Ecosyste.ms: Papers

10.1038/s41437-019-0204-4

Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate
Cited by: 24
Author(s): Pedro Henrique Bernardo, Santiago Sánchez‐Ramírez, Santiago J. Sánchez-Pacheco, Sergio Ticul Álvarez-Castañeda, Eduardo Felipe Aguilera-Miller, Fausto R. Méndez–de la Cruz, Robert W. Murphy
Software Mentions: 10
Published: over 5 years ago

10.1111/1755-0998.13266

Chromosome‐level genome assembly of <i>Paralithodes platypus</i> provides insights into evolution and adaptation of king crabs
Cited by: 11
Author(s): Boping Tang, Zhongkai Wang, Qiu-Ning Liu, Zhengfei Wang, Yandong Ren, Huayun Guo, Tingting Qi, Yue‐Tian Li, Huabin Zhang, Senhao Jiang, Baoming Ge, Fujun Xuan, Yue Sun, Shusheng She, Tin Yam Chan, Zhongli Sha, Hui Jiang, Haorong Li, Wei Jiang, Yanli Qin, Kun Wang, Qiang Qiu, Wen Wang, Xinzheng Li, Ngan Kee Ng, Dai-Zhen Zhang, Yongxin Li
Software Mentions: 9
Published: about 4 years ago

10.1111/1755-0998.13362

Chromosome‐scale assembly of the genome of <i>Salix</i><i>dunnii</i> reveals a male‐heterogametic sex determination system on chromosome 7
Cited by: 24
Author(s): Li He, Kai‐Hua Jia, Rengang Zhang, Yuan Wang, Tian-Le Shi, Zhichao Li, Si-Wen Zeng, Xin-Jie Cai, Natascha D. Wagner, Elvira Hörandl, Aline Muyle, Ke Yang, Deborah Charlesworth, Jian‐Feng Mao
Software Mentions: 9
Published: over 3 years ago

10.1111/mec.14054

The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB
Cited by: 60
Author(s): Rodrigo Pracana, Anurag Priyam, Levantis Ilya, Richard A. Nichols, Yannick Wurm
Software Mentions: 8
Published: over 7 years ago

10.1111/1755-0998.13280

The genome of <i>Draba nivalis</i> shows signatures of adaptation to the extreme environmental stresses of the Arctic
Cited by: 13
Author(s): Michael Nowak, Siri Birkeland, Terezie Mandáková, Rimjhim Roy Choudhury, Xi Guo, Lovisa Gustafsson, Abel Gizaw, Audun Schrøder-Nielsen, Marco Fracassetti, Anne K. Brysting, Loren H. Rieseberg, Tanja Slotte, Christian Parisod, Martin A. Lysak, Christian Brochmann
Software Mentions: 8
Published: about 4 years ago

10.1111/eva.12047

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
Cited by: 14
Author(s): John D. Kirwan, Michaël Bekaert, Jennifer M. Commins, Kalina T. J. Davies, Stephen J. Rossiter, Emma C. Teeling
Software Mentions: 6
Published: over 11 years ago

10.1111/mec.14123

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (<i>Dactylorhiza</i>) with distinct ecological optima
Cited by: 22
Author(s): Francisco Balao, Emiliano Trucchi, Thomas M. Wolfe, Bao Hai Hao, María Teresa Cáceres Lorenzo, Juliane Baar, Laura Sedman, Carolin Kosiol, Fabian Amman, Mark W. Chase, Mikael Hedrén, Ovidiu Paun
Software Mentions: 6
Published: over 7 years ago

10.1038/s42003-020-01593-x

Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance
Cited by: 24
Author(s): Yaodong Yang, Stéphanie Bocs, Hang Fan, Alix Armero, Luc Baudouin, Pengwei Xu, Junyang Xu, Dominique This, Chantal Hamelin, Amjad Iqbal, Rashad Qadri, Lixia Zhou, Jing Li, Yi Wu, Zhiying Ma, Auguste Emmanuel Issali, Ronan Rivallan, Na Liu, Wei Xia, Ming Peng, Yong Xiao
Software Mentions: 6
Published: almost 4 years ago

10.1111/mec.13113

Variation in promiscuity and sexual selection drives avian rate of Faster‐Z evolution
Cited by: 74
Author(s): Alison E. Wright, Peter W. Harrison, Fabian Zimmer, Stephen H. Montgomery, Marie A. Pointer, Judith E. Mank
Software Mentions: 5
Published: over 9 years ago

10.1099/jgv.0.000464

Evolution of infectious bronchitis virus in China over the past two decades
Cited by: 52
Author(s): Ye Zhao, Hui Zhang, Jing Zhao, Qi Zhong, Ji Hui Jin, Guo Zhong Zhang
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0028634

Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome
Cited by: 52
Author(s): Nicholas R. Polato, J. Cristobal Vera, Iliana B. Baums
Software Mentions: 5
Published: almost 13 years ago

10.1111/mec.13186

Ecological host fitting of <i> <scp>T</scp> rypanosoma cruzi </i> <scp>T</scp> c <scp>I</scp> in <scp>B</scp> olivia: mosaic population structure, hybridization and a role for humans in <scp>A</scp> ndean parasite dispersal
Cited by: 37
Author(s): Louisa A. Messenger, Lineth García, Mathieu Vanhove, Carlos Huaranca, Marinely Bustamante, Mary-Cruz Torrico, Faustino Torrico, Michael A. Miles, Martin S. Llewellyn
Software Mentions: 4
Published: over 9 years ago

10.1111/imb.12585

Developmental expression and evolution of hexamerin and haemocyanin from <i>Folsomia candida</i> (Collembola)
Cited by: 3
Author(s): Yangyang Liang, Wei Xie, Yigang Luan
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-018-1148-7

High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations
Cited by: 16
Author(s): Pei Zhang, Kang Huang, Bingyi Zhang, Derek W. Dunn, Dan Chen, Fan Li, Qi Xin, Songtao Guo, Baoguo Li
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-016-1145-3

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
Cited by: 539
Author(s): Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Bâa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamás Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara López-Gomollón, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel D. Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock van Oosterhout, David Swarbreck, Saskia A. Hogenhout
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes10030249

Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?
Cited by: 7
Author(s): Romain Lannes, Carène Rizzon, Emmanuelle Lerat
Software Mentions: 3
Published: over 5 years ago

10.1099/mic.0.2007/015479-0

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB
Cited by: 18
Author(s): Julia S. Bennett, Martin J. Callaghan, Jeremy P. Derrick, Martin C. J. Maiden
Software Mentions: 3
Published: over 16 years ago

10.1111/mec.15168

Dynamic virulence‐related regions of the plant pathogenic fungus <i>Verticillium dahliae</i> display enhanced sequence conservation
Cited by: 34
Author(s): Jasper R L Depotter, Xiaoqian Shi-Kunne, Hélène Missonnier, Tingli Liu, Luigi Faino, Grardy C. M. van den Berg, Thomas A. Wood, Baolong Zhang, Alban Jacques, Michael Seidl, B.P.H.J. Thomma
Software Mentions: 3
Published: over 5 years ago

10.3390/biology1030575

The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq
Cited by: 34
Author(s): Sébastien Renaut, Christopher J. Grassa, Brook T. Moyers, Nolan C. Kane, Loren H. Rieseberg
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0239558

Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis)
Cited by: 5
Author(s): Maria A. Tonione, Ke Bi, Neil D. Tsutsui
Software Mentions: 3
Published: about 4 years ago

10.1093/gigascience/giz111

Genomic evidence of neo-sex chromosomes in the eastern yellow robin
Cited by: 32
Author(s): Han Ming Gan, Stephanie Falk, Hernán E. Morales, Christopher M. Austin, Paul Sunnucks, Alexandra Pavlova
Software Mentions: 3
Published: about 5 years ago

10.1111/mec.13596

Divergence in gene expression within and between two closely related flycatcher species
Cited by: 56
Author(s): Severin Uebbing, Axel Künstner, Hannu Mäkinen, Niclas Backström, Paulina Bolívar, Reto Burri, Ludovic Dutoit, Carina F. Mugal, Alexander Nater, Bronwen Aken, Paul Flicek, Fergal J. Martin, Stephen M. J. Searle, Hans Ellegren
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0041244

Detecting the Immune System Response of a 500 Year-Old Inca Mummy
Cited by: 56
Author(s): Angélique Corthals, Antonius Koller, Dwight W. Martin, Robert Rieger, Emily I. Chen, Mario Bernaski, Gabriella Recagno, Liliana M. Dávalos
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pbio.3000255

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
Cited by: 91
Author(s): Jacob L. Steenwyk, Dana A. Opulente, Jacek Kominek, Xing‐Xing Shen, Xiaofan Zhou, Abigail L. LaBella, Noah P. Bradley, Brandt F. Eichman, Neža Čadež, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2148-9-286

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
Cited by: 26
Author(s): Alan M. Moses
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-15-718

Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins
Cited by: 72
Author(s): Sean K. McKenzie, Peter R. Oxley, Daniel J. C. Kronauer
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-503

Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica
Cited by: 37
Author(s): Laura E. Eierman, Matthew P. Hare
Software Mentions: 2
Published: almost 11 years ago

10.1099/mic.0.036475-0

Variation and molecular evolution of HmbR, the Neisseria meningitidis haemoglobin receptor
Cited by: 15
Author(s): Nicholas J. Evans, Odile B. Harrison, Kirsten Clow, Jeremy P. Derrick, Ian M. Feavers, Martin C. J. Maiden
Software Mentions: 2
Published: over 14 years ago

10.7717/peerj.7596

The complete chloroplast genome of the Jerusalem artichoke (<i>Helianthus tuberosus</i> L.) and an adaptive evolutionary analysis of the <i>ycf2</i> gene
Cited by: 22
Author(s): Qing Zhong, Shipeng Yang, Xuemei Sun, Lihui Wang, Yang Li
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1004064

Natural Selection Reduced Diversity on Human Y Chromosomes
Cited by: 90
Author(s): Melissa A. Wilson, Kirk E. Lohmueller, Rasmus Nielsen
Software Mentions: 2
Published: almost 11 years ago

10.3389/fpls.2021.662715

Highly Diverse Shrub Willows (Salix L.) Share Highly Similar Plastomes
Cited by: 11
Author(s): Natascha Wagner, Martin Volf, Elvira Hörandl
Software Mentions: 2
Published: about 3 years ago

10.3389/fpls.2019.00026

NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci
Cited by: 28
Author(s): Ying Fu, Yaofeng Zhang, Annaliese S. Mason, Baogang Lin, Dongqing Zhang, Han‐Qing Yu, Donghui Fu
Software Mentions: 2
Published: almost 6 years ago

10.1093/gbe/evy036

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa
Cited by: 33
Author(s): Germain Chevignon, Bret M. Boyd, Jayce W. Brandt, Kerry M. Oliver, Michael R. Strand
Software Mentions: 2
Published: almost 7 years ago

10.1111/jeb.12895

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy
Cited by: 21
Author(s): Luke T. Dunning, Helen Hipperson, William J. Baker, Roger K. Butlin, Céline Devaux, I. Hutton, Javier Igea, Alexander S. T. Papadopulos, Xiangqian Quan, Carole Smadja, Colin Turnbull, Vincent Savolainen
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-24939-2

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides
Cited by: 35
Author(s): Min Yang, Shengchang Duan, Xinyue Mei, Huichuan Huang, Wei Chen, Yixiang Liu, Changhong Guo, Ting Yang, Wei Wei, Xili Liu, Xiahong He, Yang Dong, Shusheng Zhu
Software Mentions: 2
Published: over 6 years ago

10.1111/mec.14466

Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant<i>Salix viminalis</i>
Cited by: 32
Author(s): Iulia Darolti, Alison E. Wright, Pascal Pucholt, Sofia Berlin, Judith E. Mank
Software Mentions: 1
Published: almost 7 years ago

10.1111/mec.13475

The rate of adaptive evolution in animal mitochondria
Cited by: 104
Author(s): Jennifer E. James, Gwenaël Piganeau, Adam Eyre‐Walker
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.cub.2019.05.060

Immediate Dosage Compensation Is Triggered by the Deletion of Y-Linked Genes in Silene latifolia
Cited by: 19
Author(s): Marc Krasovec, Yusuke Kazama, Kotaro Ishii, Tomoko Abe, Dmitry A. Filatov
Software Mentions: 1
Published: over 5 years ago

10.1093/molbev/msaa207

Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution
Cited by: 29
Author(s): Christian Rödelsperger, Annabel Ebbing, Devansh Raj Sharma, Misako Okumura, Ralf J. Sommer, Hendrik C. Korswagen
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2020.593984

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae
Cited by: 23
Author(s): Yongtan Li, Yan Dong, Yichao Liu, Xiaoyue Yu, Minsheng Yang, Yinran Huang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2018.01008

Genetic Analysis of Floral Symmetry Transition in African Violet Suggests the Involvement of Trans-acting Factor for CYCLOIDEA Expression Shifts
Cited by: 12
Author(s): Hong‐Yuan Hsu, Chengwen He, Wen-Hsi Kuo, Kuan-Ting Hsin, Jing-Yi Lu, Zhaojun Pan, Chun‐Neng Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-018-4872-x

Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems
Cited by: 8
Author(s): Katrina G. Claw, Renee D. George, Michael J. MacCoss, Willie J. Swanson
Software Mentions: 1
Published: over 6 years ago

10.1093/sysbio/syu109

Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci
Cited by: 72
Author(s): Tianqi Zhu, Mario dos Reis, Ziheng Yang
Software Mentions: 1
Published: almost 10 years ago

10.1093/molbev/msy058

Consequences of Asexuality in Natural Populations: Insights from Stick Insects
Cited by: 56
Author(s): Jens Bast, Darren J. Parker, Zoé Dumas, Kirsten M. Jalvingh, Patrick Tran Van, Kamil S. Jaroň, Emeric Figuet, Alexander Brandt, Nicolas Galtier, Tanja Schwander
Software Mentions: 1
Published: over 6 years ago

10.1186/1745-6150-6-40

Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species
Cited by: 36
Author(s): Nora Khaldi, Denis C. Shields
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-017-4059-x

Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum)
Cited by: 19
Author(s): Siqi Tao, Bin Cao, Chengming Tian, Ying‐Mei Liang
Software Mentions: 1
Published: about 7 years ago

10.1186/s13073-020-00811-9

Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care
Cited by: 9
Author(s): Andrew Bosworth, Natasha Y. Rickett, Xiaofeng Dong, Lisa F. P. Ng, Isabel García-Dorival, David A. Matthews, Tom Fletcher, Michael Jacobs, Emma C. Thomson, Miles W. Carroll, Julian A. Hiscox
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2180-6-12

Sca 1, a previously undescribed paralog from autotransporter protein-encoding genes in Rickettsia species
Cited by: 49
Author(s): Maxime Ngwamidiba, Guillaume Blanc, Didier Raoult, Pierre‐Edouard Fournier
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-14-623

Comparative genomics of emerging pathogens in the Candida glabrata clade
Cited by: 152
Author(s): Toni Gabaldón, Tiphaine Martin, Marina Marcet‐Houben, Pascal Durrens, Monique Bolotin‐Fukuhara, Olivier Lespinet, Sylvie Arnaise, Stéphanie Boisnard, Gabriela Aguileta, Ralitsa Atanasova, Christiane Bouchier, Arnaud Couloux, Sophie Créno, José Almeida Cruz, Hugo Devillers, Adela Enache-Angoulvant, Juliette Guitard, Laure Jaouen, Laurence Ma, Christian Marck, Cécile Neuveglise, Éric Pelletier, Amélie Pinard, Julie Poulain, Julien Recoquillay, Éric Westhof, Patrick Wincker, Bernard Dujon, Christophe Hennequin, Cécile Fairhead
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0018630

Change of Positive Selection Pressure on HIV-1 Envelope Gene Inferred by Early and Recent Samples
Cited by: 41
Author(s): Izumi Yoshida, Wataru Sugiura, Junko Shibata, Fengrong Ren, Ziheng Yang, Hiroshi Tanaka
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0003746

The Trouble with Sliding Windows and the Selective Pressure in BRCA1
Cited by: 37
Author(s): Karl Schmid, Ziheng Yang
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pcbi.0020130

Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Cited by: 248
Author(s): Alan M. Moses, Daniel A Pollard, David A. Nix, Venky N. Iyer, Xiaoyong Li, Mark D. Biggin, Michael B. Eisen
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0021019

Expression and Trans-Specific Polymorphism of Self-Incompatibility RNases in Coffea (Rubiaceae)
Cited by: 51
Author(s): Michael Nowak, Aaron P. Davis, François Anthony, Anne D. Yoder
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-14-103

Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway
Cited by: 27
Author(s): Odrade Nougué, Jonathan Corbi, Steven Ball, Doménica Manicacci, Maud I. Tenaillon
Software Mentions: 1
Published: over 10 years ago