Research Interests
I'm interested in the relationship between diversification processes and the generation and loss of biodiversity. I look to use integrative and comparative techniques to determine the relative impact of biotic and abiotic factors as drivers of adaptive changes in phenotype and genotype in tetrapod groups. I'm particularly interested in incorporating information from extinct lineages to better understand diversification dynamics and trait evolution.
Current Projects
Anseriform Macroevolution, Project gUCE (pronounced "goose")
In collaboration with the OpenWings project, I am using phylogenomics to investigate the relationships among several species of the Anseriformes, or waterfowl (ducks, geese, swans and screamers). The members of this order are among the most distinct and readily recognizable birds and there are over 150 species worldwide. Waterfowl occur on all continents, except Antarctica, and occupy habitat ranging from the tropics to the tundra. One of the most interesting aspects of this work is our attempt to include DNA from recently extinct species in our analyses.
In collaboration with the OpenWings project, I am using phylogenomics to investigate the relationships among several species of the Anseriformes, or waterfowl (ducks, geese, swans and screamers). The members of this order are among the most distinct and readily recognizable birds and there are over 150 species worldwide. Waterfowl occur on all continents, except Antarctica, and occupy habitat ranging from the tropics to the tundra. One of the most interesting aspects of this work is our attempt to include DNA from recently extinct species in our analyses.
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Phylogenetics and Biogeography of the Cracidae
I am also using phylogenomics to investigate the biogeographic history of the the family, Cracidae (chachalacas, currasows and guans). There are approximately 50 species of these birds and they occur primarily in the Neotropics. The range extends from the extreme southern tip of Texas, down to Argentina. These are medium to large size birds and are members of the order Galliformes which also includes birds like chickens and turkeys. There are some endangered species in this group resulting from a combination of hunting and habitat disturbance. One species has been declared extinct and Cracidae are considered one of the most endangered bird groups in the world. |
The Alagoas Currasow (Mitu mitu), now declared extinct in the wild.
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Polymorphism in the Major Histocompatibility Complex (MHC) in Cebinae
This project looks at the DNA sequence and corresponding amino acid diversity of specific exons from three MHC loci (DRB, DQA and DQB). The MHC is an important gene family involved in immune system function in vertebrates. We primarily focus on one population of Cebus capucinus imitator and include a modest sampling of additional populations as well as several other species from the subfamily Cebinae (capuchin monkeys). With the results of this study, we can begin to characterize this important gene complex for capuchins and investigate its relationship to immunity, life history traits and behavior.
This project looks at the DNA sequence and corresponding amino acid diversity of specific exons from three MHC loci (DRB, DQA and DQB). The MHC is an important gene family involved in immune system function in vertebrates. We primarily focus on one population of Cebus capucinus imitator and include a modest sampling of additional populations as well as several other species from the subfamily Cebinae (capuchin monkeys). With the results of this study, we can begin to characterize this important gene complex for capuchins and investigate its relationship to immunity, life history traits and behavior.
Publications
Lima, M.G.M, Silva-Júnior, J.S, Cerny, D, Buckner, J.C, Aleixo, A, et. al. (2018) A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America. Molecular Phylogenetics and Evolution 124, 137-150.
Buckner, J.C, Ellingson, R., Gold, D.A., Jones, T.L., Jacobs, D.K. (2018) Mitogenomics supports a novel taxonomic relationship for the extinct diving duck Chendytes lawi. Molecular Phylogenetics and Evolution 122, 102-109.
Lima, M.G.M, Buckner, J.C, et. al. (2017) Capuchin monkey biogeography: understanding Sapajus Pleistocene range expansion and the current sympatry between Cebus and Sapajus. Journal of Biogeography 44, 810-820. doi:10.1111/jbi.12945
Rylands, A., Heymann, E., Lynch Alfaro, J., Buckner, J., Roos, C., Matauschek, C., Boubli, J., Sampaio, R., Mittermeier, R. (2016) Taxonomic review of the New World tamarins (Primates: Callitrichidae). Zoological Journal of the Linnaean Society 177, 1003-1028.
Blumstein, D., Buckner, J., Shah, S., Patel, S., Alfaro, M. E., Natterson-Horowitz, B. (2015) A clinical research pathway towards developing new insights into cardiomyopathy. Evolution, Medicine, and Public Health 2015(1), 280. DOI: 10.1093/emph/eov024
Blumstein, D., Buckner, J., Shah, S., Patel, S., Alfaro, M. E., Natterson-Horowitz, B. (2015). The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy? Evolution, Medicine, and Public Health 2015 (1), 195-203. DOI:10.1093/emph/eov015
Buckner, J. C., Alfaro, J. W. L., Rylands, A. B., & Alfaro, M. E. (2015). Biogeography of the marmosets and tamarins (Callitrichidae). Molecular phylogenetics and evolution, 82, 413-425.
Buckner, J., Welsh, A.B., Sime, K.R. (2014). Evidence for population differentiation in the bog buckmoth of New York State. Northeastern Naturalist 21, 506-514.
Buckner, J.C, Ellingson, R., Gold, D.A., Jones, T.L., Jacobs, D.K. (2018) Mitogenomics supports a novel taxonomic relationship for the extinct diving duck Chendytes lawi. Molecular Phylogenetics and Evolution 122, 102-109.
Lima, M.G.M, Buckner, J.C, et. al. (2017) Capuchin monkey biogeography: understanding Sapajus Pleistocene range expansion and the current sympatry between Cebus and Sapajus. Journal of Biogeography 44, 810-820. doi:10.1111/jbi.12945
Rylands, A., Heymann, E., Lynch Alfaro, J., Buckner, J., Roos, C., Matauschek, C., Boubli, J., Sampaio, R., Mittermeier, R. (2016) Taxonomic review of the New World tamarins (Primates: Callitrichidae). Zoological Journal of the Linnaean Society 177, 1003-1028.
Blumstein, D., Buckner, J., Shah, S., Patel, S., Alfaro, M. E., Natterson-Horowitz, B. (2015) A clinical research pathway towards developing new insights into cardiomyopathy. Evolution, Medicine, and Public Health 2015(1), 280. DOI: 10.1093/emph/eov024
Blumstein, D., Buckner, J., Shah, S., Patel, S., Alfaro, M. E., Natterson-Horowitz, B. (2015). The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy? Evolution, Medicine, and Public Health 2015 (1), 195-203. DOI:10.1093/emph/eov015
Buckner, J. C., Alfaro, J. W. L., Rylands, A. B., & Alfaro, M. E. (2015). Biogeography of the marmosets and tamarins (Callitrichidae). Molecular phylogenetics and evolution, 82, 413-425.
Buckner, J., Welsh, A.B., Sime, K.R. (2014). Evidence for population differentiation in the bog buckmoth of New York State. Northeastern Naturalist 21, 506-514.
Previous Projects
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2015-2017 Phylogenetic placement of the extinct ducks, Chendytes lawi and Camptorhynchus labradorius (Labrador duck)
Abstract: "Chendytes lawi, an extinct flightless diving anseriform from coastal California, was traditionally classified as a sea duck, tribe Mergini, based on similarities in osteological characters. We recover and analyze mitochondrial genomes of C. lawi and five additional Mergini species, including the extinct Labrador Duck, Camptorhyncus labradorius. Despite its diving morphology, C. lawi is reconstructed as an ancient relictual lineage basal to the dabbling ducks (tribe Anatini), revealing an additional example of convergent evolution of characters related to feeding behavior among ducks. The Labrador Duck is sister to Steller’s Eider which may provide insights into the evolution and ecology of this poorly known extinct species. Our results demonstrate that inclusion of full length mitogenomes, from taxonomically distributed ancient and modern sources can improve phylogeny reconstruction of groups previously assessed with shorter single-gene mitochondrial sequences." - Buckner et. al. (2018) |
A phylogeny of Anatinae (true ducks) showing the placement of two extinct species.
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2016 Phylogenetic Biogeography of Capuchin monkeys (Subfamily: Cebinae)
Abstract: "Our aim was to examine gracile capuchin (Cebus) and robust capuchin monkey (Sapajus) diversification, with a focus on recent Sapajus expansion within Amazonia. We wanted to reconstruct the biogeographical history of the clade using statistical methods that model lineages’ occupation of different regions over time in order to evaluate recently proposed ‘Out of Amazonia’ and ‘Reinvasion of Amazonia’ hypotheses as alternative explanations for the extensive geographical overlap between reciprocally monophyletic gracile (Cebus) and robust (Sapajus) capuchin monkeys. We reconstructed a time-calibrated molecular phylogeny for capuchins under Bayesian inference from three mitochondrial genes. We then categorized 12 capuchin clades across four Neotropical centres of endemism and reconstructed the biogeographical history of the capuchin radiation using six models implemented in ‘BioGeoBEARS’. We performed a phylogeographical analysis for a robust capuchin clade that spans the Atlantic Forest, Cerrado, Caatinga and Amazonia. We find support for a late Miocene vicariant Cebus-Sapajus divergence and a Pleistocene Sapajus invasion of Amazonia from the Atlantic Forest. Our new analyses confirm Sapajusdiversified first in the Atlantic Forest, with subsequent range expansion into widespread sympatry with Cebus in Amazonia, as well as multiple expansions into drier savanna-like habitats. We do not find mitochondrial molecular congruence with morphological species distinctions for Sapajus flavius, S. cay, S. macrocephalus, S. libidinosus and S. apella; instead, these five morphological types together form a single widespread clade (Bayesian posterior probability = 1) with geographical substructure and shared ancestry during the Pleistocene. Our results support vicariance dividing ancestral capuchin populations in Amazonia versus the Atlantic Forest, and a Pleistocene ‘Amazonian invasion’ by Sapajus to explain the present-day sympatry of Cebus and Sapajus." - Lima, MGM et. al. (2017)
Abstract: "Our aim was to examine gracile capuchin (Cebus) and robust capuchin monkey (Sapajus) diversification, with a focus on recent Sapajus expansion within Amazonia. We wanted to reconstruct the biogeographical history of the clade using statistical methods that model lineages’ occupation of different regions over time in order to evaluate recently proposed ‘Out of Amazonia’ and ‘Reinvasion of Amazonia’ hypotheses as alternative explanations for the extensive geographical overlap between reciprocally monophyletic gracile (Cebus) and robust (Sapajus) capuchin monkeys. We reconstructed a time-calibrated molecular phylogeny for capuchins under Bayesian inference from three mitochondrial genes. We then categorized 12 capuchin clades across four Neotropical centres of endemism and reconstructed the biogeographical history of the capuchin radiation using six models implemented in ‘BioGeoBEARS’. We performed a phylogeographical analysis for a robust capuchin clade that spans the Atlantic Forest, Cerrado, Caatinga and Amazonia. We find support for a late Miocene vicariant Cebus-Sapajus divergence and a Pleistocene Sapajus invasion of Amazonia from the Atlantic Forest. Our new analyses confirm Sapajusdiversified first in the Atlantic Forest, with subsequent range expansion into widespread sympatry with Cebus in Amazonia, as well as multiple expansions into drier savanna-like habitats. We do not find mitochondrial molecular congruence with morphological species distinctions for Sapajus flavius, S. cay, S. macrocephalus, S. libidinosus and S. apella; instead, these five morphological types together form a single widespread clade (Bayesian posterior probability = 1) with geographical substructure and shared ancestry during the Pleistocene. Our results support vicariance dividing ancestral capuchin populations in Amazonia versus the Atlantic Forest, and a Pleistocene ‘Amazonian invasion’ by Sapajus to explain the present-day sympatry of Cebus and Sapajus." - Lima, MGM et. al. (2017)
2012 - 2014 Phylogenetics and Biogeography of the Marmosets and Tamarins (Family: Callitrichidae)
Abstract: "The marmosets and tamarins, Family Callitrichidae, are Neotropical primates with over 60 species and subspecies that inhabit much of South America. Although callitrichids exhibit a remarkable widespread distribution, attempts to unravel their biogeographic history have been limited by taxonomic confusion and the lack of an appropriate statistical biogeographic framework. Here, we construct a time-calibrated multi-locus phylogeny from GenBank data and the callitrichid literature for 38 taxa. We use this framework to conduct statistical biogeographic analyses of callitrichids using BioGeoBEARS. The DIVAj model is the best supported reconstruction of biogeographic history among our analyses and suggests that the most recent common ancestor to the callitrichids was widespread across forested regions c. 14 Ma. There is also support for multiple colonizations of the Atlantic forest region from the Amazon basin, first by Leontopithecus c. 11 Ma and later by Callithrix c. 5 Ma. Our results show support for a 9 million year old split between a small-bodied group and large-bodied group of tamarins. These phylogenetic data, in concert with the consistent difference in body size between the two groups and geographical patterns (small-bodied tamarins and large-bodied tamarins have an unusually high degree of geographic overlap for congeners) lend support to our suggestion to split Saguinus into two genera, and we propose the use of distinct generic names; Leontocebus and Saguinus, respectively." - Buckner et. al. (2015)
Abstract: "The marmosets and tamarins, Family Callitrichidae, are Neotropical primates with over 60 species and subspecies that inhabit much of South America. Although callitrichids exhibit a remarkable widespread distribution, attempts to unravel their biogeographic history have been limited by taxonomic confusion and the lack of an appropriate statistical biogeographic framework. Here, we construct a time-calibrated multi-locus phylogeny from GenBank data and the callitrichid literature for 38 taxa. We use this framework to conduct statistical biogeographic analyses of callitrichids using BioGeoBEARS. The DIVAj model is the best supported reconstruction of biogeographic history among our analyses and suggests that the most recent common ancestor to the callitrichids was widespread across forested regions c. 14 Ma. There is also support for multiple colonizations of the Atlantic forest region from the Amazon basin, first by Leontopithecus c. 11 Ma and later by Callithrix c. 5 Ma. Our results show support for a 9 million year old split between a small-bodied group and large-bodied group of tamarins. These phylogenetic data, in concert with the consistent difference in body size between the two groups and geographical patterns (small-bodied tamarins and large-bodied tamarins have an unusually high degree of geographic overlap for congeners) lend support to our suggestion to split Saguinus into two genera, and we propose the use of distinct generic names; Leontocebus and Saguinus, respectively." - Buckner et. al. (2015)
A time-callibrated phylogeny of the Callitrichidae. Shading refers to major geologic time periods: yellow – Miocene, orange – Pliocene, red – Pleistocene. Node bars indicate the 95% highest posterior density. Illustrations by Stephen Nash.
2009-2011 Population Genetics and Ecology of the Oswego County Bog Buckmoth
My undergraduate thesis focused on the biology of an endangered variant of a saturniid moth from the Hemileuca maia complex, the bog buckmoth. This insect occurs in the isolated bogs and fens surrounding the Great Lakes in North America. I worked on the population genetics and ecology of the insects within Oswego County, New York.
My undergraduate thesis focused on the biology of an endangered variant of a saturniid moth from the Hemileuca maia complex, the bog buckmoth. This insect occurs in the isolated bogs and fens surrounding the Great Lakes in North America. I worked on the population genetics and ecology of the insects within Oswego County, New York.
Searching for egg masses of the bog buck moth in Selkirk Fen, Oswego County, New York. Photo Credit: Karen Sime.
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Workshops and Courses
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2019 SACNAS Postdoc Leadership Institute, Honolulu, Hawaii
Role: Participant This two-part workshop for postdocs aims to assist in developing leadership skills and the ability to leverage their whole selves – including their culture – as an asset in the workplace. It also serves as an incredible networking opportunity for early career professionals to find peers and mentors to support them through their STEM journey. Find out more about the workshop here. 2018 Molecular Evolution Workshop at the MBL, Woods Hole, Massachusetts
Role: Participant This workshop, held every year since 1988 at the Marine Biological Laboratory in Woods Hole (Cape Cod), focuses on the fundamentals of molecular evolution and the application of the most recent laboratory and statistical methods to studies of micro- and macro-evolution. Students learn directly from leaders in the field and have the opportunity to engage and discuss their research with them throughout the duration of the workshop. This year it was led by Mark Holder and Joseph Bielawski. Find out more about the course here. |
First cohort of the SACNAS PLI (2019)
Participants from the Molecular Evolution Workshop in front of Eel Pond.
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2015 Latin American Macroevolutionary Analysis Workshop: Brazil
Role: Assistant Instructor This workshop, held immediately after the 2015 Evolution conference in Brazil on the island of Ilha Bela, reviewed several recent methods in macroevolutionary analysis. These included introductions to programming in R, ancestral state reconstruction, diversification rate analyses and more. Instructors: Liam Revell, Luke Harmon and Michael Alfaro. |
Participants, TAs and instructors from the Macroevolution workshop. Photo credit: Laura Alencar.
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2014 NESCent Academy Course: Phylogenetic Analysis Using RevBayes
Role: Participant A lecture/tutorial based course on using the statistical software RevBayes (http://revbayes.github.io/) for inference of evolutionary parameters in phylogenetic analysis and related analyses. The workshops were led by the developers including Tanja Stadler, Tracy Heath and Sebastian Höhna, among others. Since the workshop a number of tutorials have been made available and can be found here. |
Participants from the RevBayes NESCent Academy course. Photo Credit: Al Tanner
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2014 CABAlliance Workshop in Yauondé, Cameroon
Role: Participant The Central African Biodiversity Alliance regularly holds workshops in Central Africa for students conducting research there or with a potential interest in the region. The workshops include lectures from prominent researchers and tutorials in common biologically relevant computational programs (i.e basic R, Maxent, QGIS, etc). For more information, see the CABAlliance website. |
Participants from the CABAlliance workshop. Photo Credit: Sandie Sorelle
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2012 Field Course in Catemaco, Veracruz, Mexico
Role: Participant “Study and Conservation of Primates in Transformed Habitats: Neotropical Region” was a post-conference course that reviewed current laboratory and field methods applied to studies of wild primates. Coordinators: Pedro Dias, Ariadna Negrín, Domingo Espinosa (Veracruz University) For more information about this and other courses from the Sociedad Latinoamericana de Primatologia (Latin American Society of Primatology), check out their website. |
Participants from the Field Course.
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2011 Surveys and Phenology of Reptiles and Amphibians in the Brazilian Pantanal
As part of a winter quarter course I traveled to Brazil for ten days to participate in a survey of reptiles and amphibians in the Pantanal. In the same year I received a scholarship to spend four weeks as a research assistant in an ecology lab in Campo Grande, Mato Grosso do Sul. I continued working on the surveys in addition to preparing data for phenological analyses on various anuran species of the Brazilian Pantanal. If you are a SUNY student, check out opportunities for traveling to Brazil, Costa Rica, India, South Korea and Taiwan via Global Laboratories here. |
First cohort of the SUNY Global laboratories in Campo Grande, MS, Brazil.
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