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https://www.readbyqxmd.com/read/28713414/divergent-evolutionary-patterns-of-nac-transcription-factors-are-associated-with-diversification-and-gene-duplications-in-angiosperm
#1
Xiaoli Jin, Jing Ren, Eviatar Nevo, Xuegui Yin, Dongfa Sun, Junhua Peng
NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28695680/insights-into-the-historical-assembly-of-east-asian-subtropical-evergreen-broadleaved-forests-revealed-by-the-temporal-history-of-the-tea-family
#2
Xiang-Qin Yu, Lian-Ming Gao, Douglas E Soltis, Pamela S Soltis, Jun-Bo Yang, Liang Fang, Shi-Xiong Yang, De-Zhu Li
Subtropical evergreen broadleaved forests (EBLFs) inhabit large areas of East Asia. Although paleovegetation reconstructions have revealed that the subtropical EBLFs existed in Southwest China during the Miocene, the historical construction of these forests remains poorly known. Here, we used the tea family (Theaceae), a characteristic component of the subtropical EBLFs, to gain new insights into the assembly of this important biome. Using a robust phylogenetic framework of Theaceae based on plastome and nuclear ribosomal DNA sequence data, the temporal history of the family was reconstructed...
August 2017: New Phytologist
https://www.readbyqxmd.com/read/28694796/evolutionary-diversification-of-alanine-transaminases-in-yeast-catabolic-specialization-and-biosynthetic-redundancy
#3
Ximena Escalera-Fanjul, Carlos Campero-Basaldua, Maritrini Colón, James González, Dariel Márquez, Alicia González
Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28693418/phylogenetic-conservatism-in-skulls-and-evolutionary-lability-in-limbs-morphological-evolution-across-an-ancient-frog-radiation-is-shaped-by-diet-locomotion-and-burrowing
#4
Marta Vidal-García, J Scott Keogh
BACKGROUND: Quantifying morphological diversity across taxa can provide valuable insight into evolutionary processes, yet its complexities can make it difficult to identify appropriate units for evaluation. One of the challenges in this field is identifying the processes that drive morphological evolution, especially when accounting for shape diversification across multiple structures. Differential levels of co-varying phenotypic diversification can conceal selective pressures on traits due to morphological integration or modular shape evolution of different structures, where morphological evolution of different modules is explained either by co-variation between them or by independent evolution, respectively...
July 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#5
Áki Jarl Láruson
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28689725/phylogenetic-analysis-of-the-allometry-of-metabolic-rate-and-mitochondrial-basal-proton-leak
#6
Elias T Polymeropoulos, R Oelkrug, C R White, M Jastroch
The mitochondrial basal proton leak (MBPL) significantly contributes to high body temperatures (Tb) and basal metabolic rates (BMR) in endotherms. In endotherms at a given body mass (M), liver MBPL is higher than in ectotherms, supporting the notion that MBPL may partly explain the evolutionary increase in metabolic rate (MR), fostering endothermy. Here, we re-addressed this assumption by performing a phylogenetic analysis comparing all available liver MBPL data for ecto- and endotherms. While MBPL within endotherms negatively scales with M and BMR as shown previously, MBPL of ectotherms does not scale allometrically with M...
August 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28689721/studying-the-evolutionary-significance-of-thermal-adaptation-in-ectotherms-the-diversification-of-amphibians-energetics
#7
Roberto F Nespolo, Julio Figueroa, Jaiber J Solano-Iguaran
A fundamental problem in evolutionary biology is the understanding of the factors that promote or constrain adaptive evolution, and assessing the role of natural selection in this process. Here, comparative phylogenetics, that is, using phylogenetic information and traits to infer evolutionary processes has been a major paradigm . In this study, we discuss Ornstein-Uhlenbeck models (OU) in the context of thermal adaptation in ectotherms. We specifically applied this approach to study amphibians's evolution and energy metabolism...
August 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28685854/digest-shifting-biomes-insight-into-patterns-of-plant-radiation-and-dispersal
#8
Chloe M Nash
What determines a taxon's range? This is a deceptively simple question. It represents the intersection of ecology and evolution, requiring an understanding of the fundamental relationship between biotic and abiotic factors that can both constrain and drive assemblage structure and rates of lineage diversification. Modern methods have enabled robust analyses of this complex relationship through the integrated use of phylogenomics, community ecology, functional morphology, and biogeography. This article is protected by copyright...
July 7, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28684788/environmentally-driven-extinction-and-opportunistic-origination-explain-fern-diversification-patterns
#9
Samuli Lehtonen, Daniele Silvestro, Dirk Nikolaus Karger, Christopher Scotese, Hanna Tuomisto, Michael Kessler, Carlos Peña, Niklas Wahlberg, Alexandre Antonelli
Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679723/the-evolution-of-climatic-niches-in-squamate-reptiles
#10
Marcio R Pie, Leonardo L F Campos, Andreas L S Meyer, Andressa Duran
Despite the remarkable diversity found in squamate reptiles, most of their species tend to be found in warm/dry environments, suggesting that climatic requirements played a crucial role in their diversification, yet little is known about the evolution of their climatic niches. In this study, we integrate climatic information associated with the geographical distribution of 1882 squamate species and their phylogenetic relationships to investigate the tempo and mode of climatic niche evolution in squamates, both over time and among lineages...
July 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28674651/a-new-parrot-taxon-from-the-yucat%C3%A3-n-peninsula-mexico-its-position-within-genus-amazona-based-on-morphology-and-molecular-phylogeny
#11
Tony Silva, Antonio Guzmán, Adam D Urantówka, Paweł Mackiewicz
Parrots (Psittaciformes) are a diverse group of birds which need urgent protection. However, many taxa from this order have an unresolved status, which makes their conservation difficult. One species-rich parrot genus is Amazona, which is widely distributed in the New World. Here we describe a new Amazona form, which is endemic to the Yucatán Peninsula. This parrot is clearly separable from other Amazona species in eleven morphometric characters as well as call and behavior. The clear differences in these features imply that the parrot most likely represents a new species...
2017: PeerJ
https://www.readbyqxmd.com/read/28673048/taming-the-beast-a-community-teaching-material-resource-for-beast-2
#12
Joëlle Barido-Sottani, Veronika Bošková, Louis du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola F Müller, Julija Pecerska, David A Rasmussen, Chi Zhang, Alexei J Drummond, Tracy A Heath, Oliver G Pybus, Timothy G Vaughan, Tanja Stadler
Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic datasets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods...
June 29, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28656904/mapping-quorum-sensing-onto-neural-networks-to-understand-collective-decision-making-in-heterogeneous-microbial-communities
#13
Tahir Yusufaly, James Boedicker
Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. AI molecules bind to 'cognate' receptors, but also to 'non-cognate' receptors found in other strains, resulting in inter-strain crosstalk...
June 28, 2017: Physical Biology
https://www.readbyqxmd.com/read/28653569/the-mutable-vaccine-for-mutable-viruses
#14
Marilia Cascalho, Samuel J Balin, Jeffrey L Platt
Mutable viruses, such as HIV, pose difficult obstacles to prevention and/or control by vaccination. Mutable viruses rapidly diversify in populations and in individuals, impeding development of effective vaccines. We devised the 'mutable vaccine' to appropriate the properties of mutable viruses that undermine conventional strategies. The vaccine consists of a DNA construct encoding viral antigen and regulatory sequences that upon delivery to B cells target the enzymatic apparatus of 'somatic hypermutation' causing the construct to mutate one million-times baseline rates and allowing production and presentation of antigen variants...
June 2017: Immunotherapy
https://www.readbyqxmd.com/read/28650986/evolutionary-history-and-phylogeographic-relationships-of-shrews-from-sorex-araneus-group
#15
Paweł Mackiewicz, Magdalena Moska, Heliodor Wierzbicki, Przemysław Gagat, Dorota Mackiewicz
Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species...
2017: PloS One
https://www.readbyqxmd.com/read/28641575/phylogenetic-and-paleobotanical-evidence-for-late-miocene-diversification-of-the-tertiary-subtropical-lineage-of-ivies-hedera-l-araliaceae
#16
V Valcárcel, B Guzmán, N G Medina, P Vargas, J Wen
BACKGROUND: Hedera (ivies) is one of the few temperate genera of the primarily tropical Asian Palmate group of the Araliaceae, which extends its range out of Asia to Europe and the Mediterranean basin. Phylogenetic and phylogeographic results suggested Asia as the center of origin and the western Mediterranean region as one of the secondary centers of diversification. The bird-dispersed fleshy fruits of ivies suggest frequent dispersal over long distances (e.g. Macaronesian archipelagos), although reducing the impact of geographic barriers to gene flow in mainland species...
June 22, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28640437/repeated-evolution-of-vertebrate-pollination-syndromes-in-a-recently-diverged-andean-plant-clade
#17
Laura P Lagomarsino, Elisabeth J Forrestel, Nathan Muchhala, Charles C Davis
While specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators...
June 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28636789/out-of-the-dark-350-million-years-of-conservatism-and-evolution-in-diel-activity-patterns-in-vertebrates
#18
Samantha R Anderson, John J Wiens
Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e...
June 21, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28626938/role-of-parasite-transmission-in-promoting-inbreeding-i-infection-intensities-drive-individual-parasite-selfing-rates
#19
Jillian T Detwiler, Isabel C Caballero, Charles D Criscione
Among parasitic organisms, inbreeding has been implicated as a potential driver of host-parasite coevolution, drug-resistance evolution, and parasite diversification. Yet, fundamental topics about how parasite life histories impact inbreeding remain to be addressed. In particular, there are no direct selfing-rate estimates for hermaphroditic parasites in nature. Our objectives were to elucidate the mating system of a parasitic flatworm in nature and to understand how aspects of parasite transmission could influence the selfing rates of individual parasites...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28617640/microhabitat-and-climatic-niche-change-explain-patterns-of-diversification-among-frog-families
#20
Daniel S Moen, John J Wiens
A major goal of ecology and evolutionary biology is to explain patterns of species richness among clades. Differences in rates of net diversification (speciation minus extinction over time) may often explain these patterns, but the factors that drive variation in diversification rates remain uncertain. Three important candidates are climatic niche position (e.g., whether clades are primarily temperate or tropical), rates of climatic niche change among species within clades, and microhabitat (e.g., aquatic, terrestrial, arboreal)...
July 2017: American Naturalist
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