Family Diversification Research Articles

Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila.

Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.

Evolutionary correlates of extinction risk in Chinese angiosperm

China is widely known for its rich plant diversity, being a home for over 32,000 species of vascular plants. Approximately 11 % of them are threatened and require urgent conservation efforts. Although the major cause of species disappearance is known, the human activity does not affect all species equally. In our study we tested whether, at the family level, the risk of extinction is related to the evolutionary history and the total geographical range of the comprising family species. We gathered threat status data, evolutionary history information and range data for 27,102 Chinese angiosperm species representing 233 families. Using several Bayesian statistical approaches, we found that families with lower diversification rates had smaller geographic ranges, and that family diversification rate and geographic range size were strongly negatively associated with extinction risk. In contrast, the effect of family age on extinction risk, when its indirect effect through geographic range size was accounted for, was significantly positive. Our findings highlight the importance of considering evolutionary history in understanding the extinction dynamics and prioritization of species for protection. Our results imply that a special attention in conservation decisions should be given to species from the families with low diversification rates, old age and limited geographic ranges.

Diversification measures: Mutual fund family case

This study introduces a portfolio theory motivated approach to measuring mutual fund family-level risk diversification. The average cross-fund correlation in idiosyncratic returns measures diversification of idiosyncratic risk, while the correlation of predicted returns from the multifactor model measures factor risk diversification within a fund family. We document a substantial cross-sectional variation in family-level diversification measured with our new proxies independent of the number of funds and objectives in the family. While number of objectives is a popular yet possibly misleading measure of diversification, there is a link between portfolio theory-based diversification measures and the number of objectives in a family. On average, fund families with more investment objectives are more diversified in terms of both idiosyncratic and factor risks; yet, in large families, more investment objectives are associated with increased diversification of idiosyncratic risk but decreased diversification of factor risk. Fund family diversification improves family performance during market downturns and in large families. However, fund family diversification does not significantly affect absolute or relative family size, except for the number of investment objectives, which has a negative relation to family size.

Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function.

Nervous system function rests on the formation of functional synapses between neurons. We have identified TRMT9B as a new regulator of synapse formation and function in Drosophila. TRMT9B has been studied for its role as a tumor suppressor and is one of two metazoan homologs of yeast tRNA methyltransferase 9 (Trm9), which methylates tRNA wobble uridines. Whereas Trm9 homolog ALKBH8 is ubiquitously expressed, TRMT9B is enriched in the nervous system. However, in the absence of animal models, TRMT9B's role in the nervous system has remained unstudied. Here, we generate null alleles of TRMT9B and find it acts postsynaptically to regulate synaptogenesis and promote neurotransmission. Through liquid chromatography-mass spectrometry, we find that ALKBH8 catalyzes canonical tRNA wobble uridine methylation, raising the question of whether TRMT9B is a methyltransferase. Structural modeling studies suggest TRMT9B retains methyltransferase function and, in vivo, disruption of key methyltransferase residues blocks TRMT9B's ability to rescue synaptic overgrowth, but not neurotransmitter release. These findings reveal distinct roles for TRMT9B in the nervous system and highlight the significance of tRNA methyltransferase family diversification in metazoans.

Linking evolutionary dynamics to species extinction for flowering plants in global biodiversity hotspots

AbstractAimBiodiversity hotspots are regions with the highest species richness, and the most threatened species. Previous studies have shown that the extinction risk may be more related to evolutionary history than to species' traits. However, there is a knowledge gap on the relationship between evolutionary history and species extinction risk in biodiversity hotspots. Here, we link evolutionary history to species extinction risk for flowering plants (angiosperms) in global biodiversity hotspots.LocationGlobal biodiversity hotspots.MethodsWe calculated historical evolutionary measures (family species richness, family age, family diversification rate and the ratio of crown age to stem age) of angiosperms from 36 global biodiversity hotspots, which were grouped into 27 regions. Bayesian binomial‐logit univariate and multivariable regression models in conjunction with phylogenetic control and null models were used to identify the evolutionary history predictors of extinction risk for the 27 regions as a whole and for each of the regions.ResultsFamily species richness, family age and family diversification rate are all good indicators for predicting extinction risk. Specifically, when all the 27 regions were considered as a whole, families with higher species richness, older age and/or faster diversification rates have a higher risk of species extinction. However, high extinction risk in some regions, especially in temperate regions, tends to occur in families with low species richness and low diversification rates.Main conclusionsGeographic origin and evolutionary history of species should be jointly taken into account in conservation planning. In general, protection priority should be given to families with high species richness, ancient origins and fast diversification rate because these families seem to be prone to higher extinction risk. Additionally, different strategies should be applied to protect biodiversity in temperate versus tropical regions given that factors affecting extinction risk are different between these regions.

Biogeographic reconstruction of the migratory Neotropical fish family Prochilodontidae (Teleostei: Characiformes)

AbstractGeographically, widespread Neotropical fish lineages offer opportunities to reconstruct historical biogeography patterns and infer processes leading to modern ichthyological diversity and distribution. The characiform family Prochilodontidae is well suited for such reconstruction because their migrations limit population substructure within river systems. Therefore, their biogeographic history should match closely the history of connectivity among Neotropical river basins. Here, we combine a time‐calibrated phylogeny with biogeographic model testing to recover the history of this family's diversification. Results support the Miocene rise of the Andean Eastern Cordillera as a dispersal barrier, but also indicate a much earlier Eocene origin of the trans‐Andean genus Ichthyoelephas. Despite the early origin of the family and its three constituent genera, most prochilodontid lineages originated during the Miocene in Greater Amazonia, likely due to drainage reorganizations caused by Andean uplift. Subsequent speciation appears linked to interbasin exchanges and expansions of Amazonian lineages into Brazilian coastal systems. The modern richness of Prochilodus in easterly drainages appears to be relatively young, with only Prochilodus vimboides likely reaching that region prior to the late Miocene. The rise of the Vaupes Arch coincides with two splits between Orinocoan and Amazonian lineages circa 9 million years ago (Ma). However, two instances of later dispersal between these drainages reveal the permeability of the Vaupes Arch, suggesting that it may promote periodic speciation. This study illustrates how model‐based biogeographic studies of widespread groups can reconstruct historic paths of dispersal and help reveal how landscape evolution promoted modern diversity patterns.

Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.

The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant’s adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.

Marriage, Kids, and the Picket Fence? Household Type and Wealth among U.S. Households, 1989 to 2019.

Evidence on how parenthood impacts household wealth in the United States has been inconclusive, partially because previous studies have decontextualized parenthood from gender, marital, and relationship status. Yet, insights from economic sociology suggest that wealth-related behaviors are shaped by the intersection of identities, not by a binary classification of parental status. We examine net worth by the intersection of gender, parental, and relationship status during a period of increasing wealth inequality and family diversification. Using data from the Survey of Consumer Finances from 1989 through 2019, we show that aggregate comparisons between parents and non-parents mask substantial wealth variation across nine household types. Despite changing social selection into marriage and parenthood, married parents consistently held a wealth advantage over demographically similar adults in other household types. Married parents' wealth advantage descriptively arises from homeownership, perhaps because the combined spousal and parental identities are normatively and culturally associated with homeownership.

THE CLUSTER INITIATIVE AS A SPECIAL ECONOMIC PROJECT: EUROPEAN AND UKRAINIAN PRACTICES

Abstract. The article examines the European and Ukrainian practices, on cluster initiatives as a special development of economic projects. It is noted that in connection with the development and spread of globalization processes in the world increases competitiveness in the market and enterprises need to introduce new ways to strengthen the competitiveness and development of their production capacities. It is determined that the cluster is a stable system of enterprises and institutions associated with the production of innovative products, using the achievements of self-developing research institutions, training and education of research organizations and commercial structures, stimulating entrepreneurial activity in science and commercialization of progressive technologies. Emphasis is placed on the fact that the trends of the new cluster economy cause the following processes: Globalization and localization of business, production, capital, as processes of movement to integrated actions, targeted involvement of the country’s potentials, industries, priority resources. Primary sphere of exchange, increasing influence of financial authorities, financial oligarchy, financial markets as an element of supercontrol, hyper-power, centers of influence on changes in the reproduction of national products. Rapid information progress and sustainable priorities of comprehensive intellectualization of labor in all spheres of human activity, capacity building of the knowledge system and its tools of influence on the new man, etc. It is noted that world practice shows that when a cluster is created, all the industries within it begin to support each other. Competitive suppliers contribute to the development of consumer industries in the country. They provide them with technology, stimulate the development of common factors of production, and generate new producers. A single industry, competitive on the world market, can create a number of new interconnections, providing access to skilled labor, taking advantage of family diversification, or encouraging the emergence of new divorces. Overview that the development of cluster economy will contribute to the development of territorial communities and infrastructure of the regions, stimulate demand for education, now going through hard times, stop the outflow of human capital with subsequent employment in Ukraine, as well as stimulate innovation among young people, help improve their competitiveness in the global economic and political arena. Keywords: state, clusters, competitiveness, initiatives, market, support, stimulation. JEL Classіfіcatіon O30, F6, L25 Formulas: 0; fig. 3; tabl.: 0; bibl.: 10.

Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

BackgroundMany of genome features which could help unravel the often complex post-speciation evolution of closely related species are obscured because of their location in chromosomal regions difficult to accurately characterize using standard genome analysis methods, including centromeres and repeat regions.ResultsHere, we analyze the genome evolution and diversification of two recently diverged sister cotton species based on nanopore long-read sequence assemblies and Hi-C 3D genome data. Although D genomes are conserved in gene content, they have diversified in gene order, gene structure, gene family diversification, 3D chromatin structure, long-range regulation, and stress-related traits. Inversions predominate among D genome rearrangements. Our results support roles for 5mC and 6mA in gene activation, and 3D chromatin analysis showed that diversification in proximal-vs-distal regulatory-region interactions shape the regulation of defense-related-gene expression. Using a newly developed method, we accurately positioned cotton centromeres and found that these regions have undergone obviously more rapid evolution relative to chromosome arms. We also discovered a cotton-specific LTR class that clarifies evolutionary trajectories among diverse cotton species and identified genetic networks underlying the Verticillium tolerance of Gossypium thurberi (e.g., SA signaling) and salt-stress tolerance of Gossypium davidsonii (e.g., ethylene biosynthesis). Finally, overexpression of G. thurberi genes in upland cotton demonstrated how wild cottons can be exploited for crop improvement.ConclusionsOur study substantially deepens understanding about how centromeres have developed and evolutionarily impacted the divergence among closely related cotton species and reveals genes and 3D genome structures which can guide basic investigations and applied efforts to improve crops.

New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata.

Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.

Profitability and Efficiency of High Nature Value Marginal Farming in England

AbstractThe UK Brexit vote triggered a new wave of policy developments for a future outside the EU. In this context, we analyse the business performance of English hill and upland farms, characterised by marginal economic conditions but also high nature value (HNV). The analysis aims to help identify farm‐level management and policy options for greater economic, environmental and social sustainability. Business performance is measured as technical efficiency and the occurrence and persistence of abnormal profits, estimated through stochastic frontier analysis and static and dynamic panel‐data methods. The results help indicate rationales for recent trends including farm enlargement, farm family diversification, and agri‐environment scheme entry. The single farm payment is found to be negatively associated with farm technical efficiency while agri‐environmental subsidies were positively associated to short‐term farm profitability. Farm adaptation and resilience during a period of likely turbulence in external circumstances is discussed in light of these findings, as well as potential parallels with marginal HNV areas across Europe.

Rain Water Harvesting for Food and Livelihood Security: A case study from Pali, India

Abstract Arid zones are characterized by high evaporation, low and uneven rainfall, undulated topography, presence of salt layers at shallow depth in the soil and poor-quality ground water. Under these conditions an innovative farmer in the district of Pali in the state of Rajasthan, India explored options for farm diversification under hot-arid conditions at his farm. His motivation brought him to the ICAR-Central Arid Zone Research Institute (CAZRI), Krishi Vigyan Kendra (KVK) where he was trained in various basic aspects of rain water harvesting. KVK, Pali studied the methods and innovative ideas utilized by the farmers and the subsequent gain in yield and income by adoption of rainwater harvesting at his farm on a yearly basis. Initially he constructed a small rainwater harvesting structure by which he was able to store substantial quantities of water for longer duration. As a result of constant motivation, he constructed a concrete rainwater storage structure (40M x 40M x 3.5M) and explored further options to increase production at his farm. Also, development of goat farming, intercropping, raising fodder crops and grasses, and developing a fishery, all from the gains of water harvested from rains, gave him confidence and added to the prosperity of his farm. Presently, on farm productive activities, family labour mobilization and diversification provide him with a stable income. This experiential learning also led to new knowledge emerging from interactions among a hitherto powerful scientific hierarchy and served as role model for other farmers’ adoption of innovative techniques.

Positive Selection in the Evolution of Mammalian CRISPs.

Cysteine-RIch Secretory Proteins (CRISPs) constitute a versatile family, with functions in reptilian venom and mammalian reproduction. Mammals generally express three CRISPs, four in mice, and all are highly expressed in male reproductive tissues, either testis or accessory organs. Because reproductive proteins often evolve adaptively in response to post-copulatory sexual selection, we hypothesized that mammalian CRISPs, with important roles in male reproduction, could have undergone positive selection promoting their divergence. We explored the molecular adaptation of mammalian CRISPs applying phylogenetic methods. Our analyses revealed the evidence of positive selection in all mammalian CRISPs. The intensity of positive selection was heterogeneous among CRISP members, being stronger in CRISP3 than in CRISP1 and CRISP2, and also across functional domains, having stronger impact on Pathogenesis-Related 1 (PR-1) in CRISP2 and on Ion Channel Regulator (ICR) in CRISP1 and CRISP3. In addition, we discovered a new CRISP in some rodent species, suggesting that the acquisition of new CRISP components could contribute to male reproductive success or to acquire new physiological roles. Signatures of positive selection were not focused on any particular mammalian group, suggesting that adaptive evolution is a recurrent pattern in mammalian CRISPs. Our findings support a model of CRISP family diversification driven by episodes of duplication and posterior neofunctionalization, and provide potential adaptive changes responsible for interspecific differences in CRISPs activity.

Complex multicellularity in fungi: evolutionary convergence, single origin, or both?

Complex multicellularity represents the most advanced level of biological organization and it has evolved only a few times: in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not found in other lineages. Herein we review ecological, palaeontological, developmental and genomic aspects of complex multicellularity in fungi and discuss general principles of the evolution of complex multicellularity in light of its fungal manifestations. Fungi represent the only lineage in which complex multicellularity shows signatures of convergent evolution: it appears 8-11 times in distinct fungal lineages, which show a patchy phylogenetic distribution yet share some of the genetic mechanisms underlying complex multicellular development. To explain the patchy distribution of complex multicellularity across the fungal phylogeny we identify four key observations: the large number of apparently independent complex multicellular clades; the lack of documented phenotypic homology between these clades; the conservation of gene circuits regulating the onset of complex multicellular development; and the existence of clades in which the evolution of complex multicellularity is coupled with limited gene family diversification. We discuss how these patterns and known genetic aspects of fungal development can be reconciled with the genetic theory of convergent evolution to explain the pervasive occurrence of complex multicellularity across the fungal tree of life.

Alternative splicing after gene duplication drives CEACAM1-paralog diversification in the horse

BackgroundThe CEA gene family is one of the most rapidly evolving gene families in the human genome. The founder gene of the family is thought to be an ancestor of the inhibitory immune checkpoint molecule CEACAM1. Comprehensive analyses of mammalian genomes showed that the CEA gene family is subject to tremendous gene family expansion and contraction events in different mammalian species. While in some species (e.g. rabbits) less than three CEACAM1 related genes exist, were in others (certain microbat species) up to 100 CEACAM1 paralogs identified. We have recently reported that the horse has also an extended CEA gene family. Since mechanisms of gene family expansion and diversification are not well understood we aimed to analyze the equine CEA gene family in detail.ResultsWe found that the equine CEA gene family contains 17 functional CEACAM1-related genes. Nine of them were secreted molecules and eight CEACAMs contain transmembrane and cytoplasmic domain exons, the latter being in the focus of the present report. Only one (CEACAM41) gene has exons coding for activating signaling motifs all other CEACAM1 paralogs contain cytoplasmic exons similar to that of the inhibitory receptor CEACAM1. However, cloning of cDNAs showed that only one CEACAM1 paralog contain functional immunoreceptor tyrosine-based inhibitory motifs in its cytoplasmic tail. Three receptors have acquired a stop codon in the transmembrane domain and two have lost their inhibitory motifs due to alternative splicing events. In addition, alternative splicing eliminated the transmembrane exon sequence of the putative activating receptor, rendering it to a secreted molecule. Transfection of eukaryotic cells with FLAG-tagged alternatively spliced CEACAMs indicates that they can be expressed in vivo. Thus detection of CEACAM41 mRNA in activated PBMC suggests that CEACAM41 is secreted by lymphoid cells upon activation.ConclusionsThe results of our study demonstrate that alternative splicing after gene duplication is a potent mechanism to accelerate functional diversification of the equine CEA gene family members. This potent mechanism has created novel CEACAM receptors with unique signaling capacities and secreted CEACAMs which potentially enables equine lymphoid cells to control distantly located immune cells.

Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants.

The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C4 kranz anatomy, with implications for the engineering of C4 traits into C3 crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C4 photosynthesis and other developmental processes.

Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.

Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. About 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.

The diversification of the basic leucine zipper family in eukaryotes correlates with the evolution of multicellularity.

BackgroundMulticellularity evolved multiple times in eukaryotes. In all cases, this required an elaboration of the regulatory mechanisms controlling gene expression. Amongst the conserved eukaryotic transcription factor families, the basic leucine zipper (bZIP) superfamily is one of the most ancient and best characterised. This gene family plays a diversity of roles in the specification, differentiation and maintenance of cell types in plants and animals. bZIPs are also involved in stress responses and the regulation of cell proliferation in fungi, amoebozoans and heterokonts.ResultsUsing 49 sequenced genomes from across the Eukaryota, we demonstrate that the bZIP superfamily has evolved from a single ancestral eukaryotic gene and undergone multiple independent expansions. bZIP family diversification is largely restricted to multicellular lineages, consistent with bZIPs contributing to the complex regulatory networks underlying differential and cell type-specific gene expression in these lineages. Analyses focused on the Metazoa suggest an elaborate bZIP network was in place in the most recent shared ancestor of all extant animals that was comprised of 11 of the 12 previously recognized families present in modern taxa. In addition this analysis identifies three bZIP families that appear to have been lost in mammals. Thus the ancestral metazoan and eumetazoan bZIP repertoire consists of 12 and 16 bZIPs, respectively. These diversified from 7 founder genes present in the holozoan ancestor.ConclusionsOur results reveal the ancestral opisthokont, holozoan and metazoan bZIP repertoire and provide insights into the progressive expansion and divergence of bZIPs in the five main eukaryotic kingdoms, suggesting that the early diversification of bZIPs in multiple eukaryotic lineages was a prerequisite for the evolution of complex multicellular organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0598-z) contains supplementary material, which is available to authorized users.

Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly.

BackgroundWhile many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown.ResultsUsing next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation.ConclusionsGiven log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1832-6) contains supplementary material, which is available to authorized users.