Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

Background: New gene emergence is so far assumed to be mostly driven by duplication and divergence of existing genes. The possibility that entirely new genes could emerge out of the non-coding genomic background was long thought to be almost negligible. With the increasing availability of fully sequenced genomes across broad scales of phylogeny, it has become possible to systematically study the origin of new genes over time and thus revisit this question. Results: We have used phylostratigraphy to assess trends of gene evolution across successive phylogenetic phases, using mostly the well-annotated mouse genome as a reference. We find several significant general trends and confirm them for three other vertebrate genomes (humans, zebrafish and stickleback). Younger genes are shorter, both with respect to gene length, as well as to open reading frame length. They contain also fewer exons and have fewer recognizable domains. Average exon length, on the other hand, does not change much over time. Only the most recently evolved genes have longer exons and they are often associated with active promotor regions, i.e. are part of bidirectional promotors. We have also revisited the possibility that de novo evolution of genes could occur even within existing genes, by making use of an alternative reading frame (overprinting). We find several cases among the annotated Ensembl ORFs, where the new reading frame has emerged at a higher phylostratigraphic level than the original one. We discuss some of these overprinted genes, which include also the Hoxa9 gene where an alternative reading frame covering the homeobox has emerged within the lineage leading to rodents and primates (Euarchontoglires). Conclusions: We suggest that the overall trends of gene emergence are more compatible with a de novo evolution model for orphan genes than a general duplication-divergence model. Hence de novo evolution of genes appears to have occurred continuously throughout evolutionary time and should therefore be considered as a general mechanism for the emergence of new gene functions

Human biogeography and faunal exploitation in Diamante River basin, central western Argentina

A biogeographic model used to describe human peopling of southern Mendoza, central western Argentina, proposed an intensification process activated by an increase in population growth rate during the Late Holocene. During this process, high-ranked resources at the surroundings of residential camps were depleted, and hunter–gatherers broadened their diet by incorporating a larger number of low-ranked prey and domesticated plant resources. In this paper, we evaluate an alternative hypothesis, focusing on zooarchaeological data from the Diamante River basin. The results show that faunal resource intensification does not appear to have occurred in the Diamante River basin during the Late Holocene. Faunal consumption in Diamante River basin mainly reflects the local fauna in each ecological zone. The data do not show a lack of higher ranked resources. We suggest it is more likely that the demographic increase was not significant enough to cause an impact on the faunal resources. The archaeological evidence should be improved and analysed in smaller scales to continue with the intensification debate.Fil: Otaola, Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Giardina, Miguel Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Franchetti, Fernando Ricardo. University of Pittsburgh at Johnstown; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution

DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape..) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication"comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech

A theoretical study of the structural phases of Group 5B - 6B metals and their transport properties

In order to predict the stable and metastable phases of the bcc metals in the block of the Periodic Table defined by groups 5B to 6B and periods 4 to 6, as well as the structure dependence of their transport properties, we have performed full potential computations of the total energies per unit cell as a function of the c/a ratio at constant experimental volume. In all cases, a metastable body centered tetragonal (bct) phase was predicted from the calculations. The total energy differences between the calculated stable and metastable phases ranged from 0.09 eV/cell (vanadium) to 0.39 eV/cell (tungsten). The trends in resistivity as a function of structure and atomic number are discussed in terms of a model of electron transport in metals. Theoretical calculations of the electrical resistivity and other transport properties show that bct phases derived from group 5B elements are more conductive than the corresponding bcc phases, while bct phases formed from group 6B elements are less conductive than the corresponding bcc phases. Special attention is paid to the phases of tantalum where we show that the frequently observed beta phase is not a simple tetragonal distortion of bcc tantalum

Effect of the addition of β-mannanase on the performance, metabolizable energy, amino acid digestibility coefficients, and immune functions of broilers fed different nutritional levels

Three experiments were conducted to evaluate the effect of β-mannanase (BM) supplementation on the performance, metabolizable energy, amino acid digestibility, and immune function of broilers. A total of 1,600 broilers were randomly distributed in a 4 × 2 factorial arrangement (4 nutritional levels × 0 or 500 g/ton BM), with 10 replicates and 20 broilers per pen. The same design was used in the energy and digestibility experiments with 8 and 6 replicates, respectively, and 6 broilers per pen. The nutritional levels (NL) were formulated to meet the nutritional requirements of broilers (NL1); reductions of 100 kcal metabolizable energy (NL2); 3% of the total amino acids (NL3); and 100 kcal metabolizable energy and 3% total amino acids (NL4) from NL1. The serum immunoglobulin (Ig) concentration was determined in two broilers per pen, and these broilers were slaughtered to determine the relative weight of spleen, thymus, and bursa of Fabricius. Throughout the experiment, the lower nutritional levels reduced (P < 0.05) body weight gain (BWG) and increased (P < 0.05) feed conversion (FCR) for the NL4 treatment. The BM increased (P < 0.05) the BWG values and improved (P < 0.05) the FCR of the broilers. The apparent metabolizable energy corrected for nitrogen balance (AMEn) values were reduced (P < 0.05) for NL2 and NL3. The BM increased (P < 0.05) the AMEn values and reduced (P < 0.05) the excreted nitrogen. NL3 and NL4 reduced (P < 0.05) the true ileal digestibility coefficients (TIDc) of the amino acids cystine and glycine, and BM increased (P < 0.05) the TIDc for all amino acids. The addition of BM reduced (P < 0.05) the relative weights of the spleen and bursa. NL2 increased (P < 0.05) the Ig values, whereas BM reduced (P < 0.05) the serum IgA, IgG, and IgM values of the broilers. This study indicates that using suboptimal nutrient levels leads to losses in production parameters, whereas BM-supplemented diets were effective in improving performance, energy values, and TIDc levels of amino acids and immune response of broilers

Phytochrome B integrates light and temperature signals in Arabidopsis

Ambient temperature regulates many aspects of plant growth and development, but its sensors are unknown. Here, we demonstrate that the phytochrome B (phyB) photoreceptor participates in temperature perception through its temperature-dependent reversion from the active Pfr state to the inactive Pr state. Increased rates of thermal reversion upon exposing Arabidopsis seedlings to warm environments reduce both the abundance of the biologically active Pfr-Pfr dimer pool of phyB and the size of the associated nuclear bodies, even in daylight. Mathematical analysis of stem growth for seedlings expressing wild-type phyB or thermally stable variants under various combinations of light and temperature revealed that phyB is physiologically responsive to both signals. We therefore propose that in addition to its photoreceptor functions, phyB is a temperature sensor in plants

Electromechanical Modulations in Transition Metal Dichalcogenide Nanosheets: Implications for Environmental Sensors

Transition metal dichalcogenides (TMDs) are key players in the two-dimensional materials nanoarena due to their exquisite optoelectronic properties under a standard environment (room temperature and atmospheric pressure). Nevertheless, as reported in the literature, they may also portray interesting physical properties under different environments. Here, we show two distinct and significant electromechanical modulations in TMD nanosheets which are tuned by the environmental conditions (applied pressure and adsorbents). Using scanning probe microscopy techniques, we modify the environmental conditions and observe steplike rises in the electrical response of all studied TMDs (MoS2, WS2, MoSe2, and WSe2—monolayers and few layers). Ab initio calculations enable full understanding of specific mechanisms behind these electromechanical modulations, which may find important applications in the design of TMD-based environmental sensors

The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity

Citation: Hanschen, E. R., Marriage, T. N., Ferris, P. J., Hamaji, T., Toyoda, A., Fujiyama, A., . . . Olson, B. (2016). The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nature Communications, 7, 10. doi:10.1038/ncomms11370Additional Authors: Anderson, J.;Bakaric, R.;Luria, V.;Karger, A.;Kirschner, M. W.;Durand, P. M.;Michod, R. E.;Nozaki, H.The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions

Leptin Does Not Directly Affect CNS Serotonin Neurons to Influence Appetite

Serotonin (5-HT) and leptin play important roles in the modulation of energy balance. Here we investigated mechanisms by which leptin might interact with CNS 5-HT pathways to influence appetite. Although some leptin receptor (LepRb) neurons lie close to 5-HT neurons in the dorsal raphe (DR), 5-HT neurons do not express LepRb. Indeed, while leptin hyperpolarizes some non-5-HT DR neurons, leptin does not alter the activity of DR 5-HT neurons. Furthermore, 5-HT depletion does not impair the anorectic effects of leptin. The serotonin transporter-cre allele (Sert(cre)) is expressed in 5-HT (and developmentally in some non-5-HT) neurons. While Sert(cre) promotes LepRb excision in a few LepRb neurons in the hypothalamus, it is not active in DR LepRb neurons, and neuron-specific Sert(cre)-mediated LepRb inactivation in mice does not alter body weight or adiposity. Thus, leptin does not directly influence 5-HT neurons and does not meaningfully modulate important appetite-related determinants via 5-HT neuron function