1
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Scott MF, Mackintosh C, Immler S. Gametic selection favours polyandry and selfing. PLoS Genet 2024; 20:e1010660. [PMID: 38363804 PMCID: PMC10903963 DOI: 10.1371/journal.pgen.1010660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/29/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
Competition among pollen or sperm (gametic selection) can cause evolution. Mating systems shape the intensity of gametic selection by determining the competitors involved, which can in turn cause the mating system itself to evolve. We model the bidirectional relationship between gametic selection and mating systems, focusing on variation in female mating frequency (monandry-polyandry) and self-fertilisation (selfing-outcrossing). First, we find that monandry and selfing both reduce the efficiency of gametic selection in removing deleterious alleles. This means that selfing can increase mutation load, in contrast to cases without gametic selection where selfing purges deleterious mutations and decreases mutation load. Second, we explore how mating systems evolve via their effect on gametic selection. By manipulating gametic selection, polyandry can evolve to increase the fitness of the offspring produced. However, this indirect advantage of post-copulatory sexual selection is weak and is likely to be overwhelmed by any direct fitness effects of mating systems. Nevertheless, gametic selection can be potentially decisive for selfing evolution because it significantly reduces inbreeding depression, which favours selfing. Thus, the presence of gametic selection could be a key factor driving selfing evolution.
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Affiliation(s)
- Michael Francis Scott
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Carl Mackintosh
- CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Sorbonne Universités, UPMC Université Paris VI, Roscoff, France
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
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2
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Bertram J, Fulton B, Tourigny JP, Peña-Garcia Y, Moyle LC, Hahn MW. CAGEE: Computational Analysis of Gene Expression Evolution. Mol Biol Evol 2023; 40:msad106. [PMID: 37158385 PMCID: PMC10195155 DOI: 10.1093/molbev/msad106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023] Open
Abstract
Despite the increasing abundance of whole transcriptome data, few methods are available to analyze global gene expression across phylogenies. Here, we present a new software package (Computational Analysis of Gene Expression Evolution [CAGEE]) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. In contrast to previous methods that treat each gene independently, CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene. The statistical approach developed here makes it possible to infer lineage-specific shifts in rates of evolution across the genome, in addition to possible differences in rates among multiple tissues sampled from the same species. We demonstrate the accuracy and robustness of our method on simulated data and apply it to a data set of ovule gene expression collected from multiple self-compatible and self-incompatible species in the genus Solanum to test hypotheses about the evolutionary forces acting during mating system shifts. These comparisons allow us to highlight the power of CAGEE, demonstrating its utility for use in any empirical system and for the analysis of most morphological traits. Our software is available at https://github.com/hahnlab/CAGEE/.
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Affiliation(s)
- Jason Bertram
- Department of Biology, Indiana University, Bloomington, IN
- Department of Mathematics, Western University, London, ON, Canada
| | - Ben Fulton
- Department of Biology, Indiana University, Bloomington, IN
- University Information Technology Services, Indiana University, Bloomington, IN
| | - Jason P Tourigny
- Department of Biology, Indiana University, Bloomington, IN
- Department of Computer Science, Indiana University, Bloomington, IN
| | | | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN
- Department of Computer Science, Indiana University, Bloomington, IN
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3
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Sharpe MA, Baskin DS, Jenson AV, Baskin AM. Hijacking Sexual Immuno-Privilege in GBM-An Immuno-Evasion Strategy. Int J Mol Sci 2021; 22:10983. [PMID: 34681642 PMCID: PMC8536168 DOI: 10.3390/ijms222010983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 01/12/2023] Open
Abstract
Regulatory T-cells (Tregs) are immunosuppressive T-cells, which arrest immune responses to 'Self' tissues. Some immunosuppressive Tregs that recognize seminal epitopes suppress immune responses to the proteins in semen, in both men and women. We postulated that GBMs express reproductive-associated proteins to manipulate reproductive Tregs and to gain immune privilege. We analyzed four GBM transcriptome databases representing ≈900 tumors for hypoxia-responsive Tregs, steroidogenic pathways, and sperm/testicular and placenta-specific genes, stratifying tumors by expression. In silico analysis suggested that the presence of reproductive-associated Tregs in GBM tumors was associated with worse patient outcomes. These tumors have an androgenic signature, express male-specific antigens, and attract reproductive-associated Related Orphan Receptor C (RORC)-Treg immunosuppressive cells. GBM patient sera were interrogated for the presence of anti-sperm/testicular antibodies, along with age-matched controls, utilizing monkey testicle sections. GBM patient serum contained anti-sperm/testicular antibodies at levels > six-fold that of controls. Myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) are associated with estrogenic tumors which appear to mimic placental tissue. We demonstrate that RORC-Tregs drive poor patient outcome, and Treg infiltration correlates strongly with androgen levels. Androgens support GBM expression of sperm/testicular proteins allowing Tregs from the patient's reproductive system to infiltrate the tumor. In contrast, estrogen appears responsible for MDSC/TAM immunosuppression.
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MESH Headings
- Androgens/metabolism
- Brain Neoplasms/immunology
- Brain Neoplasms/mortality
- Brain Neoplasms/pathology
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Databases, Factual
- Estrogens/metabolism
- Female
- Glioblastoma/immunology
- Glioblastoma/mortality
- Glioblastoma/pathology
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Kaplan-Meier Estimate
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Male
- Microglia/immunology
- Microglia/metabolism
- Nuclear Receptor Subfamily 1, Group F, Member 3/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Tumor Microenvironment
- Tumor-Associated Macrophages/immunology
- Tumor-Associated Macrophages/metabolism
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Affiliation(s)
- Martyn A. Sharpe
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA; (D.S.B.); (A.V.J.); (A.M.B.)
| | - David S. Baskin
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA; (D.S.B.); (A.V.J.); (A.M.B.)
- Department of Neurological Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Amanda V. Jenson
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA; (D.S.B.); (A.V.J.); (A.M.B.)
| | - Alexandra M. Baskin
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA; (D.S.B.); (A.V.J.); (A.M.B.)
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4
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Patlar B, Jayaswal V, Ranz JM, Civetta A. Nonadaptive molecular evolution of seminal fluid proteins in Drosophila. Evolution 2021; 75:2102-2113. [PMID: 34184267 PMCID: PMC8457112 DOI: 10.1111/evo.14297] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Seminal fluid proteins (SFPs) are a group of reproductive proteins that are among the most evolutionarily divergent known. As SFPs can impact male and female fitness, these proteins have been proposed to evolve under postcopulatory sexual selection (PCSS). However, the fast change of the SFPs can also result from nonadaptive evolution, and the extent to which selective constraints prevent SFPs rapid evolution remains unknown. Using intra‐ and interspecific sequence information, along with genomics and functional data, we examine the molecular evolution of approximately 300 SFPs in Drosophila. We found that 50–57% of the SFP genes, depending on the population examined, are evolving under relaxed selection. Only 7–12% showed evidence of positive selection, with no evidence supporting other forms of PCSS, and 35–37% of the SFP genes were selectively constrained. Further, despite associations of positive selection with gene location on the X chromosome and protease activity, the analysis of additional genomic and functional features revealed their lack of influence on SFPs evolving under positive selection. Our results highlight a lack of sufficient evidence to claim that most SFPs are driven to evolve rapidly by PCSS while identifying genomic and functional attributes that influence different modes of SFPs evolution.
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Affiliation(s)
- Bahar Patlar
- Department of Biology, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada
| | - Vivek Jayaswal
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, 92697
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada
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5
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Moyle LC, Wu M, Gibson MJS. Reproductive Proteins Evolve Faster Than Non-reproductive Proteins Among Solanum Species. FRONTIERS IN PLANT SCIENCE 2021; 12:635990. [PMID: 33912206 PMCID: PMC8072272 DOI: 10.3389/fpls.2021.635990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/01/2021] [Indexed: 05/13/2023]
Abstract
Elevated rates of evolution in reproductive proteins are commonly observed in animal species, and are thought to be driven by the action of sexual selection and sexual conflict acting specifically on reproductive traits. Whether similar patterns are broadly observed in other biological groups is equivocal. Here, we examine patterns of protein divergence among wild tomato species (Solanum section Lycopersicon), to understand forces shaping the evolution of reproductive genes in this diverse, rapidly evolving plant clade. By comparing rates of molecular evolution among loci expressed in reproductive and non-reproductive tissues, our aims were to test if: (a) reproductive-specific loci evolve more rapidly, on average, than non-reproductive loci; (b) 'male'-specific loci evolve at different rates than 'female'-specific loci; (c) genes expressed exclusively in gametophytic (haploid) tissue evolve differently from genes expressed in sporophytic (diploid) tissue or in both tissue types; and (d) mating system variation (a potential proxy for the expected strength of sexual selection and/or sexual conflict) affects patterns of protein evolution. We observed elevated evolutionary rates in reproductive proteins. However, this pattern was most evident for female- rather than male-specific loci, both broadly and for individual loci inferred to be positively selected. These elevated rates might be facilitated by greater tissue-specificity of reproductive proteins, as faster rates were also associated with more narrow expression domains. In contrast, we found little evidence that evolutionary rates are consistently different in loci experiencing haploid selection (gametophytic-exclusive loci), or in lineages with quantitatively different mating systems. Overall while reproductive protein evolution is generally elevated in this diverse plant group, some specific patterns of evolution are more complex than those reported in other (largely animal) systems, and include a more prominent role for female-specific loci among adaptively evolving genes.
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6
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Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems. BMC Genomics 2018; 19:488. [PMID: 29929489 PMCID: PMC6014011 DOI: 10.1186/s12864-018-4872-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic data from various organisms have been used to study how sexual selection has shaped genetic diversity in reproductive proteins, and in particular, to elucidate how mating systems may have influenced evolution at the molecular and phenotypic levels. However, large-scale proteomic data including protein identifications and abundances are only now entering the field of evolutionary and comparative genomics. Variation in both protein sequence and expression level may play important roles in the evolution of sexual traits and behaviors. RESULTS Here, we broadly analyze the components of seminal fluid from primates with diverse mating systems ranging from monogamous to polygynous, and include genomics, proteomics, phylogenetic and quantitative characters into our framework. Our analyses show that seminal fluid proteins are undergoing rapid evolution and some of these quickly evolving proteins may be influenced by sexual selection. Through evolutionary analyses and protein abundance differences, we identified 84 genes whose evolutionary rates or expression levels were correlated with mating system and other sexual characters. We found that many proteins differ in abundance between monogamous and polygynous primate mating systems. Many of these proteins are enriched in the copulatory plug pathway, which suggests that post-zygotic selective barriers are important regardless of mating system type. CONCLUSIONS This work is the first to comprehensively compare seminal fluid proteins between human and non-human primates using high-throughput proteomics. Our findings highlight the impact of mating system variation on seminal fluid protein evolution and abundance.
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7
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Genes Integral to the Reproductive Function of Male Reproductive Tissues Drive Heterogeneity in Evolutionary Rates in Japanese Quail. G3-GENES GENOMES GENETICS 2018; 8:39-51. [PMID: 29158338 PMCID: PMC5765365 DOI: 10.1534/g3.117.300095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Early comparative genomics studies originally uncovered a nonintuitive pattern; genes involved in reproduction appeared to evolve more rapidly than other classes of genes. Currently, the emerging consensus is that genes encoding reproductive proteins evolve under variable selective pressures, producing more heterogeneous divergence patterns than previously appreciated. Here, we investigate a facet of that heterogeneity and explore the factors that drive male reproductive tissue-based heterogeneity in evolutionary rates. In Japanese quail (Coturnix japonica), genes with enriched expression in the testes evolve much more rapidly than those enriched in the foam gland (FG), a novel gland that secretes an airy foam that males transfer to females during mating. We compared molecular evolutionary patterns among (1) genes with induced expression in breeding vs. wintering conditions for both tissues and (2) genes that encode foam proteins (FPs) vs. those with varying degrees of expression specificity in the FG. We report two major findings. First, genes upregulated in breeding condition testes evolve exceptionally rapidly, while those induced in breeding condition FGs evolve slowly. These differences hold even after correcting for hormonally-dependent gene expression and chromosomal location. Second, genes encoding FPs are extremely conserved in terms of gene identity and sequence. Together, these finding suggest that genes involved in the reproductive function of each tissue drive the marked rate of heterogeneity.
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8
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Bonilla ML, Todd C, Erlandson M, Andres J. Combining RNA-seq and proteomic profiling to identify seminal fluid proteins in the migratory grasshopper Melanoplus sanguinipes (F). BMC Genomics 2015; 16:1096. [PMID: 26694822 PMCID: PMC4689059 DOI: 10.1186/s12864-015-2327-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Seminal fluid proteins control many aspects of fertilization and in turn, they play a key role in post-mating sexual selection and possibly reproductive isolation. Because effective proteome profiling relies on the availability of high-quality DNA reference databases, our knowledge of these proteins is still largely limited to model organisms with ample genetic resources. New advances in sequencing technology allow for the rapid characterization of transcriptomes at low cost. By combining high throughput RNA-seq and shotgun proteomic profiling, we have characterized the seminal fluid proteins secreted by the primary male accessory gland of the migratory grasshopper (Melanoplus sanguinipes), one of the main agricultural pests in central North America. RESULTS Using RNA sequencing, we characterized the transcripts of ~ 8,100 genes expressed in the long hyaline tubules (LHT) of the accessory glands. Proteomic profiling identified 353 proteins expressed in the long hyaline tubules (LHT). Of special interest are seminal fluid proteins (SFPs), such as EJAC-SP, ACE and prostaglandin synthetases, which are known to regulate female oviposition in insects. CONCLUSIONS Our study provides new insights into the proteomic components of male ejaculate in Orthopterans, and highlights several important patterns. First, the presence of proteins that lack predicted classical secretory tags in accessory gland proteomes is common in male accessory glands. Second, the products of a few highly expressed genes dominate the accessory gland secretions. Third, accessory gland transcriptomes are enriched for novel transcripts. Fourth, there is conservation of SFPs' functional classes across distantly related taxonomic groups with very different life histories, mating systems and sperm transferring mechanisms. The identified SFPs may serve as targets of future efforts to develop species- specific genetic control strategies.
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Affiliation(s)
- Martha L Bonilla
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, A.237. Palmira, Valle del Cauca, Colombia.
- Department of Biology, University of Saskatchewan, 112 Science Pl., Saskatoon, SK, S7N-5E2, Canada.
| | - Christopher Todd
- Department of Biology, University of Saskatchewan, 112 Science Pl., Saskatoon, SK, S7N-5E2, Canada.
| | - Martin Erlandson
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Pl., Saskatoon, SK, S7N-0X2, Canada.
| | - Jose Andres
- Department of Biology, University of Saskatchewan, 112 Science Pl., Saskatoon, SK, S7N-5E2, Canada.
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9
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Grayson P. Izumo1 and Juno: the evolutionary origins and coevolution of essential sperm-egg binding partners. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150296. [PMID: 27019721 PMCID: PMC4807442 DOI: 10.1098/rsos.150296] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/17/2015] [Indexed: 05/29/2023]
Abstract
Reproductive proteins are among the most rapidly evolving classes of proteins. For a subset of these, rapid evolution is driven by positive Darwinian selection despite vital, well-conserved, reproductive functions. Izumo1 is the only essential sperm-egg fusion protein currently known on mammalian sperm, and its egg receptor (Juno; formerly Folr4) was recently discovered. Male knockout mice for Izumo1 and female knockout mice for Juno are both healthy but sterile. Here, both sperm-egg binding proteins are shown to be evolving under positive selection. Within mammals, coevolution of Izumo1 and Juno is also uncovered, suggesting that similar forces have shaped the evolutionary histories of these binding partners within Mammalia. Additionally, genomic analyses reveal an ancient origin for the Izumo gene family, initially reported as conserved exclusively in mammals. Newly identified Izumo1 orthologues could serve reproductive functions in birds, fish and reptiles. Surprisingly, these same analyses support Juno's presence in mammals alone, suggesting a recent mammalian-specific duplication and neofunctionalization of the ancestral folate receptor. Despite the indispensability of their reproductive interaction, and their apparent coevolution within Mammalia, this binding pair arose through strikingly different evolutionary forces.
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10
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Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system. Cell Tissue Res 2015; 363:267-278. [DOI: 10.1007/s00441-015-2257-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/05/2015] [Indexed: 12/30/2022]
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11
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Wong A, Seguin K. Effects of genotype on rates of substitution during experimental evolution. Evolution 2015; 69:1772-85. [DOI: 10.1111/evo.12700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 05/26/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Alex Wong
- Department of Biology; Carleton University; Ottawa Ontario Canada
| | - Kimberley Seguin
- Department of Biology; Carleton University; Ottawa Ontario Canada
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12
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Sirot LK. Ask not (only) what proteomics can do for behavior, but (also) what behavior can do for proteomes: a comment on Valcu and Kempenaers. Behav Ecol 2015. [DOI: 10.1093/beheco/aru168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Sirot LK, Wong A, Chapman T, Wolfner MF. Sexual conflict and seminal fluid proteins: a dynamic landscape of sexual interactions. Cold Spring Harb Perspect Biol 2014; 7:a017533. [PMID: 25502515 DOI: 10.1101/cshperspect.a017533] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sexual reproduction requires coordinated contributions from both sexes to proceed efficiently. However, the reproductive strategies that the sexes adopt often have the potential to give rise to sexual conflict because they can result in divergent, sex-specific costs and benefits. These conflicts can occur at many levels, from molecular to behavioral. Here, we consider sexual conflict mediated through the actions of seminal fluid proteins. These proteins provide many excellent examples in which to trace the operation of sexual conflict from molecules through to behavior. Seminal fluid proteins are made by males and provided to females during mating. As agents that can modulate egg production at several steps, as well as reproductive behavior, sperm "management," and female feeding, activity, and longevity, the actions of seminal proteins are prime targets for sexual conflict. We review these actions in the context of sexual conflict. We discuss genomic signatures in seminal protein (and related) genes that are consistent with current or previous sexual conflict. Finally, we note promising areas for future study and highlight real-world practical situations that will benefit from understanding the nature of sexual conflicts mediated by seminal proteins.
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Affiliation(s)
- Laura K Sirot
- Department of Biology, College of Wooster, Wooster, Ohio 44691
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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14
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Finseth FR, Bondra E, Harrison RG. Selective Constraint Dominates the Evolution of Genes Expressed in a Novel Reproductive Gland. Mol Biol Evol 2014; 31:3266-81. [DOI: 10.1093/molbev/msu259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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15
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Wong A. Covariance between Testes Size and Substitution Rates in Primates. Mol Biol Evol 2014; 31:1432-6. [DOI: 10.1093/molbev/msu091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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16
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Grayson P, Civetta A. Positive selection in the adhesion domain of Mus sperm Adam genes through gene duplications and function-driven gene complex formations. BMC Evol Biol 2013; 13:217. [PMID: 24079728 PMCID: PMC3849967 DOI: 10.1186/1471-2148-13-217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sperm and testes-expressed Adam genes have been shown to undergo bouts of positive selection in mammals. Despite the pervasiveness of positive selection signals, it is unclear what has driven such selective bouts. The fact that only sperm surface Adam genes show signals of positive selection within their adhesion domain has led to speculation that selection might be driven by species-specific adaptations to fertilization or sperm competition. Alternatively, duplications and neofunctionalization of Adam sperm surface genes, particularly as it is now understood in rodents, might have contributed to an acceleration of evolutionary rates and possibly adaptive diversification. RESULTS Here we sequenced and conducted tests of selection within the adhesion domain of sixteen known sperm-surface Adam genes among five species of the Mus genus. We find evidence of positive selection associated with all six Adam genes known to interact to form functional complexes on Mus sperm. A subset of these complex-forming sperm genes also displayed accelerated branch evolution with Adam5 evolving under positive selection. In contrast to our previous findings in primates, selective bouts within Mus sperm Adams showed no associations to proxies of sperm competition. Expanded phylogenetic analysis including sequence data from other placental mammals allowed us to uncover ancient and recent episodes of adaptive evolution. CONCLUSIONS The prevailing signals of rapid divergence and positive selection detected within the adhesion domain of interacting sperm Adams is driven by duplications and potential neofunctionalizations that are in some cases ancient (Adams 2, 3 and 5) or more recent (Adams 1b, 4b and 6).
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Affiliation(s)
- Phil Grayson
- Department of Biology, University of Winnipeg, Winnipeg, Canada.
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17
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Hurtado J, Iglesias PP, Lipko P, Hasson E. Multiple paternity and sperm competition in the sibling speciesDrosophila buzzatiiandDrosophila koepferae. Mol Ecol 2013; 22:5016-26. [DOI: 10.1111/mec.12436] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 11/29/2022]
Affiliation(s)
- J. Hurtado
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Instituto de Ecología Genética y Evolución de la ciudad de Buenos Aires; CONICET-Universidad de Buenos Aires (UBA); Ciudad Universitaria; Pabellón II C1428EGA Buenos Aires Argentina
| | - P. P. Iglesias
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Instituto de Ecología Genética y Evolución de la ciudad de Buenos Aires; CONICET-Universidad de Buenos Aires (UBA); Ciudad Universitaria; Pabellón II C1428EGA Buenos Aires Argentina
| | - P. Lipko
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Instituto de Ecología Genética y Evolución de la ciudad de Buenos Aires; CONICET-Universidad de Buenos Aires (UBA); Ciudad Universitaria; Pabellón II C1428EGA Buenos Aires Argentina
| | - E. Hasson
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Instituto de Ecología Genética y Evolución de la ciudad de Buenos Aires; CONICET-Universidad de Buenos Aires (UBA); Ciudad Universitaria; Pabellón II C1428EGA Buenos Aires Argentina
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18
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Wong A, Rundle H. Selection on the Drosophila seminal fluid protein Acp62F. Ecol Evol 2013; 3:1942-50. [PMID: 23919141 PMCID: PMC3728936 DOI: 10.1002/ece3.605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 11/30/2022] Open
Abstract
Sperm competition and sexual conflict are thought to underlie the rapid evolution of reproductive proteins in many taxa. While comparative data are generally consistent with these hypotheses, few manipulative tests have been conducted and those that have provided contradictory results in some cases. Here, we use both comparative and experimental techniques to investigate the evolution of the Drosophila melanogaster seminal fluid protein Acp62F, a protease inhibitor for which extensive functional tests have yielded ambiguous results. Using between-species sequence comparisons, we show that Acp62F has been subject to recurrent positive selection. In addition, we experimentally evolved populations polymorphic for an Acp62F null allele over eight generations, manipulating the opportunities for natural and sexual selection. We found that the Acp62F null allele increased in frequency in the presence of natural selection, with no effect of sexual selection.
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Affiliation(s)
- Alex Wong
- Department of Biology, Carleton University Ottawa, Canada ; Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa Ottawa, Canada
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Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes. Genetics 2013; 194:709-19. [PMID: 23666936 DOI: 10.1534/genetics.113.152066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The population genetic behavior of mutations in sperm genes is theoretically investigated. We modeled the processes at two levels. One is the standard population genetic process, in which the population allele frequencies change generation by generation, depending on the difference in selective advantages. The other is the sperm competition during each genetic transmission from one generation to the next generation. For the sperm competition process, we formulate the situation where a huge number of sperm with alleles A and B, produced by a single heterozygous male, compete to fertilize a single egg. This "minimal model" demonstrates that a very slight difference in sperm performance amounts to quite a large difference between the alleles' winning probabilities. By incorporating this effect of paternity-sharing sperm competition into the standard population genetic process, we show that fierce sperm competition can enhance the fixation probability of a mutation with a very small phenotypic effect at the single-sperm level, suggesting a contribution of sperm competition to rapid amino acid substitutions in haploid-expressed sperm genes. Considering recent genome-wide demonstrations that a substantial fraction of the mammalian sperm genes are haploid expressed, our model could provide a potential explanation of rapid evolution of sperm genes with a wide variety of functions (as long as they are expressed in the haploid phase). Another advantage of our model is that it is applicable to a wide range of species, irrespective of whether the species is externally fertilizing, polygamous, or monogamous. The theoretical result was applied to mammalian data to estimate the selection intensity on nonsynonymous mutations in sperm genes.
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Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S. Comparative population genomics of the ejaculate in humans and the great apes. Mol Biol Evol 2013; 30:964-76. [PMID: 23329688 DOI: 10.1093/molbev/mst005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The rapid molecular evolution of reproductive genes is nearly ubiquitous across animals, yet the selective forces and functional targets underlying this divergence remain poorly understood. Humans and closely related species of great apes show strongly divergent mating systems, providing a powerful system to investigate the influence of sperm competition on the evolution of reproductive genes. This is complemented by detailed information on male reproductive biology and unparalleled genomic resources in humans. Here, we have used custom microarrays to capture and sequence 285 genes encoding proteins present in the ejaculate as well as 101 randomly selected control genes in 21 gorillas, 20 chimpanzees, 20 bonobos, and 20 humans. In total, we have generated >25× average genomic coverage per individual for over 1 million target base pairs. Our analyses indicate high levels of evolutionary constraint across much of the ejaculate combined with more rapid evolution of genes involved in immune defense and proteolysis. We do not find evidence for appreciably more positive selection along the lineage leading to bonobos and chimpanzees, although this would be predicted given more intense sperm competition in these species. Rather, the extent of positive and negative selection depended more on the effective population sizes of the species. Thus, general patterns of male reproductive protein evolution among apes and humans depend strongly on gene function but not on inferred differences in the intensity of sperm competition among extant species.
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Affiliation(s)
- Jeffrey M Good
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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21
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Positive Selection and the Evolution of izumo Genes in Mammals. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:958164. [PMID: 22957301 PMCID: PMC3432370 DOI: 10.1155/2012/958164] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/04/2012] [Indexed: 12/13/2022]
Abstract
Most genes linked to male reproductive function have been known to evolve rapidly among species and to show signatures of positive selection. Different male species-specific reproductive strategies have been proposed to underlie positive selection, such as sperm competitive advantage and control over females postmating physiology. However, an underexplored aspect potentially affecting male reproductive gene evolution in mammals is the effect of gene duplications. Here we analyze the molecular evolution of members of the izumo gene family in mammals, a family of four genes mostly expressed in the sperm with known and potential roles in sperm-egg fusion. We confirm a previously reported bout of selection for izumo1 and establish that the bout of selection is restricted to the diversification of species of the superorder Laurasiatheria. None of the izumo genes showed evidence of positive selection in Glires (Rodentia and Lagomorpha), and in the case of the non-testes-specific izumo4, rapid evolution was driven by relaxed selection. We detected evidence of positive selection for izumo3 among Primates. Interestingly, positively selected sites include several serine residues suggesting modifications in protein function and/or localization among Primates. Our results suggest that positive selection is driven by aspects related to species-specific adaptations to fertilization rather than sexual selection.
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Diz AP, Martínez-Fernández M, Rolán-Alvarez E. Proteomics in evolutionary ecology: linking the genotype with the phenotype. Mol Ecol 2012; 21:1060-80. [PMID: 22268916 DOI: 10.1111/j.1365-294x.2011.05426.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
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Affiliation(s)
- Angel P Diz
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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