Evolution 2023: Gene family expansions underlying a host-plant shift in Manduca sp. - Jay Goldberg

Summary

Jay, a post-doctoral researcher, discusses his work on gene duplications in the Manduca genus, focusing on ecological co-evolution. He highlights the challenges of confirming co-evolution in plant-insect interactions and presents his findings on gene family changes in Manduca species, particularly involving glutathione transferases and odorant receptors. These genes may play roles in detoxification and host plant shifts. Jay aims to understand how natural selection shapes these interaction genes and their role in co-evolution, supported by extensive genome sequencing and analysis.

Takeaways

• 🔬 Jay's research focuses on gene duplications across the Manduka genus.
• 🌱 His broader research interest lies in co-evolution, which involves reciprocal selection during biological interactions.
• 🌍 Jay distinguishes between ecological co-evolution (species interactions in nature) and cellular/molecular co-evolution (molecular interactions within organisms).
• 🧬 Current research emphasizes ecological co-evolution, particularly in plant-insect interactions.
• 🦠 Microbial systems are often used to study co-evolution due to clear fitness effects and rapid generation times.
• 🐍 Jay mentions the debunking of the textbook example of garter snakes and toxic newts, highlighting the complexity of co-evolution.
• 🌼 His work involves studying the Manduka genus and their interactions with the Datura plant, noting the innate attraction of Manduka moths to Datura's floral volatiles.
• 📊 Jay uses whole genome sequencing and gene family analysis to study gene gain or loss events underlying host plant shifts.
• 🧪 Significant findings include the duplication of glutathione transferase genes in Manduka and extra copies of odorant receptor 67c in Manduka sexta.
• 🌐 The research aims to identify interaction genes mediating these co-evolutionary processes, contributing to the understanding of natural selection shaping these genes.

Q & A

What is the primary focus of Jay's post-doc research?

Jay's post-doc research primarily focuses on gene duplications across the Manduca genus, with a broader emphasis on co-evolution, particularly ecological co-evolution.

What are the two types of co-evolution mentioned in the script?

The two types of co-evolution mentioned are ecological co-evolution, which occurs when species interact in nature, and cellular or molecular co-evolution, which occurs when different molecules interact within an organism.

Why are microbial systems suitable for studying co-evolution?

Microbial systems are suitable for studying co-evolution because they have clear fitness effects and rapid generation times, allowing for the observation of evolutionary changes in real time.

What challenge is associated with empirically assessing co-evolution in plant-insect interactions?

Empirically assessing co-evolution in plant-insect interactions is challenging because there are many different interactions occurring, and any given trait of interest might be influenced by various environmental factors.

What recent findings have debunked a textbook example of co-evolution involving garter snakes and toxic newts?

Recent findings have shown that the levels of toxins in newt populations are more closely related to their population structure than to the levels of resistance in their predators, indicating that selection is one-sided. The newts' toxins select for resistance in garter snakes, but the snakes' resistance does not select for higher toxin levels in the newts.

What is unique about the interaction between Datura plants and Manduca moths?

The interaction between Datura plants and Manduca moths is unique because the floral volatiles of Datura plants are innately attractive to the moths, the larvae thrive on the toxic plants, and at least one species of Datura can be completely defoliated without any cost to seed production.

What method is Jay using to understand gene family changes in Manduca species?

Jay is using whole genome sequencing and de novo assembly of Manduca species genomes, utilizing PacBio's HiFi reads for high accuracy and coverage.

What specific gene family did Jay's research find to have duplicated early in the evolution of the Manduca genus?

Jay's research found that a glutathione transferase subfamily appears to have duplicated early in the evolution of the Manduca genus, with each species sampled having six to seven copies of this gene versus only one to two in the outgroups.

Why are the duplicated glutathione transferase genes interesting in the context of host plant colonization?

The duplicated glutathione transferase genes are interesting because they are involved in detoxification of dietary compounds, which could have allowed Manduca species to colonize a diverse array of host plants by sub-functionalizing to detoxify different compounds.

How does Jay's research contribute to understanding co-evolution between Datura and Manduca?

Jay's research aims to identify interaction genes mediating the interactions between Datura and Manduca, which will help understand how natural selection has shaped these genes and whether co-evolution has played a role in their adaptation.

Outlines

00:00

🔬 Jay's Post-Doc Research on Gene Duplications and Co-evolution

Jay introduces his post-doctoral research on gene duplications within the Manduca genus, focusing on the ecological aspects of co-evolution. He explains the difference between ecological and molecular co-evolution, emphasizing the challenge of empirically assessing co-evolution in plant-insect interactions. Jay provides an example involving garter snakes and toxic newts, demonstrating one-sided selection. He compares this to his study on Datura plants and Manduca moths, which are seemingly adapted to each other. Jay highlights that despite extensive research, empirical tests to confirm co-evolution in these systems are lacking. His current focus is on the Manduca side of the interaction, with particular attention to their diverse adaptations across different host plants.

05:02

🦋 Manduca Genus Host Plant Shifts and Genomic Analysis

Jay delves into the diversity within the Manduca genus, noting the different host plants utilized by various species. He aims to understand if gene gain or loss events underpin these host plant shifts, focusing on the shift to solanaceous plants in particular. Using whole genome sequencing and de novo assembly, Jay has generated new genomic data for several Manduca species. He explains the annotation process using different pipelines and highlights a gene family analysis performed with OrthoFinder. His research indicates a specific gene duplication event in a glutathione transferase subfamily across the Manduca genus, suggesting its role in detoxification and adaptation to diverse host plants. Additionally, he finds multiple copies of an odorant receptor gene in Manduca sexta, potentially linked to host plant colonization.

10:02

🔎 Identifying Interaction Genes in Co-evolution

Jay discusses his broader research goals of identifying interaction genes that mediate plant-insect co-evolution. He aims to understand how natural selection has shaped these genes, particularly within the Datura plant and its specialist insect community. His work includes annotating and assembling multiple genomes, not just for Manduca and Datura but also for other herbivores and plant species. He highlights the significance of understanding these interactions, including the costs and benefits for the plants involved. Jay concludes by acknowledging the support he received from various collaborators, sequencing services, and funding sources. He invites further questions and provides his contact information.

Keywords

💡Gene duplications

Gene duplications refer to the process by which a region of DNA is copied and inserted into the genome. This can result in multiple copies of the same gene within an organism. In the context of the video, Jay's research focuses on gene duplications in the Manduca genus and how these duplications may have contributed to the evolutionary adaptation of these insects to their host plants.

💡Co-evolution

Co-evolution is the reciprocal evolutionary process that occurs when two or more species influence each other's evolution. Jay's research primarily focuses on ecological co-evolution, particularly the interactions between plants and insects. The video discusses how traits in both Datura plants and Manduca moths might have evolved in response to each other over time.

💡Ecological co-evolution

Ecological co-evolution occurs when species interact and influence each other's evolution within a shared environment. Jay is exploring the interactions between Datura plants and Manduca moths, aiming to determine if their traits have co-evolved due to these interactions. This involves studying how each species might have adapted traits in response to the other.

💡Molecular co-evolution

Molecular co-evolution refers to the evolutionary changes that occur between interacting molecules within an organism. Although Jay's current research focuses on ecological co-evolution, molecular co-evolution is also significant in understanding how different molecular interactions within organisms evolve together over time.

💡Manduca genus

The Manduca genus consists of various species of moths, commonly known for their interactions with toxic host plants. Jay's research includes studying different species within this genus to understand gene duplication events and how these might relate to their ability to feed on different host plants, particularly those in the nightshade family.

💡Datura plants

Datura plants are a genus of flowering plants known for their highly toxic properties. Jay's research investigates the interaction between these plants and Manduca moths, focusing on whether co-evolution has occurred. The plants' floral volatiles attract Manduca moths, and their larvae can thrive on these toxic plants.

💡Obligate interactions

Obligate interactions are relationships between species where each species is dependent on the other for survival. In the video, Jay mentions that most confirmed examples of co-evolution involve obligate interactions, often found in microbial systems, where fitness effects are clear and observable.

💡Fitness effects

Fitness effects refer to the impact of a trait on an organism's ability to survive and reproduce. Jay explains that in microbial systems, fitness effects are clear and make these systems suitable for studying co-evolution. In his research, understanding the fitness effects of traits in Datura and Manduca can help determine if these traits have co-evolved.

💡Floral volatiles

Floral volatiles are the aromatic compounds produced by flowers that attract pollinators. In Jay's research, the floral volatiles of Datura plants are innately attractive to adult Manduca moths. This innate attraction is an example of a trait that may have evolved due to the interaction between these plants and insects.

💡Genomic sequencing

Genomic sequencing is the process of determining the complete DNA sequence of an organism's genome. Jay uses whole genome sequencing to study gene duplications in Manduca species, which helps identify genetic changes that may have facilitated their adaptation to different host plants.

💡Glutathione transferase

Glutathione transferase (GST) is an enzyme involved in detoxification processes within organisms. Jay's research found that a subfamily of GST genes had duplicated in the Manduca genus, potentially allowing these insects to detoxify a variety of compounds and colonize different host plants. This gene family is a focus of his study on host plant shifts.

💡Odorant receptor 67c

Odorant receptor 67c is a gene associated with the detection of chemical signals. In Manduca sexta, extra copies of this gene were found, which might play a role in host plant detection and adaptation. Jay is investigating how these gene duplications contribute to the moths' ability to locate and thrive on specific plants.

Highlights

Introduction to ongoing post-doc research on gene duplications across the Manduca genus.

Research focuses on co-evolution, which is the reciprocal process of selection during biological interactions.

Two types of co-evolution: ecological (species interactions) and molecular (molecular interactions within organisms).

Current research emphasis on the ecological aspects of co-evolution.

Few confirmed examples of co-evolution, primarily in obligate interactions and microbial systems.

Microbial systems are advantageous for experimental manipulation due to rapid generation times.

Challenges in empirically assessing co-evolution in plant-insect interactions due to multiple environmental interactions.

Use of sequencing data to detect co-evolution by looking for evidence of past selection.

Recent study debunked a textbook example of co-evolution between garter snakes and toxic newts.

Research on Manduca sexta and its adaptation to Datura plants.

Manduca species' host plants vary significantly, indicating potential gene gain or loss events underlying host plant shifts.

Whole genome sequencing used to study gene family changes in Manduca species.

Glutathione transferase subfamily duplicated early in Manduca evolution, with multiple copies found in sampled species.

Manduca sexta has extra copies of odorant receptor 67c, potentially allowing colonization of new, highly toxic host plants.

Focus on finding interaction genes mediating plant-insect interactions to understand natural selection's role.

Transcripts

hello my name is Jay

and I'm going to tell you about some of

my ongoing post-doc research looking at

Gene duplications across the manduka

genus

my research broadly speaking focuses on

co-evolution which is the reciprocal

process of selection that can occur

during biological interactions broadly

speaking there are two types ecological

co-evolution which occurs when species

Collide in nature and also cellular or

molecular coevolution that occurs when

different molecules Collide within an

organism

right now my research is focusing on the

ecological aspects of this process

I would argue that there aren't really

that many known examples of co-evolution

that have really been confirmed

but of the ones that there are they are

primarily obligate interactions and

microbial systems this is because there

are clear Fitness effects that make them

very very suitable to experimental

manipulation and microbial systems are

particularly cool and a little jealous

that you can observe evolutionary

changes often in real time due to their

rapid generation times

in the plant insect interactions that I

work with co-evolution is often assumed

but can be difficult to empirically

assess because as shown in this figure

there are a number of different

interactions occurring and so any given

trait that you might be interested in

and want to understand if co-evolution

has shaped it

um it could be shaped by a lot of other

things that are going on in the

environment

nowadays we can detect covolution using

sequencing data and looking for evidence

of past selection

and this has actually led to textbook

examples being debunked recently and so

quite literally this was in the textbook

that I had to read as a biology

undergrad the Garter snakes and the

toxic newts that they eat in the Pacific

Northwest and so the functional trait

matching that we see in this system is

often cited as evidence of co-evolution

garter snakes that are feeding on

non-toxic newts have low if any levels

of resistance to their Toxin and the

Garter snakes that feed on highly toxic

nudes tend to have high levels of

resistance but a recent study found that

the levels of the toxins in the new

populations actually more closely relate

to their population structure and not to

the levels of resistance found in their

predators

whereas we do see signatures of

selection in the Garter snakes those

they feed on non-toxic newts have little

if any copies of the resistance genes

whereas the frequency of different

resistance alleles is much much higher

in any population of snakes that's

feeding on toxic nudes this indicates

that selection is one-sided the newts

and their toxins are selecting for

resistance in the Garter snakes but the

resistance of the Garter snakes is not

selecting for higher levels of toxins in

the newts

so in a similar fashion these systems

that I work with datura and maduka

interactions are seemingly adapted to

each other which could be the result of

co-evolution the floral volatiles of

Doterra plants are innately attractive

to the adult manduka mods there's no

learning involved on behalf of the moth

they know exactly what sense to follow

and find these flowers

the larvae of this species thrive on

these highly highly toxic host plants

and perhaps most importantly for

maintaining the mutualistic side of this

interaction there is no cost of

herbivory for at least one species of

detera they can be almost completely

defoliated and bounce back and produce

as many seeds as if they had never

experienced herbivory at all

but despite years if not Decades of

research into the traits mediating this

interaction there haven't really been

any empirical tests that show it is the

result of co-evolution

I'm doing research on both sides of this

interaction but today I'm only going to

show you um the manduca side of things

and so many of you are probably familiar

with manduka sexta the most Supreme

model insect in my opinion

but there are dozens of species in this

genus that have been described and

they're found all over North South and

Central America from Southern Canada all

the way to Argentina and Chile

and in Southern Arizona where I was

doing this research there are six

species the ones pictured

I'd hope to sample all of them for this

study but unfortunately I was only able

to acquire four of them

and I find them a fascinating study

clade because host plants vary

considerably from species to species

they're over positing on a diverse array

of plants

and I want to understand if any Gene

gain or loss events are underlying their

host plant shifts and there's one in

particular that I'm very interested in

so here we see the mandible phylogeny

most species fall within a few species

complexes

and these species complexes on the top

of the tree all exclusively feed on

non-solinacious host plants so there's a

diverse array of plant families that you

can find their caterpillars on but none

of them are in the nightshade family

which includes datura wild tobaccos and

tomato plants as well

whereas the species complexes on the

bottom of this tree the sexta and

occulta complexes exclusively use

solanaceous plants in the nitrate family

as their larval hosts

and so this shift to a soul and AC

specialist lifestyle appears to have

occurred once when Rustica diverged from

the common ancestor of the sexta and the

culta complexity

to address this question and what sort

of Gene family changes were current I

used whole genome sequencing and de novo

assembled some new genomes of manduka

species using path bios HiFi reads these

are highly accurate long reads

um I had no other sequencing data just

lots and lots of Hi-Fi reads

and in fact over 50x coverage for the

two genomes that I assembled and um my

friend and collaborator Dr Keaton

Godfrey was very generous and donated uh

commanduka Rustico assembly that she has

worked on to this project

I annotated all these genomes with the

fun annotate pipeline although I'm

currently redoing it with Helix sir

which is a brand new annotation pipeline

that I found much easier to work with

and just as robust if not better than

both fun annotate and the breaker

pipeline which I believe is the standard

nowadays

and the gene family analyzes I'm about

to show you were done with ortho finder

So This research was done with the help

of two really outstanding high school

students that I was mentoring earlier

this year

for any Arizona folks in the audience

today I highly recommend that you

participate in sarsa Star Lab program it

was a really rewarding experience for me

and helped me refine my teaching and

mentoring skills

and we found that a glutathione

transferase subfamily appears to have

duplicated in early on in the evolution

of the manduka genus

each species that we sampled had six to

seven copies of this Gene in their

genomes versus only one to two in the

out groups that we were using which was

the domestic silk mall and highly's best

for tilio which is in the same family as

manduka but about as distantly related

as two species in the same family can

feed

just to emphasize all of these branches

here on the tree

were manduka-specific copies of this

Gene whereas the top three branches were

the ones found in our outgroups

we also found that manduka's sexta

specifically has extra copies of odorant

receptor 67c there were seven copies in

its genome versus three to four in the

other Hawk moths in its family and two

in the domestic silkmonts

and most of the manduka manduka sex the

specific duplications occurred on this

branch of the gene tree

so why are these genes so interesting to

me well gsts are broadly involved in

detoxification of dietary compounds mid

gut expression is induced by the

consumption of these chemicals and

selection on them often unrealize

resistance to insecticides by pests

having multiple copies of a gene like

this could have allowed them to

sub-functionalize which compounds

they're detoxifying and subsequently

colonize a diverse array of host plants

as the gene is Diversified

or 67c is under positive selection in a

species of cactophilic drostophila

and this selection is associated with

multiple very recent host shifts to

alkaloid-rich columnar cacti so perhaps

there's some sort of convergent or

parallel Evolution going on that is

mediated by this Gene and allowing

manduca and drosophila to colonize new

highly toxic host points

and so to tie this all back to

co-evolution the driving force of my

research program this is all focused on

finding the interaction genes that are

mediating these interactions so that I

can take further steps

to understand how natural selection has

shaped these interaction genes

and I am very broadly interested in

datura and its specialist insect

Community if and how co-evolution has

shaped them and what sort of genes are

involved in these interactions and so I

have quite a few genomes that I'm

working on right now most of the

assemblies and annotations are almost

done

and so uh not just manduka and datura

but also hamifter and herbivores a few

species of Weevil and another species of

datura that has um it is not quite so

well trait matched to its herbivores for

example there is a strong cost to

refrigerate if it's defoliated it

doesn't bounce back

and so with that I'd like to acknowledge

everyone who has helped me with this

project over the years both from

developing the ideas and also all the

various Labs that have helped me carry

out this research

um of course have to acknowledge the

sequencing services that I used

and also the funding that was generously

provided by the University of Arizona

Pacific bioscience and the National

Science Foundation

and you can find me on Mastodon if you

have any further questions or anyone

you're welcome to send me an email and

thank you for watching