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Hybridization and conservation - how are they related?

Posted by Brian on October 5, 2019 at 3:25 PM Comments comments (3)

A recent interview with The Wildlife Society was just posted on their website (see below), check it out here: https://wildlife.org/researchers-discover-hummingbird-hybrid-zone/


As is pointed out in the interview article, I'm highly suspicious this hybrid zone, although it arose naturally, is larger than it would be in the absence of human disturbance and landscape alteration. Anthropogenic disturbance and habitat modification are reshaping species distributions and bringing previously isolated species into contact. Although under-studied, the potential for disturbance to erode species boundaries has enormous implications for conservation and management, especially when declining species are involved. Migratory Allen’s and Rufous Hummingbird, species of conservation concern on the Partners in Flight Watchlist, form a hybrid zone in northern California and southern Oregon. Hybrids are successful at exploiting disturbed habitat and outnumber parental species in disturbed areas across the hybrid zone.


When two species interbreed, they exchange genes, and their resultant offspring have genomes (and traits) that resemble both parental species. If hybridization spreads too far into the range of a species with a small range, it could threaten the genetic integrity of that species if the genome of the other hybridizing parent species is expanding south as a result of gene flow. I have preliminary data that shows high levels of gene flow from Rufous Hummingbird, far into the range of migratory Allen's Hummingbird, and additional data showing migratory Allen's is undergoing a population decline (although non-migratory Allen's populations are expanding rapidly and doing just fine). Thus, hybridization might be affecting the long-term viability migratory Allen's Hummingbird in the  northern part of its range. Further, non-migratory Allen’s Hummingbird is expanding its range, likely due to urbanization and landscape alteration. I also have preliminary evidence of hybridization between non-migratory and migratory Allen's at the southern end of the breeding range of migratory Allen's, so I want to investigate whether interbreeding has recently expanded north, further into the range of migratory Allen's. This is a complicated, interesting system that I want to use to show how analyses of hybridization are relevant (and needed) when addressing certain conservation issues. I plan on looking into this in the future (possibly as part of a postdoc project!) to establish whether human-enhanced hybridization is detrimental to the genetic integrity of a (likely) declining migratory subspecies.


Research updates

Posted by Brian on July 19, 2019 at 1:05 PM Comments comments (2)

Hi everybody!


It's been a while since I've updated you all on my research progress, so I thought I would do so now. 


First, my first paper, from my undergraduate research at Cal Poly Pomona, titled "Trends in bird species richness in the midst of drought", was recently published in the June 2019 edition of Western Birds! This one is based on my work as an undergraduate, and investigates the effects of drought on coastal sage scrub bird communities using long-term data. The big takeaway from this paper is that resident, non-migratory birds seem to struggle during drought, and either become more cryptic and/or experience increased mortality. However, this effect disappears when a supplemental water source was provided. Further, migratory species  richness remained the same with and without drought without supplementental water, while the number of migratory bird species detected increased during drought when a supplemental water source was provided. The main message coming from this paper is that supplemental water sources might be an important consideration for maintaining the diversity of bird species in some regions as climate change and drought become intensified over time.


The first paper regarding the hybrid zone between Allen's and Rufous Hummingbird, titled "Behavioral and morphological evidence of an Allen’s × Rufous Hummingbird (Selasphorus sasin × S. rufus) hybrid zone in southern Oregon and northern California" was recently accepted by The Auk: Ornithological Advances. This paper should be out in either the July or October issue. In this paper, we map out the hybrid zone, which spans (phenotypically) from northern California (Humboldt County) to central Oregon (Lane County) along the coast, and  inland from Humboldt County through Horse Creek in Siskiyou County, CA (although inland transect data was not completed at the time this paper was submitted). In this paper, we identify several new characters that differentiate Allen's and Rufous Hummingbird, and find, via geographic cline analysis, that sexual selection seems to be a dominant force in maintaining species boudnaries between Allen's and Rufous. 


I'm also working on three additional papers, and hope to get at least two of them submitted this year. These include behavioral sequence analysis of Allen's and Rufous Hummingbird and their hybrids, where we identify novel behavioral characters across the hybrid zone and address how evolutionary novelty might evolve, a phylogeographic study of Allen's Hummingbird using whole-genome data and ecological niche modeling, and a comparison of the genomes of Allen's and Rufous Hummingbird, especially on the Z chromosome (the sex chromosome in birds), where most species differences are found. 


I'll have an update regarding the 2019 field season, which was very brief (only two weeks this time out!) but successful, soon!. This field season closed out sampling for my dissertation, which I am completing in December 2019. 

More progress!

Posted by Brian on April 8, 2018 at 1:50 AM Comments comments (4)



The last week and a half has been really productive! To date, we've caught 40 birds in 26 days. Most species of plants seem to not be flowering yet for some reason, and although it makes it tougher on the birds (I'm sure the populations will be just fine in the long run), it makes our work a lot easier, because they storm my feeders. Out of 9 or 10 localities that I planned to sample this season, we're working on the fifth, so progress is definitely being made. Even though were 40-50 miles inland, the birds are still mostly Allen's-like, although we've seen a lot of really strange behaviors that I haven't observed in pure Allen's or Rufous. For example, I've seen birds not flying high enough to make dive sounds, and birds leaving out parts of displays that pure birds do, all multiple times-to a nerd like me, it's kinda fascinating.


Today I gave a research presentation to the South Slough National Estuarine Research Center and the Cape Arago Audubon Society in Oregon. I gave a one hour presentation to about 50 people about the Allen's x Rufous hybrid zone, discussing sexual and natural selection, and the importance of evolutionary biology in general. The audience was very interested, and many of them suspected there were hybrids here long before I knew about them! There were a lot of questions related to female choice-what is a female looking for in a potential mate? It's very difficult to study that in hummingbirds-I've never seen them actually mate, even though my dissertation focuses on courtship. I don't know what a receptive female looks like-wild females usually visit a male's territory to feed, and once the male starts harassing them, they tend to leave the area very quickly. Maybe for my next dissertation! However, through things like cline analysis, we can see which characters are important to speciation, and imply which components of sexual selection drive differences between the species, which is what I am attempting to do in my research. It was a lot of fun to have an interactive experience, bring live birds in, and showing videos of hybrid characteristics they can go outside and observe on their own. Sharing research with the general public is a rewarding part of what I do-why do all of the work if you aren't going to make your results widely available?


We stayed in a yurt for the last couple of nights, and a bat that was inside the yurt (somehow) flew by my head-that sums up the extent of wildlife that I've seen since the last post! In some other "news", I ripped two pairs of jeans in the last week-one pair was while chasing a hummingbird into a trap-at least I somehow still caught the bird. As of last week, most of the time has been spent (and will be spent) in inland northern California, working along highway 96, seeing whether the evolutionary phenomena acting on the coastal transect act similarly inland. For some reason, more snow is expected later this week where we will be working, with temperatures dipping into the low 30s at night...not looking forward to that!

Best laid plans

Posted by Brian on March 26, 2018 at 11:10 PM Comments comments (0)

It’s been an interesting couple of weeks since the field season began. Field work is nothing if not unpredictable. Broken laptop, broken recorder, snow in northern California, snow on the Oregon coast. I woke up a couple mornings ago, nearly slipping and falling in the slush at my feet, then looked around and saw that snow was falling from the sky. Unfortunately, after leaving northern California a couple weeks ago due to excessive snow, birds had not yet arrived in Florence, OR, so we decided to sample the center of the hybrid zone some more while we wait for those slackers to arrive up north. We just finished up working at the South Slough reserve (which is a beautiful place!), and started working at New River, an “Area of Critical Environmental Concern”. After that, we will try again north in Florence, and then head to northern California for the inland transect. I’m not in a hurry to leave, as we’ve been lucky enough to have a research station and yurt all to ourselves. Through the first eight days, we caught a total of zero birds…however, in the last few days, we’ve caught 16, so things have gone pretty well overall! And today was the first day that was saw the sun for more than a few minutes, so things are headed in the right direction.


It’s always funny to watch people’s faces as they walk by while we’re working. A female hummingbird flying around in a cage, a weird dude with a microphone, and a strange trap set up at a feeder. Everybody always looks so confused. We catch wild females because they elicit courtship displays from a territorial male. We observe and record the male behavior with a shotgun microphone, catch the male, sample his DNA, and take a bunch of measurements to go alongside our behavioral data. Then, not only can we map out the hybrid zone and assess phenomena such as selection, but with enough samples, we can correlate specific components of courtship displays with the genes behind them, using recombination occurring in the hybrid zone. Recombination is when the genes of one species, say, Allen’s Hummingbird, and the genes of another, Rufous Hummingbird, recombine as a result of interbreeding (hybridization). As a result, their genetic material gets rearranged, and their hybrid offspring has a genome representative of both parent species. Thus, the hybrid might perform bits and pieces of courtship displays from each parent species, and with high enough sampling, we hope to correlate the portions of the genome that trigger certain components of courtship displays, namely the pendulum display in Allen’s Hummingbird.


Finally…we are in the center of the hybrid zone sampling, even though we have a lot of samples from here already. Why? Well, variation is the highest in the center of a hybrid zone, where there is the greatest interaction of parental phenotypes (physical expressions of traits). Thus, to try and account for all of the variation present, its important to sample the center of the zone as much as possible. Thanks for reading! I’ll try to update at least once a week from this point forward.


Wildlife thus far: not too much! Some garter snakes, tree frogs, Bald Eagle, and a Varied Thrush (life bird for me, and a really, really cool one!). My field assistant (Zach) saw a bobcat unsuccessfully ambush a squirrel…I wasn’t too happy I missed that.

And so it begins

Posted by Brian on March 14, 2018 at 1:20 AM Comments comments (0)

Hi everybody! I’m doing the same thing as last year, attempting to blog my experiences in the field at least once a week to keep in touch (and show that I’m still alive). This year, the first task on the agenda is to start (and finish) the inland transect in northern California along Bigfoot Highway. Now that the coastal transect is mapped out, it will be interesting to see whether selection acts in similar ways on the system inland as it does along the coast. After that, I will probably head north to Florence, OR for a week or so to see if any Allen’s-like characters/genes have poured into the range of Rufous Hummingbird, outside the hybrid zone…this is called introgression.


So, what is selection, and why it selection matter? Natural selection is a process in which species adapt to their environment based on their fitness, which is the ability to survive and reproduce, and contribute to the gene pool of future generations. When individuals with certain characteristics have greater fitness than other individuals in the population, they will tend to be most successful at passing on their genes over time, leading to evolutionary change. Selection allows us to understand how species evolve and adapt in the natural world.


I spent the day driving from San Diego to Davis, CA, where I am staying with collaborator Lisa Tell, who is a veterinarian working on hummingbirds. When I take blood samples, I usually take an extra blood sample for her, and she looks for hemoparasites, which are types of parasites living in the blood. She also does a lot of other interesting work on hummingbirds; for example, she just finished studying how different types of water (tap water versus deionized water) affect the bacteria found in sugar water at hummingbird feeders, and found that iron in tap water might contribute to bacterial growth, and promote an increase in the types of bacteria found in the water. Not too many people like talking about hummingbird research for hours on end, so it’s always fun to catch up with her!


Something I’m definitely excited about this year is a collaboration with photographer Keith Morey, who is going to help me try and capture high quality photos and videos of the hummingbird courtship displays that I’m studying. If you check the “videos” page here, I’ve shared some lower quality displays I’ve captured as well as some videos of how I capture my birds in the first place!

Back in San Diego!

Posted by Brian on May 26, 2017 at 4:15 PM Comments comments (0)

I recently just wrapped up a 75-day field season. I caught a total of 132 birds, making the last few months successful. I'll be slowly uploading pictures and videos from the trip in the coming days. Here's a breakdown of my travel by county: San Diego-Los Angeles-Santa Barbara-San Luis Obispo-Monterey-Mendocino-Humboldt-Del Norte-Curry, OR-Lane, OR-Coos, OR. That's eight counties along the California coast, and three more from southern to central Oregon.

Although I enjoyed my time out there, it feels great to be back home and sleep in my own bed. Also, I can finally put together all of my data and map out the hybrid zone! Plans for the summer include submitting a manuscript describing the Allen’s x Rufous Hummingbird hybrid zone for the first time to a scientific journal, presenting my research at the American Ornithological Society conference in Michigan, and beginning genetic work on all of my samples from the last several field seasons.

Highlights from the trip include some awesome wildlife sightings: Mountain Lion (although I never want to see one again), American Black Bear, Rubber Boa, a lot of garter snakes, Gopher Snake, Pileated Woodpecker, tree frogs, a few foxes, and some raccoons (including the one that jumped into the back of my vehicle and stole my tortilla chips). I also saw several instances of aggression between territorial males of hummingbirds, including a couple instances physical attacks (one bird flies into the other by repeatedly hitting him on the side). One time I even saw a female hummingbird attack a displaying male. Most of the time, females are simply looking for their next meal, and if they happen to be on a male’s territory while searching for that meal, the male sees it as an opportunity to mate. Pretty much every single time. Give them a break; during the breeding season, the testes of a male hummingbird can expand to become 10% of his body weight. Thanks for checking out my blog throughout the field season, and check back for more pictures and videos soon!


I've Got 99 Problems but a Bird Ain't One

Posted by Brian on May 12, 2017 at 5:20 PM Comments comments (0)

I’m in the homestretch! The transect is finished-it officially runs from Arcata, CA to Florence, OR, gradually shifting smoothly from an Allen’s-like phenotype in the south to a Rufous-like phenotype in the north. Over the next couple weeks, I’ll be posting a lot of pictures and a few videos that show what it is I’m doing out here-videos of how I catch birds and the data I gather. All of them were taken over the last few months. It’s been a successful trip, as I accomplished sampling for phylogeography and finished the coastal transect of the hybrid zone. Next year, the goal will be to find out how far it extends inland, as migratory Allen’s Hummingbird is a strictly coastal species in northern California and southern Oregon, with Rufous found both inland and along the coast throughout Oregon.

Here’s a summary of my travel over the last several weeks: it all started in Los Angeles County, shifted to Santa Barbara, then to San Luis Obispo, Monterey, Mendocino, Humboldt County, Del Norte County, southern Oregon, central Oregon, and will end either in Bandon, Oregon (in the center of the hybrid zone) or inland as I might search for some hybrid populations to get a head start on next year.

Most people know that a lot of birds migrate, but how do they do it? It’s pretty amazing to think something weighing three grams can fly thousands of miles over a short period of time, back and forth from Mexico as far north as Alaska and Canada, year in and year out, like the Rufous Hummingbird does. Although there might be some movement from year to year depending on mating success in the previous year and the presence of adequate resources, birds often return to the same population for the mating season, which is how populations, such as the hybrid hummingbird populations I’m studying, can be compared to each other at the genetic and phenotypic level. They don’t live there year-round, but migrate in and out of the area every year! Birds are able to use the stars, the sun, the Earth’s magnetic field, topography, and odor to figure out both how to find their mating grounds and how to return where they came from. Experiments have shown that, because sometimes information is complete or unavailable (such as overcast nights or an inability to detect the sun), birds can also get lost using other cues.

In a week or so, the cold temperatures and rainy weather will have to wait until next year to come around again, while I work on presenting and publishing all of this data. Thanks for checking in!

Oregon

Posted by Brian on May 5, 2017 at 2:15 AM Comments comments (0)

As of last Saturday, sampling in California has concluded for this year. I’ll be working along the southern Oregon coast for the next few weeks, I might head to central Oregon in the Florence area (where the hybrid zone ends, and pure Rufous Hummingbird populations begin), and end the field season. The weather has gotten a lot better; less rain, more sun, and highs in the high 50s, which sometimes feels like a heat wave. I saw my first bear of the season last week at Del Norte Coast Redwoods State Park in California; one of the few black bear that actually had black fur that I’ve seen.

Where I’m at now presents the largest unknown of the transect. The Siskiyou mountain range rises to about 6,000 feet in elevation really close to the coast, potentially keeping Rufous Hummingbirds from interbreeding or interfering with potentially pure Allen’s populations. However, thus far, the populations seem to be just as intermediate as the one in Crescent City, northern California. There seem to be two possibilities, which will (hopefully) be sorted out in the coming weeks: the hybrid zone is disjunct, meaning there is a transition from a Rufous-like to an Allen’s-like phenotype (a summary of overall physical characteristics) from Florence, Oregon, to Port Orford, Oregon, a stretch of about 40-50 miles where no hybrids (and possibly pure Allen’s) are found due to the presence of the Siskiyou mountains, and a recurrence of hybrids in northern California where that mountain range is no longer present. The other possibility is that the hybrid zone forms a fairly smooth cline, where there is an overall transition from a Rufous-like to an Allen’s-like phenotype from Florence, OR, straight to the Eureka, CA, area. As of now, the latter seems most likely. One thing is certain; the populations are sparse (or at least less accessible) in this area compared to anywhere else I’ve worked.

After a couple weeks of field work in my first year, two months of field work last year, and nearly three months of field work this year, I’ll have sampled over 200 birds. Over the course of my dissertation, I will probably have sampled in the neighborhood of 400 birds. Why so many? First off, the hybrid zone is a lot larger than any of us anticipated, and sample size will thus need to increase. Also, using a technique called admixture mapping, we’re going to try to find the genes responsible for the pendulum display in Allen’s Hummingbird using recombination that takes place in the hybrid zone. If you have pure Allen’s and pure Rufous interbreed, a hybrid’s genome will include the genetic makeup of both species. Because of this, only bits and pieces of the phenotypes expressed by a “pure parent” might be present, as is the case with the pendulum display. So, we’re looking to correlate the genomes of hybrid birds with the different elements of the pendulum display they perform, and determine how it might have evolved.

Sometimes territorial male hummingbirds I’m getting courtship data from will visit feeders as often as every five minutes. Hummingbirds feed about 14 times an hour because of their extremely high metabolic rates, so some of these guys are getting most of the nectar in their diet from my feeders! When a hummingbird consumes nectar, it fills its crop, which is a storage space for food in birds. Often an individual will perch somewhere for a short while following feeding. This is so the crop can empty and digest the food into its system. Once the crop is about half full, the bird will go feed again. When a bird doesn’t go to a feeder, it can seem impossible to catch it. That’s where mist nets can be useful. A few weeks ago, we built a mist net that has been working out well in catching target birds that won’t visit the feeders. When a bird flies into a mist net, it gets tangled in the net and is typically stuck until safely removed by somebody (with no harm done to the bird). Lots of pictures and videos to share when things start slowing down, including a video of myself and the lab tech at UCR (David) catching a bird using such a net.

Wildlife!

Posted by Brian on April 20, 2017 at 11:45 PM Comments comments (0)

The last couple weeks have been characterized by a raccoon that jumped into my car, some questionable deer, and elk herds walking nearby. Last Thursday I had to wake up super early, and I left the back hatch of the car open as I went to grab my tent. I walked back to the car, and a raccoon jumped out and left a trail of tortilla chips behind. Just before I left, he reappeared, and wouldn’t run when I approached him. I had to honk the horn to scare him off and get open the back of the car! At Prairie Creek Redwoods State Park, I was walking through a meadow, and as I approached the hummingbird I wanted to set up a feeder for, a couple deer popped up in the grass a few yards away. It startled me, but no big deal. I took another step forward, and a few more did the same, then I turned around, and there were more. Lots of fawns with their moms, so I got out quick. Today, I began work at a field site with a huge elk population. As I was getting recordings, I’d see them trying to get a feel for me from far away, and every hour or so one would run by for some reason. I kept imagining the entire herd running at full speed, trying to figure out if I’d be able to climb a tree in time to get out of the way, but remembered this isn’t The Lion King and I’d probably be okay. However, nearby I did see a herd of about 50 or so elk. Finally, I saw my first ever mountain lion, and it scared the hell out of me. I was walking on the roadside to get back to camp, and the sun had just set, and I thought I saw a deer a few yards away. It wasn’t a deer.

I finished up in Mendocino and arrived in Humboldt Sunday afternoon. There’s only been one day without rain in the last week, although things have still been pretty productive given the circumstances. A couple of my field sites are in redwood forest, which has been awesome to work in. I’ve even been able to work in a closed campground surrounded by redwoods. Northern California is beautiful-endless redwoods, pine trees, ocean, wetlands, etc. I’m grateful to have met CJ Ralph, a legend up here who runs a banding station on his property and contributes a lot to ornithological research.

As far as hummingbirds go, it looks like the hybrid zone extends at least as far south as Arcata, CA, which is much further south than initially expected. The next few weeks of sampling should paint a complete picture of my coastal transect, which will allow me to study phenomenon such as sexual versus natural selection, which characters might be most important in divergence between Allen’s and Rufous Hummingbird, and the role of the environment in their evolution. If a species winds up needing protection, how can you protect it if unsure about the climate, resources, and it’s evolutionary history?

Six weeks down with a few more to go! 

In Mendocino County now; Humboldt is up next

Posted by Brian on April 6, 2017 at 10:15 PM Comments comments (0)

When it rains in southern California, it usually stops after a short while. When it rains in Mendocino, it doesn’t seem to have an end. At least there’s time for an update! I’ve traveled from San Diego, to Los Angeles, Santa Barbara, San Luis Obispo, Monterey, and now Mendocino. Next up (hopefully by the end of the weekend!) will be Humboldt County. It’s beautiful out here. Freezing, but beautiful. Tons of pine trees, dense forest, and riparian areas to aid the transition from forest to ocean. Also, I can’t forget the invasive Himalayan Blackberry (Rubus armeniacus) and it’s painful thorns. However, the hummingbirds love it. The campground I’ve been staying in at MacKerricher State Park, is my favorite of the trip. Towering pine trees, lots of separation between campsites, the sound of the ocean, peace and quiet after dark, and rain pattering the tent throughout the night. Nothing better than that.

I'm pretty excited to get into Humboldt County, because earlier in the year I made a model based on rainfall and temperature data predicting the hybrid zone would begin there. It has consistently aligned with the localities and divisions of the hybrid zone I've sampled thus far (divisions include pure Rufous Hummingbird populations, Rufous-like hybrids, 50/50, Allen's-like hybrids, and pure Allen's Hummingbird populations), so I am hopeful. Humboldt County would comprise the beginning of the Allen's-like part of the hybrid zone. If so, it might highlight the relationship between the climate and these two species, the types of habitats they are able to hybridize in, and the habitats and conditions they are dependent upon. Basically, Rufous Hummingbird requires wetter, colder, habitat than Allen's Hummingbird.

Rufous Hummingbird are still migrating, and they often make things very confusing when I’m trying to track and capture breeding Allen’s Hummingbird. Outside of courtship behavior, it’s very difficult to tell the two species apart. Often (but not always), the back of Rufous Hummingbird males is relatively close to being 100% orange in color, while the back color of Allen’s Hummingbird males is usually 60-100% green. Other than that, unless you have a bird in your hand, or they are performing courtship displays, good luck telling them apart. Females are even more difficult to differentiate, and have to be “in the hand”. There are a lot of Rufous passing through here, and several of them are displaying, which might seem strange considering they haven’t yet arrived at their breeding grounds. They just have a little trouble holding in their…excitement. This morning I watched a male Rufous Hummingbird perform a really long shuttle display (which is a close quarters courtship display that can also be used as a form of aggression) to a White-crowned Sparrow (Zonotrichia leucophrys) who was probably a little puzzled.

How often do you think a hummingbird beats it’s wings per second? Some can beat their wings well beyond 50 times in a second! Everyone knows they’re exceptional performers in flight with the ability to hover, but they can also fly backwards with ease (watch a video here). Did you know the Ruby-throated Hummingbird (Archilochus colubris), found in the eastern United States, has a metabolic rate nearly 100 times that of an elephant? If you have a feeder up at home, you might notice the same hummingbird visit several times a day, and probably even more often than you think. This is because of their high metabolic rates and the fact that they burn so many calories so quickly. Some hummingbirds consume up to three times their bodyweight in nectar and insects per day!

That's all I've got for now. See you all soon!


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