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The State of Software for Evolutionary Biology [PDF]

Molecular Biology and Evolution, 2018
With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently ...
Diego Darriba, Tomas Flouri, Alexandros Stamatakis, Alexandros Stamatakis   +3 more
openaire   +5 more sources

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts [PDF]

, 2018
Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory.
A Etxeberria, A Fuentes, A Parravicini, A Vianello, A Wagner, AC Love, Alejandro Fábregas-Tejeda, AV Badyaev, B Bocxlaer Van, BS Lieberman, BS Lieberman, D Noble, D Sepkoski, D Sloan-Wilson, DD Turner, DJ Depew, DJ Futuyma, DJ Nicholson, DL Hull, DM Walsh, DR Piperno, DT Campbell, E Danchin, E Jablonka, E Jablonka, E Jablonka, E Mayr, E Mayr, E Serrelli, E Szathmáry, EI Svensson, ES Vrba, ES Vrba, ES Vrba, F Suman, F Vergara-Silva, FJ Odling-Smee, FJ Odling-Smee, Francisco Vergara-Silva, GB Müller, GB Müller, GG Simpson, GJ Cooper, GP Wagner, GP Wagner, I Tëmkin, I Tëmkin, I Tëmkin, J Beatty, J Griesemer, J Griesemer, J Odling-Smee, J Odling-Smee, JJ Welch, JW Pepper, K Laland, K Laland, K Stotz, KN Laland, KN Laland, KN Laland, KN Laland, M Bertolaso, M Blute, M Lynch, M Martínez, M Nei, M Pavličev, M Pigliucci, M Pigliucci, MD Laubichler, MJ Denton, MW Kirschner, N Eldredge, N Eldredge, N Eldredge, N Eldredge, N Eldredge, N Eldredge, N Eldredge, N Eldredge, P Alberch, P Bateson, P Godfrey-Smith, PJ Bowler, R Amundson, R Amundson, R Riedl, R Sansom, RG Delisle, RG Winther, S Caianiello, S Okasha, S Okasha, S Oyama, S Sultan, SF Gilbert, SJ Gould, SJ Gould, T Ingold, T Ingold, T Pievani, T Pievani, T Pievani, T Pievani, TA Grantham, TS Kemp, TS Kemp, U Dieckmann, W Miller III, W Miller III, WB Provine, WD Allmon, WE Reif   +113 more
core   +1 more source

Neofunctionalization of ciliary BBS proteins to nuclear roles is likely a frequent innovation across eukaryotes

iScience, 2023
Summary: The eukaryotic BBSome is a transport complex within cilia and assembled by chaperonin-like BBS proteins. Recent work indicates nuclear functions for BBS proteins in mammals, but it is unclear how common these are in extant proteins or when they ...
Alexander Ewerling, Vanessa Maissl, Bill Wickstead, Helen Louise May-Simera   +3 more
doaj  

Complete mitochondrial genomes provide current refined phylogenomic hypotheses for relationships among ten Hirundo species

Mitochondrial DNA. Part B. Resources, 2020
Hirundo is the most species-rich genus of the passerine swallow family (Hirundinidae) and has a cosmopolitan distribution. Here we report the complete, annotated mitochondrial genomes for 25 individuals from 10 of the 14 extant Hirundo species; these ...
Javan K. Carter, Peter Innes, April M. Goebl, Benjamin Johnson, Matthew Gebert, Ziv Attia, Zachariah Gabani, Ruiqi Li, Tina Melie, Chiara Dart, Ali Mares, Chrisopher Greidanus, Jaime Paterson, Brianna Wall, Gabriela Cortese, Kevin Thirouin, Gabrielle Glime, Joseph Rutten, Cameron Poyd, Erin Post, Brianna Wall, Ahmed A. Elhadi, Katherine Feldmann, August Danz, Thomas Blanchard, Samantha Amato, Stephan Reinert, Cloe S. Pogoda, Elizabeth S. C. Scordato, Amanda K. Hund, Rebecca J. Safran, Nolan C. Kane   +31 more
doaj   +1 more source

Towards a quantum evolutionary scheme: violating Bell's inequalities in language [PDF]

, 2004
We show the presence of genuine quantum structures in human language. The neo-Darwinian evolutionary scheme is founded on a probability structure that satisfies the Kolmogorovian axioms, and as a consequence cannot incorporate quantum-like evolutionary ...
Aerts, Diederik, Czachor, Marek, D'Hooghe, Bart   +2 more
core   +5 more sources

The evolutionary biology of dance without frills [PDF]

, 2016
Recently psychologists have taken up the question of whether dance is reliant on unique human adaptations, or whether it is rooted in neural and cognitive mechanisms shared with other species 1, 2. In its full cultural complexity, human dance clearly has
Cook, P., Ravignani, A.
core   +2 more sources

Transcriptional effects of a positive feedback circuit in Drosophila melanogaster

BMC Genomics, 2017
Background Synthetic systems that use positive feedback have been developed to control human disease vectors and crop pests. The tTAV system, which has been deployed in several insect species, relies on a positive feedback circuit that can be inhibited ...
Jarosław Bryk, R. Guy Reeves, Floyd A. Reed, Jai A. Denton   +3 more
doaj   +1 more source

The relationship between evolutionary biology and religion [PDF]

, 2009
Belief in creationism and intelligent design is widespread and gaining in significance in a number of countries. This article examines the characteristics of science and of religions and the possible relationship between science and religion.
Reiss, Michael
core   +3 more sources

FishPIE: A universal phylogenetically informative exon markers set for ray-finned fishes

iScience, 2022
Summary: Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR
Xidong Mu, Yexin Yang, Jinhui Sun, Yi liu, Meng Xu, Changwei Shao, Ka Hou Chu, Wei Li, Chao Liu, Dangen Gu, Miao Fang, Chi Zhang, Fei Liu, Hongmei Song, Xuejie Wang, Jiehu Chen, Ka Yan Ma   +16 more
doaj  

Resynthesizing Evolutionary and Developmental Biology [PDF]

Developmental Biology, 1996
A new and more robust evolutionary synthesis is emerging that attempts to explain macroevolution as well as microevolutionary events. This new synthesis emphasizes three morphological areas of biology that had been marginalized by the Modern Synthesis of genetics and evolution: embryology, macroevolution, and homology.
Gilbert, Scott F., Opitz, J. M., Raff, R. A.   +2 more
openaire   +3 more sources