Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair

Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes

Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.

Hybridization and gene expression: Beyond differentially expressed genes

Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.

Dynamics of seminal fluid production after mating

Seminal fluid proteins (SFPs) play vital roles for optimizing reproductive success in diverse animals. Underlining their significance, SFP production and transfer are highly plastic, e.g., depending on the presence of rivals or mating status of partners. However, surprisingly little is known about replenishing SFPs after mating. This is especially relevant in species that mate multiple times, as they continuously produce and use SFPs throughout their reproductive life. Here we examined the expression pattern of SFP genes after mating in the great pond snail, Lymnaea stagnalis. Our results show that two out of the six SFP genes investigated here were upregulated 1 week after mating. Surprisingly, most SFP genes did not change their expression immediately after mating. Even after 1 week, when supposedly seminal fluid is fully replenished, the expression of SFP genes is rather high. In addition, the difference with previous studies hints at the possibility that SFP production after mating is plastic and depends on the mating history of female-acting snails. Our results shed light on unexplored aspects of SFP production, thereby expanding the understanding of reproductive strategies in animals.

The uterine secretory cycle: recurring physiology of endometrial outputs that setup the uterine luminal microenvironment

Conserved in female reproduction across all mammalian species is the estrous cycle and its regulation by the hypothalamic-pituitary-gonadal (HPG) axis, a collective of intersected hormonal events that are crucial for ensuring uterine fertility. Nonetheless, knowledge of the direct mediators that synchronously shape the uterine microenvironment for successive yet distinct events, such as the transit of sperm and support for progressive stages of preimplantation embryo development, remain principally deficient. Toward understanding the timed endometrial outputs that permit luminal events as directed by the estrous cycle, we used Bovidae as a model system to uniquely surface sample and study temporal shifts to in vivo endometrial transcripts that encode for proteins destined to be secreted. The results revealed the full quantitative profile of endometrial components that shape the uterine luminal microenvironment at distinct phases of the estrous cycle (estrus, metestrus, diestrus, and proestrus). In interpreting this comprehensive log of stage-specific endometrial secretions, we define the "uterine secretory cycle" and extract a predictive understanding of recurring physiological actions regulated within the uterine lumen in anticipation of sperm and preimplantation embryonic stages. This repetitive microenvironmental preparedness to sequentially provide operative support was a stable intrinsic framework, with only limited responses to sperm or embryos if encountered in the lumen within the cyclic time period. In uncovering the secretory cycle and unraveling realistic biological processes, we present novel foundational knowledge of terminal effectors controlled by the HPG axis to direct a recurring sequence of vital functions within the uterine lumen.NEW & NOTEWORTHY This study unravels the recurring sequence of changes within the uterus that supports vital functions (sperm transit and development of preimplantation embryonic stages) during the reproductive cycle in female Ruminantia. These data present new systems knowledge in uterine reproductive physiology crucial for setting up in vitro biomimicry and artificial environments for assisted reproduction technologies for a range of mammalian species.

A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster

Sperm competition is a crucial aspect of male reproductive success in many species, including Drosophila melanogaster, and seminal fluid proteins (Sfps) can influence sperm competitiveness. However, the combined effect of environmental and genotypic variation on sperm competition gene expression remains poorly understood. Here, we used Drosophila Genetic Reference Panel (DGRP) inbred lines and manipulated developmental population density (i.e. larval density) to test the effects of genotype, environment and genotype-by-environment interactions (GEI) on the expression of the known sperm competition genes Sex Peptide, Acp36DE and CG9997. High larval density resulted in reduced adult body size, but expression of sperm competition genes remained unaffected. Furthermore, we found no significant GEI but genotypic effects in the expression of SP and Acp36DE. Our results also revealed GEI for relative competitive paternity success (second male paternity; P2), with genes' expression positively correlated with P2. Given the effect of genotype on the expression of genes, we conducted a genome-wide association study (GWAS) and identified polymorphisms in putative cis-regulatory elements as predominant factors regulating the expression of SP and Acp36DE. The association of genotypic variation with sperm competition outcomes, and the resilience of sperm competition genes' expression against environmental challenges, demonstrates the importance of genome variation background in reproductive fitness.

Genotype-by-environment interactions influence the composition of the Drosophila seminal proteome

Ejaculate proteins are key mediators of post-mating sexual selection and sexual conflict, as they can influence both male fertilization success and female reproductive physiology. However, the extent and sources of genetic variation and condition dependence of the ejaculate proteome are largely unknown. Such knowledge could reveal the targets and mechanisms of post-mating selection and inform about the relative costs and allocation of different ejaculate components, each with its own potential fitness consequences. Here, we used liquid chromatography coupled with tandem mass spectrometry to characterize the whole-ejaculate protein composition across 12 isogenic lines of Drosophila melanogaster that were reared on a high- or low-quality diet. We discovered new proteins in the transferred ejaculate and inferred their origin in the male reproductive system. We further found that the ejaculate composition was mainly determined by genotype identity and genotype-specific responses to larval diet, with no clear overall diet effect. Nutrient restriction increased proteolytic protein activity and shifted the balance between reproductive function and RNA metabolism. Our results open new avenues for exploring the intricate role of genotypes and their environment in shaping ejaculate composition, or for studying the functional dynamics and evolutionary potential of the ejaculate in its multivariate complexity.

Evolutionary Quantitative Proteomics of Reproductive Protein Divergence in Drosophila

Reproductive traits often evolve rapidly between species. Understanding the causes and consequences of this rapid divergence requires characterization of female and male reproductive proteins and their effect on fertilization success. Species in the Drosophila virilis clade exhibit rampant interspecific reproductive incompatibilities, making them ideal for studies on diversification of reproductive proteins and their role in speciation. Importantly, the role of intraejaculate protein abundance and allocation in interspecific divergence is poorly understood. Here, we identify and quantify the transferred male ejaculate proteome using multiplexed isobaric labeling of the lower female reproductive tract before and immediately after mating using three species of the virilis group. We identified over 200 putative male ejaculate proteins, many of which show differential abundance between species, suggesting that males transfer a species-specific allocation of seminal fluid proteins during copulation. We also identified over 2000 female reproductive proteins, which contain female-specific serine-type endopeptidases that showed differential abundance between species and elevated rates of molecular evolution, similar to that of some male seminal fluid proteins. Our findings suggest that reproductive protein divergence can also manifest in terms of species-specific protein abundance patterns.

Indel driven rapid evolution of core nuclear pore protein gene promoters

Nuclear pore proteins (Nups) prominently are among the few genes linked to speciation from hybrid incompatibility in Drosophila. These studies have focused on coding sequence evolution of Nup96 and Nup160 and shown evidence of positive selection driving nucleoporin evolution. Intriguingly, channel Nup54 functionality is required for neuronal wiring underlying the female post-mating response induced by male-derived sex-peptide. A region of rapid evolution in the core promoter of Nup54 suggests a critical role for general transcriptional regulatory elements at the onset of speciation, but whether this is a general feature of Nup genes has not been determined. Consistent with findings for Nup54, additional channel Nup58 and Nup62 promoters also rapidly accumulate insertions/deletions (indels). Comprehensive examination of Nup upstream regions reveals that core Nup complex gene promoters accumulate indels rapidly. Since changes in promoters can drive changes in expression, these results indicate an evolutionary mechanism driven by indel accumulation in core Nup promoters. Compensation of such gene expression changes could lead to altered neuronal wiring, rapid fixation of traits caused by promoter changes and subsequently the rise of new species. Hence, the nuclear pore complex may act as a nexus for species-specific changes via nucleo-cytoplasmic transport regulated gene expression.

Sperm morphology and performance in relation to postmating prezygotic isolation in two recently diverged passerine species

Divergence in sperm phenotype and female reproductive environment may be a common source of postmating prezygotic (PMPZ) isolation between species. However, compared to other reproductive barriers it has received much less attention. In this study, we examined sperm morphology and velocity in two hybridizing passerine species, the common nightingale (Luscinia megarhynchos) and thrush nightingale (L. luscinia). In addition, we for the first time characterized a passerine female reproductive tract fluid proteome. We demonstrate that spermatozoa of the common nightingale have significantly longer and wider midpiece (proximal part of the flagellum containing mitochondria) and longer tail compared to spermatozoa of thrush nightingale. On the other hand, they have significantly shorter and narrower acrosome. Importantly, these differences did not have any effect on sperm velocity. Furthermore, the fluid from the reproductive tract of common nightingale females did not differentially affect velocity of conspecific and heterospecific sperm. Our results indicate that the observed changes in the flagellum and acrosome size are unlikely to contribute to PMPZ isolation through differential sperm velocity of conspecific and heterospecific sperm in the female reproductive tract. However, they could affect other postcopulatory processes, which might be involved in PMPZ isolation, such as sperm storage, longevity or sperm-egg interaction.

Discovering novel reproductive genes in a non-model fly using de novo GridION transcriptomics

Gene discovery has important implications for investigating phenotypic trait evolution, adaptation, and speciation. Male reproductive tissues, such as accessory glands (AGs), are hotspots for recruitment of novel genes that diverge rapidly even among closely related species/populations. These genes synthesize seminal fluid proteins that often affect post-copulatory sexual selection-they can mediate male-male sperm competition, ejaculate-female interactions that modify female remating and even influence reproductive incompatibilities among diverging species/populations. Although de novo transcriptomics has facilitated gene discovery in non-model organisms, reproductive gene discovery is still challenging without a reference database as they are often novel and bear no homology to known proteins. Here, we use reference-free GridION long-read transcriptomics, from Oxford Nanopore Technologies (ONT), to discover novel AG genes and characterize their expression in the widespread dung fly, Sepsis punctum. Despite stark population differences in male reproductive traits (e.g.: Body size, testes size, and sperm length) as well as female re-mating, the male AG genes and their secretions of S. punctum are still unknown. We implement a de novo ONT transcriptome pipeline incorporating quality-filtering and rigorous error-correction procedures, and we evaluate gene sequence and gene expression results against high-quality Illumina short-read data. We discover highly-expressed reproductive genes in AG transcriptomes of S. punctum consisting of 40 high-quality and high-confidence ONT genes that cross-verify against Illumina genes, among which 26 are novel and specific to S. punctum. Novel genes account for an average of 81% of total gene expression and may be functionally relevant in seminal fluid protein production. For instance, 80% of genes encoding secretory proteins account for 74% total gene expression. In addition, median sequence similarities of ONT nucleotide and protein sequences match within-Illumina sequence similarities. Read-count based expression quantification in ONT is congruent with Illumina's Transcript per Million (TPM), both in overall pattern and within functional categories. Rapid genomic innovation followed by recruitment of de novo genes for high expression in S. punctum AG tissue, a pattern observed in other insects, could be a likely mechanism of evolution of these genes. The study also demonstrates the feasibility of adapting ONT transcriptomics for gene discovery in non-model systems.

Mating strategy predicts gene presence/absence patterns in a genus of simultaneously hermaphroditic flatworms

Gene repertoire turnover is a characteristic of genome evolution. However, we lack well-replicated analyses of presence/absence patterns associated with different selection contexts. Here, we study ∼100 transcriptome assemblies across Macrostomum, a genus of simultaneously hermaphroditic flatworms exhibiting multiple convergent shifts in mating strategy and associated reproductive morphologies. Many species mate reciprocally, with partners donating and receiving sperm at the same time. Other species convergently evolved to mate by hypodermic injection of sperm into the partner. We find that for orthologous transcripts annotated as expressed in the body region containing the testes, sequences from hypodermically inseminating species diverge more rapidly from the model species, Macrostomum lignano, and have a lower probability of being observed in other species. For other annotation categories, simpler models with a constant rate of similarity decay with increasing genetic distance from M. lignano match the observed patterns well. Thus, faster rates of sequence evolution for hypodermically inseminating species in testis-region genes result in higher rates of homology detection failure, yielding a signal of rapid evolution in sequence presence/absence patterns. Our results highlight the utility of considering appropriate null models for unobserved genes, as well as associating patterns of gene presence/absence with replicated evolutionary events in a phylogenetic context.

Biofluids manipulation methods for liquid biopsy in minimally-invasive assays

The Liquid Biopsy (LB) is an opportunity for non-invasive diagnosis and prognosis of various diseases. To date, it isn't possible to consider that tissue biopsy can represent a pathology entirety. Then, body fluids are rich in a large number and variety of biomarkers and they can provide information about several diseases.•

Recently, other biological fluids, easy to be collected are rising for their significant content of biomarkers and for the possibility to collect and manipulate them without the intervention of medical staff.

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The management of biological fluids requires suitable storage methods. Temperature, storage time and physical stresses due to sample handling can lead to chemical and physical changes that may induce sample degradation and incorrect analysis.

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The reliability of a diagnostic or screening test depends on its sensitivity and specificity. As the liquid biopsy is a 'snapshot' of a pathophysiological condition, it is crucial that its components do not degrade due to the improper handling of the body fluid.

In this review, some handling methods of Saliva, Urine, Stool, Seminal Fluid, Tears and Sweat samples will be described, as well as protocols to facilitate the analysis of metabolites, nucleic acids, proteins and Extracellular Vesicles (EVs) from those unusual body fluids.

Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow

Hybridization can result in novel allelic combinations which can impact the hybrid phenotype through changes in gene expression. While misexpression in F₁ hybrids is well documented, how gene expression evolves in stabilized hybrid taxa remains an open question. As gene expression evolves in a stabilizing manner, break‐up of co‐evolved cis‐ and trans‐regulatory elements could lead to transgressive patterns of gene expression in hybrids. Here, we address to what extent gonad gene expression has evolved in an established and stable homoploid hybrid, the Italian sparrow (Passer italiae). Through comparison of gene expression in gonads from individuals of the two parental species (i.e., house and Spanish sparrow) to that of Italian sparrows, we find evidence for strongly transgressive expression in male Italian sparrows—2530 genes (22% of testis genes tested for inheritance) exhibit expression patterns outside the range of both parent species. In contrast, Italian sparrow ovary expression was similar to that of one of the parent species, the house sparrow (Passer domesticus). Moreover, the Italian sparrow testis transcriptome is 26 times as diverged from those of the parent species as the parental transcriptomes are from each other, despite being genetically intermediate. This highlights the potential for regulation of gene expression to produce novel variation following hybridization. Genes involved in mitochondrial respiratory chain complexes and protein synthesis are enriched in the subset that is over‐dominantly expressed in Italian sparrow testis, suggesting that selection on key functions has moulded the hybrid Italian sparrow transcriptome.

Seminal fluid gene expression and reproductive fitness in Drosophila melanogaster

Background

The rapid evolution of seminal fluid proteins (SFPs) has been suggested to be driven by adaptations to postcopulatory sexual selection (e.g. sperm competition). However, we have recently shown that most SFPs evolve rapidly under relaxed selective pressures. Given the role of SFPs in competition for fertilization phenotypes, like the ability to transfer and store sperm and the modulation of female receptivity and ovulation, the prevalence of selectively relaxed SFPs appears as a conundrum. One possible explanation is that selection on SFPs might be relaxed in terms of protein amino acid content, but adjustments of expression are essential for post-mating function. Interestingly, there is a general lack of systematic implementation of gene expression perturbation assays to monitor their effect on phenotypes related to sperm competition.

Results

We successfully manipulated the expression of 16 SFP encoding genes using tissue-specific knockdowns (KDs) and determined the effect of these genes’ perturbation on three important post-mating phenotypes: female refractoriness to remating, defensive (P1), and offensive (P2) sperm competitive abilities in Drosophila melanogaster. Our analyses show that KDs of tested SFP genes do not affect female refractoriness to remating and P2, however, most gene KDs significantly decreased P1. Moreover, KDs of SFP genes that are selectively constrained in terms of protein-coding sequence evolution have lower P1 than KDs of genes evolving under relaxed selection.

Conclusions

Our results suggest a more predominant role, than previously acknowledged, of variation in gene expression than coding sequence changes on sperm competitive ability in D. melanogaster.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01975-1.

Ejaculate Allocation and Sperm Characteristics Differ among Alternative Male Types in a Species of Fish with Cooperation and Competition among Unrelated Males

Sexual selection arising from sperm competition has driven the evolution of immense variation in ejaculate allocation and sperm characteristics not only among species, but also among males within a species. One question that has received little attention is how cooperation among males affects these patterns. Here we ask how male alternative reproductive types differ in testes size, ejaculate production, and sperm morphology in the ocellated wrasse, a marine fish in which unrelated males cooperate and compete during reproduction. Nesting males build nests, court females and provide care. Sneaker males only “sneak” spawn, while satellite males sneak, but also help by chasing away sneakers. We found that satellite males have larger absolute testes than either sneakers or nesting males, despite their cooperative role. Nesting males invested relatively less in testes than either sneakers or satellites. Though sneakers produced smaller ejaculates than either satellite or nesting males, we found no difference among male types in either sperm cell concentration or sperm number, implying sneakers may produce less seminal fluid. Sperm tail length did not differ significantly among male types, but sneaker sperm cells had significantly larger heads than either satellite or nesting male sperm, consistent with past research showing sneakers produce slower sperm. Our results highlight that social interactions among males can influence sperm and ejaculate production.

Pronounced Postmating Response in the Drosophila Female Reproductive Tract Fluid Proteome

Fertility depends on the progression of complex and coordinated postmating processes within the extracellular environment of the female reproductive tract (FRT). Molecular interactions between ejaculate and FRT proteins regulate many of these processes, including sperm motility, migration, storage, and modification, along with concurrent changes in the female. Although extensive progress has been made in the proteomic characterization of the male-derived components of sperm and seminal fluid, investigations into the FRT have remained more limited. To achieve a comparable level of knowledge regarding female-derived proteins that comprise the reproductive environment, we utilized semiquantitative MS-based proteomics to study the composition of the FRT tissue and, separately, the luminal fluid, before and after mating in Drosophila melanogaster. Our approach leveraged whole-fly isotopic labeling to delineate female proteins from transferred male ejaculate proteins. Our results revealed several characteristics that distinguish the FRT fluid proteome from the FRT tissue proteome: (1) the fluid proteome is encoded by genes with higher overall levels of FRT gene expression and tissue specificity, including many genes with enriched expression in the fat body, (2) fluid-biased proteins are enriched for metabolic functions, and (3) the fluid exhibits pronounced postmating compositional changes. The dynamic mating-induced proteomic changes in the FRT fluid inform our understanding of secretory mechanisms of the FRT, serve as a foundation for establishing female contributions to the ejaculate-female interactions that regulate fertility, and highlight the importance of applying proteomic approaches to characterize the composition and dynamics of the FRT environment.

Nonadaptive molecular evolution of seminal fluid proteins in Drosophila

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.

The Female Snark Is Still a Boojum: Looking toward the Future of Studying Female Reproductive Biology

Philosophical truths are hidden in Lewis Carroll's nonsense poems, such as "The hunting of the snark." When the poem is used as a scientific allegory, a snark stands for the pursuit of scientific truth, while a boojum is a spurious discovery. In the study of female biology, boojums have been the result of the use of cultural stereotypes to frame hypotheses and methodologies. Although female reproduction is key for the continuation of sexually reproducing species, not only have females been understudied in many regards, but also data have commonly been interpreted in the context of now-outdated social mores. Spurious discoveries, boojums, are the result. In this article, we highlight specific gaps in our knowledge of female reproductive biology and provide a jumping-off point for future research. We discuss the promise of emerging methodologies (e.g., micro-CT scanning, high-throughput sequencing, proteomics, big-data analysis, CRISPR-Cas9, and viral vector technology) that can yield insights into previously cryptic processes and features. For example, in mice, deoxyribonucleic acid sequencing via chromatin immunoprecipitation followed by sequencing is already unveiling how epigenetics lead to sex differences in brain development. Similarly, new explorations, including microbiome research, are rapidly debunking dogmas such as the notion of the "sterile womb." Finally, we highlight how understanding female reproductive biology is well suited to the National Science Foundation's big idea, "Predicting Rules of Life." Studies of female reproductive biology will enable scholars to (1) traverse levels of biological organization from reproductive proteins at the molecular level, through anatomical details of the ovum and female reproductive tract, into physiological aspects of whole-organism performance, leading to behaviors associated with mating and maternal care, and eventually reaching population structure and ecology; (2) discover generalizable rules such as the co-evolution of maternal-offspring phenotypes in gestation and lactation; and (3) predict the impacts of changes to reproductive timing when the reliability of environmental cues becomes unpredictable. Studies in these key areas relative to female reproduction are sure to further our understanding across a range of diverse taxa.

Deconvoluting complex protein interaction networks through reductionist strategies in peptide biochemistry: Modern approaches and research questions

Following the decoding of the first human genome, researchers have vastly improved their understanding of cell biology and its regulation. As a result, it has become clear that it is not merely genetic information, but the aberrant changes in the functionality and connectivity of its encoded proteins that drive cell response to periods of stress and external cues. Therefore, proper utilization of refined methods that help to describe protein signalling or regulatory networks (i.e., functional connectivity), can help us understand how change in the signalling landscape effects the cell. However, given the vast complexity in 'how and when' proteins communicate or interact with each other, it is extremely difficult to define, characterize, and understand these interaction networks in a tangible manner. Herein lies the challenge of tackling the functional proteome; its regulation is encoded in multiple layers of interaction, chemical modification and cell compartmentalization. To address and refine simple research questions, modern reductionist strategies in protein biochemistry have successfully used peptide-based experiments; their summation helping to simplify the overall complexity of these protein interaction networks. In this way, peptides are powerful tools used in fundamental research that can be readily applied to comparative biochemical research. Understanding and defining how proteins interact is one of the key aspects towards understanding how the proteome functions. To date, reductionist peptide-based research has helped to address a wide range of proteome-related research questions, including the prediction of enzymes substrates, identification of posttranslational modifications, and the annotation of protein interaction partners. Peptide arrays have been used to identify the binding specificity of reader domains, which are able to recognise the posttranslational modifications; forming dynamic protein interactions that are dependent on modification state. Finally, representing one of the fastest growing classes of inhibitor molecules, peptides are now begin explored as "disruptors" of protein-protein interactions or enzyme activity. Collectively, this review will discuss the use of peptides, peptide arrays, peptide-oriented computational biochemistry as modern reductionist strategies in deconvoluting the functional proteome.

Rapid divergence of the male reproductive proteins in the Drosophila dunni group and implications for postmating incompatibilities between species

Proteins involved in post-copulatory interactions between males and females are among the fastest evolving genes in many species, usually attributed to their involvement in reproductive conflict. As a result, these proteins are thought to often be involved in the formation of postmating-prezygotic incompatibilities between species. The Drosophila dunni subgroup consists of a dozen recently diverged species found across the Caribbean islands with varying levels of hybrid incompatibility. We performed experimental crosses between species in the dunni group and see some evidence of hybrid incompatibilities. We also find evidence of reduced survival following hybrid mating, likely due to postmating-prezygotic incompatibilities. We assessed rates of evolution between these species genomes and find evidence of rapid evolution and divergence of some reproductive proteins, specifically the seminal fluid proteins. This work suggests the rapid evolution of seminal fluid proteins may be associated with postmating-prezygotic isolation, which acts as a barrier for gene flow between even the most closely related species.

Ovarian fluid proteome variation associates with sperm swimming speed in an externally fertilizing fish

Sperm velocity is a key trait that predicts the outcome of sperm competition. By promoting or impeding sperm velocity, females can control fertilization via postcopulatory cryptic female choice. In Chinook salmon, ovarian fluid (OF), which surrounds the ova, mediates sperm velocity according to male and female identity, biasing the outcome of sperm competition towards males with faster sperm. Past investigations have revealed proteome variation in OF, but the specific components of OF that differentially mediate sperm velocity have yet to be characterized. Here we use quantitative proteomics to investigate whether OF protein composition explains variation in sperm velocity and fertilization success. We found that OF proteomes from six females robustly clustered into two groups and that these groups are distinguished by the abundance of a restricted set of proteins significantly associated with sperm velocity. Exposure of sperm to OF from females in group I had faster sperm compared to sperm exposed to the OF of group II females. Overall, OF proteins that distinguished between these groups were enriched for vitellogenin and calcium ion interactions. Our findings suggest that these proteins may form the functional basis for cryptic female choice via the biochemical and physiological mediation of sperm velocity.

Seminal fluid and accessory male investment in sperm competition

Sperm production and allocation strategies have been a central concern of sperm competition research for the past 50 years. But during the 'sexual cascade' there may be strong selection for alternative routes to maximizing male fitness. Especially with the evolution of internal fertilization, a common and by now well-studied example is the accessory ejaculate investment represented by seminal fluid, the complex mixture of proteins, peptides and other components transferred to females together with sperm. How seminal fluid investment should covary with sperm investment probably depends on the mechanism of seminal fluid action. If seminal fluid components boost male paternity success by directly enhancing sperm function or use, we might often expect a positive correlation between the two forms of male investment, whereas trade-offs seem more likely if seminal fluid acts independently of sperm. This is largely borne out by a broad taxonomic survey to establish the prevailing patterns of seminal fluid production and allocation during animal evolution, in light of which I discuss the gaps that remain in our understanding of this key ejaculate component and its relationship to sperm investment, before outlining promising approaches for examining seminal fluid-mediated sperm competitiveness in the post-genomic era. This article is part of the theme issue 'Fifty years of sperm competition'.

Within-population sperm competition intensity does not predict asymmetry in conpopulation sperm precedence

Postcopulatory sexual selection can generate evolutionary arms races between the sexes resulting in the rapid coevolution of reproductive phenotypes. As traits affecting fertilization success diverge between populations, postmating prezygotic (PMPZ) barriers to gene flow may evolve. Conspecific sperm precedence is a form of PMPZ isolation thought to evolve early during speciation yet has mostly been studied between species. Here, we show conpopulation sperm precedence (CpSP) between Drosophila montana populations. Using Pool-seq genomic data we estimate divergence times and ask whether PMPZ isolation evolved in the face of gene flow. We find models incorporating gene flow fit the data best indicating populations experienced considerable gene flow during divergence. We find CpSP is asymmetric and mirrors asymmetry in non-competitive PMPZ isolation, suggesting these phenomena have a shared mechanism. However, we show asymmetry is unrelated to the strength of postcopulatory sexual selection acting within populations. We tested whether overlapping foreign and coevolved ejaculates within the female reproductive tract altered fertilization success but found no effect. Our results show that neither time since divergence nor sperm competitiveness predicts the strength of PMPZ isolation. We suggest that instead cryptic female choice or mutation-order divergence may drive divergence of postcopulatory phenotypes resulting in PMPZ isolation.

This article is part of the theme issue ‘Fifty years of sperm competition’.

Three decades of sperm competition in birds

In the three decades, since Birkhead and Møller published Sperm competition in birds (1992, Academic Press) more than 1000 papers have been published on this topic, about half of these being empirical studies focused on extrapair paternity. Both technological innovations and theory have moved the field forward by facilitating the study of both the mechanisms underlying sperm competition in both sexes, and the ensuing behavioural and morphological adaptations. The proliferation of studies has been driven partly by the diversity of both behaviours and morphologies in birds that have been influenced by sperm competition, but also by the richness of the theory developed by Geoff Parker over the past 50 years. This article is part of the theme issue 'Fifty years of sperm competition'.

Divergence of seminal fluid gene expression and function among natural snail populations

Seminal fluid proteins (SFPs) can trigger drastic changes in mating partners, mediating post-mating sexual selection and associated sexual conflict. Also, cross-species comparisons have demonstrated that SFPs evolve rapidly and hint that post-mating sexual selection drives their rapid evolution. In principle, this pattern should be detectable within species as rapid among-population divergence in SFP expression and function. However, given the multiple other factors that could vary among populations, isolating divergence in SFP-mediated effects is not straightforward. Here, we attempted to address this gap by combining the power of a common garden design with functional assays involving artificial injection of SFPs in the simultaneously hermaphroditic freshwater snail, Lymnaea stagnalis. We detected among-population divergence in SFP gene expression, suggesting that seminal fluid composition differs among four populations collected in Western Europe. Furthermore, by artificially injecting seminal fluid extracted from these field-derived snails into standardized mating partners, we also detected among-population divergence in the strength of post-mating effects induced by seminal fluid. Both egg production and subsequent sperm transfer of partners differed depending on the population origin of seminal fluid, with the response in egg production seemingly closely corresponding to among-population divergence in SFP gene expression. Our results thus lend strong intraspecific support to the notion that SFP expression and function evolve rapidly, and confirm L. stagnalis as an amenable system for studying processes driving SFP evolution.

Functional Aspects of Seminal Plasma in Bird Reproduction

This review provides an updated overview of the seminal plasma composition, and the role of metabolic and protein components on the sperm function of avian species. In addition, the implication of seminal plasma on assisted reproductive techniques of birds was discussed. The semen of birds usually has exceptionally high sperm concentration with relatively little seminal plasma, but this contributes to very fast changes in sperm metabolism and function. The biochemical characteristics and physiological roles of the various seminal plasma components in birds (carbohydrates, lipids, amino acids, hormones, and proteins) are poorly understood. Seminal plasma content of proteins has an action on most cellular functions: metabolism, immunity, oxido-reduction regulation, proteolysis, apoptosis, ion homeostasis, and antimicrobial defenses. The variable amount of many proteins is related to a different fertility capacity of poultry sperm. The role of seminal plasma on semen conservation (chilling and freezing) remains largely a matter of speculation, as both inhibitory and stimulating effects have been found. Whereas the presence of seminal plasma did not seem to affect the sperm survival after freezing-thawing, DNA fragmentation is lower in the absence of seminal plasma. The molecular basis of the influence of seminal plasma on sperm cryo-resistance was also discussed in the present review.

The house sparrow in the service of basic and applied biology

From the northernmost tip of Scandinavia to the southernmost corner of Patagonia, and across six continents, house sparrows (Passer domesticus) inhabit most human-modified habitats of the globe. With over 7,000 articles published, the species has become a workhorse for not only the study of self-urbanized wildlife, but also for understanding life history and body size evolution, sexual selection and many other biological phenomena. Traditionally, house sparrows were studied for their adaptations to local biotic and climatic conditions, but more recently, the species has come to serve as a focus for studies seeking to reveal the genomic, epigenetic and physiological underpinnings of success among invasive vertebrate species. Here, we review the natural history of house sparrows, highlight what the study of these birds has meant to bioscience generally, and describe the many resources available for future work on this species.