Uncertainty in the reconstruction of ancestral character states and limitations on the use of phylogenetic comparative methods

Phylogenies and the Comparative Method

Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793

The comparative method in evolutionary biology

Harvey, P., & Pagel, M. (1991) · Choice Reviews Online · doi:10.5860/choice.29-5104 · Cited by 4,778

The Comparative Method in Evolutionary Biology

Harvey, P. H., & Pagel, M. D. (1991) · doi:10.1093/oso/9780198546412.001.0001 · Cited by 4,337

Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts

Garland, T., Harvey, P. H., & Ives, A. R. (1992) · Systematic Biology · doi:10.1093/sysbio/41.1.18 · Cited by 2,151

Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data

Martins, E. P., & Hansen, T. F. (1997) · The American Naturalist · doi:10.1086/286013 · Cited by 1,718

LIKELIHOOD OF ANCESTOR STATES IN ADAPTIVE RADIATION

Schluter, D., Price, T. D., Mooers, A. Ø., & Ludwig, D. (1997) · Evolution · doi:10.1111/j.1558-5646.1997.tb05095.x · Cited by 936

Ecological morphology: Integrative organismal biology

Sinervo, B. (1995) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)89062-x · Cited by 909

Phylogeny, Ecology, and Behavior. A Research Program in Comparative Biology

Crother, B. I., Brooks, D. R., & McLennan, D. A. (1991) · Copeia · doi:10.2307/1446122 · Cited by 798

THE QUANTITATIVE ASSESSMENT OF PHYLOGENETIC CONSTRAINTS IN COMPARATIVE ANALYSES: SEXUAL DIMORPHISM IN BODY WEIGHT AMONG PRIMATES

Cheverud, J. M., Dow, M. M., & Leutenegger, W. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb05699.x · Cited by 671

An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values

Garland, T., Midford, P. E., & Ives, A. R. (1999) · American Zoologist · doi:10.1093/icb/39.2.374 · Cited by 568

Functional Morphology of the Postcranial Skeleton

Dunn, R. H. (2018) · Vertebrate paleobiology and paleoanthroplogy series/Vertebrate paleobiology and paleoanthropology series · doi:10.1007/978-3-319-94265-0_3 · Cited by 28

The evolution of egg size in socially polyandrous shorebirds

Liker, A., Reynolds, J. D., & Székely, T. (2001) · Oikos · doi:10.1034/j.1600-0706.2001.950101.x · Cited by 26

Spiny trapdoor spiders (Euoplos) of eastern Australia: Broadly sympatric clades are differentiated by burrow architecture and male morphology

Wilson, J. D., Hughes, J. M., Raven, R. J., Rix, M. G., & Schmidt, D. J. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.01.022 · Cited by 23

Preexisting Male Traits Are Important in the Evolution of Elaborated Male Sexual Display

Borgia, G. (2006) · Advances in the study of behavior · doi:10.1016/s0065-3454(06)36006-8 · Cited by 23

Vireo song repertoires and migratory distance: three sexual selection hypotheses fail to explain the correlation

Mountjoy, D. J., & Leger, D. W. (2001) · Behavioral Ecology · doi:10.1093/oxfordjournals.beheco.a000385 · Cited by 23

Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds

Merwin, J. T., Seeholzer, G. F., & Smith, B. T. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-020-1577-y · Cited by 22

Sexual selection and ‘species recognition’ revisited: serial processing and order-of-operations in mate choice

Gray, D. A. (2022) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2021.2687 · Cited by 22

Which plant traits promote growth in the low-light regimes of vegetation gaps?

Seidlová, L., Verlinden, M. S., Gloser, J., Milbau, A., & Nijs, I. (2008) · Plant Ecology · doi:10.1007/s11258-008-9454-6 · Cited by 22

Evolution and Development of Tendrils in Bignonieae (Lamiales, Bignoniaceae)1

Sousa‐Baena, M. S., Sinha, N. R., & Lohmann, L. G. (2014) · Annals of the Missouri Botanical Garden · doi:10.3417/2011018 · Cited by 24

Grounded Ground Birds and Surfing Canopy Birds: Variation of Foraging Stratum Breadth Observed in Neotropical Forest Birds and Tested With Simulation Models Using Boundary Constraints

Walther, B. A. (2002) · The Auk · doi:10.1093/auk/119.3.658 · Cited by 21

FEMALE RED THROAT COLORATION IN TWO POPULATIONS OF THREESPINE STICKLEBACK

McKinnon, J. S., Demayo, R., Granquist, R. M., & Weggel, L. (2000) · Behaviour · doi:10.1163/156853900502556 · Cited by 20

Ventral and sub-caudal scale counts are associated with macrohabitat use and tail specialization in viperid snakes

Hampton, P. M. (2010) · Evolutionary Ecology · doi:10.1007/s10682-010-9432-z · Cited by 19

Phylogenetic signal and evolutionary relationships among traits of inland fishes along elevational and longitudinal gradients

Cano‐Barbacil, C., Radinger, J., Grenouillet, G., & García‐Berthou, E. (2022) · Freshwater Biology · doi:10.1111/fwb.13890 · Cited by 18

Where have all the trees gone? The declining use of phylogenies in animal behaviour journals

Price, J. J., Clapp, M. K., & Omland, K. E. (2011) · Animal Behaviour · doi:10.1016/j.anbehav.2010.12.004 · Cited by 18

Form function of sulcus acusticus of the sagittal otolith in seven Sciaenidae ( Acanthuriformes ) species using geometric morphometrics ( southwestern Atlantic )

Verocai, J. E., Cabrera, F., Lombarte, A., & Norbis, W. A. (2023) · Journal of Fish Biology · doi:10.1111/jfb.15521 · Cited by 17

The climatic niche diversity of Malagasy primates: A phylogenetic approach

Kamilar, J. M., & Muldoon, K. M. (2010) · ScholarWorks@UMassAmherst (University of Massachusetts Amherst) · doi:10.7275/1748 · Cited by 17

Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

Moen, D. S., Cabrera‐Guzmán, E., Caviedes-Solis, I. W., González‐Bernal, E., & Hanna, A. R. (2022) · Journal of Experimental Biology · doi:10.1242/jeb.243292 · Cited by 16

Parental care in the Cuatro Ciénegas cichlid, Herichthys minckleyi (Teleostei: Cichlidae)

Oldfield, R. G., Mandrekar, K., Nieves, M. X., Hendrickson, D. A., Chakrabarty, P., Swanson, B. O., & Hofmann, H. A. (2014) · Hydrobiologia · doi:10.1007/s10750-014-2081-4 · Cited by 15

A phylogenetic approach to the study of sexual size dimorphism in Felidae and an assessment of Rensch´s rule.

Martínez, P. A., Amado, T. F., & Bidau, C. J. (2014) · Ecosistemas · doi:10.7818/ecos.2014.23-1.05 · Cited by 15

Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa

Masters, L. E., Tomaszewska, P., Schwarzacher, T., Hackel, J., Zuntini, A. R., Heslop-Harrison, J. S., & Vorontsova, M. S. (2024) · Annals of Botany · doi:10.1093/aob/mcae022 · Cited by 17

Evolutionary rates and adaptive radiations

Hernández‐Hernández, T. (2019) · Biology & Philosophy · doi:10.1007/s10539-019-9694-y · Cited by 16

Phylogeny and evolution of sexually selected tail ornamentation in widowbirds and bishops (Euplectesspp.)

Prager, M., & Andersson, S. (2009) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2009.01818.x · Cited by 14

Evolution of Breeding Systems in Acrocephaline Warblers

Leisler, B., Winkler, H., & Wink, M. (2002) · The Auk · doi:10.1093/auk/119.2.379 · Cited by 13

Using Integrative Biology to Infer Adaptation from Comparisons of Two (or a Few) Species

Cox, C. L., & Logan, M. L. (2021) · Physiological and Biochemical Zoology · doi:10.1086/714018 · Cited by 10

Morphological and Molecular Analysis of Australian Earwigs (Dermaptera) Points to Unique Species and Regional Endemism in the Anisolabididae Family

Stuart, O. P., Binns, M. R., Umina, P. A., Holloway, J. C., Severtson, D. L., Nash, M., Heddle, T., van Helden, M., & Hoffmann, A. A. (2019) · Insects · doi:10.3390/insects10030072 · Cited by 10

Evolution of Microsporogenesis in Palms (Arecaceae)

Sannier, J., Lange, C. B. A., Harley, M. M., & Nadot, S. (2007) · International Journal of Plant Sciences · doi:10.1086/518265 · Cited by 10

Bridging Performance and Adaptive Landscapes to Understand Long-Term Functional Evolution

Simon, M. N., & Moen, D. S. (2023) · Physiological and Biochemical Zoology · doi:10.1086/725416 · Cited by 11

Review and phylogeny of the geniculata group, genus Chinavia (Heteroptera: Pentatomidae), with notes on biogeography and morphological evolution

Genevcius, B. C., & SCHWERTNER, C. F. (2014) · Zootaxa · doi:10.11646/zootaxa.3847.1.2 · Cited by 9

Phylogenetic Character Reconstruction

Albert, J. S. (2007) · Evolution of Nervous Systems · doi:10.1016/b0-12-370878-8/00108-7 · Cited by 9

EVOLUTION OF COLORFUL DISPLAY

Borgia, G., Coyle, B. J., & Zwiers, P. B. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00051.x · Cited by 8

Phylogeny and Historical Ecology of Rhodocoma (Restionaceae) from the Cape Floristic Region

Hardy, C., & Linder, P. (2007) · Aliso · doi:10.5642/aliso.20072301.16 · Cited by 8

Comparison of Natural and Nonnative Two-Species Communities ofAnolisLizards

Poe, S. (2014) · The American Naturalist · doi:10.1086/676523 · Cited by 7

A Novel Clade of Unique Eukaryotic Ribonucleotide Reductase R2 Subunits is Exclusive to Apicomplexan Parasites

Munro, J. B., Jacob, C. G., & da Silva, J. C. F. (2013) · Journal of Molecular Evolution · doi:10.1007/s00239-013-9583-y · Cited by 6

Phylogenetic signals in ecological properties of parasites

Krasnov, B. R., Morand, S., & Poulin, R. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139794749.024 · Cited by 6

RESOURCE PARTITIONING OF SYMPATRIC NOROPS (BETA ANOLIS) IN A SUBTROPICAL MAINLAND COMMUNITY

D'Cruze, Neil, C. M., Stafford, & Peter, J. M. (2006) · Herpetological Journal · Cited by 6

Evolution of ecological diversity in the neotropical tanagers of the genus Tangara (Aves: Thraupidae)

Naoki, K. (2003) · doi:10.31390/gradschool_dissertations.2021 · Cited by 6

A Phylogenetic Morphometric Investigation of Interspecific Relationships of Lyponia s. str. (Coleoptera, Lycidae) Based on Male Genitalia Shapes

Fang, C., Yang, Y., Yang, X., & Liu, H. (2023) · Insects · doi:10.3390/insects15010011 · Cited by 5

Phylogeny of the Saxifraga-associated species of Dichotrachelus (Insecta: Coleoptera: Curculionidae), with remarks on their radiation in the Alps

Meregalli, M., Menardo, F., Klass, K., & Cervalla, P. (2013) · Arthropod Systematics & Phylogeny · doi:10.3897/asp.71.e31765 · Cited by 4

Grounded Ground Birds and Surfing Canopy Birds: Variation of Foraging Stratum Breadth Observed in Neotropical Forest Birds and Tested with Simulation Models Using Boundary Constraints

Walther, B. A. (2002) · The Auk · doi:10.2307/4089965 · Cited by 4

Phylogenomic analysis reveals the evolutionary origins of five independent clades of forage grasses within the African genus UrochloaPreprint

Masters, L. E., Tomaszewska, P., Schwarzacher, T., Zuntini, A. R., Heslop-Harrison, J. S., & Vorontsova, M. S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.03.547487 · Cited by 4

Phylogenetic Hypothesis Testing

Irisarri, I., & Zardoya, R. (2013) · Wiley eBooks · doi:10.1002/9780470015902.a0025163 · Cited by 4

Phylogenetic Character Reconstruction

Albert, J. S. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-820584-6.00002-7 · Cited by 2

A Review on the Use of Geodesign Processes in Managing Flood Vulnerability

Pang, B., & Deal, B. M. (2024) · Land · doi:10.3390/land13060723 · Cited by 2

Linguistic Phylogenetics of the Austronesian Family: A Performance Review of Methods Adapted from Biology

Saunders, A. B. (2006) · Cited by 2

Mother knows best: maternal egg-clutch size predicts larval group size in pine sawflies (genus Neodiprion )Preprint

Terbot, J. W., & Linnen, C. R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/761528 · Cited by 2

Evolution of Breeding Systems in Acrocephaline Warblers

Leisler, B., Winkler, H., & Wink, M. (2002) · The Auk · doi:10.2307/4089885 · Cited by 2

Una aproximación filogenética al estudio del dimorfismo sexual de tamaño en Felidae y la evaluación de la regla de Rensch

Ecología, R. C. D., & Ambiente, Y. M. (2014) · Cited by 1

Challenges and Possible Solutions

Zhadko, O., & Ko, S. (2019) · Routledge eBooks · doi:10.4324/9780429030017-10 · Cited by 1

Plants as biotic indicators of Neogene palaeoenvironmental evolution in the Cape Floristic Region

Hoffmann, V. (2012) · Open University of Cape Town (University of Cape Town) · Cited by 1

The implementation of phylogenetic structural equation modeling for biological data from variance-covariance matrices, phylogenies, and comparative analyses

Santos, J. C. (2009) · Texas ScholarWorks (Texas Digital Library) · Cited by 1

DNA methyltransferase enzymes (MTases) may not enhance genomic protection against exogenous DNA invasions

Wijenayake, S. (2012) · doi:10.22215/etd/2012-07415 · Cited by 1

Los Métodos Comparativos Filogenéticos en el estudio de las aves

Mahler, B., & Tubaro, P. L. (2002) · El Hornero · doi:10.56178/eh.v17i1.883 · Cited by 1

Aspectos evolutivos da história de vida e estrutura da casca do ovo de lagartos tropiduríneos

Nunes, R. B. (2010) · doi:10.11606/t.41.2010.tde-06122010-103251

LIFE HISTORY AND POPULATION GENETIC STRUCTURE OF SEA STARS FROM THE FAMILY ASTERINIDAE

Keever, C. C. (2010) · Summit (Simon Fraser University)

What Makes Our Minds Human? Comparative Phylogenetic Perspectives on the Evolution of Cognition

MacLean, E. L. (2012) · DukeSpace (Duke University)

SYNTHESIS Of mice and mammoths: generality and antiquity of the island rule

Lomolino, M. V., van der Geer, A. A., Lyras, G., Palombo, M. R., Sax, D. F., & Rozzi, R. (2013)

ARTICLE Body size, biomic specialization and range size of African large mammals

Fernández, M. H., & Vrba, E. S. (2005)

Uso de marcadores moleculares na taxonomia de Dissomphalus (Hymenoptera, Bethylidae) e gêneros correlatos.

AZEVEDO, C. O., Almeida, E. A. B., & Costa, L. P. (2016)

Fossil Energy Technology Environmental Program information system: making the data accessible

Gove, N. B., Genung, R. K., Huffstetler, J. K., & Oen, C. (1984) · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)

Different phylogenetic characteristics of Icterids: would they be evolutionary strategies to avoid parasitism by Molothrus spp.?Preprint

Barbosa, V. M., da Silva, B. D., da Silva, V. X., & Hasui, É. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.30.601453

Écomorphologie et évolution phénotypique : méthodes et applications aux ruminants actuels et aux « ongulés » fossiles lors de la Crise de Salinité Messinienne à la limite Mio-Pliocène

Clavel, J. (2014) · theses.fr (ABES) · doi:10.70675/16a4b1fezdc18z4a53zb938z667ab690ce9b

Utilisation of next generation sequencing to characterise novel lyssaviruses, improve phylogenetic inferences and investigate cross species transmission events

Marston, D. A. (2017) · doi:10.70675/754f7fa9z8762z482azb11az4abac5fa2a90

MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data

Mongad, D., Chavan, N. S., Narwade, N. P., Dixit, K. K., Shouche, Y. S., & Dhotre, D. P. (2021) · Genomics · doi:10.1016/j.ygeno.2021.08.016 · Cited by 66

Meinicke P. Tax4Fun: predicting functional profiles frommetagenomic 16S rRNA data. Bioinformatics. 2015; 31:2882–2884. doi: 10.1093/bioinformatics/btv287 PMID

Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2016)

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv287 · Cited by 1,615

Sequence analysis Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2016)

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

Wemheuer, F., Taylor, J. A., Daniel, R., Johnston, E. L., Meinicke, P., Thomas, T., & Wemheuer, B. (2020) · Environmental Microbiome · doi:10.1186/s40793-020-00358-7 · Cited by 804