Lindsay Scarpitta Project Description
Title: Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular Data from Three Mitochondrial Loci
Abstract:
The Zeiformes (dories) are mid-water or deep (to 1000 m) marine acanthomorph fishes with a global, circumtropical, and circumtemperate distribution. Some species have a near-worldwide distribution, while others appear to be regional endemics, e.g., near New Zealand. Six families, 16 genera, and 33 species are currently recognized as valid. Relationships among them, however, remain unsettled, especially in light of recent proposals concerning the phylogenetic placement of zeiforms within the Paracanthopterygii rather than allied with beryciforms or percomorphs. The present study uses mtDNA characters to investigate zeiform interrelationships given their revised phylogenetic placement and attendant changes to their close outgroups, carried out as part of a larger study by Grande et al. (2018) also including nDNA + morphological characters in their assessment of zeiform phylogeny. Results indicate that revised outgroups affected the phylogenetic conclusions, particularly among genus and species level relationships, and that mtDNA analyses recover a different arrangement of family and genus relationships than proposed by prior morphology-only hypotheses. All analyses recovered monophyletic Zeidae, Cyttidae, and Oreosomatidae, and Zeniontidae, and non-monophyletic Parazenidae. Overall, results reflect the particular usefulness of mtDNA characters for examination of recent evolutionary events that shaped genus and species level relationships within Zeiformes, and the necessity of considering multiple lines of evidence to reveal the wider picture of zeiform evolution.
Acknowledgements:
I would like to thank the many people who have helped me in the preparation of this degree. I especially would like to thank my adviser Dr. Terry Grande for welcoming me into her lab and for her invaluable support at every step of the project. The breadth of Dr. Grande’s knowledge and expertise in her field has been inspiring since the very beginning of my time at Loyola. Her enthusiasm for fishes is infectious, and her encouragement and confidence in the strength of my work have buoyed me through the ups and downs of research and the curveballs life will throw at you. I am deeply grateful to have had the opportunity to build the relationship I have with Dr. Grande, without which my efforts to unravel the evolutionary history of these fascinating fishes would not be what it is today.
I am incredibly grateful to my co-advisor Dr. Mark Wilson for his far-reaching expertise and unflinching generosity in sharing that knowledge with me. His guiding hand was instrumental in everything from technical troubleshooting to asking just the right questions that would lead to my fitting tough evolutionary puzzle pieces together, and I cannot thank him enough for taking the time and care to steer me back on-course when I found myself struggling with the bigger picture.
Many thanks go to the members of my committee, Dr. Howard Laten and Dr. Marty Berg, for their valuable time, instruction, and attention to detail over the course of this project. I am eminently grateful to their patience and encouragement through the entire process, and I am privileged to have reaped the benefits of their involvement in my growth as a researcher.
I would also like to thank former Grande Lab post-doc Cal Borden for all his help in the initial stages of the project, through contacting research collections for tissue acquisition and for his aid in getting the molecular bench work off the ground.
I am grateful to the members of the Grande Lab for their camaraderie and friendship, as well as all of their generous help in troubleshooting software and instruments, studying for shared classes, and teaching me programs and techniques that contributed to the strength of my project. Many thanks to Meg Malone for welcoming me into the lab, to Cheryl Theile, John Belcik, Josh Hittie, and Jeff Peters for being wonderful labmates and classmates during my tenure working on-campus, and for their always-thoughtful questions and suggestions during lab meetings. Thanks also go to Michael Hanson for his beautiful line drawings of the fishes under study for this thesis.
Many thanks are also due to Audrey Berry, Virginia Lorenzo, and all the Loyola University Department of Biology staff for providing me with the funding to complete my graduate study, for their daily close attention and advocacy for Biology graduate students, and for guiding me through the administrative requirements of this program. Thanks go as well to Dr. Sushma Reddy for the use of her molecular biology laboratory space to carry out the bench work for this thesis.
Throughout my course of study, the support of my friends in the Biology Department, family, and loved ones has been a much-needed port in the storm when I felt daunted by the scope of what I hoped to accomplish in this program. I could not have done it without them. Thank you.
Vita:
Lindsay A. Scarpitta graduated from Merrimack College in North Andover, Massachusetts in May 2011 with a B.S. in Biology, concentrating in Molecular Biology and Bioinformatics. As an undergraduate, she studied mate choice in the sailfin molly (Poecilia latipinna) using microsatellite sequence elements to determine inheritance patterns in the Genetics lab of Dr. Janine Leblanc-Straceski. Her undergraduate research laid the foundation of a collaborative research initiative between the Genetics and Ecology laboratories and developed the protocols by which future undergraduate genetic research would be conducted for the ongoing project. She also worked as an undergraduate teaching assistant in the Biology Department under Dr. Leblanc-Straceski, where she assisted in facilitating Introduction to Biology practical laboratories for incoming students.
Upon graduating from Merrimack College, Lindsay moved to the Midwest to begin her Master of Science in Biology at Loyola University Chicago in 2011, focusing on evolution and phylogenetics in the Zeiformes order of paracanthopterygian fishes under Dr. Terry Grande. She obtained a Lerner-Gray research grant from the American Museum of Natural History to carry out her work, and completed this thesis as part of a larger study conducted by the Grande Lab and published in the journal Copeia (now called Ichthyology & Herpetology) in 2018. During her time at Loyola, Lindsay enjoyed teaching Evolution BIOL 319 under Dr. Grande as a teaching assistant, and Introduction to Biology Laboratory BIOL 111 and 112 as Instructor of Record.
In 2015, Lindsay accepted a full-time position as a Research Specialist under Dr. Pieter Faber at the University of Chicago Functional Genomics Facility, where she now manages a team facilitating sample preparation and processing for client-submitted Next-Generation Sequencing experiments. She credits her time at Loyola for developing the scientific knowledge and experimental rigor that have earned her to two promotions at the Genomics Facility since beginning her tenure in the lab.
Committee: Members:
Terry Grande
Mark Wilson
Howard Laten
Marty Berg
Title: Phylogenetic Relationships among Fishes in the Order Zeiformes Based on Molecular Data from Three Mitochondrial Loci
Abstract:
The Zeiformes (dories) are mid-water or deep (to 1000 m) marine acanthomorph fishes with a global, circumtropical, and circumtemperate distribution. Some species have a near-worldwide distribution, while others appear to be regional endemics, e.g., near New Zealand. Six families, 16 genera, and 33 species are currently recognized as valid. Relationships among them, however, remain unsettled, especially in light of recent proposals concerning the phylogenetic placement of zeiforms within the Paracanthopterygii rather than allied with beryciforms or percomorphs. The present study uses mtDNA characters to investigate zeiform interrelationships given their revised phylogenetic placement and attendant changes to their close outgroups, carried out as part of a larger study by Grande et al. (2018) also including nDNA + morphological characters in their assessment of zeiform phylogeny. Results indicate that revised outgroups affected the phylogenetic conclusions, particularly among genus and species level relationships, and that mtDNA analyses recover a different arrangement of family and genus relationships than proposed by prior morphology-only hypotheses. All analyses recovered monophyletic Zeidae, Cyttidae, and Oreosomatidae, and Zeniontidae, and non-monophyletic Parazenidae. Overall, results reflect the particular usefulness of mtDNA characters for examination of recent evolutionary events that shaped genus and species level relationships within Zeiformes, and the necessity of considering multiple lines of evidence to reveal the wider picture of zeiform evolution.
Acknowledgements:
I would like to thank the many people who have helped me in the preparation of this degree. I especially would like to thank my adviser Dr. Terry Grande for welcoming me into her lab and for her invaluable support at every step of the project. The breadth of Dr. Grande’s knowledge and expertise in her field has been inspiring since the very beginning of my time at Loyola. Her enthusiasm for fishes is infectious, and her encouragement and confidence in the strength of my work have buoyed me through the ups and downs of research and the curveballs life will throw at you. I am deeply grateful to have had the opportunity to build the relationship I have with Dr. Grande, without which my efforts to unravel the evolutionary history of these fascinating fishes would not be what it is today.
I am incredibly grateful to my co-advisor Dr. Mark Wilson for his far-reaching expertise and unflinching generosity in sharing that knowledge with me. His guiding hand was instrumental in everything from technical troubleshooting to asking just the right questions that would lead to my fitting tough evolutionary puzzle pieces together, and I cannot thank him enough for taking the time and care to steer me back on-course when I found myself struggling with the bigger picture.
Many thanks go to the members of my committee, Dr. Howard Laten and Dr. Marty Berg, for their valuable time, instruction, and attention to detail over the course of this project. I am eminently grateful to their patience and encouragement through the entire process, and I am privileged to have reaped the benefits of their involvement in my growth as a researcher.
I would also like to thank former Grande Lab post-doc Cal Borden for all his help in the initial stages of the project, through contacting research collections for tissue acquisition and for his aid in getting the molecular bench work off the ground.
I am grateful to the members of the Grande Lab for their camaraderie and friendship, as well as all of their generous help in troubleshooting software and instruments, studying for shared classes, and teaching me programs and techniques that contributed to the strength of my project. Many thanks to Meg Malone for welcoming me into the lab, to Cheryl Theile, John Belcik, Josh Hittie, and Jeff Peters for being wonderful labmates and classmates during my tenure working on-campus, and for their always-thoughtful questions and suggestions during lab meetings. Thanks also go to Michael Hanson for his beautiful line drawings of the fishes under study for this thesis.
Many thanks are also due to Audrey Berry, Virginia Lorenzo, and all the Loyola University Department of Biology staff for providing me with the funding to complete my graduate study, for their daily close attention and advocacy for Biology graduate students, and for guiding me through the administrative requirements of this program. Thanks go as well to Dr. Sushma Reddy for the use of her molecular biology laboratory space to carry out the bench work for this thesis.
Throughout my course of study, the support of my friends in the Biology Department, family, and loved ones has been a much-needed port in the storm when I felt daunted by the scope of what I hoped to accomplish in this program. I could not have done it without them. Thank you.
Vita:
Lindsay A. Scarpitta graduated from Merrimack College in North Andover, Massachusetts in May 2011 with a B.S. in Biology, concentrating in Molecular Biology and Bioinformatics. As an undergraduate, she studied mate choice in the sailfin molly (Poecilia latipinna) using microsatellite sequence elements to determine inheritance patterns in the Genetics lab of Dr. Janine Leblanc-Straceski. Her undergraduate research laid the foundation of a collaborative research initiative between the Genetics and Ecology laboratories and developed the protocols by which future undergraduate genetic research would be conducted for the ongoing project. She also worked as an undergraduate teaching assistant in the Biology Department under Dr. Leblanc-Straceski, where she assisted in facilitating Introduction to Biology practical laboratories for incoming students.
Upon graduating from Merrimack College, Lindsay moved to the Midwest to begin her Master of Science in Biology at Loyola University Chicago in 2011, focusing on evolution and phylogenetics in the Zeiformes order of paracanthopterygian fishes under Dr. Terry Grande. She obtained a Lerner-Gray research grant from the American Museum of Natural History to carry out her work, and completed this thesis as part of a larger study conducted by the Grande Lab and published in the journal Copeia (now called Ichthyology & Herpetology) in 2018. During her time at Loyola, Lindsay enjoyed teaching Evolution BIOL 319 under Dr. Grande as a teaching assistant, and Introduction to Biology Laboratory BIOL 111 and 112 as Instructor of Record.
In 2015, Lindsay accepted a full-time position as a Research Specialist under Dr. Pieter Faber at the University of Chicago Functional Genomics Facility, where she now manages a team facilitating sample preparation and processing for client-submitted Next-Generation Sequencing experiments. She credits her time at Loyola for developing the scientific knowledge and experimental rigor that have earned her to two promotions at the Genomics Facility since beginning her tenure in the lab.
Committee: Members:
Terry Grande
Mark Wilson
Howard Laten
Marty Berg