in this area has focused on male reproductive traits. However, a more comprehensive understanding of female reproductive adaptations and their relationship to male characters is crucial to uncover the relative roles of sexual cooperation and conflict in driving co-evolutionary dynamics between the sexes. We focus on the physiology of a complex female reproductive adaptation in butterflies and moths: a stomach-like organ in the female reproductive tract called the bursa copulatrix that digests the male ejaculate (spermatophore). Little is known about how the bursa digests the spermatophore. We characterized bursa proteolytic capacity in relation to female state in the polyandrous butterfly Pieris rapae. We found that the virgin bursa exhibits extremely high levels of proteolytic activity. Furthermore, in virgin females, bursal proteolytic capacity increases with time since eclosion and ambient temperature, but is not sensitive to the pre-mating social environment. Post copulation, bursal proteolytic activity decreases rapidly before rebounding toward the end of a mating cycle, suggesting active female regulation of proteolysis and/or potential quenching of proteolysis by male ejaculate constituents. Using transcriptomic and proteomic approaches, we report identities for nine proteases actively transcribed by bursal tissue and/or expressed in the bursal lumen that may contribute to observed bursal proteolysis. We discuss how these dynamic physiological characteristics may function as female adaptations resulting from sexual conflict over female remating rate in this polyandrous butterfly.
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Affiliation(s)
- Melissa S Plakke
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aaron B Deutsch
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Camille Meslin
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nathan L Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nathan I Morehouse
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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