cran: adephylo | Projects | Ecosyste.ms: Papers

10.1093/gbe/evab127

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild <i>Drosophila</i> Gut Microbiome
Cited by: 4
Author(s): Jeffery S. McMullen, Eduardo Bueno, Frances Blow, Angela E. Douglas
Software Mentions: 16
Published: over 3 years ago

10.1111/mec.13636

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event
Cited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pone.0151959

Physiological Limits along an Elevational Gradient in a Radiation of Montane Ground Beetles
Cited by: 28
Author(s): R. O. Slatyer, Sean D. Schoville
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pone.0138031

The Effect of Host-Plant Phylogenetic Isolation on Species Richness, Composition and Specialization of Insect Herbivores: A Comparison between Native and Exotic Hosts
Cited by: 16
Author(s): Julio Miguel Grandez-Rios, Leonardo Lima Bergamini, Walter Santos de Araújo, Fabricio Villalobos, Mário Almeida‐Neto
Software Mentions: 10
Published: about 9 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0036664

Functional Morphometric Analysis of the Furcula in Mesozoic Birds
Cited by: 33
Author(s): Roger A. Close, Emily J. Rayfield
Software Mentions: 9
Published: over 12 years ago

10.1002/ece3.6390

Can ancestry and morphology be used as surrogates for species niche relationships?
Cited by: 5
Author(s): Friedrich W. Keppeler, Kirk O. Winemiller
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2148-13-134

Phylogenetic signal in the acoustic parameters of the advertisement calls of four clades of anurans
Cited by: 42
Author(s): Bruno Gingras, Elmira Mohandesan, Drasko Boko, W. Tecumseh Fitch
Software Mentions: 8
Published: over 11 years ago

10.1186/1471-2148-14-79

Do pre- and post-copulatory sexually selected traits covary in large herbivores?
Cited by: 18
Author(s): Mariona Ferrandiz‐Rovira, Jean‐François Lemaître, Sophie Lardy, Bernat Claramunt López, Aurélie Cohas
Software Mentions: 7
Published: over 10 years ago

10.1155/2014/851425

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence
Cited by: 22
Author(s): Edgar E. Lara-Ramírez, Ma Isabel Salazar, María de Jesús López-López, Juan Santiago Salas-Benito, Alejandro Sánchez-Varela, Xianwu Guo
Software Mentions: 7
Published: over 10 years ago

10.7554/eLife.63650

Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates
Cited by: 8
Author(s): Rylan Shearn, Alison E. Wright, Sylvain Mousset, Corinne Régis, Simon Penel, Jean‐François Lemaître, Guillaume Douay, Brigitte Crouau‐Roy, Émilie Lecompte, Gabriel Marais
Software Mentions: 7
Published: almost 4 years ago

10.3390/insects11050278

Thermal Tolerance of Fruit-Feeding Butterflies (Lepidoptera: Nymphalidae) in Contrasting Mountaintop Environments
Cited by: 9
Author(s): Vanessa Diniz e Silva, Marina do Vale Beirão, Danon Clemes Cardoso
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0094246

Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast Torulaspora delbrueckii
Cited by: 60
Author(s): Warren Albertin, Laura Chasseriaud, Guillaume Comte, Aurélie Panfili, Adline Delcamp, Franck Salin, Philippe Marullo, Marina Bely
Software Mentions: 7
Published: over 10 years ago

10.1186/s12862-018-1300-4

A phylogenomic resolution of the sea urchin tree of life
Cited by: 37
Author(s): Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E. G. Briggs, Rich Mooi, Greg W. Rouse
Software Mentions: 6
Published: almost 6 years ago

10.1128/AEM.02111-18

Resistance Gene Carriage Predicts Growth of Natural and Clinical Escherichia coli Isolates in the Absence of Antibiotics
Cited by: 7
Author(s): Richard C. Allen, Daniel C Angst, Alex R. Hall
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.6597

Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
Cited by: 6
Author(s): María Eugenia Arnaudo, Néstor Toledo, Leopoldo Héctor Soibelzon, Paula Bona
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.ppat.1008686

Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes
Cited by: 7
Author(s): Laura Jackson, Barney Potter, Sean E. Schneider, Matthew Fitzgibbon, Kris M. Blair, Hajirah Farah, U. Murali Krishna, Trevor Bedford, Richard M. Peek, Nina R. Salama
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2017.01530

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar
Cited by: 67
Author(s): Molly C. Bletz, Holly Archer, Reid N. Harris, Valerie J. McKenzie, Falitiana C. E. Rabemananjara, Andolalao Rakotoarison, Miguel Vences
Software Mentions: 6
Published: about 7 years ago

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: about 8 years ago

10.3389/fgene.2021.693541

The Evolutionary Patterns of Genome Size in Ensifera (Insecta: Orthoptera)
Cited by: 15
Author(s): Hao Yuan, Yuan Huang, Ying Mao, Nan Zhang, Yimeng Nie, Xue Zhang, Yafu Zhou, Shao-Li Mao
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0104787

Relationship between Phylogeny and Immunity Suggests Older Caribbean Coral Lineages Are More Resistant to Disease
Cited by: 36
Author(s): H C Jorge Pinzón, Joshuah Beach-Letendre, Ernesto Weil, Laura D. Mydlarz
Software Mentions: 5
Published: about 10 years ago

10.3389/fmicb.2020.596589

The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession
Cited by: 24
Author(s): Stacey J. Doherty, Robyn A. Barbato, A. Stuart Grandy, W. Kelley Thomas, Sylvain Monteux, Ellen Dorrepaal, Margareta Johansson, Jessica G. Ernakovich
Software Mentions: 5
Published: almost 4 years ago

10.3390/v10100576

Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
Cited by: 10
Author(s): Phillip Seitzer, Adrien Jeanniard, Fangrui Ma, James L. Van Etten, Marc T. Facciotti, David D. Dunigan
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-019-3020-1

LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference
Cited by: 3
Author(s): Carlos Rivera-Rivera, Juan I. Montoya‐Burgos
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2738-7

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102
Cited by: 22
Author(s): Nathan Brown, Robert F. Mueller, Jonathan W. Shepardson, Zachary C. Landry, Jeff Morré, Christoph Maier, F. Joan Hardy, Theo W. Dreher
Software Mentions: 4
Published: over 8 years ago

10.1099/mgen.0.000070

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network
Cited by: 53
Author(s): Tim Dallman, Thomas Inns, Thibaut Jombart, Philip Ashton, Nicholas J. Loman, Carol Chatt, Ute Messelhaeusser, Wolfgang Rabsch, Sandra Simon, Sergejs Nikisins, Helen Bernard, Simon Le Hello, Nathalie Jourdan da-Silva, Christian Kornschober, Joël Mossong, Peter M. Hawkey, Elizabeth de Pinna, Kathie Grant, Paul Cleary
Software Mentions: 4
Published: about 8 years ago

10.1002/ece3.3564

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales
Cited by: 22
Author(s): Oliver Purschke, Stefan G. Michalski, Helge Bruelheide, Walter Durka
Software Mentions: 4
Published: almost 7 years ago

10.1002/ece3.7005

Plant phylogeny drives arboreal caterpillar assemblages across the Holarctic
Cited by: 8
Author(s): Carlo L. Seifert, Martin Volf, Leonardo Ré Jorge, Tomokazu Abe, Grace Carscallen, Pavel Drozd, Rajesh Kumar, Greg P. A. Lamarre, Martin Libra, María Eugenia Losada, Scott E. Miller, Masashi Murakami, Geoffrey Nichols, Petr Pyszko, Martin Šigut, David L. Wagner, Vojtěch Novotný
Software Mentions: 4
Published: almost 4 years ago

10.1111/evo.13865

Altitude and life‐history shape the evolution of<i>Heliconius</i>wings
Cited by: 25
Author(s): Gabriela Montejo‐Kovacevich, Jennifer E. Smith, Joana I. Meier, Caroline Bacquet, Eva Whiltshire-Romero, Nicola J. Nadeau, Chris D. Jiggins
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2016.00703

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil
Cited by: 122
Author(s): Charles Pepe-Ranney, Ashley Campbell, Chantal Koechli, Sean T. Berthrong, Daniel H. Buckley
Software Mentions: 4
Published: over 8 years ago

10.3389/fphys.2020.00312

Living on the Edge: Physiological and Kinetic Trade-Offs Shape Thermal Tolerance in Intertidal Crabs From Tropical to Sub-Antarctic South America
Cited by: 7
Author(s): Samuel Coelho Faria, Adalto Bianchini, Mariana Machado Lauer, Ana Lúcia Ribeiro Latorre Zimbardi, Federico Tapella, M. Carolina Romero, John Campbell McNamara
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2015.00004

Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms
Cited by: 84
Author(s): Conchita Alonso, Rocío Silva Pérez, Pilar Bazaga, Carlos M. Herrera
Software Mentions: 3
Published: over 9 years ago

10.1002/ece3.2051

phylosignal: an R package to measure, test, and explore the phylogenetic signal
Cited by: 327
Author(s): François Keck, Frédéric Rimet, Agnès Bouchez, Alain Franc
Software Mentions: 3
Published: over 8 years ago

10.1002/ece3.2385

The influence of variability in species trait data on community‐level ecological prediction and inference
Cited by: 9
Author(s): Karen M. Alofs
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0067463

Trypanosoma cruzi Infection in Neotropical Wild Carnivores (Mammalia: Carnivora): At the Top of the T. cruzi Transmission Chain
Cited by: 71
Author(s): Fabiana Lopes Rocha, André Luiz Rodrigues Roque, Juliane Saab de Lima, Carolina Carvalho Cheida, Frederico Gemesio Lemos, Fernanda Cavalcanti de Azevedo, Ricardo Corassa Arrais, Daniele Bilac, Heitor Miraglia Herrera, Guilherme Mourão, Ana María Jansen
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0086231

Has Pollination Mode Shaped the Evolution of Ficus Pollen?
Cited by: 18
Author(s): Gang Wang, Jin Chen, Zongbo Li, Fengping Zhang, Da‐Rong Yang
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.ppat.1009714

First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence
Cited by: 6
Author(s): Paola Campos, Clara Groot Crego, Karine Boyer, Myriam Gaudeul, Cláudia Baider, Damien Richard, Olivier Pruvost, Philippe Roumagnac, Boris Szurek, Norbert Becker, Lionel Gagnevin, Adrien Rieux
Software Mentions: 2
Published: about 3 years ago

10.3389/fevo.2021.630207

Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish
Cited by: 8
Author(s): Alison L. Gould, Allison Fritts-Penniman, Ana Gaisiner
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2020.588550

Plant Salinity Tolerance Conferred by Arbuscular Mycorrhizal Fungi and Associated Mechanisms: A Meta-Analysis
Cited by: 40
Author(s): Khondoker M. G. Dastogeer, Mst Ishrat Zahan, Md. Tahjib‐Ul‐Arif, Masuda Akter, Shin Okazaki
Software Mentions: 2
Published: almost 4 years ago

10.3390/plants10071356

Differential Evolutionary History in Visual and Olfactory Floral Cues of the Bee-Pollinated Genus Campanula (Campanulaceae)
Cited by: 1
Author(s): Paulo Milet‐Pinheiro, Paulo Henrique Dias Dos Santos, Samuel Prieto‐Benítez, Manfred Ayasse, Stefan Dötterl
Software Mentions: 1
Published: about 3 years ago

10.1002/ece3.2888

Infochemical use and dietary specialization in parasitoids: a meta‐analysis
Cited by: 27
Author(s): Louise van Oudenhove, Ludovic Mailleret, Xavier Fauvergue
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-4417-8

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments
Cited by: 21
Author(s): Rui Borges, Warren E. Johnson, Stephen J. O’Brien, Cidália Gomes, Christopher P. Heesy, Agostinho Antunes
Software Mentions: 1
Published: over 6 years ago

Projects: cran: adephylo

Papers Mentioning adephylo 42