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Ancestral character reconstruction

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https://www.readbyqxmd.com/read/29125205/reconstructing-pectoral-appendicular-muscle-anatomy-in-fossil-fish-and-tetrapods-over-the-fins-to-limbs-transition
#1
Julia L Molnar, Rui Diogo, John R Hutchinson, Stephanie E Pierce
The question of how tetrapod limbs evolved from fins is one of the great puzzles of evolutionary biology. While palaeontologists, developmental biologists, and geneticists have made great strides in explaining the origin and early evolution of limb skeletal structures, that of the muscles remains largely unknown. The main reason is the lack of consensus about appendicular muscle homology between the closest living relatives of early tetrapods: lobe-finned fish and crown tetrapods. In the light of a recent study of these homologies, we re-examined osteological correlates of muscle attachment in the pectoral girdle, humerus, radius, and ulna of early tetrapods and their close relatives...
November 10, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29123238/reconstructing-yeasts-phylogenies-and-ancestors-from-whole-genome-data
#2
Bing Feng, Yu Lin, Lingxi Zhou, Yan Guo, Robert Friedman, Ruofan Xia, Fei Hu, Chao Liu, Jijun Tang
Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29113924/why-are-there-so-many-sedges-sumatroscirpeae-a-missing-piece-in-the-evolutionary-puzzle-of-the-giant-genus-carex-cyperaceae
#3
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford
For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers...
November 4, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29111476/phylogenomics-and-evolution-of-floral-traits-in-the-neotropical-tribe-malmeeae-annonaceae
#4
J C Lopes, L W Chatrou, R Mello-Silva, P J Rudall, M G Sajo
Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have arisen several times in different lineages. The majority of androdioecious species of Annonaceae belong to the Neotropical tribe Malmeeae. In addition to these species, Pseudoxandra spiritus-sancti was recently confirmed to be androdioecious...
October 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29024751/phylogenomics-reveals-habitat-associated-body-shape-divergence-in-oryzias-woworae-species-group-teleostei-adrianichthyidae
#5
Daniel F Mokodongan, Javier Montenegro, Koji Mochida, Shingo Fujimoto, Asano Ishikawa, Ryo Kakioka, Lengxob Yong, Mulis, Renny K Hadiaty, Ixchel F Mandagi, Kawilarang W A Masengi, Nakatada Wachi, Yasuyuki Hashiguchi, Jun Kitano, Kazunori Yamahira
The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations...
October 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29020180/molecular-tracing-of-the-geographical-origin-of-hiv-1-infection-and-patterns-of-epidemic-spread-among-migrants-who-inject-drugs-in-athens
#6
D Paraskevis, E Kostaki, G K Nikolopoulos, V Sypsa, M Psichogiou, J Del Amo, I Hodges-Mameletzis, D Paraskeva, A Skoutelis, M Malliori, L Williams, S R Friedman, G L Daikos, A Hatzakis
Background: High numbers of HIV-1 infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrant who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. Methods: Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1/1/2011-31/10/2014. Phylogenetic analyses used maximum likelihood estimation...
August 16, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28993971/ancestral-sequence-reconstruction-with-maximum-parsimony
#7
Lina Herbst, Mareike Fischer
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees...
October 5, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28948216/glaciation-as-a-migratory-switch
#8
Robert M Zink, Aubrey S Gardner
Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28878063/mitochondrial-phylogenomics-of-hemiptera-reveals-adaptive-innovations-driving-the-diversification-of-true-bugs
#9
Hu Li, John M Leavengood, Eric G Chapman, Daniel Burkhardt, Fan Song, Pei Jiang, Jinpeng Liu, Xuguo Zhou, Wanzhi Cai
Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes...
September 13, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28819805/diversity-and-evolution-of-leaf-anatomical-characters-in-taxaceae-s-l-fluorescence-microscopy-reveals-new-delimitating-characters
#10
Christoph Elpe, Patrick Knopf, Thomas Stützel, Christian Schulz
Taxaceae s.l. comprise six genera (including Cephalotaxus) and about 35 species; The present study aims to give new insights into the evolution of this family, especially into the phylogenetic position of Cephalotaxus. Moreover, only little is known about comparative leaf anatomy of this family and this study aims to expose and interpret the diversity and evolution of leaf anatomical characters and to assess their applicability to identify taxa at the generic and species level. A detailed phylogeny was reconstructed, using both maximum likelihood and Bayesian inference, with a combined dataset of four molecular markers from the plastid and nuclear genomes...
August 17, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28819749/time-dependent-asymmetric-linear-parsimonious-ancestral-state-reconstruction
#11
Gilles Didier
The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter...
October 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28790088/transitions-from-distyly-to-homostyly-are-associated-with-floral-evolution-in-the-buckwheat-genus-fagopyrum
#12
Ling-Yun Wu, Bo Wang, Daniel J Schoen, Shuang-Quan Huang
PREMISE OF THE STUDY: Documenting trait transitions among species with dimorphic flowers can help to test whether similar patterns of selection are responsible for divergence in floral traits among different species. Heterostyly is thought to promote outcrossing. Theory suggests that the evolutionary transition from heterostylous to homostylous flowers should be accompanied by a reduction in floral size in which pollen size and style length are expected to covary. Patterns of such correlated floral trait evolution have not, however, been widely examined...
August 8, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28776667/relating-appendicular-skeletal-variation-of-sigmodontine-rodents-to-locomotion-modes-in-a-phylogenetic-context
#13
Ludmilla Carvalho Coutinho, João Alves de Oliveira
Sigmodontinae rodents constitute the second-largest subfamily among mammals. Alongside the taxonomic diversity, they are also ecologically diverse, exhibiting a wide array of locomotion modes, with semifossorial, terrestrial, semiaquatic, scansorial, arboreal, and saltatorial forms. To understand the ecomorphologic aspects that allow these rodents to display such locomotion diversity, we analyzed 35 qualitative characters of the appendicular skeleton (humerus, ulna, radius, scapula, femur, tibia, ilium, ischium and pubis) in 795 specimens belonging to 64 species, 34 genera and 10 tribes, representing all locomotion modes assigned to this subfamily...
August 4, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28763051/the-ancestral-flower-of-angiosperms-and-its-early-diversification
#14
Hervé Sauquet, Maria von Balthazar, Susana Magallón, James A Doyle, Peter K Endress, Emily J Bailes, Erica Barroso de Morais, Kester Bull-Hereñu, Laetitia Carrive, Marion Chartier, Guillaume Chomicki, Mario Coiro, Raphaël Cornette, Juliana H L El Ottra, Cyril Epicoco, Charles S P Foster, Florian Jabbour, Agathe Haevermans, Thomas Haevermans, Rebeca Hernández, Stefan A Little, Stefan Löfstrand, Javier A Luna, Julien Massoni, Sophie Nadot, Susanne Pamperl, Charlotte Prieu, Elisabeth Reyes, Patrícia Dos Santos, Kristel M Schoonderwoerd, Susanne Sontag, Anaëlle Soulebeau, Yannick Staedler, Georg F Tschan, Amy Wing-Sze Leung, Jürg Schönenberger
Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled...
August 1, 2017: Nature Communications
https://www.readbyqxmd.com/read/28747803/phylogeny-of-locusts-and-grasshoppers-reveals-complex-evolution-of-density-dependent-phenotypic-plasticity
#15
Hojun Song, Bert Foquet, Ricardo Mariño-Pérez, Derek A Woller
Locusts are grasshoppers that can form dense migrating swarms through an extreme form of density-dependent phenotypic plasticity, known as locust phase polyphenism. We present a comprehensive phylogeny of the genus Schistocerca, which contains both non-swarming grasshoppers and swarming locusts. We find that the desert locust, S. gregaria, which is the only Old World representative of the genus, is the earliest diverging lineage. This suggests that the common ancestor of Schistocerca must have been a swarming locust that crossed the Atlantic Ocean from Africa to America approximately 6 million years ago, giving rise to the current diversity in the New World...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743759/anatolian-origins-and-diversification-of-aethionema-the-sister-lineage-of-the-core-brassicaceae
#16
Setareh Mohammadin, Kim Peterse, Sara J van de Kerke, Lars W Chatrou, Ali A Dönmez, Klaus Mummenhoff, J Chris Pires, Patrick P Edger, Ihsan A Al-Shehbaz, M Eric Schranz
PREMISE OF THE STUDY: The Irano-Turanian region harbors three biodiversity hotspots and ∼25% of Brassicaceae species are endemic to the region. Aethionema (∼61 species) is the sister lineage to the core Brassicaceae and occurs mainly in the Irano-Turanian region. The evolutionary important position of Aethionema makes it an ideal reference for broader comparative genetics and genomics. To understand the evolution of Aethionema, and for a broader understanding of crucifer evolution, a time-calibrated phylogenetic tree and biogeographical history of the genus is needed...
July 25, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28726643/reconstructed-ancestral-enzymes-reveal-that-negative-selection-drove-the-evolution-of-substrate-specificity-in-adp-dependent-kinases
#17
Víctor Castro-Fernandez, Alejandra Herrera-Morande, Ricardo Zamora, Felipe Merino, Felipe Gonzalez-Ordenes, Felipe Padilla-Salinas, Humberto M Pereira, Jose Brandão-Neto, Richard C Garratt, Victoria Guixe
One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales, Methanosarcinales, and Methanococcales, as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes...
September 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28713346/distribution-of-2-4-diacetylphloroglucinol-biosynthetic-genes-among-the-pseudomonas-spp-reveals-unexpected-polyphyletism
#18
Juliana Almario, Maxime Bruto, Jordan Vacheron, Claire Prigent-Combaret, Yvan Moënne-Loccoz, Daniel Muller
Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG(+)Pseudomonas strains in the "P. corrugata" and "P. protegens" subgroups of the "Pseudomonas fluorescens" group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG(+)Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28709985/molecular-phylogeny-of-miltogramminae-diptera-sarcophagidae-implications-for-classification-systematics-and-evolution-of-larval-feeding-strategies
#19
Marcin Piwczyński, Thomas Pape, Edyta Deja-Sikora, Marcin Sikora, Kamran Akbarzadeh, Krzysztof Szpila
Miltogramminae is one of the phylogenetically most poorly studied taxa of the species-rich family Sarcophagidae (Diptera). Most species are kleptoparasites in nests of solitary aculeate wasps and bees, although parasitoids and saprophagous species are also known, and the ancestral miltogrammine life habit remains unsettled. Here, we present for the first time a comprehensive phylogenetic tree consisting of 58 representatives of Miltogramminae, reconstructed using sequence data from three mitochondrial (COI, cytB, ND4) and one nuclear (Ef-1α) genes...
November 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28674236/molecular-systematics-of-indian-alysicarpus-fabaceae-based-on-analyses-of-nuclear-ribosomal-dna-sequences
#20
Akram Gholami, Shweta Subramaniam, R Geeta, Arun K Pandey
Alysicarpus Necker ex Desvaux (Fabaceae, Desmodieae) consists of ~30 species that are distributed in tropical and subtropical regions of theworld. In India, the genus is represented by ca. 18 species, ofwhich seven are endemic. Sequences of the nuclear Internal transcribed spacer from38 accessions representing 16 Indian specieswere subjected to phylogenetic analyses. The ITS sequence data strongly support the monophyly of the genus Alysicarpus. Analyses revealed four major well-supported clades within Alysicarpus...
June 2017: Journal of Genetics
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