Coevolution Hypothesis Research Articles

Sub-Saharan African information potential to unveil adaptations to infectious disease.

Sub-Saharan Africa is the most promising region of the world to conduct high-throughput studies to unveil adaptations to infectious diseases due to several reasons, namely, the longest evolving time-depth in the Homo sapiens phylogenetic tree (at least two-third older than any other worldwide region); the continuous burden of infectious diseases (still number one in health/life threat); and the coexistence of populations practising diverse subsistence modes (nomadic or seminomadic hunter-gatherers and agropastoralists, and sedentary agriculturalists, small urban and megacity groups). In this review, we will present the most up-to-date results that shed light on three main hypotheses related with this adaptation. One is the hypothesis of coevolution between host and pathogen, given enough time for the establishment of this highly dynamic relationship. The second hypothesis enunciates that the agricultural transition was responsible for the increase of the infectious disease burden, due to the huge expansion of the sedentary human population and the cohabitation with domesticates as main reservoirs of pathogens. The third hypothesis states that the boosting of our immune system against pathogens by past selection may have resulted in maladaptation of the developed hygienic societies, leading to an increase of allergic, inflammatory and autoimmune disorders. Further work will enlighten the biological mechanisms behind these main adaptations, which can be insightful for translation into diagnosis, prognosis and treatment interventions.

Late Quaternary extinctions in the Indian Subcontinent

Over the last 50,000 years, a majority of megafauna went extinct globally. Only two regions, Africa, and tropical Asia retain megafaunal communities today. Their persistence in Africa has been attributed to co-evolution with hominins, but faunal dynamics are largely understudied in South Asia. Focusing on the Indian Subcontinent and using a novel dataset compiled from the published literature, we report an extremely size biased, but low magnitude extinction during the terminal Pleistocene and early Holocene—approximately 30,000 years after the arrival of Homo sapiens in the region. We document four mammalian extinctions—Palaeoloxodon namadicus, Stegodon namadicus, Hexaprotodon sp., and Equus namadicus; the extirpation of ostriches (Struthio camelus); and a pseudo-extinction of Indian aurochs (Bos namadicus). The per-capita extinction rate is comparable to eastern and southern Africa, but much lower than elsewhere. Given the long history of hominins in the Indian Subcontinent, and similar extinction patterns to those seen in Africa, we provide the first independent test of the co-evolution hypothesis, and further, suggest that robust population networks and climatic refugia may have allowed for the persistence of megafauna in this region.

A cross-country and country-specific modelling of stock market performance, bank development and global equity index in emerging market economies: A case of BRICS countries.

This study investigated in cross-country and panel form the interactions of bank development, stock market development and global equity index, focusing on the BRICS countries covering the period 1990 to 2018. We found a bidirectional causation between bank development (CPSGDP) and stock market performance as proxied by the depth of the markets (MCAPGDP) in the BRICS countries. Cointegration was also found using the panel cointegration framework and the bounds test for the ARDL estimators. This largely proves that a long-run relationship of both direct and reverse nature exists between bank development and stock market performance. For the bank development and market performance models respectively, all the error-correction terms were found to be negatively significant, indicating that they both share dynamic profile and adjust appreciably to deviations from equilibrium between the short run and the long run. The global equity index showed that stock market development interacts more with the global financial environment than bank development in the BRICS countries. Our findings support the complementarity and coevolution hypothesis in the stock market and bank development nexus.

Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis

BackgroundCommonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over 3500 km along the Brazilian coast, with several rocky shores displaying high substrate coverage. Apart from its singular invasiveness capacity, the documentation and, therefore, understanding of the role of symbiotic microorganisms in the sun-coral invasion is still scarce. However, in general, the broad and constant relationship between corals and microorganisms led to the development of co-evolution hypotheses. As such, it has been shown that the microbial community responds to environmental factors, adjustment of the holobiont, adapting its microbiome, and improving the hosts’ fitness in a short space of time. Here we describe the microbial community (i.e. Bacteria) associated with sun-coral larvae and adult colonies from a locality displaying a high invasion development.ResultsThe usage of high throughput sequencing indicates a great diversity of Bacteria associated with T. tagusensis, with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, and Firmicutes corresponding to the majority of the microbiome in all samples. However, T. tagusensis’ microbial core consists of only eight genera for colonies, and, within them, three are also present in the sequenced larvae. Overall, the microbiome from colonies sampled at different depths did not show significant differences. The microbiome of the larvae suggests a partial vertical transfer of the microbial core in this species.ConclusionAlthough diverse, the microbiome core of adult Tubastraea tagusensis is composed of only eight genera, of which three are transferred from the mother colony to their larvae. The remaining bacteria genera are acquired from the seawater, indicating that they might play a role in the host fitness and, therefore, facilitate the sun-coral invasion in the Southwestern Atlantic.

First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments.

Stereochemical nucleotide-amino acid interactions, in the form of noncovalent nucleotide-amino acid interactions, potentially produced the genetic code's codon-amino acid assignments. Empirical estimates of single nucleotide-amino acid affinities on surfaces and in solution are used to test whether trinucleotide-amino acid affinities determined genetic code assignments pending the principle "first arrived, first served": presumed early amino acids have greater codon-amino acid affinities than ulterior ones. Here, these single nucleotide affinities are used to approximate all 64 × 20 trinucleotide-amino acid affinities. Analyses show that (1) on surfaces, genetic code codon-amino acid assignments tend to match high affinities for the amino acids that integrated earliest the genetic code (according to Wong's metabolic coevolution hypothesis between nucleotides and amino acids) and (2) in solution, the same principle holds for the anticodon-amino acid assignments. Affinity analyses match best genetic code assignments when assuming that trinucleotides competed for amino acids, rather than amino acids for trinucleotides. Codon-amino acid affinities stick better to genetic code assignments than anticodon-amino acid affinities. Presumably, two independent coding systems, on surfaces and in solution, converged, and formed the current translation system. Proto-translation on surfaces by direct codon-amino acid interactions without tRNA-like adaptors coadapted with a system emerging in solution by proto-tRNA anticodon-amino acid interactions. These systems assigned identical or similar cognates to codons on surfaces and to anticodons in solution. Results indicate that a prebiotic metabolism predated genetic code self-organization.

Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids.

The conditions that led to the formation of the first organisms and the ways that life originates from a lifeless chemical soup are poorly understood. The recent hypothesis of “RNA-peptide coevolution” suggests that the current close relationship between amino acids and nucleobases may well have extended to the origin of life. We now show how the interplay between these compound classes can give rise to new self-replicating molecules using a dynamic combinatorial approach. We report two strategies for the fabrication of chimeric amino acid/nucleobase self-replicating macrocycles capable of exponential growth. The first one relies on mixing nucleobase- and peptide-based building blocks, where the ligation of these two gives rise to highly specific chimeric ring structures. The second one starts from peptide nucleic acid (PNA) building blocks in which nucleobases are already linked to amino acids from the start. While previously reported nucleic acid-based self-replicating systems rely on presynthesis of (short) oligonucleotide sequences, self-replication in the present systems start from units containing only a single nucleobase. Self-replication is accompanied by self-assembly, spontaneously giving rise to an ordered one-dimensional arrangement of nucleobase nanostructures.

Divergent molecular and growth responses of young \u201cCabernet Sauvignon\u201d (Vitis vinifera) plants to simple and mixed infections with Grapevine rupestris stem pitting-associated virus

Grapevine rupestris stem pitting associated virus (GRSPaV) is one of the most widely distributed viruses; even so, little is known about its effect on Vitis vinifera. To provide new insights, the effects of single and mixed GRSPaV infections on the V. vinifera cultivar “Cabernet Sauvignon” were studied by evaluating growth parameters, such as measurements of the total plant length, the number and distance of internodes and the number of leaves per shoot. In addition, parameters relating to gas exchange, i.e., the stomatal conductance, net photosynthetic rate, internal CO2 concentration and leaf transpiration, were also assessed. All the measurements were performed in one- and two-year-old plants with a single GRSPaV infection or mixed infections of GRSPaV and Grapevine fanleaf virus (GFLV). The results show that the plant phytosanitary status did not significantly alter the growth and gas exchange parameters in one-year-old plants. However, in two-year-old plants, single GRSPaV infections increased shoot elongation, which was accompanied by the overexpression of genes associated with the gibberellic acid response pathway. The gas exchange parameters of these plants were negatively affected, despite exhibiting higher LHCII gene expression. Plants with mixed infections did not have modified growth parameters, although they presented a greater reduction in the primary photosynthetic parameters evaluated with no change in LHCII expression. The results presented here confirm the co-evolution hypothesis for V. vinifera and GRSPaV during the early stages of plant development, and they provide new evidence about the effects of GRSPaV and GFLV co-infections on the “Cabernet Sauvignon” cultivar.

The social coevolution hypothesis for the origin of enzymatic cooperation.

At the start of life, the origin of a primitive genome required individual replicators, or genes, to act like enzymes and cooperatively copy each other. The evolutionary stability of such enzymatic cooperation poses a problem, because it would have been susceptible to parasitic replicators that did not act like enzymes but could still benefit from the enzymatic behaviour of other replicators. Existing hypotheses to solve this problem require restrictive assumptions that may not be justified, such as the evolution of a cell membrane before the evolution of enzymatic cooperation. We show theoretically that, instead, selection itself can lead to replicators grouping themselves together in a way that favours cooperation. We show that the tendency to physically associate with others and cooperative enzymatic activity can coevolve, leading to the evolution of physically linked cooperative replicators. Our results shift the empirical problem from a search for special environmental conditions to questions about what types of phenotypes can be produced by simple replicators.

Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms

Clonal reproduction is thought to facilitate polyploid establishment in the angiosperms, but the evolutionary relationship between polyploidy and clonality has not been thoroughly tested. A perennial life history may confer many of the same advantages, and the relative importance of clonality versus perenniality is unknown. We used phylogenetic comparative analyses of 1751 species to examine associations between polyploidy, clonality, and life history. We test hypotheses of co-evolution by determining the sequence of trait development. Polyploidy is associated with both clonality and perenniality across species, and analyses show that clonality can be an important predictor of polyploidy beyond perenniality. Tests of directionality on our full dataset suggest that polyploidy is more likely to promote clonality or perenniality than vice versa, although there are significant differences in patterns of co-evolution among major angiosperm groups. Our results suggest that polyploidy and clonal reproduction are evolutionarily associated across the angiosperms, even when perenniality is considered, but we find little evidence at the whole-angiosperm level for the hypothesis that clonality promotes polyploidy. However, variation among different clades indicates that polyploidy and clonality are interacting in diverse ways, likely to be due to the variable roles of clonality in their evolutionary histories.

Interspecific Differences in the Larval Performance of Pieris Butterflies (Lepidoptera: Pieridae) Are Associated with Differences in the Glucosinolate Profiles of Host Plants.

The tremendous diversity of plants and herbivores has arisen from a coevolutionary relationship characterized by plant defense and herbivore counter adaptation. Pierid butterfly species feed on Brassicales plants that produce glucosinolates as a chemical deterrent against herbivory. In turn, the larvae of pierids have nitrile specifier proteins (NSPs) that are expressed in their gut and disarm glucosinolates. Pierid butterflies are known to have diversified in response to glucosinolate diversification in Brassicales. Therefore, each pierid species is expected to have a spectrum of host plants characterized by specific glucosinolate profiles. In this study, we tested whether the larval performance of different Pieris species, a genus in Pieridae (Lepidoptera: Pieridae), was associated with plant defense traits of putative host plants. We conducted feeding assays using larvae of three Pieris species and 10 species of the Brassicaceae family possessing different leaf physical traits and glucosinolate profile measurements. The larvae of Pieris rapae responded differently in the feeding assays compared with the other two Pieris species. This difference was associated with differences in glucosinolate profiles but not with variations in physical traits of the host plants. This result suggests that individual Pieris species are adapted to a subset of glucosinolate profiles within the Brassicaceae. Our results support the idea that the host ranges of Pieris species depend on larval responses to glucosinolate diversification in the host species, supporting the hypothesis of coevolution between butterflies and host plants mediated by the chemical arms race.

Tempo and mode in coevolution of Agave sensu lato (Agavoideae, Asparagaceae) and its bat pollinators, Glossophaginae (Phyllostomidae)

The genus Agave sensu lato contains ca. 211 described species, many of which are considered keystone species because of their ecological dominance and the quantity of resources they provide with their massive, nectar-rich inflorescences. The large diversity of Agave species has been hypothesized as being related to their reproductive strategy (predominantly monocarpic) and diverse pollinators (e.g., bats, hummingbirds, hawkmoths). In particular, Agave species provide resources that a few genera of nectar feeding bats from the subfamily Glosophaginae are dependent upon. To explore a possible coevolutionary relationship between Agave and the bat species that pollinate them, we calibrated molecular phylogenies of both groups and looked for a correlation in their dates of divergence. One coding and two non-coding regions of the chloroplast genome were sequenced from 49 species of the Agavoideae (Asparagaceae), and the mitochondrial gene Cyt-b and nuclear coding gene RAG2 were either sequenced or obtained from gene bank for 120 Phyllostomid bats. Results from the analyses indicate that Agave sensu lato is a young genus (estimated crown age 2.7–8.5/stem age 4.6–12.3 Ma), with an increasing diversification rate, and the highest speciation rate among Agavoideae’s clades. The origin of the Glossophaginae bats (stem age 20.3–23.5 Ma) occurred prior to the stem age of Agave sensu lato, while the origin of the current pollinators of Agave species, members of the genera Glossophaga, Leptonycteris, Anoura, Choeronyscus, Musonycteris and Choeronycteris, was estimated to be around 6.3–16.2 Ma, overlapping with the stem age of Agave sensu lato, supporting the hypothesis of diffuse coevolution.

Yeast XRS2 and human NBN gene: Experimental evidence for homology using codon optimized cDNA.

The genes, XRS2 in Saccharomyces cerevisiae and NBN in mammals, have little sequence identity at the amino acid level. Nevertheless, they are both found together with MRE11 and RAD50 in a highly conserved protein complex which functions in the repair of DNA double-strand breaks. Here, we have examined the evolutionary and functional relationship of these two genes by cross-complementation experiments. These experiments necessitated sequence correction for specific codon usage before they could be successfully conducted. We present evidence that despite extreme sequence divergence nibrin can, at least partially, replace Xrs2 in the cellular DNA damage response, and Xrs2 is able to promote nuclear localization of MRE11 in NBS cells. We discuss that the extreme sequence divergence reflects a unique adaptive pressure during evolution related to the specific eukaryotic role for both Xrs2 and nibrin in the subcellular localisation of the DNA repair complex. This, we suggest, is of particular relevance when cells are infected by viruses. The conflict hypothesis of co-evolution of DNA repair genes and DNA viruses may thus explain the very low sequence identity of these two homologous genes.

Sobre a coevolução das estruturas comercial e tecnológica: teoria e evidência empírica

O objetivo deste artigo é analisar em que medida os padrões de especialização tecnológica coevoluem com os de especialização comercial. Para isso, o artigo assume que existe interdependência entre as estruturas produtiva, tecnológica e comercial e, portanto, os choques de demanda subjacentes aos processos de integração econômica gerarão impactos na estrutura tecnológica. A hipótese de coevolução é testada para 35 países e 38 setores no período de 1996 a 2013 por meio de estimações em dados em painel. Os resultados mostram que ambos os padrões (comercial e tecnológico) coevoluíram, especialmente nos setores mais intensivos em conhecimento, registrando-se um importante efeito demand pull nos setores mais internacionalizados. A ação das empresas multinacionais se revelou como um direcionador menor da evolução dos padrões de especialização tecnológica dos países hospedeiros. Entre os determinantes autônomos da especialização tecnológica, a cumulatividade parece jogar um papel crucial, enquanto a oportunidade tecnológica só se mostrou relevante nas indústrias intensivas em recursos naturais.

Metabolite-Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks.

How individual enzymes evolved is relatively well understood. However, individual enzymes rarely confer a physiological advantage on their own. Judging by its current state, the emergence of metabolism seemingly demanded the simultaneous emergence of many enzymes. Indeed, how multicomponent interlocked systems, like metabolic pathways, evolved is largely an open question. This complexity can be unlocked if we assume that survival of the fittest applies not only to genes and enzymes but also to the metabolites they produce. This review develops our current knowledge of enzyme evolution into a wider hypothesis of pathway and network evolution. We describe the current models for pathway evolution and offer an integrative metabolite-enzyme coevolution hypothesis. Our hypothesis addresses the origins of new metabolites and of new enzymes and the order of their recruitment. We aim to not only survey established knowledge but also present open questions and potential ways of addressing them.

In the Beginning was a Mutualism - On the Origin of Translation.

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.

Modification and functional adaptation of the MBF1 gene family in the lichenized fungus Endocarpon pusillum under environmental stress

The multiprotein-bridging factor 1 (MBF1) gene family is well known in archaea, non-lichenized fungi, plants, and animals, and contains stress tolerance-related genes. Here, we identified four unique mbf1 genes in the lichenized fungi Endocarpon spp. A phylogenetic analysis based on protein sequences showed the translated MBF1 proteins of the newly isolated mbf1 genes formed a monophyletic clade different from other lichen-forming fungi and Ascomycota groups in general, which may reflect the evolution of the biological functions of MBF1s. In contrast to the lack of function reported in yeast, we determined that lysine114 in the deduced Endocarpon pusillum MBF1 protein (EpMBF1) had a specific function that was triggered by environmental stress. Further, the Endocarpon-specific C-terminus of EpMBF1 was found to participate in stress tolerance. Epmbf1 was induced by a number of abiotic stresses in E. pusillum and transgenic yeast, and its stress-resistant ability was stronger than that of the yeast mbf1. These findings highlight the evolution and function of EpMBF1 and provide new insights into the co-evolution hypothesis of MBF1 and TATA-box-binding proteins.

Teaching to make stone tools: new experimental evidence supporting a technological hypothesis for the origins of language

The relationship between lithic technology, learning and language is a topic of growing interest in human evolution studies, and has therefore been the subject of numerous scientific papers in recent years. To evaluate the role of language in the social transmission of lithic technology, we designed and developed an experimental protocol through which we compared the acquisition of knapping skills in thirty non-experts in the early stages of learning, by means of three mechanisms of social transmission: imitation-emulation, gestural communication, and verbal communication. All the apprentice knappers carried out the experimental task with blanks that were equal in shape and size, and were requested to replicate what the expert knapper was doing: the alternating method, a sufficiently simple, but systematic technique for detaching flakes from a core. We analysed each participant’s actions, including those of the master knapper, the final products (flakes and cores), and the knapping sequences, by analysing the refits. Our results show that the apprentices improved their knapping skills in teaching conditions -both gestural and verbal communication-, and specially through the latter. In conclusion, our study supports the hypothesis of co-evolution between lithic technology and social learning, which could have favoured the emergence of verbal language.

A field study with geometrid moths to test the coevolution hypothesis of red autumn colours in deciduous trees

AbstractRed autumn colouration of trees is the result of newly synthesized anthocyanin pigments in senescing autumn leaves. As anthocyanin accumulation is costly and the trait is not present in all species, anthocyanins must have an adaptive significance in autumn leaves. According to the coevolution hypothesis of autumn colours, red autumn leaves warn herbivorous insects – especially aphids that migrate to reproduce in trees in the autumn – that the tree will not be a suitable host for their offspring in spring due to a high level of chemical defence or lack of nutrients. The signalling allows trees to avoid herbivores and herbivores to choose better host trees. In this study the coevolution hypothesis was tested with four deciduous tree species that have red autumn leaf colouration – European aspen (Populus tremula L.) (Salicaceae), rowan (Sorbus aucuparia L.) (Rosaceae), mountain birch [Betula pubescens ssp. czerepanovii (NI Orlova) Hämet‐Ahti], and dwarf birch (Betula nana L.) (Betulaceae), and with two generalist herbivores, the autumnal moth [Epirrita autumnata (Borkhausen)] and the winter moth [Operophtera brumata (L.)] (both Lepidoptera: Geometridae). Anthocyanin concentrations of autumn leaves were determined from leaf samples and the growth performance parameters of the moth larvae on the study trees were measured in the spring. Trees with higher anthocyanin concentration in the autumn were predicted to be low‐quality food for the herbivores. Our results clearly showed that anthocyanin concentration was not correlated with the growth performance of the moths in any of the studied tree species. Thus, our study does not support the coevolution hypothesis of autumn colours.

Putting the Cart Before the Horse: Co-evolution of the Universe and Observers as an Explanatory Hypothesis

The answer to the fine-tuning problem of the universe has been traditionally sought in terms of either design or multiverse. In philosophy circles, this is sometimes expanded by adding the option of explanatory nihilism—the claim that there is no explanation for statements of that high level of generality: fine-tunings are brute facts. In this paper, we consider the fourth option which, at least in principle, is available to us: co-evolution of the universe and observers. Although conceptual roots of this approach could be found already in ancient stoicism, it is still the least investigated explanatory option for resolving the problem of empirical fine tunings. We offer two preliminary models along which the co-evolution hypothesis could be developed further. They are still on the level of speculative metaphysics, but there are opportunities along the way to generate predictions which are in principle testable, especially in the domain of large-scale numerical simulations.

Phylogenies of symbiotic genes of Bradyrhizobium symbionts of legumes of economic and environmental importance in Brazil support the definition of the new symbiovars pachyrhizi and sojae

Bradyrhizobium comprises most tropical symbiotic nitrogen-fixing strains, but the correlation between symbiotic and core genes with host specificity is still unclear. In this study, the phylogenies of the nodY/K and nifH genes of 45 Bradyrhizobium strains isolated from legumes of economic and environmental importance in Brazil (Arachis hypogaea, Acacia auriculiformis, Glycine max, Lespedeza striata, Lupinus albus, Stylosanthes sp. and Vigna unguiculata) were compared to 16S rRNA gene phylogeny and genetic diversity by rep-PCR. In the 16S rRNA tree, strains were distributed into two superclades—B. japonicum and B. elkanii—with several strains being very similar within each clade. The rep-PCR analysis also revealed high intra-species diversity. Clustering of strains in the nodY/K and nifH trees was identical: 39 strains isolated from soybean grouped with Bradyrhizobium type species symbionts of soybean, whereas five others occupied isolated positions. Only one strain isolated from Stylosanthes sp. showed similar nodY/K and nifH sequences to soybean strains, and it also nodulated soybean. Twenty-one representative strains of the 16S rRNA phylogram were selected and taxonomically classified using a concatenated glnII-recA phylogeny; nodC sequences were also compared and revealed the same clusters as observed in the nodY/K and nifH phylograms. The analyses of symbiotic genes indicated that a large group of strains from the B. elkanii superclade comprised the novel symbiovar sojae, whereas for another group, including B. pachyrhizi, the symbiovar pachyrhizi could be proposed. Other potential new symbiovars were also detected. The co-evolution hypotheses is discussed and it is suggested that nodY/K analysis would be useful for investigating the symbiotic diversity of the genus Bradyrhizobium.