Interview with Dr. David Maddison Director of OSAC

Summary

Dr. David Maddison, a renowned professor at Oregon State University, shares his journey and expertise in the field of integrative biology with a particular focus on beetle evolution and phylogenetics. With over 11 years at OSU and a prior tenure at the University of Arizona, Dr. Maddison combines research, teaching, and software development to unravel the mysteries of beetle diversity and evolutionary relationships. His work encompasses fieldwork across continents, lab-based DNA analysis, and innovative methods like sequencing historical specimens. Through courses and mentoring, he integrates students into genuine research experiences, making substantial contributions to the understanding of beetle phylogenetics and broader biodiversity challenges.

Highlights

• Dr. Maddison's fascination with beetles began as a teenager and led to a scholarly career 🚀.
• His transition from University of Arizona to Oregon State marks over two decades of impact in integrative biology 🌿.
• Mesquite software, co-developed with his brother, underpins critical evolutionary analyses 🔍.
• Sequencing technology can unlock genetic mysteries in centuries-old specimens, offering insights into historical biodiversity 🌱.
• Dr. Maddison involves students directly in research, fostering a dynamic learning environment where discovery and education go hand-in-hand 👩‍🔬.

Key Takeaways

• Dr. Maddison has over 11 years of experience at OSU, focusing on beetle evolution and phylogenetics 🐞.
• His educational journey spans top universities, culminating in a Ph.D. from Harvard, fueled by a teenage love for beetles 🏫.
• He develops software like Mesquite for phylogenetic analysis, showcasing the blend of biology and technology 💻.
• Historical specimens hold hidden genomic secrets, revolutionized by modern sequencing techniques 📜.
• Dr. Maddison's hands-on teaching approach turns classrooms into research labs, engaging students in real-world discovery 🌍.

Overview

Dr. David Maddison’s journey in the world of integrative biology is nothing short of fascinating. With an enduring passion for beetles, he leverages his extensive academic background to explore the evolutionary intricacies of these incredible creatures. His career path, marked by significant tenure at the University of Arizona and currently at Oregon State, highlights his profound impact on the field.

Beyond teaching, Dr. Maddison is actively engaged in research that spans continents. His work in phylogenetics not only involves the study of beetle diversity but also includes the development of specialized software like Mesquite, which he co-created to assist in graphic analyses of evolutionary trees. This integration of technology in biological research exemplifies the evolving nature of scientific exploration.

In addition to his research, Dr. Maddison’s commitment to education is evident through his innovative courses, which immerse students in real-world scientific inquiries. By incorporating hands-on projects such as DNA sequencing of historical specimens, he ensures that his teaching is as impactful as his research, preparing a new generation of scientists to explore and understand the vast world of biodiversity.

Chapters

• 00:00 - 00:30: Introduction Introduction: The chapter introduces the session with a welcome to Z365, featuring Dr. David Madison. Dr. Madison shares his excitement for the course and provides an overview of his background, including his tenure and position at Oregon State University.
• 00:30 - 02:00: David Maddison's Background David Maddison is a professor at Oregon State University in the field of integrative biology, having been there for over 11 years. Prior to this, he spent 17 years at the University of Arizona. Originally from Southern Ontario, Canada, Maddison completed his undergraduate degree at the University of Toronto, followed by a master's degree.
• 02:00 - 04:30: Research Focus and Interests The chapter discusses the speaker's educational journey, beginning at the University of Alberta in Edmonton and continuing with a doctorate at Harvard University. The speaker developed a passion for beetles during their teenage years, which significantly influenced their academic and research interests. The chapter sets up a discussion about the speaker's current roles and responsibilities at Oregon State University.
• 04:30 - 05:00: Undergraduate Projects in the Lab The chapter discusses the speaker's research interests and focus areas, which revolve around fetal evolution, phylogenetics, and species diversity, with a particular interest in beetles. The speaker is engaged in discovering and documenting beetle species and is also fascinated by broader phylogenetic studies that explore evolutionary relationships and the tree of life.
• 05:00 - 07:00: Graphic Novels and Scientific Communication The chapter titled 'Graphic Novels and Scientific Communication' discusses the development of a software program as part of core research. It highlights extensive fieldwork conducted across North America and recently in New Zealand and Australia. The research aims to find various beetle lineages and understand their place in the tree of life, involving significant field and lab work.
• 07:00 - 11:00: The Mesquite Software Project The chapter titled 'The Mesquite Software Project' describes various activities related to DNA sequence analysis and scientific research. The speaker mentions their involvement in preparing specimens and studying them under a compound microscope. Additionally, the speaker is involved in teaching, conducting classes in phylogenetics, and scientific illustration. The chapter also touches on the speaker's contributions to departmental administration through various service roles.
• 11:00 - 15:00: Research Approach in Entomology The chapter titled 'Research Approach in Entomology' discusses the structure and activities within a lab focused on entomology research. Graduate and undergraduate students work under mentorship to conduct diverse research projects. Graduate students typically have their own specific projects, while undergraduate projects are varied and depend on both the students' interests and the lab's current needs. This setup provides a comprehensive learning and research environment for all students involved.
• 15:00 - 19:00: Interest in Ground Beetles The chapter delves into the lab activities related to ground beetles, specifically highlighting the involvement of undergraduate students in ongoing research. Four undergraduates are currently engaged in lab work, with two of them focusing on conducting PCR (polymerase chain reaction) to aid in gene sequencing of different beetle species. These students are contributing to a larger research project overseen by a senior researcher, although there is potential for them to develop their own independent projects as they gain experience.
• 19:00 - 24:00: Molecular Characters in Systematics The chapter discusses the integration of molecular characters into systematics, exploring how genomic data is analyzed using bioinformatics to aid in statistical analyses. It highlights the interdisciplinary collaboration between students interested in biology and art, who are working on graphic novels, underscoring the value of scientific illustration and diverse perspectives in scientific communication.
• 24:00 - 30:00: Advances in DNA Sequencing The chapter titled 'Advances in DNA Sequencing' discusses the efforts of scientists to communicate their work to a wider audience through engaging means such as graphic novels. These novels depict real research projects from the lab, including topics covered in recent lab sessions in a specific course. The initiative aims to make scientific research more accessible and interesting to the general public.
• 30:00 - 37:00: DNA Barcoding vs. Full Genomic Data The chapter begins with a conversation that diverts briefly into a personal anecdote about graphic novels, before addressing DNA barcoding versus full genomic data. The speaker shares a personal interest in graphic novels which was reignited by two events, not detailed in this excerpt. The mention suggests a parallel between the complexity and detail in graphic novels compared to DNA data, though the full exploration of this topic is cut off in the transcript provided.
• 37:00 - 42:00: Complex Speciation Cases The chapter discusses the concept of scientific posters, particularly in the field of forestry, presented at scientific conferences. These posters, often text-heavy, serve as a medium for researchers to describe their work. They resemble scientific papers in a large page format, including sections like methods and results. The chapter likely touches on the educational aspect of preparing students for such presentations by exposing them to the nuances of scientific poster creation and presentation.
• 42:00 - 52:00: Discovering Insect Species Course Experience In this chapter titled 'Discovering Insect Species Course Experience,' the author describes an innovative approach to presenting research. The story begins with the author's daughter, Julia, who decided to present her research poster as a comic or graphic novel instead of the traditional standard format. Julia's creative presentation style, which depicted her conducting research and discussing her findings in a visually appealing manner, inspired the author. This inspiration led to the author contemplating the possibility of narrating their own research stories in a similar, engaging format.

Interview with Dr. David Maddison Director of OSAC Transcription

• 00:00 - 00:30 well welcome to z365 thanks so much for taking time to talk to us uh this is dr david madison uh could you tell us uh your job title and uh how much time you've been at oregon state university uh sure andy thanks um and i just wanna say i'm really excited about this aspect of the course so david
• 00:30 - 01:00 madison i'm a professor here at oregon state university in integrative biology i've been here for a little over 11 years now i was at university of arizona for 17 years before that great so uh where did you get your degree and um where are you from originally so i'm from southern ontario in canada uh and i did my undergrad degree at the university of toronto and then i did a master's degree in
• 01:00 - 01:30 alberta edmonton albert at the university of alberta and then i came to the states to do my doctorate at harvard university and and uh i should say that most of that way there was lots of beetles involved uh i fell in love i fell in love with beatles when i was a teenager so great so can you tell us some of the things that you do as part of your job here at oregon state
• 01:30 - 02:00 well uh so i do research i do research on fetal evolution phylogenetics species diversity i'm i do a lot of work on discovering and documenting species of beetles i am also very interested in general aspects of phylogenetics the ways we study the evolutionary tree of life i associate with that research is also
• 02:00 - 02:30 development of a software program and so all of that is part of my core research i do a lot of field work uh in i've done field a lot of field work around north america but i've done recently done field work in new zealand australia and this is to find various lineages of beetles and understand where they fit into the tree of life i've done uh yeah so so lots of field work lots of lab work
• 02:30 - 03:00 with dna sequences and looking at specimens under the microscopes preparing bits of them to study under a compound microscope and so on i also teach i teach several classes i teach a phylogenetics class i teach a scientific illustration class i within the department i do have a bunch of service jobs so i do various things to help out with administration of the department
• 03:00 - 03:30 i have students within my lab that i mentor both graduate students and undergrads many of the grad students have their own pride phone research projects the undergrads have a diversity of things they do within the lab as well oh yeah interesting uh can you can you just tell us briefly maybe about the kinds of projects you have undergraduates doing in your lab so it's it's it varies uh and it partly varies on the undergrad uh and what's needed in
• 03:30 - 04:00 the lab at the time so right now i've got four undergrads working in the lab two of them are are doing pcr reactions polymerase chain reactions and this is to basically allow us to sequence genes in various beetles they right now don't have their own research projects they're working on on one of my research projects um sometimes in my lab when the undergrads transition to working on their own projects
• 04:00 - 04:30 i also have had undergrads that do various bioinformatics studies so that they basically do statistical analyses of genomic data for example the other two undergrads that i have in my lab right now are students who are interested in both biology and art and they're doing graphic novels and so that's very exciting to me because i've had a long history of doing scientific illustrations and i think it's really valuable to look at other ways for
• 04:30 - 05:00 scientists to express what they do and make it available and appealing to a broader audience so both of these graphic novels are about research projects that have happened in the lab and one of them is actually about the the subject of last week's lab in your course and this week's lap and so um so that's uh that's very exciting we can
• 05:00 - 05:30 talk a little bit more about that later yeah that's that's really interesting just a a quick question on that have you always been into graphic novels is that something you've been into since you're a kid no well i mean when i was a kid i used to buy comics at the grocery store but um uh but not you know i went through a long period where i wasn't at all interested in it but uh there were two things that happened that changed that one is that my daughter who when she was doing a master's degree in
• 05:30 - 06:00 forestry did a poster for a scientific conference and posters of these things that uh for your if your students haven't been into a scientific conference they might not realize that there's this phenomenon of presenting posters uh describing your research and they tend to be fairly they're tend to be fairly text heavy and they're basically just like a scientific paper but in a big big page format uh with with text and the little a little uh methods section and a results section
• 06:00 - 06:30 and a few figures here and there well my daughter julia decided to present her poster not in that standard way but as a comic as a graphic novel and uh and so she had this spectacular poster that showed her doing her research and talking about her results and that was so appealing uh that when i started thinking about some of my research i thought oh god wouldn't it be cool to actually tell the story of the
• 06:30 - 07:00 research so not just tell them not just present in a scientific paper what the results were but tell the history of it tell the how that science happened and what the and what the excitement was try to portray the excitement of the discoveries that were made in that context so that the process of science was was more evident but also just to really portray the fact that it's very much a human enterprise and that there's many things about it
• 07:00 - 07:30 that uh that are exciting and that as you'll see from from your exercises that that students can get involved with too yeah so you touched on this a minute ago but you and your brother wayne wrote the program mesquite that we're actually working with as a class and i wonder if you could tell us a little bit about uh why you and wayne decided to embark on that project and uh what you know what sort of effort did it take to put that together
• 07:30 - 08:00 well it's a long history but i'll be very brief that we we basically we so we it was back in the 1980s that uh when it was 1986 that wayne started writing a little computer program called mcclaid and it was this baby little program that allowed you to do to look at evolutionary trees on this was a macintosh 512 i think it was so like the second
• 08:00 - 08:30 macintosh computer that was made uh and this knows 85 he started doing it and i quickly joined the effort and basically we started doing that because we had our own data that we wanted to look at and examine and there was no software available that did what we wanted to do and so mcclaid grew into this program to allow graphic analysis uh to analysis using graphical tools of phylogeny's evolutionary trees and
• 08:30 - 09:00 character evolution upon the branches of that tree and it got to the point in the late 90s where mcclaid was too creaky and so we basically started from scratch to rebuild mclead and that became mesquite and so mesquite is a program that is now gosh so that's now 24 years old from when it first started but of course we've been doing a lot of revisions
• 09:00 - 09:30 and really it's the it's our work it tends to be our workhouse force for our own data so it's how we manage our data it's how we analyze it uh using some filogenic tools we of course use lots of other software because there's fantastic other software involved but in our field of science there's a lot of analyses that you can most analyses you can't do by uh buying an off-the-shelf computer program from a company because uh we have the sorts of analyses
• 09:30 - 10:00 we do are unique enough to our field that no company has built that so the scientists themselves actually tend to build their own software there's a group of scientists that build we build our own software to do this um and so that's and so what's actually involved is a lot of work uh but it's fantastically fun because that's a part of my life where so much of it is about
• 10:00 - 10:30 problem solving it's it's about how how do we okay we want to build something how do we do that and you start it's like you start building some cool thing it's like you're building this lego thing that that's just gigantic and fantastic and there's you get such a high when it actually works right and you can see these things working as you build it up the amazing thing about the software world is basically anything you can imagine you can build right it may take a while but you can build and so
• 10:30 - 11:00 um so that's a fun thing but one thing that uh i we actually haven't been super active in it recently just because it takes so much more time and the beatles for me and the spiders which is what my jumping spiders which is what my brother works on uh have been taking a lot of our time well our students uh recently constructed a cladogram by hand so i think they very much appreciate the necessity of uh computational tools like what you and wayne have developed right right
• 11:00 - 11:30 right it's a challenge well it was yeah it's this i mean it's in the old days people did do these things by hand but they didn't have massive quantities of dna data back then and with it now it's just like i mean you just simply can't do it by hand anymore oh with even even with morphological data it's tough oh yeah it's tough it's tough yep yeah well great um could you comment just in general how you pursue uh you started to get into this a little bit but how you pursue
• 11:30 - 12:00 uh research questions in your field um and maybe you could compare what you do say to another part of entomology say insect physiology how maybe is it different uh what you do how do you ask questions how do you preserve pursue research topics it may be similar or different to yeah another sub discipline of entomology yeah so this is a very interesting topic uh uh because i think about this a lot
• 12:00 - 12:30 um so i bet that many of the students in your in your class learned about at some point in their career learned about the scientific method uh being a a method in which you have a hypothesis about something in the world and whatever it might happen to be and you make a prediction if that hypothesis were true what we would expect to observe uh if we did some experiment so you
• 12:30 - 13:00 imagine an experiment and say well if the hypothesis were true then we'd expect to see this particular result and you go and you do the the experiment and if the result you get matches your what you predicted then your hypothesis is confirmed if it disagrees then your hypothesis is rejected uh that's what's often called the scientific method but there are other components to science as well and the field that i'm in uh is less is it
• 13:00 - 13:30 much of it is not built that way we we what i do is tends to not be hypothesis driven we tend to i tend to not do as much hypothesis testing um because word that we're at the early phases of our science uh we're just still mapping the world we're still understanding what the shape of the we're getting the first get first inference of what the shape of the evolutionary tree is we're getting the first sense as to what
• 13:30 - 14:00 species are out there that's not true in groups like mammals but in in groups like beetles where there's still a lot to be discovered and even more so in groups like fungi or bacteria the microbes where there's a tremendous amount to be discovered we're like an explorer going in with a machete and going into the amazon rainforest for the first time and just saying like what's out there um and uh and so we're we're more building i view myself as somebody who's
• 14:00 - 14:30 more a biodiversity explorer who is who's creating a lot of them the map of the world and yes as i go along there's lots of little hypotheses that i generate my brain and i test them but the bigger picture structure is more is more is more about building an initial map rather than testing aspects of that map uh or that that that view of history um so uh i tend to i tend to think of
• 14:30 - 15:00 what i do as less hypothesis driven even though there's lots of little hypotheses as i'm puzzling things out and more about uh that in building the initial model that can then later be tested that's really interesting and it uh leads us into the next question i had about just um maybe you could talk a little bit about in general the research that you're doing and the the group of uh insects you're working on and maybe
• 15:00 - 15:30 what drew you to that group to begin with in your search for you know the part of the map of life you want to work on yeah uh so when i was a a teenager i became interested in a group a family of of beetles called coravity their common name in english is usually ground beetle um and it's a it's a family of beetles that has about 40 000 species so a lot
• 15:30 - 16:00 of species uh remember that beetles have well over close to 400 000 species known species many many unknown species that haven't been seen by science yet um but uh and so the the ground beetles are a significant chunk of that it's about one-tenth of beetle diversity and i was interested in that and i this was in southern ontario and i would go out as a 15 year old 16 year old and and go along the rivers and creeks
• 16:00 - 16:30 there and find along the shorelines all these little ground beetles that i soon discovered were the genus bambidion and and i became fascinated by their diversity because they're many many species in one particular area um as it turns out just we're in oregon now i now know of about a hundred 120 species of that genus just in oregon um uh wow i i at the time and back when i was 15 or 16 i didn't
• 16:30 - 17:00 know that much diversity in southern ontario but just in my local area i could see you know a couple dozen species and i had a microscope at the time that my my dad had got for me and i could just see these beautiful structures right they were just these amazing little little structures and and all different colors and metallic colors and but even the ones that weren't weren't colorful had these beautiful shapes and and that diversity just fascinated me and it really i was thinking i was really that really
• 17:00 - 17:30 solidified and i really like fell in love with that group uh associated with my reaching out to a professor at the university of alberta george ball uh who i didn't know but he had written a book about the ground beetles of the united states not a book he written a chapter in a book about the ground beetles of the united states and i wrote him not expecting a response i was a 16 year old at the time and uh and to my utter shock he sent
• 17:30 - 18:00 back an eight-page letter uh to me uh and uh and that's that at that moment he became my mentor uh and uh and he encouraged me to work on bimbidion and and so the combination of those factors had just totally solidified my love of bambidian and now what i do with bimbition is i've got one project i've got many projects i've got one large project trying to
• 18:00 - 18:30 figure out the phylogeny of videos as a whole across the world and oh i'll just show you something quickly and this is an old version of it but this is i don't know if you'll be able to see this but this is uh part of the phylogeny so each of those tech names is one species and the colors indicate different groups and it just goes on and on and on so we've now got in our phylogenetic tree and this is based on dna sequence data
• 18:30 - 19:00 about 800 species of embition which is about two-thirds of the known fauna in the world and this is part of a big international collaborative effort to figure out the phylogeny of this group so that's one aspect of what i do i also work on especially in the north american fauna trying to figure out what species live in north america and so i've got a big project on that and that involves all that fieldwork and and dna
• 19:00 - 19:30 gathering dna material and so forth um more and more where the lab is starting to get into genomics of these beetles and so this is less about actually understanding how the genome works in their and the the you know the cell biology but more using that as data for phylogenetics i also do cytogenetics so i look at chromosomal variation so how many chromosomes they have whether they have a y chromosome or not
• 19:30 - 20:00 that sort of thing so i've got projects on that clarifying question would you consider that a morphological character is that a or is that a uh is that an a character i mean yeah that's a good question it's not a dna sequence character uh it's i mean most people it effectively is a morphological character it's a structural character um yeah that's a good question um and uh let's see i mean basically i
• 20:00 - 20:30 i will do anything with that video just about but uh but my focus is on species what the species are on in the world uh and uh uh details about those species and what how they're all related to one another that's kind of the core core of what i do great could you then explain uh in your group what you think the importance of molecular characters is uh both for your group and then for insect
• 20:30 - 21:00 systematics in general so um systematics which is the study of biodiversity uh is uh under uh for many many years of course we only had morphological data you know we could look at a specimen look at it under the microscope and we could see their structures we could dissect it to see the structures inside of it uh but until relatively recently in the history of biology
• 21:00 - 21:30 we just simply couldn't we didn't know anything about the dna sequences and so a lot of the early work including my early work uh when i started in this business my early projects were all morphological it was all looking at specimens under the microscope and seeing comparing structures so okay so this species has this structure on this part of the body this other species has a different has a different looking structure oh here's a third species that looks just like the second one and what does that tell us about relationships and puzzling all that out
• 21:30 - 22:00 just it sounds like that's partly what your your group did your class did in the cladogram exercise so that was my history uh and it turns out that that was that is for one thing it's a an awful lot of work it's a huge amount of work to do that morphological stuff it's very valuable but uh there's so much vastly more data in the genome than than there is easily accessible in by looking at the external structure
• 22:00 - 22:30 and so uh the study of dna sequences has revealed so many things that we just couldn't see with the morphological data there are species that are that that i've discovered using molecular data or phylogenetic results that i've discovered using molecular data that i did not see with the morphological data i i couldn't have seen some of those the moment that i the
• 22:30 - 23:00 moment that i saw those that i had the molecular data they rearranged the landscape such that i could see the variation that the more the more the variation i could see the morphological data level suddenly made sense right um so there's some there's some c species complexes that i couldn't figure out what the species were i did the molecular work oh wait a minute now i can see what the species are because it's very clear with molecular data it's much clearer
• 23:00 - 23:30 who's sharing genes with whom which is really what species are about right is that is it groups of specimens that are sharing genes within one another are one species and if they don't share genes with this other group of specimens that's a different species and that's easier to that those patterns are easier to see when you're looking straight at the dna level and so i've discovered species by looking at the dna level that i never saw it was all the morphological variation was way too confusing but the moment that i sorted them out
• 23:30 - 24:00 with the molecular data then i can see oh wait a minute all of these ones have this structure on them all of the ones in this species so forth so that said it's not a silver bullet i've got there are some species some some species complexes in which it's way easier to see i've yet to be able to i can't tell them apart with dna sequence data yet i can easily tell them apart with morphological data and that you know that why that is is a very interesting question in in in terms of what's going on
• 24:00 - 24:30 genomically my suspicion is is that there's only a very few loci that are the ones that are they're fairly recently speciated those species only recently split and there's only a few loci that involved with reproductive isolation that are really the ones that if i could sequence those and know what they were i'd see the pattern there but otherwise i can only see the pattern in the reproductive parts structures of the organisms and so um so the dna sequence data
• 24:30 - 25:00 is a fantastic addition to our toolkit like it really clarifies a lot of what's going on and especially at the phylogenetic level we're without in some cases we need to go all the way to the full genome to understand the phylogeny and actually it turns out in some cases we still haven't been able to figure out parts of the shape of the phylogenetic tree even if we have the whole genome but we can do a lot better with it than we can do with
• 25:00 - 25:30 only morphological data well that's really interesting um so my next question was about then uh what are some of the things that new technology has enabled in in your field and um specifically i'm thinking about uh sequencing of historical specimens so maybe you could talk in general about new technology cheap dna sequencing what it allows and then specifically uh historical specimens yeah so
• 25:30 - 26:00 sometimes i'm i i i'm amazed and i think back to i think back to when i was a grad student or when i was a teenager and i think can that per could that person back then ever have imagined that i would be sitting here with data on the genome of this benvidia and i just i just can't quite believe it right and yet
• 26:00 - 26:30 these days you can take uh well okay so when i first started out doing dna sequencing and this would have been in the late in the early 1990s was it painful it was mind-boggling amounts of work and you had to deal with radioactivity and you had it was just so painful and you would spend like two days and you get a few sequences of a few species and and these are sequences that are short right
• 26:30 - 27:00 these are not genomes these are just some small part of some one gene and and and there were very few genes that you could actually do that way at the time right you could only a very few genes were were accessible to somebody like me working on beetles um and now with uh the next gen generation sequencing methods you can get uh you can basically we can we can take a little bit of dna
• 27:00 - 27:30 that we've extracted from a beetle and we can give it to our local sequencing facility here at oregon state and for about well i mean it depends on the beetle because it depends on how big their genome is but for a thousand dollars or less we can get dna sequences of most of the genome of of of the beetles uh and uh that just is still i just still can't quite believe that uh
• 27:30 - 28:00 uh but how much how much did it cost how much did it cost steve jobs to have his genome sequenced remember uh a hundred thousand right and now now for humans like humans are actually cheaper to get it to get a uh that per per nucleotide cost for humans to get their genome is way less than it is for beetles and that's because of all the background information that we've got around humans but still even for beetles it's it's like absurdly cheap compared to
• 28:00 - 28:30 what it would have been um so one of the key things about many of the next generation sequencing methods and the ones that we've used so far is that they're all built around sequencing short pieces of dna so basically you take the genome of the organism and you you you break it up and then you throw those into a sequencer and they sequence these short pieces and then you get all these short pieces and you have to in using software stitch them back together and so
• 28:30 - 29:00 do you talk about this in your in your class do they would your students have background in this uh we we don't really talk about how sequencing works just what it's used for yeah okay so it's the way i tend to think about it is imagine that you've got a you you have a book and you have and the in this case the book the sentences and the words in the book are the genomes the that nuclear string of acgts that represent the full sequence and you break that up into uh
• 29:00 - 29:30 chunks that are like like 60 letters long or actually in my case 150 letters long so you've got a sentence and then maybe it ends partly there and then the next sentence and there's just random where are they starting in those fragments is random right but you you've got so many of them that any particular part you you've actually got it represented many many times so it's like you've got it's almost like you've got 80 copies of a book and you just cut it up into these little
• 29:30 - 30:00 fragments and then you can basically stitch it back together by saying oh wait a minute the end of this 150 letter fragment exactly matches the first 40 letters in this other fragment and so you see that overlap and then you can base and then you just do that again and again and engage you can just sort of stitch everybody back together so that's what you can do with these tools um well in old specimens one of the problems with old specimens say some specimen that's
• 30:00 - 30:30 been sitting in the museum a little beetle spinning that wasn't collected for preserving dna there was just collected in whatever method they collected back in the 19 early 1900s or 1800s killed with cyanide or whatever saved by charles darwin himself right they're saved by charles darwin himself uh that that those specimens the dna in there as it as both when they were killed not to be preserved for dna and as it sits in the museum dried over all those years the dna degrades
• 30:30 - 31:00 and and basically naturally breaks up into small pieces and so it's almost pre-built for sequencing using these tools and so um and so we've got there was one uh one historical specimen that from that was collected in oregon well what was then oregon because this was in the mid 1850s and oregon had a different was bigger than it is now um it was collected in the mid-1850s and
• 31:00 - 31:30 it was an historically important specimen and and we needed to know to what species it belonged and and that allowed us knowing in figuring that out we would know what the name of that species was right it was key to the whole nomenclature nomenclatural puzzle of figuring out what the name of that species was and this was a key uh it's what was called a type specimen it was the the name bear it was the one that it if any species was going to be called
• 31:30 - 32:00 bambini on erasum it was that species uh that spec it was the species to which that specimen belonged this historical specimen and so we needed to get sequence data from it and it turned out much to my utter shock we got much of the genome from that it was when we see when we sequenced it it was 159 years old uh since it had been collected about 159 years old we don't exactly know what year it was collected and that just is stunning to me that here sitting in
• 32:00 - 32:30 that city this specimen was sitting in the museum of comparative zoology at harvard university they've been sitting in there for 159 years and that it can still contain the genome that you could recover from it and that is a stunning thing about what's sitting in the museums of the world is that it's that suddenly these new sequencing tools have turned those museums that sometimes are thought of these dusty old warehouses of old material
• 32:30 - 33:00 that nobody cares about anymore it's suddenly that it suddenly contains the genome of the world like they contain the genome of earth like all the genomes of earth that we know about are sitting there in those museums it's just that we can actually get now we just didn't know that before and that's this is stunning it's just stunning plus lots of extinct species plus lots of extinct species and one of my projects actually was doing exact using these tools to sequence what are surely the extinct species that are on top of uh the isle the
• 33:00 - 33:30 the mountain on the the the peaks on the top of saint helena the an island in the middle of the atlantic ocean which has this amazing diversity of had this amazing diversity of bambidion on top of it uh and they're there most of those species are surely extinct because the habitats are gone uh there might be one left uh and but we were able to see they were sitting those specimens were sitting
• 33:30 - 34:00 some of them from the 1800s in uh the natural history museum in london and some in tehran uh belgium uh and we managed to get get the dna sequences from them it's just it's still i still can't quite believe it we just did a a lab on dna barcoding using the c01 gene yep um i wonder if you could just briefly explain how what you do is different from a dna barcoding approach yeah so right so
• 34:00 - 34:30 uh dna barcode i just full disclaimer i don't like the the word dna barcoding because it it's nature is not simple there's no barcode on the butt of these beetles it just doesn't work that way there's no silver bullet that said and and sometimes when the the concept of dna barcoding was presented uh i think was 2003 2002 2003 it was suggested that it was this silver
• 34:30 - 35:00 bullet right that it would solve all of our problems and understanding what species are out there uh and uh and it's not it's not a silver bullet that said it's a fantastic thing like it's really really improved our ability to quickly understand uh by patterns of what the species are that are out there uh species boundaries um uh so what i do is similar to that but i
• 35:00 - 35:30 like i use that scene i use that same piece i don't call it barcoding because it's it makes it too it sound makes it sound too simplistic i use that piece for evidence but i use other genes too and one of the key things is is that is that there's reasons to expect that the bar coding gene which is mitochondrial it's part of the mitochondrion uh mitochondrial genome that that it has some flaws in it that mean that it sometimes can be more likely to give you a false
• 35:30 - 36:00 signal as to what the species boundaries are um than some other genes might um again that said you can learn a lot from it but it's not i've got groups of of bambidion in which the worst gene is co1 to try to figure out what the species boundaries are i've got other ones which are the best gene uh it varies like there's just the nature has there's a lot of ways in which in this world you have to watch out for simple rules right and
• 36:00 - 36:30 and they rarely rarely work so i use my standard genes i use are cytochrome co1 uh 28s which is a part of the ribosomal cistron 28s ribosomal dna uh a gene called the short name of the the acronym for the gene is cad cad another one that's topoisomerase one uh and then sometimes we use muscle specific protein 300 and those are all genes that that evolve quickly enough
• 36:30 - 37:00 that you can get signals about gene flow or lack of gene flow using them and we're also starting now to switch to genomic data like not just four or five genes but many more and that having the multiple genes especially these are genes that are at least in part surely part of different linkage groups like they're not genetically the co1 is certainly not genetically linked to say 28s because one's mitochondrial
• 37:00 - 37:30 one's in the nuclear genome that you you get different signals and just just as sometimes sometimes having only one piece of evidence leads you in one path but if you have two pieces of evidence if they conflict you it wakes you up to the fact wait a minute things are not simple that's one of the biggest reasons why why we want to use more than one piece of evidence and just to follow up then if you were at a point where you got a
• 37:30 - 38:00 fork in the road where you have two different ways that the data look like they're going would you then sequence more genes or would you potentially sequence the entire genome how would you uh move past that so uh uh good question um we have very few cases where i've got very few cases in my work where i don't get a clear signal with the four genes that we
• 38:00 - 38:30 typically use and one of the genes like so say for example we do co1 and we don't get a clear signal we get a mass and we do 20 s and it's got conflicting signal maybe also a little what might be a mess you don't really know but then you get cad and it confirms 20 s then you get toppo and it get topoisomerase and it confirms 28 say or it confirms co1 right so it's usually the case that when we get to the
• 38:30 - 39:00 when we sequence four or five genes we haven't a signal that wins out right the the weight of the evidence goes in one direction especially when you combine when you start then using the morphological data it's usually the case that the combination of four or five genes and the morphological data the picture is normally clear we have some examples where that's not the case and and actually curiously enough one of the most puzzling and the hardest cases that we've got
• 39:00 - 39:30 is subgenus trapan bambidion subgenus trapanodorus which is the which is the one that uh that you i i had a class on which we could talk about um but it's also one the one that your students are analyzing sub-genius tripanodors it's actually i i mean i i it's one thing one way in which it's maybe not a little bit less than ideal for your class too because it's actually one of the most complicated if they they you know they're not your class is not dealing with all the genes
• 39:30 - 40:00 and they're not dealing with all the specimens that we had but when you get the full picture oh it's it's it's probably the single messiest group of bambidion in the sense that the dna data didn't just have a really really clear signal that made the the the genetic structure of the group obvious which is normally the case for other bimbian so uh a quick follow-up to that and then i i want i do want you to talk about
• 40:00 - 40:30 your class uh so the quick follow-up is is that evidence of a rapidly speciating group where there's lots of young species if you say that the molecular data aren't necessarily always clear or perhaps it's a more complicated story so i uh i think that that's likely the case but there i just i think that it's fair to say
• 40:30 - 41:00 that i just don't understand it well enough yet to know what's going on so one thing that's one thing that we have not done is attempt to uh put dates on the various events on the phylogenetic tree for that group uh to actually time how like how old are these species for example the ones that we we we think we know what the species are now like we've got well we have a hypothesis now as to what the species are within trepanodorus
• 41:00 - 41:30 uh again unlike most species of most groups of bembidian in which i tend to be very confident of those hypotheses for this group i'm not and you know future future studies that will test those hypotheses may may disrupt them they may prove that we're wrong or may show that we're wrong about some of them um but uh but actually dating those those presumed species we haven't done like so like how long has it been since the speciation event we've not attempted that and to really
• 41:30 - 42:00 do that well you need to bring fossil data into the into the story to do it what really well and we're where we have not yet incorporated the available fossils and there are some fossils have been video we haven't incorporated the fossil denvidian into the sort of the bigger picture that's that's part of the long-term plan but we haven't done it yet so we don't so basically it's i'm waffling here i don't really know i think that in some cases you're exactly right but another but i just there's that the re one of the big
• 42:00 - 42:30 reasons i hesitate there's odd things going on in some of these big marshes like it really shocks me how genetically differentiated the populations are in in different areas uh of or even oregon uh within this group of bambidian in what looks like one species and i just don't see that in other benvidia that sort of geographic structure and and so i and i haven't delved into the history of the marshes like i haven't
• 42:30 - 43:00 looked at the the scientific literature on how old are these marshes and and so forth so i i just it's hard for me to say well that's what makes it an interesting group to study right yeah yeah oh yeah oh there's and yeah there's lots to be done in it well that's great uh so can you tell us about um this course that you taught in 2015 i believe it was it was titled discovering insect species you taught it here at oregon state yeah so i
• 43:00 - 43:30 uh as i was starting to work on this project to document the species of bambidion in north america i there i don't remember exactly what the seminal moment was but i thought god it'd be really cool to to uh have it so that a group of undergraduate students were engaged in the research directly and not just just people in the lab but they were like part of a a research team and that it was done in the context of a course a
• 43:30 - 44:00 class and so uh as this was mulling around in my brain i was talking to a an entomologist well actually no i talked to the entomologist before then before it started mulling around in my brain uh kenneth cooper at uh uh he's now he's deceased now but he was at the university of california at riverside when i talked about it and he told me that this group of bambidion that i didn't know all that well subgenus trepanodorus
• 44:00 - 44:30 there was a lot of interesting things going on in california and uh i saw that was in the back of my mind and then when i thought about this course i thought oh i should do that and i should do trypanodorus uh as the subject matter for the course and i had it up to that point i had done a little bit of research on trafanadoris uh i've done some dna sequencing and i did enough that i thought oh this is an interesting group but i didn't know how complex it was
• 44:30 - 45:00 going to be uh and and so uh at the moment i decided that's what the topic of the class was going to be i stopped research on it and that data set is what your class is analyzing uh analyzed last week uh was that that was that was part of the data set that i had at that time pre-class and then so uh so for the course i advertised the course i had a bunch of
• 45:00 - 45:30 students apply they had to apply to it and i chose nine students i had a graduate teaching assistant uh john johns brow and the 11 of us formed a research team and i made it a point to do nothing behind the scenes uh that was in well i mean obviously i i got supplies behind the scenes and so forth right i organized things but i didn't do any research behind the scenes at all while we were doing the class and
• 45:30 - 46:00 so any discoveries that were made any of the core work that was done the students participated in um and they uh participated in some of the field work and why they participate in the decisions about the fieldwork they did morphological work they look under the microscope of the specimens they sorted things out the specimens that we collected they extracted dna from them they did the pcr they processed the sequence data we got back and so forth
• 46:00 - 46:30 and so um at this point early on in the course we had decided that klamath marsh because these were a group of bambini that tended to live on marsh in marshes the klamath marsh which is uh just east of the cascades in southern oregon this big marsh complex that we would go out there as our first major weekend field trip and so we went out there and uh and at the national wildlife refuge the people in the refuge were great to us they gave us a
• 46:30 - 47:00 cabin to stay in we drove there from corvallis we ended up at the refuge everybody was excited about it because they had learned enough about subgenius trypanodorus at that point to be able to recognize them in the field and to know some of the things that i had learned about them including that i knew about an undescribed species a specie a new species that didn't have a name it lived in the cascades of oregon uh and it was called i called it lost lake
• 47:00 - 47:30 uh because i'd first found it at lost lake um and uh here's a i'll show you a picture of lost lake here's a picture of lost lake uh so where i found that that species and uh so i i they knew about that they thought that was really cool that there was a new species in the group and so we might we drove off to klamath marsh and uh we were going to collect the next two days so friday night we get there and we
• 47:30 - 48:00 decided there was a little part of the marsh that was right next to our cabin we thought oh let's just go out and look there and so we went out there and uh at night with headlamps and here's what the the klamath marsh looks like uh that that particular site uh this is a picture of the next day not uh not at night um but it shows where we're we're just we're in there we're looking in between the sedges and the grasses like just digging around
• 48:00 - 48:30 crawling around on our hands and knees looking for these little little beetles because they're small small little beetles uh you know these ones are about between 2.5 and 4.5 millimeters long and so we're we're digging around in there and we're finding we found a few species of the class was really excited about that and then one of us picked up a specimen and i looked at it with my hand lens and i said oh this is lost late and they were really excited about
• 48:30 - 49:00 that because here was this species lost lake that uh that they had learned about uh that didn't have a name yet it wasn't in the scientific literature so they were seeing this thing that the rest of the world didn't know about and they were very excited about that um it turned out that in the next couple days the trip we got lots of specimens of this subgenus trypanodorus and we found one other specimen at a different site within klamath marsh that uh i looked at and said oh that's lost lake too
• 49:00 - 49:30 and so we we after this great field trip we went back to uh corvallis we took a lot of our specimens we decided the class decided which ones we were going to sequence which ones were going to look at morphologically and so forth we extracted dna from the ones that we're going to sequence and of course we extracted dna from the two specimens that i had thought were lost late um and but during that time uh uh after we got back to corvallis we
• 49:30 - 50:00 were looking at the specimens those two specimens from the two different places at klamath marsh that i thought were lost lake when i was in the field i thought were last lake but looking under the microscope not just the hand lands they just looked a little bit they looked disturbingly different like just they're a little bit paler they're a little bit bigger and i started thinking about it i realized that that was lower elevation than any of the sites that i had found lost lake at in the cascades and so i started like we were starting
• 50:00 - 50:30 to question is this really lost lake or not those two specimens i mean i was waffling like you had probably lost late but maybe they're not lost late i didn't really know right and so we we um sent our our we did the pcrs on those and all the other specimens that we had collected at at klamath marsh we uh prepared them the pcr products uh so after the dna amplification we we did we amplified uh uh
• 50:30 - 51:00 cytochrome oxidase one so co1 28s cad topoisomerase those four genes i mentioned before we sent those pcr products off to be sequenced at the university of arizona where i get still get my my dna sequenced in this way the basic sequencing the next generation sequencing we do here at oregon state sent it off and then again because everything was done with the class we uh at about a week later the next
• 51:00 - 51:30 week's class we're all in class we get a note from the sequencing facility in arizona saying the sequences are ready to be downloaded uh so they get downloaded in class uh and the initial processing is done and now we're at exactly the point that your class is for today for this week's class okay so uh the data set that you've got is the same background back uh historical data set that i gave that
• 51:30 - 52:00 we had at the start of the class in 2015 the discovering insect species class and we just downloaded the in class that the data from arizona and we had 28s and co1 from a whole bunch of specimens we also had cad and topoloy summaries but uh that's a different story so we had 28 s and c01 from those two specimens from klamath marsh uh that i had thought were were uh lost
• 52:00 - 52:30 lake and uh and so now your students can basically step into the shoes of the students in my class in 2015 and see what the data the dna sequence data tells them you