Publications

 

Carvajal-Rodríguez A. (2024)

iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2.

Biology Methods and Protocols bpae089. Doi: 10.1093/biomethods/bpae089.
Carvajal-Rodríguez A. (2024)

On Non-Random Mating, Adaptive Evolution, and Information Theory.

Biology 13 (12): 970. Doi: 10.3390/biology13120970.
Carvajal-Rodríguez A. (2024)

Unifying quantification methods for sexual selection and assortative mating using information theory.

Theoretical Population Biology 158: 206-215. Doi: 10.1016/j.tpb.2024.06.007. Mathematical Appendix and Supplementary tables and figures available HERE


Carvajal-Rodríguez A. (2023)

QInfoMating: Sexual selection and assortative mating estimation.

bioRxiv. Doi: 10.1101/2023.09.06.556585
Carvajal-Rodríguez A. (2023)

1LocusSim a mobile-friendly simulator for teaching population genetics.

Bioinformatics Advances 3(1):vbad087. Doi: 10.1093/bioadv/vbad087
Gabián M., Morán P., Saura M., Carvajal-Rodríguez A. (2022)

Detecting Local Adaptation between North and South European Atlantic Salmon Populations.

Biology 11: 933. Doi: 10.3390/biology11060933
Fernández-Meirama M., Rolán-Alvarez E., Carvajal-Rodríguez A. (2022)

A simulation study of the ecological speciation conditions in the Galician marine snail Littorina saxatilis.

Frontiers in Genetics 13: 680792. Doi: 10.3389/fgene.2022.680792
Antonio Carvajal-Rodríguez (2021)

Bioinformatics of Correction of Multiple Testing: An Introduction for Life Scientists.

in Bioinformatics and Human Genomics Research. CRC Press. Doi: 10.1201/9781003005926-17 [PDF].
Sarah L.Y. Lau, Gray A. Williams, Antonio Carvajal-Rodríguez, Emilio Rolán-Alvarez (2021)

An integrated approach to infer the mechanisms of mate choice for size.

Animal Behaviour 175: 33-43. Doi: 10.1016/j.anbehav.2021.02.020.
Daniel Estévez, Eugene Kozminsky, Antonio Carvajal-Rodríguez, Armando Caballero, Rui Faria, Juan Galindo and Emilio Rolán-Alvarez (2020)

Mate choice contributes to the maintenance of shell color polymorphism in a marine snail via frequency-dependent sexual selection.

Front. Mar. Sc 14. Doi: 10.3389/fmars.2020.614237.
Ponte-Fernández, C., González-Domínguez, J., Carvajal-Rodríguez, A., Martín, M.J. (2020)

Evaluation of Existing Methods for High-Order Epistasis Detection.

IEEE/ACM Transactions on Computational Biology and Bioinformatics . Doi: 10.1109/TCBB.2020.3030312.
Ponte-Fernández, C., González-Domínguez, J., Carvajal-Rodríguez, A., Martín, M.J. (2020)

Toxo: a library for calculating penetrance tables of high-order epistasis models.

BMC Bioinformatics 21: 138. Doi: 10.1186/s12859-020-3456-3.
Eugenio López-Cortegano, Carla Carpena-Catoira, Antonio Carvajal-Rodríguez, Emilio Rolán-Alvarez (2020)

Mate choice based on body size similarity in sexually dimorphic populations causes strong sexual selection.

Animal Behaviour 160: 69-78. Doi: 10.1016/j.anbehav.2019.12.005.
A. Carvajal-Rodríguez (2020)

Multi-model inference of non-random mating from an information theoretic approach.

Theoretical Population Biology 131: 38-53. Doi: 10.1016/j.tpb.2019.11.002. Peer-reviewed and recommended by PCI Evolutionary Biology. [PDF].


A. Carvajal-Rodríguez (2020)

Data and models from multi-model inference of non-random mating from an information theoretic approach.

Data in Brief 28: 104969. Doi: 10.1016/j.dib.2019.104969.


Martínez-Rodríguez P, Rolán-Alvarez E, Pérez-Ruiz M. del Mar, Arroyo-Yebras F, Carpena-Catoira C, A. Carvajal-Rodríguez, Bella J.L. (2019)

Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism?

Microbial Ecology 77: 1-12. Doi: 10.1007/s00248-019-01338-2.


A. Carvajal-Rodríguez (2019)

A generalization of the informational view of non-random mating: Models with variable population frequencies.

Theoretical Population Biology. 125: 67-74. Doi: 10.1016/j.tpb.2018.12.004.


Estévez D, Ng TPT, Fernández-Meirama M, Voois Jorien M, Carvajal-Rodríguez A, Williams GA, Galindo J, Rolán-Alvarez E. (2018)

A novel method to estimate the spatial scale of mate choice in the wild.

Behavioral Ecology and Sociobiology 72: 195. Doi: 10.1007/s00265-018-2622-3.


A. Carvajal-Rodríguez (2018)

MateSim: Monte Carlo simulation for the generation of mating tables.

BioSystems 171: 26-30 Doi: 10.1016/j.biosystems.2018.07.001. (biorxiv preprint) doi:10.1101/239178
A. Carvajal-Rodríguez (2018)

Non-random mating and information theory.

Theoretical Population Biology 120: 103-113. Doi: 10.1016/j.tpb.2018.01.003. Preprint (bioRxiv)


A. Carvajal-Rodríguez (2018)

Myriads: p-value-based multiple testing correction.

Bioinformatics 34 (6): 1043-1045. Doi: 10.1093/bioinformatics/btx746
Fernández-Meirama M, A. Carvajal-Rodríguez, Rolán-Alvarez E. (2017)

Testing the role of mating preference in a case of incomplete ecological speciation with gene flow.

Biological Journal of the Linnean Society 122 (3): 549-557. Doi: 10.1093/biolinnean/blx107
A. Carvajal-Rodríguez (2017)

HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations.

PLOS ONE 12(4): e0175944. Doi: 10.1371/journal.pone.0175944


Fernández-Meirama M, Estévez D, Ng TPT, Williams GA, Carvajal-Rodríguez A, Rolán-Alvarez E. (2017)

A novel method for estimating the strength of positive mating preference by similarity in the wild.

Ecol Evol. 7:1-11. Doi: 10.1002/ece3.2835
A. Carvajal-Rodríguez (2015)

Incorporación de la programación informática en el currículum de Biología.

Magister. Vol. 27, pp. 76-82. Doi: 10.1016/j.magis.2015.12.002
E. Rolán-Alvarez, A. Carvajal-Rodríguez, A. de Coo, B. Cortés, D. Estévez, M. Ferreira, R. González and A. D. Briscoe (2015)

The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples.

Evolution. Vol. 67, pp. 1845-1857. Doi: 10.1111/evo.12691
M. J. Rivas, S. Dominguez-Garcia and A. Carvajal-Rodríguez (2015)

Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow.

Current Genomics. Vol. 16, pp. 203-212. Doi: 10.2174/1389202916666150313230943
A. Carvajal-Rodríguez, E. Rolán-Alvarez (2014)

A comparative study of Gaussian mating preference functions: a key element of sympatric speciation models.

Biological Journal of the Linnean Society. Vol. 113, pp. 642-657. Doi: [Journal Link]
M. J. García-Pereira, A. Carvajal-Rodríguez, Simon Whelan, A. Caballero, H. Quesada (2014)

Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers

Molecular Phylogenetics and Evolution. Vol. 76, pp. 102-109 [Journal Link]
A. Carvajal-Rodríguez (2012)

Teaching the fluctuation test in silico by using Mutate: A program to distinguish between the adaptive and spontaneous mutation hypotheses

Biochemistry and Molecular Biology Education. Vol. 40, No. 4, pp. 277–283. [Journal Link]
M. J. García-Pereira, H. Quesada, A. Caballero, A. Carvajal-Rodríguez (2012)

AFLPMax: a user-friendly application for computing the optimal number of amplified fragment length polymorphism markers needed in phylogenetic reconstruction

Molecular Ecology Resources. 12 (3): 566-569. Doi: 10.1111/j.1755-0998.2011.03113.x
A. Carvajal-Rodríguez and de Uña-Alvarez (2011)

Assessing significance in high-throughput experiments by sequential goodness of fit and q-value estimation

PLoS ONE. 6 (9): e24700. [Journal Link]
A. Carvajal-Rodríguez and de Uña-Alvarez (2011)

A Simulation Study on the Impact of Strong Dependence in High-Dimensional Multiple-Testing I: The Case without Effects

PACBB. Advances in Intelligent and Soft Computing 93: 241-246. Doi: [10.1007/978-3-642-19914-1_32]
AP. Diz, A. Carvajal-Rodríguez and David O. F. Skibinski (2011)

Multiple hypothesis testing in proteomics: A strategy for experimental work

Molecular & Cellular Proteomics 10: M110.004374. Doi: 10.1074/mcp.M110.004374
de Uña-Alvarez and A. Carvajal-Rodríguez (2010)

SGoFicance Trace: Assessing Significance in High Dimensional Testing Problems

PLoS ONE. 5 (12):e15930. Doi: 10.1371/journal.pone.0015930
A. Carvajal-Rodríguez (2010)

Simulation of Genes and Genomes Forward in Time.

Current Genomics 11 (1): 58-61.
A. Carvajal-Rodríguez, Jacobo de Uña-Alvarez and Emilio Rolan-Alvarez (2009)

A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests

BMC Bioinformatics 10:209 [PDF]
Antonio Carvajal-Rodríguez and Fernando Carvajal-Rodriguez (2009)

Population Extinction in Genetic Algorithms: Application in Evolutionary Studies

LNCS (IWANN 2009) 5518: 1028-1034
A. Carvajal-Rodríguez (2008)

Detecting recombination and diversifying selection in human alpha-papillomavirus

Infection, Genetics and Evolution 8: 689-692 [PDF] (see also Figure 1 corrigendum)


A. Carvajal-Rodríguez (2008)

GENOMEPOP: A program to simulate genomes in populations

BMC Bioinformatics 9: 223 [PDF]
A. Carvajal-Rodríguez (2008)

Simulation of genomes: A review.

Current Genomics 9 (3): 155-159.
A. Carvajal-Rodríguez (2008)

The role of recombination in the post-genomic era: Challenges and Perspectives.

in Genetic Recombination Research Progress pp. 205-227. Ed. Jacob H. Schulz. Nova Science Publishers, Inc. New York.
Antonio Carvajal-Rodríguez, David Posada,Marcos Pérez-Losada, Emily Keller, Elaine J. Abrams,Raphael P. Viscidi and Keith A. Crandall (2008)

Disease progression and evolution of the HIV-1 C2V3C3 env gene region from 24 infected infants

Infection, Genetics and Evolution 8: 110-120. Doi: 10.1016/j.meegid.2007.10.009
A. Carvajal-Rodríguez (2007)

Simulating Genomes and Populations in the Mutation Space: An example with the evolution of HIV drug resistance.

arXiv:0801.0124v1
Manuel Angulo and Antonio Carvajal-Rodríguez (2007)

Evidence of recombination within human Alpha-Papillomavirus.

Virology Journal 4 :33. Doi: 10.1186/1743-422X-4-33]


Antonio Carvajal-Rodríguez, Keith A. Crandall and David Posada (2007)

Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy

Infection, Genetics and Evolution 7: 476-483. Doi: 10.1016/j.meegid.2007.02.001
Antonio Carvajal-Rodríguez (2007)

The importance of bio-computational tools for predicting HIV drug resistance

Recent Patents on DNA & Gene Sequences.Volume 1, Number 1: 63-68 [PDF]
Gonzalo Bello, Concepción Casado, Soledad García, Carmen Rodríguez, Jorge del Romero, Antonio Carvajal-Rodríguez, David Posada and Cecilio López-Galíndez (2007)

Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients.

Virology 362: 294-303. Doi: 10.1016/j.virol.2006.11.039
Conde-Padín P, A. Carvajal-Rodríguez, Carballo M, Caballero A and Rolán-Álvarez E. (2007)

Genetic variation for shell traits in a direct-developing marine snail involved in a putative sympatric ecological speciation process

Evolutionary Ecology 21: 635-650. Doi: 10.1007/s10682-006-9142-8
Antonio Carvajal-Rodríguez (2007)

FamSphere: A computer program for parental allocation from known genotypic pools.

Molecular Ecology Notes. 7: 213-216. Doi: 10.1111/j.1471-8286.2006.01599.x
A. Carvajal-Rodríguez, Guerra-Varela, J.,  Fernández, B., Rolán, E. and E. Rolán-Alvarez (2006)

An example of application of the geometric morphometric tools to the morphological diagnosis of two sibling species in Nassarius (Mollusca, Prosobranchia). 

Iberus 24 (2): 81-88 [PDF]
Antonio Carvajal-Rodríguez and Emilio Rolán-Alvarez (2006)

JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data.

BMC Evolutionary Biology 6:40.[Abstract][PDF]
Antonio Carvajal-Rodríguez, Keith A. Crandall and David Posada (2006)

Recombination Estimation under Complex Evolutionary Models with the Coalescent Composite Likelihood Method.

Molecular Biology and Evolution 23(4): 817-827. Doi: 10.1093/molbev/msj102.
Antonio Carvajal-Rodríguez, Keith A. Crandall y David Posada (2005)

Caracterización y modelado computacional de la recombinación en secuencias de ADN en el virus del SIDA (VIH-1).

Biojournal.net 2 [PDF].
A. M. Rodríguez-Piñeiro, A. Carvajal-Rodríguez, E. Rolán-Álvarez , F. J. Rodríguez-Berrocal, M. Martínez-Fernández and M. Páez de la Cadena (2005)

Application of relative warp analysis to the evaluation of two-dimensional gels in proteomics: Studying isoelectric point and relative molecular mass variation

Journal of Proteome Research. Volume 4 (4): 1318 - 1323.


A. Carvajal-Rodríguez, P. Conde Padín and E Rolán Álvarez (2005)

Decomposing shell form into size and shape by geometric-morphometric methods in two sympatric ecotypes of Littorina saxatilis.

Journal of Molluscan Studies 71: 313-318 PDF
A. Carvajal-Rodríguez, E. Rolán-Alvarez and A. Caballero (2005)

Quantitative variation as a tool for detecting human-induced impacts on genetic diversity

Biological Conservation. 124: 1-13 PDF
A. Carvajal-Rodríguez, Rodríguez MG (2005)

MODICOS: Morphometric and Distance Computation Software for evolutionary studies.

Online Journal of Bioinformatics  6 : 34-40 Abstract
A. Pérez-Figueroa, F. Cruz, A. Carvajal-Rodríguez, E. Rolán-Alvarez and A. Caballero (2005)

The evolutionary forces maintaining a  wild polymorphism of Littorina saxatilis: model selection by  computer simulations

Journal of Evolutionary Biology 18: 191-202.
A. Carvajal-Rodríguez (2004)

GASP: A new Genetic Algorithm (based on) Surviving Probability

Online Journal of Bioinformatics 5:23-31.[PDF]


A. Carvajal (2001)

A system of complementary Genes in hybrids between D. koepferae and D. buzzatii: A Markov chain model allows to make inferences about their number and relationships.

Genes and Genetic Systems 76:345-353. Doi: 10.1266/ggs.76.345
A. Carvajal (1996)

Developmental disruption in hybrids between D. koepferae and D. buzzatii

Int. Journ. of Dev. Biol. Suplement: 93s-94s [PDF].
A. Carvajal, M. Gandarela and H Naveira (1996)

A three-locus system of interspecific incompatibility underlies male inviability in hybrids between Drosophila buzzatii and D.koepferae

Genetica 98:1-19 [PDF].

A. Carvajal-Rodriguez - Departamento de Bioquímica Genética e Inmunología - Universidad de Vigo. ( Last update: November 2019). Return Home