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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 84,502 bioRxiv papers from 363,737 authors.

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in category evolutionary biology

5,169 results found. For more information, click each entry to expand.

4041: Existence and functions of hypothalamic kisspeptin neuropeptide signaling system in a non-chordate deuterostome species
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Posted to bioRxiv 21 Nov 2019

Existence and functions of hypothalamic kisspeptin neuropeptide signaling system in a non-chordate deuterostome species
234 downloads evolutionary biology

Tianming Wang, Zheng Cao, Zhangfei Shen, Jingwen Yang, Xu Chen, Zhen Yang, Ke Xu, Xiaowei Xiang, Qiuhan Yu, Yimin Song, Weiwei Wang, Yanan Tian, Lina Sun, Libin Zhang, Su tGuo, Naiming Zhou

The kisspeptin (Kp) system is a central modulator of the hypothalamic-pituitary-gonadal axis in vertebrates. Its existence outside the vertebrate lineage remains largely unknown. Here we report the identification and characterization of Kp system in the sea cucumber Apostichopus japonicus . The gene encoding the Kp precursor, generates two mature neuropeptides, AjKiss1a and AjKiss1b. The Kp receptors, AjKissR1 and AjKissR2, are strongly activated by synthetic A. japonicus and vertebrate Kps, triggering a rapid intracellular mobilization of Ca2+, followed by receptor internalization. AjKissR1 and AjKissR2 share similar intracellular signaling pathways via Gαq/PLC/PKC/MAPK cascade, when activated by C-terminal decapeptide (AjKiss1b-10). The A. japonicus Kp system functions in mutiple tissues which are closely related to reproduction and metabolism. Overall, our findings uncover for the first time, to our knowledge, the existence and functions of the Kp system in a non-chordate species and provide new evidence to support the ancient origin of the hypothalamic neurosecretory system.

4042: The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs. autosomes
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Posted to bioRxiv 13 Apr 2020

The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs. autosomes
233 downloads evolutionary biology

Christelle Fraïsse, Himani Sachdeva

Interspecific crossing experiments have shown that sex chromosomes play a major role in the reproductive isolation of many species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has hardly been evaluated quantitatively in relation to autosomes. Yet, this genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of a XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow of the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression of the X (or Z) compared to autosomes. This effect is enhanced by certain types of dosage compensation or sex-biased forces; but it remains overall small (except when incompatibilities are recessive). We discuss these predictions in light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems. ### Competing Interest Statement The authors have declared no competing interest.

4043: Divergence in Thermostability of Arabidopsis Mitochondrial Nucleotide Exchange Factors Encoded by Duplicate Genes, MGE1 and MGE2
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Posted to bioRxiv 18 Feb 2019

Divergence in Thermostability of Arabidopsis Mitochondrial Nucleotide Exchange Factors Encoded by Duplicate Genes, MGE1 and MGE2
233 downloads evolutionary biology

Zih-teng Chen, Meng-Ju Hung, Shih-Jiun Yu, Tai-Yan Liao, Yao-Pin Lin, Rita P.-Y. Chen, Chien-Chih Yang, Yee-yung Charng

The divergence of duplicate genes links to organismic adaptation. In Arabidopsis thaliana two nuclear genes encode mitochondrial GrpEs, MGE1 and MGE2, the nucleotide exchange factors of DnaK/HSP70 chaperone. MGE1 and MGE2 are duplicate genes originated from a whole genome duplication event. They respond differentially to high temperature; MGE2 is heat-inducible and is required for Arabidopsis seedlings to tolerate prolonged heat stress, while MGE1 is constitutively expressed. Heterologous expression of MGE2 but not MGE1 restored the growth of E. coli grpE mutant cells at elevated temperatures, suggesting that MGE2 is more thermostable than MGE1. In this study, we directly compared the thermostability of the purified recombinant MGE1 and MGE2 by circular dichroism spectroscopy. The temperature midpoints of the unfolding transition (Tm) of MGE1 and MGE2 were about 38 and 46 °C, respectively, indicating that MGE2 is remarkably more stable than MGE1 at a higher temperature. Domain swapping between the two homologous proteins showed that the N-terminal region, including an unstructured sequence and a long α-helix domain, is the major determinant of the thermostability. Although MGE2 contains a conserved sequence derived from an exonized intron within the N-terminus unstructured region, deletion of this sequence did not substantially affect protein thermostability in vitro and complementation of E. coli and Arabidopsis heat sensitive mutants. Taken together, our results suggest that Arabidopsis MGE1 and MGE2 had diverged not only in transcriptional response but also in the thermostability of the encoded proteins, which may contribute to adaptation of plants to higher temperatures.

4044: Evolutionary Response to Resource Deprivation: Parallelism and Nonmonotonicity
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Posted to bioRxiv 05 Dec 2019

Evolutionary Response to Resource Deprivation: Parallelism and Nonmonotonicity
233 downloads evolutionary biology

Megan G Behringer, Wei-Chin Ho, Samuel F Miller, John C Meraz, Gwyneth F Boyer, Michael Lynch

Establishing reliable frameworks for predicting unknown outcomes from empirical observations is of great interest to ecologists and evolutionary biologists. Strong predictability in evolutionary responses has been previously demonstrated by the repeated observation of similar phenotypes or genotypes across multiple natural or experimental populations in analogous environments. However, the degree to which evolutionary outcomes can be predicted across environmental gradients, or in fluctuating environments, remains largely unexplored. Presumably, the phenotypic evolution in an intermediate environment could be interpolated from the evolved phenotypes observed in two extreme environments, but this assumption remains to be fully tested. Here, we report on the experimental evolution of Escherichia coli under three nutritional transfer periods: every day, every 10 days, and every 100 days, representing increasing severity in feast/famine cycles. After 900 days of experimental evolution, populations experiencing intermediate durations of starvation had evolved longer times to reach maximum growth rate, smaller colony sizes, higher biofilm formation, and higher mutation rates than populations evolving in the other environmental extremes. Because the intermediately starved populations exhibit significantly high molecular parallelism, these distinct phenotypes are likely due to non-monotonic deterministic forces instead of increased stochastic forces commonly associated with fluctuating environments. Our results demonstrate novel complexities associated with evolutionary predictability across environmental gradients and highlight the risk of using interpolation in evolutionary biology. ### Competing Interest Statement The authors have declared no competing interest.

4045: Density-dependent selection mediates harvest-induced evolution
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Posted to bioRxiv 27 Feb 2019

Density-dependent selection mediates harvest-induced evolution
233 downloads evolutionary biology

Alix Bouffet-Halle, Jacques Mériguet, David Carmignac, Simon Agostini, Alexis Millot, Samuel Perret, Eric Motard, Beatriz Decenciere, Eric Edeline

Harvesting has been demonstrated to cause rapid, yield-decreasing trait change towards slower somatic growth and earlier maturation in wild populations. These changes are largely considered to result from direct, density-independent harvest selection on traits. Here, we show that exact same trait changes may also indirectly result from a harvest-induced relaxation of density-dependent (K) natural selection for faster growth and delayed maturation. We exposed 12 pond populations of medaka fish (Oryzias latipes) to contrasted size-selective harvesting during 5 years, and show that harvesting effectively changed juvenile natural mortality from density-dependent to density-independent. We then laboratory-reared medaka progeny under contrasted food levels mimicking the environmental effects of a harvest-induced density gradient. Interaction between past harvest regime and present food environment on progeny traits revealed that harvest-induced trait changes in medaka resulted from selection in a low-food environment only, i.e., were driven by relaxed K-selection only, not by direct harvest selection. Feeding trials further demonstrated that trait changes were associated with reorganizations in rates of food acquisition, assimilation and allocation that were contingent upon the food environments. This is the first study to demonstrate that harvesting can induce undesirable distortions of natural selection that impair productivity traits. We conclude that sustaining harvesting yields over extended time scales requires a preservation of high population densities.

4046: Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice
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Posted to bioRxiv 12 Jun 2019

Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice
233 downloads evolutionary biology

Andrew D. Sweet, Kevin P Johnson, Stephen L Cameron

Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes ("minicircles") are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between 9 and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2-3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. All three methods indicated Columbicola spp. genomes are highly fragmented into 15-17 minicircles between 1,119 and 3,173 bp in length, with 1-4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

4047: CaMKII oxidation is a performance/disease trade-off in vertebrate evolution
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Posted to bioRxiv 12 Sep 2019

CaMKII oxidation is a performance/disease trade-off in vertebrate evolution
233 downloads evolutionary biology

Qinchuan Wang, Erick O. Hernández-Ochoa, Meera C Viswanathan, Ian D. Blum, Jonathan M. Granger, Kevin R. Murphy, An-Chi Wei, Susan Aja, Naili Liu, Corina M. Antonescu, Liliana D. Florea, C. Conover Talbot, David Mohr, Kathryn R Wagner, Sergi Regot, Richard M. Lovering, Mark N. Wu, Anthony Cammarato, Martin F. Schneider, Gabriel S. Bever, Mark E. Anderson

Reactive oxygen species (ROS) contribute to health and disease. CaMKII is a widely expressed enzyme whose activation by oxidation of regulatory domain methionines (ox-CaMKII) contributes to cardiovascular disease, asthma, and cancer. Here we integrate comparative genomic and experimental data to show that CaMKII activation by ROS arose more than half-a-billion years ago on the vertebrate stem lineage where it constituted a bridge between ROS and increased intracellular Ca2+ release, exercise responsive gene transcription, and improved performance in skeletal muscle. These enhancements to fight-or-flight physiology were likely key in facilitating a well-evidenced shift in the behavioural ecology of our immediate chordate ancestors, and, in turn, the evolutionary success of vertebrates. Still, the ox-CaMKII innovation for augmenting performance must be considered a critical evolutionary trade-off, as it rendered us more susceptible to common and often fatal diseases linked to excessive ROS.

4048: Genome-wide misexpression associated with hybrid sterility in Mimulus (monkeyflower)
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Posted to bioRxiv 30 Aug 2019

Genome-wide misexpression associated with hybrid sterility in Mimulus (monkeyflower)
232 downloads evolutionary biology

Rachel E. Kerwin, Andrea L Sweigart

Divergence in gene expression regulation is common between closely related species and may give rise to incompatibilities in their hybrid progeny. In this study, we investigated the relationship between regulatory evolution within species and reproductive isolation between species. We focused on a well-studied case of hybrid sterility between Mimulus guttatus and M. nasutus, two closely related yellow monkeyflower species, that is caused by two epistatic loci, hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2). We quantified and compared global transcript abundance across male and female reproductive tissues (i.e. stamens and carpels) of M. guttatus and M. nasutus, as well as sterile and fertile progeny from an advanced M. nasutus-M. guttatus introgression line that carries the hms1-hms2 incompatibility. We observed substantial variation in transcript abundance between M. guttatus and M. nasutus, including distinct but overlapping patterns of tissue-biased expression, providing evidence for regulatory divergence between these species. Furthermore, we found pervasive genome-wide misexpression exclusively associated with hybrid sterility - only observed in the affected tissues (i.e. stamens) of sterile introgression hybrids. Examining patterns of allele-specific expression in sterile and fertile hybrids, we found evidence of cis- and trans-regulatory divergence, as well as cis-trans compensatory evolution (likely to be driven by stabilizing selection). However, regulatory divergence does not appear to cause misexpression in sterile hybrids, which instead likely manifests as a downstream consequence of sterility itself.

4049: Preadaptation of pandemic GII.4 noroviruses in hidden virus reservoirs years before emergence
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Posted to bioRxiv 03 Jun 2019

Preadaptation of pandemic GII.4 noroviruses in hidden virus reservoirs years before emergence
232 downloads evolutionary biology

Christopher Ruis, Lisa C. Lindesmith, Michael L. Mallory, Paul D Brewer-Jensen, Josephine M Bryant, Veronica Costantini, Christopher Monit, Jan Vinjé, Ralph S. Baric, Richard A. Goldstein, Judith Breuer

The control of pandemic pathogens depends on early prediction of pandemic variants and, more generally, understanding origins of such variants and factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have suggested that new GII.4 pandemic viruses evolve from previous pandemic variants through substitutions in the antigenic region of the VP1 protein that enable evasion of host population immunity, leading to global spread. In contrast, we show here that the acquisition of new genetic and antigenic characteristics is not the proximal driver of new pandemics. Instead, pandemic GII.4 viruses circulate undetected for years before causing a new pandemic, during which time they diversify and spread over wide geographical areas. Serological data demonstrate that by 2003, some nine years before it emerged as a new pandemic, the ancestral 2012 pandemic strain had already acquired the antigenic characteristics that allowed it to evade prevailing population immunity against the previous 2009 pandemic variant. These results provide strong evidence that viral genetic changes are necessary but not sufficient for GII.4 pandemic spread. Instead, we suggest that it is changes in host population immunity that enable pandemic spread of an antigenically-preadapted GII.4 variant. These results indicate that predicting future GII.4 pandemic variants will require surveillance of currently unsampled reservoir populations. Furthermore, a broadly acting GII.4 vaccine will be critical to prevent future pandemics.

4050: Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses
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Posted to bioRxiv 16 Oct 2019

Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses
232 downloads evolutionary biology

Carlos Reding, Mark Hewlett, Tobias Bergmiller, Ivana Gudelj, R. E. Beardmore

Fisher suggested advantageous genes would spread through populations as a wave so we sought genetic waves in evolving populations, as follows. By fusing a fluorescent marker to a drug efflux protein (AcrB) whose expression provides Escherichia coli with resistance to some antibiotics, we quantified the evolution and spread of drug-resistant E. coli through spacetime using image analysis and quantitative PCR. As is done in hospitals routinely, we exposed the bacterium to a gradient of antibiotic in a 'disk diffusion' drug susceptibility test that we videoed. The videos show complex spatio-genomic patterns redolent of, yet more complex than, Fisher's predictions whereby a decelerating wave front of advantageous genes colonises towards the antibiotic source, forming bullseye patterns en route and leaving a wave back of bacterial sub-populations expressing AcrB at decreasing levels away from the drug source. qPCR data show that E. coli sited at rapidly-adapting spatial hotspots gain 2 additional copies of acr, the operon that encodes AcrB, within 24h and imaging data show resistant sub-populations thrive most near the antibiotic source due to non-monotone relationships between inhibition due to antibiotic and distance from the source. In the spirit of Fisher, we provide an explicitly spatial nonlinear diffusion equation that exhibits these properties too. Finally, linear diffusion theory quantifies how the spatial extent of bacterial killing scales with increases in antibiotic dosage, predicting that microbes can survive chemotherapies that have been escalated to 250x the clinical dosage if the antibiotic is diffusion-limited.

4051: Fungal adaptation to plant defenses through convergent assembly of metabolic modules
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Posted to bioRxiv 11 Jun 2018

Fungal adaptation to plant defenses through convergent assembly of metabolic modules
232 downloads evolutionary biology

Emile Gluck-Thaler, Vinod Vijayakumar, Jason C. Slot

The ongoing diversification of plant defense compounds exerts dynamic selection pressures on the microorganisms that colonize plant tissues. Evolutionary processes that generate resistance towards these compounds increase microbial fitness by giving access to plant resources and increasing pathogen virulence. These processes entail sequence-based mechanisms that result in adaptive gene functions, and combinatorial mechanisms that result in novel syntheses of existing gene functions. However, the priority and interactions among these processes in adaptive resistance remains poorly understood. Using a combination of molecular genetic and computational approaches, we investigated the contributions of sequence-based and combinatorial processes to the evolution of fungal metabolic gene clusters encoding stilbene cleavage oxygenases (SCOs), which catalyze the degradation of biphenolic plant defense compounds known as stilbenes into monophenolic molecules. We present phylogenetic evidence of convergent assembly among three distinct types of SCO gene clusters containing alternate combinations of phenolic catabolism. Multiple evolutionary transitions between different cluster types suggest recurrent selection for distinct gene assemblages. By comparison, we found that the substrate specificities of heterologously expressed SCO enzymes encoded in different clusters types were all limited to stilbenes and related molecules with a 4'-OH group, and differed modestly in substrate range and activity under the experimental conditions. Together, this work suggests a primary role for genome structural rearrangement, and the importance of enzyme modularity, in promoting fungal metabolic adaptation to plant defense chemistry.

4052: Multivariate phenotypic divergence along an urbanization gradient
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Posted to bioRxiv 11 Jul 2019

Multivariate phenotypic divergence along an urbanization gradient
232 downloads evolutionary biology

James S. Santangelo, Carole Advenard, L. Ruth Rivkin, Ken A. Thompson

A growing body of evidence suggests that natural populations can evolve to better tolerate the novel environmental conditions associated with urban areas. Invariably, studies of adaptive divergence in urban areas examine only one or a few traits at a time from populations residing only at the most extreme urban and nonurban habitats. Thus, whether urbanization is driving divergence in many traits simultaneously in a manner that varies with the degree of urbanization remains unclear. To address this gap, we generated seed families of white clover ( Trifolium repens ) collected from 27 populations along an urbanization gradient in Toronto, Canada, and grew them up to measure multiple phenotypic traits in a common garden. Overall, urban populations had later phenology and germination, larger flowers, thinner stolons, reduced cyanogenesis, greater biomass, and were more attractive to pollinators. Pollinator observations revealed near complete turnover between urban and nonurban sites, which may explain some of the observed divergence in floral traits and phenology. Our results suggest that adaptation to urban environments involves multiple organismal traits.

4053: Parsimonious scenario for the emergence of viroid-like replicons de novo
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Posted to bioRxiv 30 Mar 2019

Parsimonious scenario for the emergence of viroid-like replicons de novo
232 downloads evolutionary biology

Pablo Catalán, Santiago F. Elena, José A. Cuesta, Susanna Manrubia

Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluate the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g. RNA polymerases, RNases and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.

4054: Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles.
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Posted to bioRxiv 25 Sep 2018

Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles.
232 downloads evolutionary biology

Ivain Martinossi-Allibert, Emma Thilliez, Göran Arnqvist, David Berger

Whether sexual selection impedes or aids adaptation has become a pressing question in times of rapid environmental change and parallels the debate about how the evolution of individual traits impacts on population dynamics and viability. The net effect of sexual selection on population viability results from a balance between genetic benefits of good genes effects and costs of sexual conflict. Depending on how these facets of sexual selection are affected under environmental change, extinction of maladapted populations could either be avoided or accelerated. Here, we evolved seed beetles under three alternative mating regimes (polygamy, monogamy and male-limited selection) to disentangle the contributions of sexual selection, fecundity selection and male-female coevolution to individual reproductive success and population fitness. We compared these contributions between the ancestral environment and two new stressful environments (temperature and host plant shift). Evolution under polygamy resulted in the highest individual reproductive success in competitive context for both sexes. Moreover, females evolving only via sexual selection on their male siblings in the male-limited regime had similar reproductive success and higher fertility than females evolving under monogamy, suggesting that sexual selection on males had positive effects on female fitness components. Interestingly, male-limited sexual selection resulted in males that were robust to stress, compared to males from the two evolution regimes applying fecundity selection. We quantified the population-level consequences of this sex-specific adaptation and found evidence that costs of socio-sexual interactions were higher in male-limited lines compared to polygamous lines, and that this difference was particularly pronounced at elevated temperature to which males from the male-limited regime were more robust compared to their conspecific females. These results illustrate the tension between individual-level adaptation and population-level viability in sexually reproducing species and suggest that sex-specific selection can cause differences in environmental robustness that may impact population demography under environmental change.

4055: Mitochondrial genome of non-photosynthetic mycoheterotrophic plant Hypopitys monotropa,its structure, gene expression and RNA editing
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Posted to bioRxiv 25 Jun 2019

Mitochondrial genome of non-photosynthetic mycoheterotrophic plant Hypopitys monotropa,its structure, gene expression and RNA editing
232 downloads evolutionary biology

Viktoria Y. Shtratnikova, Mikhail I. Schelkunov, Aleksey A. Penin, Maria D. Logacheva

Heterotrophic plants – the plants that lost the ability to photosynthesis – are characterized by a number of changes at all levels of organization. Heterotrophic plants divide into two large categories – parasitic and mycoheterotrophic. The question of to what extent these changes are similar in these two categories is still open. Plastid genomes of non-photosynthetic plants are well characterized and they demonstrate similar patterns of reduction in both groups. In contrast, little is known about mitochondrial genomes of mycoheterotrophic plants. We report the structure of the mitochondrial genome of Hypopitys monotropa , a mycoheterotrophic member of Ericaceae, and the expression of mitochondrial genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon , its complete size is ~810 Kbp. We found an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations on parasitic non-photosynthetic plants. Transcriptome sequencing revealed trans-splicing of several genes and RNA editing in 33 genes of 38. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites which extensively integrate genetic material from their hosts.

4056: Comparative transcriptomics of albino and warningly coloured caterpillars
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Posted to bioRxiv 02 Jun 2018

Comparative transcriptomics of albino and warningly coloured caterpillars
231 downloads evolutionary biology

Juan A. Galarza

Colouration is perhaps one of the most prominent adaptations for survival and reproduction of most taxa. Colouration is of particular importance for aposematic species, which rely on their colouring and patterning to act as a warning signal against predators. Most research has focused on the evolution of warning colouration by natural selection. However, little information is available for colour mutants of aposematic species, particularly at the genomic level. Here I compare the transcriptomes of albino mutant caterpillars of the wood tiger moth (Arctia plantaginis) to those of their full-sibs having their distinctive orange-black warning colouration. The results showed >300 differentially expressed genes transcriptome-wide. Genes involved in the immune system, structural constituents of cuticle, and peptidase activity were mostly down-regulated in the albino larvae. Surprisingly, higher expression was observed in core melanin genes from albino larvae, suggesting that melanin synthesis may be disrupted in terminal ends of the pathway during its final conversion. I further identified 25 novel genes uniquely expressed in the albino larvae. Functional annotation showed that these genes are involved in nucleotide biosynthesis, copper ion transmembrane transport, and nucleic acid binding. Taken together, these results suggest that caterpillar albinism may not be due to a depletion of melanin precursor genes. In contrast, the albino condition may result from the combination of faulty melanin conversion late in its synthesis and structural deficiencies in the cuticle preventing its deposition.

4057: Control of Genetic Parasites Mediated Through Nucleoporin Evolution
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Posted to bioRxiv 07 Nov 2017

Control of Genetic Parasites Mediated Through Nucleoporin Evolution
231 downloads evolutionary biology

Paul A. Rowley, Kurt Patterson, Suzanne B. Sandmeyer, Sara L Sawyer

Yeasts serve as long-term hosts to several types of genetic parasites. Few studies have addressed the evolutionary trajectory of yeast genes that control the stable co-existence of these parasites with their host cell. In Saccharomyces yeasts, the retrovirus-like Ty retrotransposons must access the nucleus. We show that several genes encoding components of the yeast nuclear pore complex have experienced natural selection for substitutions that change the encoded protein sequence. By replacing these S. cerevisiae genes with orthologs from other Saccharomyces species, we discovered that natural sequence changes have affected the control of Ty retrotransposons. Specifically, changing the genetic sequence of NUP84 or NUP82 to what is found in other Saccharomyces species alters the retrotransposition of S. cerevisiae Ty1 and Ty3, respectively. Importantly, all tested housekeeping functions of NUP84 and NUP82 remained equivalent across species. The nuclear pore complex is the gatekeeper of the nucleus. It appears that nucleoporins are adapting to modulate the control of genetic parasites which access the nucleus, which is achieved despite the strict constraints imposed by host nuclear pore complex function.

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Posted to bioRxiv 29 Aug 2018

231 downloads evolutionary biology

Alzugaray María Eugenia, Bruno María Cecilia, Villalobos Sambucaro María José, Ronderos Jorge Rafael

Cell-cell communication is a basic principle in all organisms, necessary to facilitate the coordination and integration between cell populations. These systems act by mean of chemical messengers. Peptides constitute a highly diversified group of intercellular messengers widely distributed in nature, and regulate a great number of physiological processes in Metazoa. Being crucial for life, it would seem that they have appeared in the ancestral group from which Metazoa evolved, and were highly conserved along the evolutionary process. Peptides act mainly through G-protein coupled receptors (GPCRs), a great family of transmembrane molecules. GPCRs are also widely distributed in nature being present not only in metazoan, but also in Choanoflagellata (unicellular eukariotes related with metazoans), and even in Fungi. Among GPCRs, the Allatotropin/Orexin (AT/Ox) family is particularly characterized by the presence of the DRW motif in the second intracellular loop (IC Loop 2), and seems to be present in Cnidaria, Placozoa and in Bilateria, suggesting that it also was present in the common ancestor of Metazoa. Looking for the evolutionary history of this GPCR family we searched in the GenBank for sequences corresponding to this family of receptors (i.e. seven transmembrane domain and the E/DRW motif at the second IC Loop 2). Our results show that AT/Ox receptors were highly conserved along evolutionary history of Metazoa, and that they might be defined by the presence of the E/DRWYAI motif at the level of IC Loop 2. Molecular phylogenetic analyses performed by Maximum Likelihood method suggest that AT/Ox family of receptors reflects evolutionary relationships that agree with current understanding of phylogenetic relationships in Actinopterygii and Sauropsida, including also the largely discussed position of Testudines.

4059: The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms
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Posted to bioRxiv 28 Jul 2019

The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms
231 downloads evolutionary biology

Jan A. Veenstra

The primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

4060: The Deep(er) Roots of Eukaryotes and Akaryotes
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Posted to bioRxiv 17 Jan 2020

The Deep(er) Roots of Eukaryotes and Akaryotes
231 downloads evolutionary biology

Ajith Harish, David A. Morrison

Locating the root-node of the "tree of life" (ToL) is one of the hardest problems in phylogenetics. The root-node or the universal common ancestor (UCA) divides the descendants into organismal domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently, though, Williams and colleagues (W&C) claim that one is better supported than the other. Here, we argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well known that different character-types present different perspectives on evolutionary history that relate to different phylogenetic depths. Which of the 2D-ToL hypotheses is better supported depends on which kind of molecular features -- protein-domains or their component amino-acids -- are better for resolving the common ancestors (CA) at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA.

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