BY245/BY555 Fundamentals of Scientific Investigation (Summer 2020, Fall 2020)
The course covers the basics of scientific investigation with an emphasis on understanding methods of the scientific process, experimental design, data interpretation and presentation and scientific writing. Special emphasis will be placed on the use of data management and statistical packages to address the most common types of data analysis used to investigate specific applications in biology. Quantitative Literacy is a significant component of this course. Recommend course is taken before junior year.
BY555 Design and Analysis of Biological Data (Fundamentals of Scientific Investigation) (Fall 2020)
Whitehead C (2021) NOT Seeing Double: The Gecko Epiphany
BY555 Design and Analysis of Biological Data (Fundamentals of Scientific Investigation) (Summer 2020)
O'Connor A (2020) Gene-culture coevolution in humpback whales
Bradley A (2020) What role do pedigrees play in the preservation of the Galapagos giant tortoise?
Ferguson R (2020) Habitat fragmentation of the catfish Hemibagrus spilopterus: damned if we do
The course covers the basics of scientific investigation with an emphasis on understanding methods of the scientific process, experimental design, data interpretation and presentation and scientific writing. Special emphasis will be placed on the use of data management and statistical packages to address the most common types of data analysis used to investigate specific applications in biology. Quantitative Literacy is a significant component of this course. Recommend course is taken before junior year.
BY555 Design and Analysis of Biological Data (Fundamentals of Scientific Investigation) (Fall 2020)
Whitehead C (2021) NOT Seeing Double: The Gecko Epiphany
BY555 Design and Analysis of Biological Data (Fundamentals of Scientific Investigation) (Summer 2020)
O'Connor A (2020) Gene-culture coevolution in humpback whales
Bradley A (2020) What role do pedigrees play in the preservation of the Galapagos giant tortoise?
Ferguson R (2020) Habitat fragmentation of the catfish Hemibagrus spilopterus: damned if we do
BY429/491/629 Evolutionary Processes (Fall 2017, Spring 2018, Fall 2019, Spring 2021)
This course will introduce the history of evolutionary thought and modern evolutionary theory. Our discussions will cover (but are not limited to) the history of life, mechanisms of evolutionary change, adaptation, speciation, life-history evolution, sexual selection and molecular evolution. We will also discuss historical and contemporary studies of evolution on a wide variety of topics and organisms.
It's been said that "nothing in biology makes sense except in the light of evolution" (Theodosius Dobzhansky, 1973). Why? We'll consider that question in depth in this course, taking a look at the science of biological evolution from a number of perspectives. We will follow the Zimmer textbook closely and will read a few other sources as well. A lot of what we do will involve in-class discussions and problem solving of the readings as well as applying concepts to novel questions, and you will be expected to actively work with the course material to develop an intuitive understanding of evolution. Some overarching themes we will cover are:
Here are related posts written by students for The Molecular Ecologist:
Fitch M (2020) It's the city life for me ... or maybe not
Edwards R (2020) Does it pay to be parasitized?
Livett S (2018) Racing against the climate
Here are related posts written by students for The AGA Blog:
Weddle D (2021) No Hair Dye? No Problem: How CRISPER/Cas 9 alters fur color
Oswalt H (2021) Do male crickets create symphonies?
Gregory S (2020) The difference 70 miles can make
Edwards R (2019) Pelagic to Coastal: The expansion of Bottlenose Dolphins
This course will introduce the history of evolutionary thought and modern evolutionary theory. Our discussions will cover (but are not limited to) the history of life, mechanisms of evolutionary change, adaptation, speciation, life-history evolution, sexual selection and molecular evolution. We will also discuss historical and contemporary studies of evolution on a wide variety of topics and organisms.
It's been said that "nothing in biology makes sense except in the light of evolution" (Theodosius Dobzhansky, 1973). Why? We'll consider that question in depth in this course, taking a look at the science of biological evolution from a number of perspectives. We will follow the Zimmer textbook closely and will read a few other sources as well. A lot of what we do will involve in-class discussions and problem solving of the readings as well as applying concepts to novel questions, and you will be expected to actively work with the course material to develop an intuitive understanding of evolution. Some overarching themes we will cover are:
- Evolution is a necessary property of any finite, self-replicating system.
- Evolution is both (mathematical) theory and (measureable) fact.
- Evolution is not a "deep time" question, but happening constantly, measurably, around us every day.
- Evolution ≠ natural selection.
- Evolution occurs because of random chance, but yields non-random outcomes
- The theoretical framework of biological evolution is broadly applicable, with influence on computer science, economics, medicine, psychology, politics, etc.
Here are related posts written by students for The Molecular Ecologist:
Fitch M (2020) It's the city life for me ... or maybe not
Edwards R (2020) Does it pay to be parasitized?
Livett S (2018) Racing against the climate
Here are related posts written by students for The AGA Blog:
Weddle D (2021) No Hair Dye? No Problem: How CRISPER/Cas 9 alters fur color
Oswalt H (2021) Do male crickets create symphonies?
Gregory S (2020) The difference 70 miles can make
Edwards R (2019) Pelagic to Coastal: The expansion of Bottlenose Dolphins
BY468/668/768 Conservation Genetics (Fall 2018, Spring 2019, Spring 2020)
This intensive course will introduce students to the genetic tools of modern population biology – which ones are available, practical, and useful for particular questions – and how these genetic analyses have been applied to a wide variety of ecological topics, including: dispersal, life cycles, recruitment, habitat and mate choice, local selection, genetic differentiation, the conservation of biodiversity, and speciation. Importantly, this course is an opportunity to become proficient at applying molecular tools to bolster ecological studies. Time will be spent in lectures, discussions, reviewing the primary literature, and learning practical coding and data analyses.
At the end of the course, students will understand how to apply population genetics principles to understand genetic variation in natural populations. This requires an understanding of the appropriate theory, designing appropriate experiments and/or sampling, collecting the appropriate data, and understanding how to analyze these data. Students will learn each step in this process through lectures, discussions, independent projects, and practical application of population genetic tools. This course will help students create an informed framework for thought about issues in evolutionary ecology, with an emphasis on applying concepts and tools of genetics to problems in conservation.
If you are an undergrad, it is highly recommended that you have already passed BY311 Molecular Genetics (or equivalent) AND BY429 Evolution. For grad students, it is also recommended that you have an undergrad- or grad-level genetics and evolution course. We will briefly review fundamental concepts, but we will not spend as much time as in a genetics or evolution course.
Here are related posts written by students for The Molecular Ecologist:
Gregory S (2020) Where did this flower come from?
Shainker SJ (2020) Genes rolling down the river
Conner N (2019) Snapshots of biodiversity: eDNA as a methodology of species detection
Bonka A (2019) Genetics of returning turtles
Curtis M (2019) The ultimate party animal
Keister E (2019) Is taxonomy still relevant to innovative science?
Heiser S (2019) "Through endurance we conquer*" Are humans really the only ones who can make it across the Drake's Passage?
O'Connor A (2019) Kelp forests: the underwater woodlands
This intensive course will introduce students to the genetic tools of modern population biology – which ones are available, practical, and useful for particular questions – and how these genetic analyses have been applied to a wide variety of ecological topics, including: dispersal, life cycles, recruitment, habitat and mate choice, local selection, genetic differentiation, the conservation of biodiversity, and speciation. Importantly, this course is an opportunity to become proficient at applying molecular tools to bolster ecological studies. Time will be spent in lectures, discussions, reviewing the primary literature, and learning practical coding and data analyses.
At the end of the course, students will understand how to apply population genetics principles to understand genetic variation in natural populations. This requires an understanding of the appropriate theory, designing appropriate experiments and/or sampling, collecting the appropriate data, and understanding how to analyze these data. Students will learn each step in this process through lectures, discussions, independent projects, and practical application of population genetic tools. This course will help students create an informed framework for thought about issues in evolutionary ecology, with an emphasis on applying concepts and tools of genetics to problems in conservation.
If you are an undergrad, it is highly recommended that you have already passed BY311 Molecular Genetics (or equivalent) AND BY429 Evolution. For grad students, it is also recommended that you have an undergrad- or grad-level genetics and evolution course. We will briefly review fundamental concepts, but we will not spend as much time as in a genetics or evolution course.
Here are related posts written by students for The Molecular Ecologist:
Gregory S (2020) Where did this flower come from?
Shainker SJ (2020) Genes rolling down the river
Conner N (2019) Snapshots of biodiversity: eDNA as a methodology of species detection
Bonka A (2019) Genetics of returning turtles
Curtis M (2019) The ultimate party animal
Keister E (2019) Is taxonomy still relevant to innovative science?
Heiser S (2019) "Through endurance we conquer*" Are humans really the only ones who can make it across the Drake's Passage?
O'Connor A (2019) Kelp forests: the underwater woodlands
BY655/755 Biometry (Spring 2019)
This is an introductory course for graduate students for application and implementation of statistical analyses in the biological sciences. The course will cover many topics covered in the first two semesters of introductory statistics, from samples means to linear regression. All analyses will be completed either by hand or with the statistical program R. Each class meeting will consist of both lecture and working practice problems in R. At the end of the course, students should feel well versed enough to apply basic statistical concepts to data collected from their own experiments. Students will also gain some basic knowledge of the R programming language in order to store, manipulate, graph, and analyze data.
This is an introductory course for graduate students for application and implementation of statistical analyses in the biological sciences. The course will cover many topics covered in the first two semesters of introductory statistics, from samples means to linear regression. All analyses will be completed either by hand or with the statistical program R. Each class meeting will consist of both lecture and working practice problems in R. At the end of the course, students should feel well versed enough to apply basic statistical concepts to data collected from their own experiments. Students will also gain some basic knowledge of the R programming language in order to store, manipulate, graph, and analyze data.
BY670/770 Scientific Communication (Fall 2016, Spring 2018, Fall 2019)
Becoming a professional biologist is challenging and requires mastering a variety of skills. This course complements the biological knowledge graduate students gain from other courses and their thesis research by providing training, experience, and critical feedback in the following areas. Students will gain valuable experience in:
• Science and social media
• Professional presentations (oral, PowerPoint, and poster)
• Grant writing
• Curriculum vitae
• Peer-review system and giving/receiving constructive criticism
• Scientific ethics
• Interviewing for graduate schools and employment
Here are related posts written by Stacy and her students for The Molecular Ecologist:
O'Connor A (2020) Kelp Connections
Mishra B (2020) Tapping social networks to explore biological systems
Detchemendy T (2020) Yeast 2-Hybrid: discovering protein-protein interactions from yeast to west
Gregory S (2020) Everything about ant reproductive biology is bizarre
Sirgo C (2020) Bobbing for Bobcats
Walker, M (2020) The Virosphere’s Own Trojan HorseMishra B (2020) Tapping social networks to explore biological systems
Oswalt H (2020) Digging for knowledge … and nematodes
Jones A (2020) “Of all the Islands in all the Seas in all the World…”
Gantt S (2020) Brood Parasitism or adoption? Mixed parentage of brooding damselfishes
Krueger-Hadfield SA (2020) #StudentSciComm
Jackson J (2018) In it to win it: selective advantage through host-selected mutations
Momeni M (2018) Cricket plays a song of systems biology
Sahawneh K (2018) A master manipulator: how a bacterium tells a plant what to do
Keister E (2018) Are we restoring coral reefs for today or for tomorrow?
Krueger-Hadfield SA (2018) To present data is human, to communicate data is divine
Aida V (2017) Mapping genomes and navigating behavior for wildlife conservation.
Hayes M (2017) Like turtles, terrapin research moves a little slow.
Latimer M (2017) Small Molecules, Big Differences.
Roegner M (2017) Molting on the molecular level: how blue crabs become soft-shell crabs.
Adkins S (2017) Dishing out art: 'Soiling' our microbiology curriculum.
Heiser S (2017) Have we got the power?
Krueger-Hadfield SA (2017) I think we're NOT alone now.
Here are related posts written by students for The AGA Blog:
Thrash R (2020) Do marine species of a fin flock together
Becoming a professional biologist is challenging and requires mastering a variety of skills. This course complements the biological knowledge graduate students gain from other courses and their thesis research by providing training, experience, and critical feedback in the following areas. Students will gain valuable experience in:
• Science and social media
• Professional presentations (oral, PowerPoint, and poster)
• Grant writing
• Curriculum vitae
• Peer-review system and giving/receiving constructive criticism
• Scientific ethics
• Interviewing for graduate schools and employment
Here are related posts written by Stacy and her students for The Molecular Ecologist:
O'Connor A (2020) Kelp Connections
Mishra B (2020) Tapping social networks to explore biological systems
Detchemendy T (2020) Yeast 2-Hybrid: discovering protein-protein interactions from yeast to west
Gregory S (2020) Everything about ant reproductive biology is bizarre
Sirgo C (2020) Bobbing for Bobcats
Walker, M (2020) The Virosphere’s Own Trojan HorseMishra B (2020) Tapping social networks to explore biological systems
Oswalt H (2020) Digging for knowledge … and nematodes
Jones A (2020) “Of all the Islands in all the Seas in all the World…”
Gantt S (2020) Brood Parasitism or adoption? Mixed parentage of brooding damselfishes
Krueger-Hadfield SA (2020) #StudentSciComm
Jackson J (2018) In it to win it: selective advantage through host-selected mutations
Momeni M (2018) Cricket plays a song of systems biology
Sahawneh K (2018) A master manipulator: how a bacterium tells a plant what to do
Keister E (2018) Are we restoring coral reefs for today or for tomorrow?
Krueger-Hadfield SA (2018) To present data is human, to communicate data is divine
Aida V (2017) Mapping genomes and navigating behavior for wildlife conservation.
Hayes M (2017) Like turtles, terrapin research moves a little slow.
Latimer M (2017) Small Molecules, Big Differences.
Roegner M (2017) Molting on the molecular level: how blue crabs become soft-shell crabs.
Adkins S (2017) Dishing out art: 'Soiling' our microbiology curriculum.
Heiser S (2017) Have we got the power?
Krueger-Hadfield SA (2017) I think we're NOT alone now.
Here are related posts written by students for The AGA Blog:
Thrash R (2020) Do marine species of a fin flock together