Research Interests


My current research interests stem from my desire to understand fundamental aspects of biological diversity. These fundamental aspects include the relationships of organisms and their morphological complexity. I study these aspects using phylogenetic systematics, geometric morphometrics and other tools. These tools allow us to understand broader themes such as historical biogeography, molecular evolution, conservation and the evolution of morphological diversity. As an ichthyologist, my focus is on process oriented evolutionary biology in marine fishes and pattern oriented evolutionary biology in freshwater fishes. As a systematist, I use molecular and morphological tools to help discover relationships among species and resolve taxonomy in order to better understand the evolutionary history of a taxon.

My most recent research focuses on understanding the phylogenetic and biogeographic relationships of freshwater fishes from Middle America (Central America, Mexico, Greater Antillean Islands) and on the phylogenetic and evolutionary history of deep-sea fishes in the Gulf of Mexico and the Indo-West Pacific. I am also conducting studies of blind cave fishes of Gondwanan origin and bioluminescent fishes from the deep ocean.



Systematics of Deep-Sea and Bioluminescent Fishes
Part of my current research focus is to resolve some of the difficult phylogenetic problems associated with bioluminescent and deep-sea fishes. In recent years I have focused on the Indo-Pacific family of ponyfishes (Leiognathidae; with collaborator John Sparks, AMNH) and on deep-sea forms including batfishes and tripod fishes. Many deep-sea fishes are bioluminescent and co-opt the light produced by bacteria for sexually dimorphic photic communication. By resolving the relationships among these fishes we can better understand how this ability may have influenced their evolutionary history (e.g. increased speciation rates or morphological disparity). My lab is also currently resolving the many taxonomic problems that plague these group using molecular, morphological and behavioral (flashing) characters in phylogenetic analyses. Much of this work is associated with the products of recent field trips to Vietnam, Madagascar, Sri Lanka, Indonesia, the Malay Peninsula and Taiwan. The phylogenies being prepared for these families will be used to revise the taxonomy of these group, identify new species, and test hypotheses about the role of sexual selection and photic communication on morphological diversity and species richness.

Selected Systematics Publications:
-Chakrabarty, P., Davis, M.P., Smith, W.L. Smith, Baldwin, Z.H., Sparks, J.S. (2011) Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)? Molecular Ecology 20, 2818-2834.
-McMahan, C.D., Matamoros, W.A., Piller, K.R., Chakrabarty, P. (2015) Taxonomy and systematics of the herichthyins (Cichlidae: Tribe Heroini), with the description of eight new Middle American Genera. Zootaxa 3999 (2): 211-234.
-Derouen, V., Ludt, W.L., Ho, H.C., Chakrabarty, P., (2015) Examining Evolutionary Relationships and Shifts in Depth Preferences in the Enigmatic Batfishes (Lophiiformes: Ogcocephaloidei) Molecular Phylogenetics and Evolution 84: 27-33



Biogeography
I am also currently interested in the historical biogeography of Neotropical fishes. I hope to better understand the biogeographic relationships of Greater Antillean, Middle and South American fishes. One of the great unknowns in biogeographic studies is the origin of the fauna of the Greater Antillean islands and the four different geological blocks that have united to form Central America. I found evidence through phylogenetic analysis that the origin of some of the freshwater ichthyofauna is linked to ancient vicariance events. Vicariance was favored over alternatives because both the pattern of the recovered phylogeny and divergence time estimates were congruent with this hypothesis. I continue testing these hypotheses and several large-scale phylogenies that include a much broader sampling of taxa including fossils. The relationships of each of these groups are unique but all of them can potentially test biogeographic patterns for the region through phylogenetic analyses.

Recent Biogeography Publications:
-Ludt, W.B., Rocha, L.A., Erdmann, M.V., Chakrabarty, P., (2015) Skipping across the tropics: the evolutionary history of sawtail surgeonfishes (Acanthuridae: Prionurus). Molecular Phylogenetics and Evolution 84: 166-172.
-Bacon, C.D., Silvestro, D., Jaramillo, C.A., Smith, B.T., Chakrabarty, P., Antonelli, A. (2015) Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Sciences 112: 6110-6115.
Matamoros, W.A., McMahan, C.D., Chakrabarty, P., Albert, J.S., (2015) Derivation of the Freshwater Fish Fauna of Central America Revisited: Myer's hypothesis in the twenty-first century. Cladistics 31: 177-188.



Geometric Morphometrics And Analyses of Disparity
I have done a number of projects measuring and comparing morphological diversity as it is distributed among groups. I used geometric morphometric techniques and analyses of disparity to test hypotheses about morphological evolution in several fish clades. Hypotheses about the origins of various groups can often be tested by quantifying morphological diversity. I have published on how African Rift Lake cichlid taxa differ in morphological diversity relative to species richness and ecological diversity. Researchers in the past have tied the rich diversity of these cichlids to different evolutionary hypotheses (e.g., microallopatric speciation, sympatric speciation). Some of these evolutionary hypotheses were based on assumptions made about the morphological diversity of some cichlid clades. I quantified morphological diversity to test these hypotheses. I have also used geometric morphometric tools to clarify taxonomy and to test the role of sexual selection on the morphological evolution of bioluminescent fishes.

Selected GM Publications:
-Chakrabarty, P., Chu, J., Luthfun, N., and Sparks, J.S. (2010) Geometric morphometrics uncovers an undescribed ponyfish (Teleostei: Leiognathidae: Equulites) with a note on the taxonomic status of Equula berbis Valenciennes. Zootaxa 2427:15-24.


Taxonomy and Morphological Studies
Morphological character analyses are essential in phylogenetics and descriptive work to ensure proper diagnoses, taxonomy and rigorous sampling of all phylogenetically informative material. As a collections-based scientist I will always continue to have morphological systematics as a major part of my research program. Phylogenies that include morphological characters lead to the discovery of morphological synapomorphies that can be used in descriptive works diagnosing novel taxa or higher groups. Another important use of morphological work is in the use of fossil calibrations in molecular studies. Calibrations based on fossil taxa are widely used to age different nodes in molecular phylogenies. Unfortunately, these fossils are often incorrectly placed on the molecular phylogeny because of the lack of any morphological data from extant taxa in the character matrix. When fossils are available I often incorporate them into my analyses and sometimes redescribe them, as I did with Nandopsis woodringi (Chakrabarty, 2006). Taxonomy is an important part of systematics and it is a study that collections-based scientists should view as an important part of their research program.

Recent Morphological Publications:
-Sparks, J.S., Chakrabarty, P. (2015) Description of a new genus of ponyfishes (Teleostei: Leiognathidae), with a discussion of the current generic-level composition of the family. Zootaxa 3947:181-190.
-Chakrabarty, P., Davis, M.P., Smith, W.L., Berquist, R., Gledhill, K., Sparks, J.S., and Frank, L. (2011) Evolution of the light organ system in ponyfishes (Teleostei: Leiognathidae) Journal of Morphology 272, 704-721.



Philosophy
As a scientist I sometimes think it is important to comment on philosophical matters related to biology and to articulate justifications for one side of a particular scientific debate. Recently, I’ve found a number of different outlets to make philosophical comments. In one example, I found that molecular phylogenetics and taxonomy were working independently of each other and proposed a new approach. This approach introduces a new nomenclature to molecular taxonomy called “genetypes.” Genetypes are sequence data from type specimens. Being able to identify sequence data from type specimens (particularly topotypes) creates a new dimension by which taxa can be compared. In a second example, I’ve commented on what is seen by some traditionalists as a paradigm shift in systematic ichthyology. This shift is caused by the recent trend in ichthyology to change higher-level fish taxonomy based on molecular data. I think the incorporation of molecular data into this aspect of systematic ichthyology is a positive step and provides a shift from the authority-based taxonomy that dominated the field in the past.

Recent Philosophy Publications:
-Chakrabarty, P., Warren, M., Page, L., Baldwin, C. (2013) GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources. ZooKeys 346:29-41.
-Rocha, L. et al., Chakrabarty, P., with 115 other authors (including E.O.Wilson), (2014) Specimen collection: an essential tool. Science 344, 814-815.