Publications

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	70) Ecker N., Huchon D., Mansour Y., Mayrose I. & Pupko T. (2024). A machine-learning based alternative to phylogenetic bootstrap. Bioinforamtics. (Accepted).
	69) Sandberg T.O.M., Yahalomi D., Bracha N., Haddas-Sasson M., Pupko T., Atkinson S.D., Bartholomew J.L., Zhang J.Y. & Huchon D. (2024). Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC genomics. 25:388 https://doi.org/10.1186/s12864-024-10254-w. [pdf]
	68) Montesanto F., Hadjez R., Mastrototaro F., Huchon D., Gissi C., Novak L. & Shenkar N. (2024) Against the flow: Integrated taxonomy and environmental suitability of a cold-water species dispersing to warmer waters. Biological Invasions. 26:953-973 https://doi.org/10.1007/s10530-023-03222-0. [pdf]
	67) Dotan E., Alburquerque M., Wygoda E., Huchon D. & Pupko T. (2023) GenomeFLTR: filtering reads made easy. Nucleic Acids Research. gkad410. https://doi.org/10.1093/nar/gkad410. [pdf] [Web server link]	[Source code]
	66) Liberman R., Benayahu Y. & Huchon D. (2022) Octocorals in the Gulf of Aqaba exhibit high photosymbiont fidelity. Frontiers in Microbiology. 13:1005471. https://doi.org/10.3389/fmicb.2022.1005471. [pdf]
	65) Novosolov M., Yahalomi D., Chang E. S., Fiala I., Cartwright P. & Huchon D. (2022) The phylogenetic position of the enigmatic, Polypodium hydriforme (Cnidaria, Polypodiozoa): Insights from mitochondrial genomes. Genome Biology and Evolution 14(8):evac112. https://doi.org/10.1093/gbe/evac112. [pdf]
	64) Gupta A., Haddas-Sasson M., Gayer K. & Huchon D. (2022) Myxozoan infection in thinlip mullet Chelon ramada (Mugiliformes: Mugilidae) in the Sea of Galilee. Scientific Reports 12:10049. https://doi.org/10.1038/s41598-022-13215-z. [pdf]
	63) Van Le M.-L., Novosolov M., Huchon D. & Stach T. (2021) The pericardium of Oikopleura dioica (Tunicata, Appendicularia) contains two distinct cell types and is rotated by 90 degrees to the left. Zoomorphology. 140:527–537. https://doi.org/10.1007/s00435-021-00538-0. [pdf]
	62) Alama-Bermejo G., Hernandez-Orts J. S., Huchon D. & Atkinson S. D. (2021) Two novel myxosporean parasite species of Ceratomyxa Thelohan, 1892 from the banded cusk-eel Raneya brasiliensis (Kaup) (Ophidiiformes: Ophidiidae) off Patagonia, Argentina. Parasitology International. 85:102433. https://doi.org/10.1016/j.parint.2021.102433. [pdf]
	61) Gordon T., Upadhyay A. K., Manni L., Huchon D. & Shenkar N. (2021) And then there were three…: extreme regeneration ability of the solitary chordate Polycarpa mytiligera. Frontiers in Cell and Developmental Biology. 9:793. https://doi.org/10.3389/fcell.2021.652466. [pdf]	[Datasets]
	60) Salonna M., Gasparini F., Huchon D., Montesanto F., Haddas-Sasson M., Ekins M., McNamara M., Mastrototaro F. & Gissi C. (2021) An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode. Scientific reports. 11, 4078. https://doi.org/10.1038/s41598-021-83127-x. [pdf]
	59) Kyger R., Luzuriaga-Neira A., Layman T., Sandberg T. O. M., Singh D., Huchon D., Peri S., Atkinson S. D., Bartholomew J. L., Yi S. V. & Alvarez-Ponce D. (2021) Myxosporea (Myxozoa, Cnidaria) lack DNA cytosine methylation. Molecular Biology and Evolution. 38:393–404. [pdf]
	58) Shpirer E., Haddas-Sasson M., Spivak-Glater M., Feldstein T., Meiri S. & Huchon D. (2021) Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome-b sequences. Mammalia. 85:79-89. [pdf]
	57) Anava S., Neuhof M., Gingold H., Sagy O., Munters A., Svensson E. M. , Afshinnekoo E., Danko D., Foox J., Shor P., Riestra B., Huchon D., Mason C. E., Mizrahi N., Jakobsson M. & Rechavi O. (2020) Illuminating the genetic mysteries of the Dead Sea Scrolls. Cell. 181:1218–1231. [pdf]
	56) Yahalomi D., Atkinson S. D., Neuhof M., Chang E. S., Philippe H., Cartwright P., Bartholomew J.L. & Huchon D. (2020) A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome. Proceedings of the National Academy of Sciences USA. 117:5358-5363. [pdf]	[Datasets]
	55) Fromm A., Atkinson S. D., Alama-Bermejo G., Cartwright P., Bartholomew J. L. & Huchon D. (2019) A new mitochondrial gene order in the banded cusk-eel Raneya brasiliensis (Actinopterygii, Ophidiiformes). Mitochondrial DNA Part B. 4:1-4. [pdf]
	54) Shenkar N., Shmuel Y. & Huchon D. (2018) The invasive ascidian Ciona robusta recorded from a Red Sea marina. Marine Biodiversity. 48:2211–2214. [pdf]
	53) Shpirer E., Diamant A., Cartwright P. & Huchon D. (2018) A genome wide survey reveals multiple nematocyst-specific genes in Myxozoa. BMC Evolutionary Biology. 18:138. [pdf]
	52) Arafat H., Adamaru A., Gissi C. & Huchon D. (2018) Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida. BMC Evolutionary Biology. 18:65. [pdf]
	51) Idan T., Shefer S., Feldstein T., Yahel R., Huchon D. & Ilan M. (2018) Shedding light on an East-Mediterranean mesophotic sponge ground community and the regional sponge fauna. Mediterranean Marine Science. 19:84-106. [pdf]
	50) Ostersetzer-Biran O., Lane N., Pomiankowski A., Burton R., Arnqvist G., Filipovska A., Huchon D. & Mishmar D. (2017) The first Mitochondrial Genomics and Evolution SMBE-satellite meeting: a new scientific symbiosis. Genome Biology and Evolution. 9:3054–3058. [pdf]
	49) Alamaru A., Hoeksema B. W., van der Meij S. E. T. & Huchon D. (2017) Molecular diversity of benthic ctenophores (Coeloplanidae). Scientific Reports 7:6365. [pdf]
	48) Yahalomi D., Haddas-Sasson M., Rubinstein N., Feldtein T., Diamant A. & Huchon D. (2017) The multipartite mitochondrial genome of Enteromyxum leei (Myxozoa): eight fast evolving megacircles. Molecular Biology and Evolution. 34:1551-1556. [pdf]
	47) Meiri M., Stockhammer P. W., Marom N., Bar-Oz G., Sapir-Hen L., Morgenstern P., Macheridis S., Rosen B., Huchon D., Maran J. & Finkelstein I. (2017) Eastern Mediterranean mobility in the Bronze and Early Iron Ages: inferences from ancient DNA of pigs and cattle. Scientific reports. 7:701. [pdf]
	46) Shenkar N., Koplovitz G., Dray L., Gissi C. & Huchon D. (2016) Back to solitude: solving the phylogenetic position of the Diazonidae using molecular and developmental characters. Molecular Phylogenetics and Evolution. 100:51-56. [pdf]
	45) Dray L., Neuhof M., Diamant A. & Huchon D. (2016) The complete mitochondrial genome of the devil firefish Pterois miles (Bennett, 1828) (Scorpaenidae). Mitochondrial DNA Part A. 27:783-784. [pdf]
	44) Dray L., Neuhof M., Diamant A. & Huchon D. (2016) The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae). Mitochondrial DNA Part A. 27:781-782. [pdf]
	43) Huchon D., Szitenberg A., Shefer S., Ilan M. & Feldstein T. (2015) Mitochondrial Group I and Group II introns in the sponge orders Agelasida and Axinellida. BMC Evolutionary Biology. 15:278. [pdf]
	42) Chang S. E., Neuhof M., Rubinstein N. D., Diamant A., Philippe H., Huchon D. & Cartwright P. (2015) Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. Proceedings of the National Academy of Sciences USA. 112:14912–14917. [pdf]	[Datasets]
	41) Ashkenazy H., Cohen O., Pupko T. & Huchon D. (2014) Indel reliability in indel-based phylogenetic inference. Genome Biology and Evolution. 6:3199–3209. [pdf]
	40) Shpirer E., Chang S., Diamant A., Rubinstein N., Cartwright P. & Huchon D. (2014) Diversity and evolution of myxozoan minicollagens and nematogalectins. BMC Evolutionary Biology. 14:205. [pdf]
	39) Diamant A., Rothman S. B.-S., Goren M., Galil B.S., Yokes M.B., Szitenberg A. & Huchon D. (2014) Biology of a new xenoma-forming gonadotropic microsporidium in the invasive blotchfin dragonet Callionymus filamentosus. Diseases of Aquatic Organisms. 109:35-54. [pdf]	[Datasets]
	38) Meiri M., Huchon D., Bar-Oz G., Boaretto E., Kolska Horwitz L., Maeir A. M., Sapir-Hen L., Larson G., Weiner S. & Finkelstein I. (2013) Ancient DNA and population turnover in Southern Levantine pigs - signature of the Sea Peoples migration? Scientific Reports. 3:3035. [pdf]
	37) Rubinstein N. D., Feldstein T., Shenkar N., Botero-Castro F., Griggio F., Mastrotorato F., Delsuc F., Douzery E. J. P., Gissi C. & Huchon D. (2013) Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes. Genome Biology and Evolution. 5:1185–1199. [pdf]	[Datasets]
	36) Szitenberg A., Becking L. E., Vargas S., Fernandez J. C. C., Santodomingo N., Wörheide G., Ilan M., Kelly M. & Huchon D. (2013) Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers. Molecular Phylogenetics and Evolution. 67:509-519. [pdf]	[Datasets]
	35) Belinky F., Goldfarb I., Szitenberg A., Feldstein T., Wörheide G., Ilan M. & Huchon D. (2012) ALG11 – a new variable DNA marker for sponge phylogeny. Comparison of phylogenetic performances with the 18S rDNA and the COI gene. Molecular Phylogenetics and Evolution. 63:702-713. [pdf]	[Datasets]
	34) Szitenberg A., Goren M., & Huchon D. (2012) Mitochondrial and morphological variation of Tilapia zillii in Israel. BMC Research Notes. 5:172. [pdf]	[Datasets]
	33) Erpenbeck D., Schmitz J., Churakov G., Huchon D., Wörheide G. & Degnan B. M. (2012) First evidence of miniature transposable elements in sponges (Porifera). Hydrobiologia. 687:43-47. [pdf]
	32) Edrey Y. H., Casper D., Huchon D., Gelfond J. A., Mele J., Kristan D. M., Nevo E., & Buffenstein R. (2012) Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity. Aging Cell. 11:213–222. [pdf]	[Datasets]
	31) Shneor O., Perlman G., Balaban A., Yom-Tov Y., Huchon D. & Geffen E. (2010) Origin of passerine migratory waves: evidence from the blackcap at a stopover site. Israel Journal of Ecology and Evolution. 56:135–151. [pdf]
	30) Cohen O., Ashkenazy H., Belinky F., Huchon D. & Pupko T. (2010) GLOOME: Gain Loss Mapping Engine. Bioinformatics. 26:2914-2915. [pdf]	[Web server]
	29) Szitenberg A., Rot C., Ilan M. & Huchon D. (2010) Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae. BMC Evolutionary Biology. 10:288. [pdf]
	28) Diamant A., Goren M., Yokes M. B., Galil B. S., Klopman Y., Huchon D., Szitenberg A. & Karhan S.Ü. (2010) Dasyatispora levantinae gen. et sp. nov., a new microsporidian parasite from the common stingray Dasyatis pastinaca (Linnaeus, 1758) in the eastern Mediterranean. Diseases of Aquatic Organisms. 91:137–150. [pdf]
	27) Churakov G., Sadasivuni M.K., Rosenbloom K., Huchon D., Brosius J. & Schmitz J. (2010) Rodent evolution: back to the root. Molecular Biology and Evolution. 27:1315-1326. [pdf]
	26) Belinky F., Cohen O. & Huchon D. (2010) Large-scale parsimony analysis of metazoan indels in protein-coding genes. Molecular Biology and Evolution. 27:441–451. [pdf]	[Datasets]
	25) Singh T. R., Tsagkogeorga G., Delsuc F., Blanquart S., Shenkar N., Loya Y. Douzery E. J. P. & Huchon D. (2009) Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny. BMC Genomics. 10:534. [pdf]	[Datasets]
	24) Tsagkogeorga G., Turon X., Hopcroft R. R., Tilak M.-K., Feldstein T., Shenkar N., Loya Y., Huchon D., Douzery E. J. P. & Delsuc F. (2009) An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models. BMC Evolutionary Biology. 9:187. [pdf]	[Datasets]
	23) Shemesh E., Huchon D., Simon-Blecher N. & Achituv Y. (2009) The distribution and molecular diversity of the Eastern Atlantic and Mediterranean chthamalids (Crustacea, Cirripedia). Zoologica Scripta. 38:365-378 [pdf]
	22) Blanga-Kanfi S., Miranda H., Penn O., Pupko T., DeBry R.W. & Huchon D. (2009) Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evolutionary Biology. 9:71. [pdf]
	21) Levin E., Yom-Tov Y., Barnea A. & Huchon D. (2008) Genetic diversity and phylogeography of the greater mouse-tailed bat (Rhinopoma microphyllum) in the Levant. Acta Chiropterologica. 10:207-212. [pdf]
	20) Belinky F., Rot C., Ilan M. & Huchon D. (2008) The complete mitochondrial genome of the demosponge Negombata magnifica (Poescilosclerida). Molecular Phylogenetics and Evolution. 47:1238–1243. [pdf]
	19) Singh T. R., Shneor O. & Huchon D. (2008) Bird mitochondrial gene order: insight from three warbler mitochondrial genomes. Molecular Biology and Evolution. 25:475–477. [pdf]
	18) Steppan S. J., Ramirez O., Banbury J., Huchon, D., Pacheco V., Walker L. I. & Spotorno, A.E. (2007) A molecular reappraisal of the systematics of the leaf-eared mice Phyllotis and their relatives. Pp. 799-826. In Kelt, D. A., Lessa, E. P., Salazar-Bravo, J. and Patton, J. L. (eds). The quintessential naturalist: honoring the life and legacy of Oliver P. Pearson. University of California, Publications in Zoology 134:1-981. [pdf]
	17) Simon-Blecher N., Huchon D. & Achituv Y. (2007) Phylogeny of coral-inhabiting barnacles (Cirripedia; Thoracica; Pyrgomatidae) based on 12S, 16S and 18S rDNA analysis. Molecular Phylogenetics and Evolution. 44:1333-1341. [pdf]
	16) Huchon D., Chevret P., Jordan U., Kilpatrick W. C., Ranwez V., Jenkins P. D., Brosius J. & Schmitz J. (2007) Multiple molecular evidences for a living mammalian fossil. Proceedings of the National Academy of Sciences USA. 104:7495–7499. [pdf]
	15) Farwick A., Jordan U., Fuellen G., Huchon D., Catzeflis F., Brosius J. & Schmitz J. (2006) Automated scanning for phylogenetically informative transposed elements in rodents. Systematic Biology. 55:936-948. [pdf]
	14) Davidov Y., Huchon D., Koval S. F. & Jurkevitch E. (2006) A new α-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory. Environmental Microbiology. 8:2179-2188. [pdf]
	13) Rot C., Goldfarb I., Ilan M. & Huchon D. (2006) Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria. BMC Evolutionary Biology. 6:71. [pdf]
	12) Poux C., Chevret P., Huchon D., De Jong W. W. & Douzery E. J. P. (2006) Arrival and diversification of caviomorph rodents and plathyrrhine primates in South America. Systematic Biology. 55:228-244. [pdf]	[Datasets]
	11) Steindler L., Huchon D., Avni A. & Ilan M. (2005) 16S rRNA phylogeny of sponge-associated cyanobacteria. Applied and Environmental Microbiology. 71:4127-4131. [pdf]
	10) Douzery E. J. P., & Huchon D. (2004) Rabbits, if anything, are likely glires. Molecular Phylogenetics and Evolution. 33:922 - 935. [pdf]
	9) Douzery E. J. P., Delsuc F., Stanhope M. J. & Huchon D. (2003) Local molecular clocks in three nuclear genes: divergence ages of rodents and other mammals, and incompatibility between fossil calibrations. Journal of Molecular Evolution. 57:S201-S213. [pdf]	[Datasets]
	8) Huchon D., Nikaido M. & Okada N. (2002) Use of SINE retroposon in phylogeny. Mיdecine/Science. 18:1276-1281. [pdf]
	7) Pupko T., Huchon D., Cao Y., Norihiro Okada N. & Hasegawa M. (2002) Combining multiple data sets in a likelihood analysis: which models are the best? Molecular Biology and Evolution. 19:2294-2307. [pdf]
	6) Huchon D., Madsen O., Sibbald M. J. J. B., Ament K., Stanhope M. J., Catzeflis F., de Jong W. W. & Douzery E. J. P. (2002) Rodent Phylogeny and a Timescale for the Evolution of Glires: evidence from an Extensive Taxon Sampling using three Nuclear Genes. Molecular Biology and Evolution. 19:1053-1065. [pdf]	[Datasets]
	5) Huchon D. & Douzery E. J. P. (2001) From the old-world to the new-world: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents. Molecular Phylogenetics and Evolution. 20:238-351. [pdf]
	4) Robinson-Rechavi M. & Huchon D. (2000) RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. Bioinformatics. 16:296-297. [pdf]	[Source code]
	3) Huchon D., Catzeflis F. & Douzery E. J. P. (2000) Variance of molecular datings, evolution of rodents, and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. The Proceedings of the Royal Society of London serie B. 267:393-402. [pdf]
	2) Huchon D., Delsuc F., Catzeflis F. M. & Douzery E. J. P. (1999) Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm the founder effect in Dasypus novemcinctus (Xenarthra). Molecular Ecology. 8:1743-1748. [pdf]
	1) Huchon D., Catzeflis F. M. & Douzery E. J. P. (1999) Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. Molecular Biology and Evolution. 16:577-589. [pdf]

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Dorothee Huchon's Lab

Publications