Outreach and Media
 Teaching




Publications (including book chapters)




Pdfs of most of the following papers are available here
Pre-print articles (non peer-reviewed) are indicated with pp


Graduate students in the lab are indicated with **, undergraduate and high school students with *






66) E. Maki**, T. Glimm, P. Pramanik, Y. Chiari, M. Kiskowski (2025) New approaches for capturing and estimating variation in complex animal color patterns from digital photographs: application to the Eastern Box turtle (Terrapene carolina). Accepted, PeerJ






65) S. Bulls**, E. Finn, P. Sykora, V.J. Lynch, P. Pramanik, S. Glaberman, Y. Chiari (2025) Assessing CometChip technology for DNA damage studies in non-model species: distinct UV-induced responses in turtles and mammals. BMC Rsearch Notes, 18: 243.






64) C. Blanchard, AT. Gomeiz, K. Avery, E. El Gazzah, AM. Alsubaie, M. Sikaroodi, Y. Chiari, C. Ward, J. Sanchez, V. Espina, E. Petricoin, E. Baldelli, M. Pierobon (2024) Signaling dynamics in coexisting monoclonal cell subpopulations unveil mechanisms of resistance to anti-cancer compounds. Cell Communication and Signaling, 22: 377






63) E. White**, S. Kim*, G. Wegh*, Y. Chiari (2024) Thermal tolerance plasticity and dynamics of thermal tolerance in Eublepharis macularius: implications for future climate- driven heat stress. Journal of Thermal Biology, 123: 103912






pp12) E. White**, S. Kim*, G. Wegh*, Y. Chiari (2024) Thermal tolerance plasticity and dynamics of thermal tolerance in Eublepharis macularius: implications for future climate- driven heat stress. Pre-print on bioRxiv https://www.biorxiv.org/content/10.1101/2024.01.13.575519v1






62)  BT. Hastings**, A. Melnyk*, M. Ghyabi, E. White**, FM. Barroso, MA. Carretero, D. Lattanzi, J. Claude, Y. Chiari (2023) Melanistic coloration does not influence thermoregulation in the crepuscular gecko Eublepharis macularius. Biology Open, 12(10): bio060114

Software pipeline to extract melanistic coloration @ https://github.com/brandon-hastings/Lumeleon

Dataset and R codes on Dryad @ doi:10.5061/dryad.1zcrjdfzq

Outreach video summary @ https://youtu.be/iPT_4RG1OVA?si=6Ivlhzogm-IWXO_g

First author interview @ https://journals.biologists.com/bio/article/12/10/bio060176/334528/First-person-Brandon-Hastings






pp11) BT. Hastings**, A. Melnyk*, M. Ghyabi, E. White**, FM. Barroso, MA. Carretero, D. Lattanzi, J. Claude, Y. Chiari (2023) On the role of melanistic coloration on thermoregulation in the crepuscular gecko Eublepharis macularius. Publicly available pre-print on bioRxiv https://www.biorxiv.org/content/10.1101/2023.05.18.541382v1






61) S. Weber Hertel, J. Stupavsky, K. Alford*, HR. Hicks*, A. Heaton**, N. Katlein**, BT. Hastings**, A. Stern*, S. Jett, AY. Wang*, B. Wang, S. Glaberman, Y. Chiari (2023) Dominant attitudes and values towards wildlife and the environment in coastal Alabama. Conservation Science and Practice, 5(8): e12957

Data visualization available @
https://public.tableau.com/app/profile/ylenia.chiari/viz/WeberHerteletal__16599728420070/1Demographics-AtGlance

Outreach video summary @ https://youtu.be/3hlaDQnokXQ?si=Lm7lv7rNbHwqMV3b





pp10) S. Glaberman, R. Posont, H. Swain, Y. Chiari, J. Claude (2023) Baseline corticosterone is not an indicator of population health during non-El Nino conditions in Galapagos marine iguanas. Publicly available pre-print on SSRN https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4437567




60) BJ. Pinto, T. Gamble, CH. Smith, SE. Keating, JC. Havird, Y. Chiari (2023) The revised leopard gecko (Eublepharis macularius) reference genome provides insight into the consideration of genome phasing and assembly. Journal of Heredity, esad016






59) Y. Chiari, L. Howard, N. Moreno**, S. Relyea, J. Dunnigan, MC. Boyer, M. Kardos, S. Glaberman, G. Luikart (2023) Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation. Molecular Ecology Resources, 23: 803-817

Outreach video summary @ https://youtu.be/ExPVCY-w2ZY?si=CL7dEjKd52rDuaXX






pp9) BJ. Pinto, T. Gamble, CH. Smith, SE. Keating, JC. Havird, Y. Chiari (2023) The revised leopard gecko (Eublepharis macularius) reference genome provides insight into the consideration of genome phasing and assembly. Publicly available pre-print on bioRxiv https://www.biorxiv.org/content/10.1101/2023.01.20.523807v1






pp8) S. Weber Hertel, J. Stupavsky, K. Alford*, HR. Hicks*, A. Heaton**, N. Katlein**, B. Hastings**, A. Stern*, S. Jett, AY. Wang*, B. Wang, S. Glaberman, Y. Chiari (2023) Dominant attitudes and values towards wildlife and the environment in coastal Alabama.  Publicly available preprint on ecoevoRxiv https://ecoevorxiv.org/repository/view/4871/






58) JD. Daza, Y. Chiari, E. Daza-Herrera, MS. Glaberman, S. Glaberman, O. Heide, A. Herrera-Martinez, R. Thomas (2022) A rare case of caudal bifurcation in a miniaturized gecko from Puerto Rico. The Anatomical Record, 1-4






pp7) S. Bulls**, L. Platner, W. Ayub*, N. Moreno**, J-P. Arditi*, S. McCain, P. Wagner, LGR. Bruins- van Sonsbeek, VJ. Lynch, J. Claude, S. Glaberman, Y. Chiari (2022) Cancer prevalence is remarkably low in turtles and is correlated with life history traits in birds, mammals, and squamates. Publicly available pre-print on bioRxiv
https://www.biorxiv.org/content/10.1101/2022.07.12.499088v1






57) N. Moreno**, A. Heaton**, K. Bruening*, E. Milligan*, D. Nelson, S. Glaberman, Y. Chiari (2022) Hybridization and low genetic diversity in the endangered Alabama red-bellied turtle (Pseudemys alabamensis). Ecology and Evolution, 12: e8964


Photo credit: N. Moreno




56) N. Katlein**, M. Ray*, A. Wilkinson, J. Claude, MA. Kiskowski, B. Wang, S. Glaberman, Y. Chiari (2022) Does colour impact responses to images in geckos? Journal of Zoology, 317: 138-146


Photo credit: R. Moreau




55) EL. Jensen, MC. Quinzin, JM. Miller, MA. Russello, RC. Garrick, DL. Edwards, S. Glaberman, Y. Chiari, N. Poulakakis, W. Tapia, JP. Gibbs, A. Caccone (2022) A new lineage of Galapagos giant tortoises identified from museum samples. Heredity, 128: 261-270









54) R. Roy, N. Moreno**, SA. Brockman, A. Kostanecki, A. Zambre, C. Holl, EM. Solhaug, A. Minami, E. Snell-Rood, M. Hampton, MA. Bee, Y. Chiari, AD. Hegeman, CJ. Carter (2022) Convergent evolution of a novel blood-red nectar pigment in vertebrate-pollinated flowers. PNAS, 119: e2114420119






53) S. Glaberman, SE. Bulls, JM. Vazquez, Y. Chiari, VJ. Lynch (2021) Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles. Genome Biology and Evolution, evab244




pp6) S. Glaberman, SE. Bulls, JM. Vazquez, Y. Chiari, VJ. Lynch (2021) Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles.
Publicly available pre-print on bioRxiv
https://www.biorxiv.org/content/10.1101/2021.07.07.451454v1





52) T. Glimm, M.A. Kiskowski, N. Moreno**, Y. Chiari (2021) Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos. PeerJ, 9: e11829

Matlab codes to extract the gecko color pattern are available @ https://osf.io/zauwe/?view_only=97c4846fb5f34357b0943c2f5c6bc571






51) MM. Lamont, N. Moreno**, FY. Camacho-Sanchez, HH. Acosta-Sanchez, S. Glaberman, MA. Reyes-Lopez, Y. Chiari (2021) Genetic diversity of immature Kemp's ridley (Lepidochelys kempii) individuals from the northern Gulf of Mexico. Aquatic Conservation: Marine and Freshwater Ecosystems, 31(10): 3003 - 3010






50) K. Pabis^, Y. Chiari^, C. Sala, E. Straka, R. Giacconi, M. Provinciali, X. Li, H. Brown-Borg, K. Novikowski, T. Valancak, C. Gundacker, P. Garagnani, M. Malavolta (2021) Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. GeroScience, 43: 1975 - 1993
^Shared first authorship





pp5) R. Roy, N. Moreno**, SA. Brockman, A. Kostanecki, A. Zambre, C. Holl, EM. Solhaug, A. Minami, E. Snell-Rood, M. Hampton, MA. Bee, Y. Chiari, AD. Hegeman, CJ. Carter (2021) Convergent evolution of a novel blood-red nectar pigment in vertebrate-pollinated flowers. Publicly available pre-print on bioRxiv
https://www.biorxiv.org/content/10.1101/2021.03.24.436888v1






pp4) T. Glimm, M.A. Kiskowski, N. Moreno**, Y. Chiari (2021) Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos. Publicly available pre-print on bioRxiv
https://www.biorxiv.org/content/10.1101/2021.03.23.436685v1






pp3) N. Katlein**, M. Ray*, A. Wilkinson, J. Claude, M.A. Kiskowski, B. Wang, S. Glaberman, Y. Chiari (2021) Does colour impact attention towards 2D images in geckos? Publicly available pre-print on bioRxiv
https://www.biorxiv.org/content/10.1101/2021.02.03.429594v1






pp2) N. Moreno**, L. Howard, S. Relyea, J. Dunnigan, M. Boyer, M. Kardos, S. Glaberman, G. Luikart, Y. Chiari (2021) Gene expression estimates: influence of sequencing library construction, fish sampling methods, and tissue harvesting time. Publicly available pre-print on Authorea
https://www.authorea.com/users/391297/articles/505449-gene-expression-estimates-influence-of-sequencing-library-construction-fish-sampling-methods-and-tissue-harvesting-time






49) Y. Chiari Morphology (2020) In "Galapagos Giant Tortoises" J. Gibbs, L. Cayot, W.A. Tapia (Eds.). Section III, Chapter 8. Publisher Elsevier





48) WL Allen, N. Moreno*, T. Gamble, Y. Chiari (2020) Ecological, behavioral, and phylogenetic influences on the evolution of dorsal color pattern in gecko. Evolution, 74: 1033 - 1047
               Digest on this article available here






47) M.A. Kiskowski, T. Glimm, N. Moreno*, T. Gamble, Y. Chiari (2019) Isolating and quantifying the role of developmental noise in generating phenotypic variation. PLoS Computational Biology, 15(4): e1006943

Outreach video summary @ https://youtu.be/pM7YGBrAutQ?si=SQrUFpk3TF3h4vHl






46) Quesada et al. (2019) Giant tortoise genomes provide insights into longevity and age-related disease. Nature Ecology and Evolution, 3: 87 - 95




pp1) M.A. Kiskowski, T. Glimm, N. Moreno*, T. Gamble, Y. Chiari (2018) Isolating and quantifying the role of developmental noise in generating phenotypic variation. Publicly available pre-print on bioRxiv 334961
https://www.biorxiv.org/content/10.1101/334961v1






45) Y. Chiari, S. Glaberman, V.J. Lynch (2018) Insights on cancer resistance in vertebrates: reptiles as a parallel system to mammals. Nature Reviews Cancer, 18: 5252 (Correspondence)






44) P. Sykora , Y. Chiari, A. Heaton**, N. Moreno**, S. Glaberman, R. Sobol (2018) Application of the CometChip platform to assess DNA damage in field collected blood samples from turtles. Environmental and Molecular Mutagenesis, 59: 322 - 333






43) A. Hylton**, Y. Chiari, I. Capellini, MG. Barron, S. Glaberman (2018) Mixed phylogenetic signal in fish acute toxicity across chemical classes. Ecological Applications, 28: 605 - 611 






42) Y. Chiari, A. van der Meijden, A. Caccone, J. Claude, B. Gilles (2017) Self-righting potential and the evolution of shell shape in Galapagos tortoises. Scientific Reports, 7: 15828







41) Y. Chiari, N. Moreno*, J. Elmore**, A. Hylton**, A. Ray*, R. Burkhardt**, S. Glaberman (2017) Widespread occurrence of Batrachochytrium dendrobatidis in Southern Alabama, USA. Herpetological Review, 48: 356 - 359





40) Y. Chiari, S. Glaberman, P. Tarroso, A. Caccone, J. Claude (2016) Ecological and evolutionary influences on body size and shape in Galapagos marine iguana (Amblyrhynchus cristatus). Oecologia, 181: 885 - 894.






39) DL. Martin, Y. Chiari, E. Boone, TD. Sherman, C. Ross, S. Wyllie-Echeverria, JK. Gaydos, AA. Boettcher (2016) Functional, phylogenetic and host-geographic signatures of Labyrinthula spp. provide for putative species delimitation and a global-scale view of seagrass wasting disease. Estuaries and Coasts 39: 1403 - 1421.





38) N. Poulakakis, DL. Edwards, Y. Chiari, RC. Garrick, E. Benavides, MA. Russello, GJ. Watkins-Colwell, S. Glaberman, W. Tapia, JP. Gibbs, LJ. Cayot, A. Caccone (2015) Description of a new Galapagos giant tortoise species (Chelonoidis, Testudines, Testudinidae) from Cerro Fatal on Santa Cruz Island. PLoS One 10: e0138779.






37) B. Gasse, Y. Chiari, J. Silvent, T. Davit-Beal, J-Y. Sire (2015) Amelotin: an enamel matrix protein that experienced distinct evolutionary pathways in amphibians, sauropsids and mammals. BMC Evolutionary Biology 15: 47.






36) Y. Chiari, S. Glaberman, N. Serén**, MA. Carretero, I. Capellini (2015) Phylogenetic signal in amphibian sensitivity to copper sulfate relative to experimental temperature. Ecological Applications 25: 596 - 602.






35) J. Romiguier, P. Gayral, M. Ballenghien, A. Bernard, V. Cahais, A. Chenuil, Y. Chiari, R. Dernat, L. Duret, N. Faivre, E. Loire, JM. Lourenco, B. Nabholz, C. Roux, G. Tsagkogeorga, AA-T. Weber, LA. Weinert, K. Belkhir, N. Bierne, S. Glemin, N. Galtier (2014) Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515: 261 - 263.






34) N. Serén**, S. Glaberman, MA. Carretero, Y. Chiari (2014) Molecular evolution and functional divergence of the metallothionein gene family in vertebrates. Journal of Molecular Evolution 78: 217 - 233. Journal Cover


33) E. Loire, Y. Chiari, A. Bernard, V. Cahais, J. Romiguier, B. Nabholz, JM. Lourenço, N. Galtier (2013) Population genomics of the endangered giant Galapagos tortoises. Genome Biology 14: R136.


32) Y. Chiari, A. van der Meijden, M. Mucedda, N. Wagner, M. Veith (2013) No detection of the pathogen Batrachochytrium dendrobatis in Sardinian cave salamanders, genus Hydromantes. Amphibia-Reptilia 34: 136 -141.







31) P. Orozco-terWengel, Y. Chiari, DR. Vieites, M. Perdono, E. Louis Jr (2013) Isolation and characterization of four polymorphic microsatellite loci for the Malagasy spider tortoise Pyxis arachnoides and cross-amplification in Pyxis planicauda. Amphibia-Reptilia 34: 125 - 128.






30) JM. Lourenco**, S. Glemin, Y. Chiari, N. Galtier (2013) The determinants of the molecular substitution process in turtles. Journal of Evolutionary Biology 26: 38-50.






29) Y. Chiari, V. Cahais, N. Galtier, F. Delsuc (2012) Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biology 10: 65.






28) V. Cahais, P. Gayral, G. Tsagkogeorga, J. Melo-Ferreira, M. Ballenghien, L. Weinert, Y. Chiari, K. Belkhir, V. Ranwez, N. Galtier (2012) Reference-free transcritpome assembly in non-model animals from next-generation sequencing data. Molecular Ecology Resources 12: 834-845.






27) Y. Chiari, A. van der Meijden, M. Mucedda, JM. Lourenco**, A. Hochkirch, M. Veith (2012) Phylogeography of Sardinian cave salamanders (genus Hydromantes) is mainly determined by geomorphology. PLoS One 7(3): e32332.








26) JM. Lourenco**, J. Claude, N. Galtier, Y. Chiari (2012) Dating the cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Molecular Phylogenetics and Evolution 62: 496- 507.

 




25) Y. Chiari, J. Claude (2012) Morphometric identification of individuals when there are more shape variables than reference specimens: a case study in Galapagos tortoises. Comptes rendus Biologies 335: 62-68.






24) P. Gayral, L. Weinert, Y. Chiari, G. Tsagkogeorga, M. Ballenghien, N. Galtier (2011) Next-generation sequencing of transcriptomes: a guide to RNA isolation in non-model animals. Molecular Ecology Resources 11: 650-661.






23) Y. Chiari, N. Galtier (2011) RNA extraction from sauropsids blood: evaluation and improvement of methods. Amphibia-Reptilia 32: 136-139.






22) Y. Chiari, J. Claude (2011) Study of the carapace shape and growth in two Galapagos tortoise lineages. Journal of Morphology 272: 379-386.






21) Y. Chiari^, K. Dion^, J. Colborn^, A. Parmakelis, J. Powell (2010) On the possible role of tRNA base modifications in the evolution of codon usage: Queuosine and Drosophila. Journal of Molecular Evolution 70: 339-345.
^Authors contributed equally






20) Y. Chiari, A. van der Meijden, O. Madsen, M. Vences, A. Meyer (2009) Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates. Frontiers in Zoology 6: 32.






19) Y. Chiari, DR. Vieites, J. Guo*, P. Bora, M. Vences (2009) High haplotype diversity in a microendemic Malagasy gecko species, Lygodactylus mirabilis (Pasteur, 1962). Zootaxa 2269: 43-52.






18) Y. Chiari^, C. Hyseni^*, TH. Fritts, S. Glaberman, C. Marquez, JP. Gibbs, J. Claude, A. Caccone (2009) Morphometrics parallel genetics in a newly discovered and endangered taxon of Galapagos tortoise. PLoS One 4(7): e6272.
^Authors contributed equally






17) A. van der Meijden, Y. Chiari, M. Mucedda, S. Carranza, C. Corti, M. Veith (2009) Phylogenetic relationships of Sardinian cave salamanders, genus Hydromantes, based on mitochondrial and nuclear DNA sequence data. Molecular Phylogenetics and Evolution 51: 399-404.






16) A. Crottini, Y. Chiari, V. Mercurio, A. Meyer, M. Vences, F. Androne (2008) Into the canyons: the phylogeography of the Malagasy frogs Mantella expectata and Scaphiophryne gottlebei in the arid Isalo Massif and its significance for conservation (Amphibia: Mantellidae and Microhylidae). Organism Diversity and Evolution 8: 368-377.






15) M. Vences, Y. Chiari, M. Teschke, RD. Randrianiaina, L. Raharivololoniaina, P. Bora, DR. Vieites, F. Glaw (2008). Which frogs are out there? A preliminary evaluation of survey techniques and identification reliability of Malagasy amphibians. In: Andreone F. (ed), A Conservation Strategy for the Amphibians of Madagascar. Monografie, 45. Museo Regionale di Scienze Naturali, Turin.






14) Y. Chiari^, B. Wang^, H. Rushmeier, A. Caccone (2008) Using digital images to reconstruct 3D biological forms: a new tool for morphological studies. Biological Journal of the Linnean Society 95: 425-436.
^Authors contributed equally


13) F. Rabemananjara, A. Crottini, Y. Chiari, F. Andreone, F. Glaw, R. Duguet, P. Bora, OR. Ravoahangimalala, M. Vences (2007) Molecular systematics of Malagasy poison frogs in the Mantella betsileo and M. leavigata species groups. Zootaxa 1501: 31-44.








12) M. Vargas-Ramirez**, Y. Chiari, OV. Castaño-Mora, SBJ. Menken (2007) Low genetic variability in the endangered endemic Colombian freshwater turtle Podocnemis lewyana (Testudinides, Podocnemididae). Contributions to Zoology 76 (1): 1-7.






11) F. Rabemananjara, Y. Chiari, OR. Ravoahangimalala, M. Vences (2007) Evidence for recent gene flow between north-eastern Madagascan poison frogs from a phylogeography of the Mantella cowani group. Frontiers in Zoology 4: article 1.






10) JG. Measey, M. Vences, RC. Drewes, Y. Chiari, M. Melo, B. Bourles (2007) Freshwater paths into the ocean: molecular phylogeny of the frog Ptychadena gives insights into amphibian colonisation of the oceanic islands. Journal of Biogeography 34: 7-20.






9) DR. Vieites, Y. Chiari, M. Vences, F. Andreone, F. Rabemananjara, P. Bora, S. Nieto-Roman, A. Meyer (2006) Mitochondrial evidence for distinct phylogeographic units in the endangered Malagasy poison frog Mantella bernhardi. Molecular Ecology 15: 1617-1625.






8) Y. Chiari, P. Orozco-terWengel, M. Vences, DR. Vieites, A. Sarovy, J. Randrianirina, A. Meyer, E. Louis Jr (2006) Genetic identification of units for conservation in tomato frogs, Dyscophus. Conservation Genetics 7: 473-482.






7) Y. Chiari, D. Malala Ravelonkasina, E. Faliarisoa (2006) Observation of Liopholidophis sexlineatus at 2498 m of elevation. Herpetological Review 37(3): 363.






6) A. van der Meijden, Y. Chiari (2006) Observation of Natrix tesselata in a seawater environment. Herpetological Review 37(1): 94






5) Y. Chiari, M. Thomas, M. Pedrono, DR. Vieites (2005) First data on genetic differentiation within the Madagascar spider tortoise, Pyxis arachnoides (BELL 1827). Salamandra 41: 35-43.






4) M. Vences, M. Thomas, A. van der Meijden, Y. Chiari, DR. Vieites (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology 2: article 5.






3) Y. Chiari, F. Andreone, M. Vences, A. Meyer (2005) Genetic variation of an endangered Malagasy frog, Mantella cowani, and its phylogeographic relationship to the widespread M. baroni. Conservation Genetics 6: 1041-1047.






2) Y. Chiari, M. Vences, DR. Vieites, F. Rabemananjara, P. Bora, OR. Ravoahangimalala, A. Meyer (2004) New evidence for parallel evolution of color patterns in Malagasy poison frogs (Mantella). Molecular Ecology 13: 3763-3774.






1) M. Vences, Y. Chiari, L. Raharivoloniaina, A. Meyer (2004) High mitochondrial diversity within and among populations of Malagasy poison frogs. Molecular Phylogenetics and Evolution 30: 295-307.










Other peer-reviewed publications

2) U. Fritz, Y. Chiari (2013) Conservation actions for European pond turtles - a summary of current efforts in distinct European countries. Herpetology Notes 6: 105


1) M. Thomas, Y. Chiari (2004) Untersuchungen der genetischen Differenzierung der Landschildkröten Südmadagaskars als Basis für Phylogeographie und Artenschutz. Elaphe 12: 56-58.










Last update May 2025
Copyright Ylenia Chiari