Appendix 5: Example Research Interests for Job Application

Transcription

1 Appendix 5: Example Research Interests for Job Application SUMMARY OF RESEARCH INTERESTS Prosanta Chakrabarty 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 fishes. 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 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 Donn Starks, AMNH) and on deep-sea forms including batfishes and tripod fishes (with Hans Ho of the Academia A Guide to Academia: Getting into and Surviving Grad School, Postdocs, and a Research Job, First Edition. Prosanta Chakrabarty. C 2012 John Wiley & Sons, Inc. Published 2012 by John Wiley & Sons, Inc. 141

2 142 Appendix 5: Example Research Interests for Job Application Sinica and Matthew Davis of the University of Kansas). 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). I am also currently resolving the many taxonomic problems that plague these groups using molecular, morphological and behavioral (flashing) characters in phylogenetic analyses. Much of this work is associated with the products of my 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. Recent Publications on Deep-Sea Fish Systematics: Ho, H.C., Chakrabarty, P., Sparks, J.S.(2010) Review of the Halieutichthys aculeatus species complex (Lophiiformes: Ogcocephalidae), with descriptions of two new species. Journal of Fish Biology 77: Davis, M.P., Chakrabarty, P. (in press) Video Observation of a Tripodfish (Aulopiformes: Bathypterois) from Bathypelagic Depths in the Campos Basin of Brazil. Marine Biology Research. Pending Deep-Sea Grants: $ 601,414* submitted NSF DEB: The Timing and Evolutionary History of Deep-Sea Invasions and Habitat Shifts: Systematics and diversification within lizardfishes, cods and batfishes. PC is CO-PI, PI is Matthew P. Davis (LSU) *submitted July 9, Historical 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

3 Appendix 5: Example Research Interests for Job Application 143 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: Smith, W.L., Chakrabarty, P., Sparks, J.S., (2008) Phylogeny, taxonomy and evolution of Neotropical cichlids (Percomorpha: Cichlidae: Cichlinae). Cladistics 24, Chakrabarty, P. Albert, J. (in press.) Not so Fast: Freshwater Fishes and the Great American Biotic Interchange. In: Historical Biogeography of Neotropical Freshwater Fishes (J. S. Albert and R.E. Reis, eds.) Current Biogeography Grants: $ 519,944 AWARDED NSF REVSYS: Reconstructing Heroini (Teleostei:Cichlidae) Of Heroes, Convicts, Angels and Red Devils. PC is sole PI. September 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. Recent Geometric Morphometric 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: Chakrabarty, P., Davis, M.P., Smith, W.L., Baldwin, Z.H., Sparks, J.S. (submitted) Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)? Molecular Ecology (September 24, 2010).

4 144 Appendix 5: Example Research Interests for Job Application 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 collectionsbased 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-Taxonomic status of the Hispaniolan Cichlidae). 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 Taxonomy and Morphological Publications: Chakrabarty, P., (2010) Status and phylogeny of Milyeringidae, with the description of a new blind cave fish from Australia, Milyeringa brooksi, n. sp. Zootaxa 2557: Schaefer, S.A, Chakrabarty, P., Geneva, A., Sabaj-Perez, M.H. (in press) Nucleotide sequence data confirm monophyly and local endemism of variable morphospecies of Andean astroblepid catfishes (Siluriformes: Astroblepidae). Zool. J. Linn. Soc. 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

5 Appendix 5: Example Research Interests for Job Application 145 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., (2010) Genetypes: a concept to help integrate molecular systematics and traditional taxonomy. Zootaxa 2632: Chakrabarty, P. (2010) The transitioning state of systematic ichthyology. Copeia 2010 (3):