Showing posts with label DNA. Show all posts
Showing posts with label DNA. Show all posts

Monday, November 16, 2015

Where is south? Uncovering bird migration routes

Guest post by John Viengkone, currently enrolled in the Professional Masters of Environmental Science program at the University of Toronto-Scarborough
Wilson’s Warbler
There are approximately 450 native migrating bird species that for at least part of the year reside in Canada, but where do they go when they aren’t in the True North Strong and Free? If you ask just about anyone, they’ll tell you that birds fly south for the winter, but where exactly is south? South could be as close as the next city, the USA or as far as Tierra Del Fuego. Also do they make stops on their way to this “south” and do they mix with other populations? The truth is there isn’t much information on where many migrating species go or the route they take to get there.

But why should we care where they go when they leave Canada, they seem to always come back in the spring. The truth is not all birds are coming back, there has been a marked decline in the population size of many migrating neotropical bird species. As the leading cause of species loss, humans need to figure out whether these bird populations are facing stressors in their breeding, wintering, stopover range or some combination of the three so we can help manage them. The first step in doing this is learning the birds’ migration route. 

The effort to understand the movement patterns of birds began in North America during the 1800s when the famous ornithologist John James Audubon started tying silver string to the legs of eastern phoebes, Sayornis phoebe, to see if individuals that left in the fall returned in the spring. Of all the birds Audubon marked, 2 returned in the spring. This little experiment transformed into the bird banding/ringing program we know today with different coloured metal bands replacing the pieces of silver string.

Though the bird banding program has been essential to the understanding of bird ecology, life history and migration it is has one major flaw. This flaw is that banded birds must be spotted again and it’s estimated that only 1 in 10,000 banded birds are recaptured, leaving a large data gap. So why use bands, why not use GPS tracking devices? Well, they do for larger birds but for many bird species the size and weight of a tracker is too much of stress so a better solution is needed. This solution is up and coming from Dr. Kristen Ruegg’s lab at UCLA and it has been dubbed The Bird Genoscape Project.

Ruegg and company have taken on the task of creating a protocol that will allow them to identify where a migrating bird has come from by using just a feather. To get a full comprehensive understanding of this protocol please refer to Ruegg et al. 2014 but I’ll briefly explain their methods here: Variation in DNA is what makes individuals unique but a huge portion of an organism is actually shared with the individuals of the same species. As groups or populations of a species become more isolated and breed with other individuals in their populations more, the populations start to diverge, this is population differentiation. Individuals in a breeding population will be more similar to each other than to other populations.

The UCLA team used the concept of population differentiation to find the small bits of DNA, called single nucleotide polymorphisms (SNPs), that are unique to each breeding population, a genetic fingerprint some might say. For their study they looked at the Wilson’s warbler, Cardellina pusilla, taking small blood samples from individuals in each breeding population and each population’s genetic fingerprint was made.

With a genetic fingerprint for each breeding population Dr. Ruegg and her collaborators were able to collect feathers from Wilson’s warblers across North America and identify where it came from with an 80-100% success rate. So a feather collected in Colorado in the late fall could be traced back to the British Columbia breeding population, meaning Colorado is a stop off point. This solves the major problem that banding had; you don’t need to come in contact with the same bird to get information, any bird in the species will work. 

From Ruegg et al. 2014. Each colour depicts a breeding population, arrows are stopovers and circles are wintering grounds
An interesting finding from UCLA’s study was that there are 6 breeding populations of Wilson’s warblers opposed to the 2-3 that biologist previously thought and that 3 of the breeding populations actually share a wintering ground and flight path. Two of these three breeding populations are stable but one population is declining, suggesting the cause of decline stems from the declining population’s breeding ground. If the issue stemmed from the wintering ground of the flight path, the other populations should be affected too.

So what’s next? Ecological managers now know where the issue is likely originating from for the Wilson’s warbler but still need to identify the root cause. As for The Bird Genoscape Project, Dr. Ruegg has moved on to repeating this study with the American Kestrel. There is also work being done with museum samples to see if ranges and flight paths have shifted with time. It’s looking like The Bird Genoscape Project can only get bigger, spreading to more migrating bird species and become an essential tool for bird conservation just as bird banding did in the past.

For more information see:
Ruegg K.C., Anderson E.C., Paxton K.L., Apkenas V., Lao S., Siegel R.B., Desante D.F., Moore F., and Smith T.B. 2014. Mapping migration in a songbird using high-resolution genetic markers. Molecular Ecology 23:5726-5739.
Kristen’s interview with Podcast Eye’s on Conservation is available on iTunes

Thursday, January 7, 2010

Double or nothing

As I finished my undergrad career and started thinking about graduate school, I was totally infatuated with the chromosomal speciation of treefrogs in the genus Hyla. Hyla versicolor and H. chrysoscelis, the 'gray treefrogs', have similar geographic distributions and look almost identical - except that one is a tetraploid version of the other. The increase in genome size is associated with a slight increase in cell size, which has trickle-down effects into physiology, the sound of their call, and other ecological factors, and of course they are reproductively isolated. As it turns out, Margaret Ptacek and colleagues were unraveling this mystery at the genetic level just as I was learning of it, and while I was disappointed not to be able to explore this for my graduate work, Margaret made up for it by paying for all the drinks when I visited Clemson a few years back.

So it was with considerable interest that I stumbled across one of the first tables of contents of the new year, in BMC Evolutionary Biology. Two co-occurring populations of the diatom Ditylum brightwellii, it turns out, differ in genome size. In this case, the belief is that there is a single taxonomic species harboring a very recent genome duplication polymorphism (which are likely cryptic species). Of course, a species by any other name... well, that's the problem isn't it? In the world of diatoms, according to Koester and colleagues, the 'barcode' standard is to use the 18S rDNA gene sequences and silica cell wall morphology in diagnosing species. However, already armed with evidence that two substantially distinct populations could be identified with the more rapidly-evolving ITS gene region, these researchers explored how differences in reproductive rates and size distributions might be associated with genome size.

See, diatoms are the petri dishes of the natural world. In order to reproduce, each side of the interlocking silica case separates and generates a new nested case. One of the offspring of this fission will be the same size as the parental individual, the other will be slightly smaller - the smaller of the two original cell walls, with an even smaller one nested within. At least that is how I understand it. Over time, these clonal lineages reduce substantially in size, and cell size is eventually limited by genome size; sexual reproduction then allows them to regain a larger cell size and the process repeats. So, the life history of this species requires an interesting interaction among the genome (which places a lower bound on cell size, and a lower bound on reproductive rate) and the population.

In Ditylum, Koester et al. were able to show that there are not only two very distinct genetic lineages, but that the one that is regionally localized to Puget Sound appears to have been generated through genome duplication. That is, there is a cosmopolitan species, and an offshoot lineage that was formed through some form of genome duplication, with concomitant changes in cell size, rates of population growth, and reproductive isolation. Koester et al. conclude that these lineages are cryptic species, and that this form of isolation may be common in marine diatoms.

More generally, this shows another way in which our understanding of biodiversity is changing rapidly thanks to molecular diversity analysis. The latest term to be coined by John Avise, biodiversity genetics, reflects the fact that we must now consider all of the new ways in which this technology can accelerate the rate of discovery in our natural world. Taxonomists trained in the morphology and phenotypic diversity of life are few; certainly too few to keep up with growing scientific collections, and the bottleneck in describing species can be a difficult one for management and conservation. The '18S or bust' approach in diatoms may be one standard that will change as more studies like this one, out of Armbrust's lab at Washington, illuminate how dynamic biological diversity can be.

Sunday, November 22, 2009

Something fishy

Of the many victories wrought by DNA barcoding - the ability to place an unknown sample in a phylogenetic, and often taxonomic, context using short fragments of DNA sequence data - some of the most useful applications for management have come from the sea. One of the best citation-to-data ratios in this regard belongs to a 2004 study by Peter Marko. This project extended naturally from Marko's molecular ecology course: students purchased samples of "red snapper" from various fish markets, and sequence data from the mitochondrial cytochrome b gene region showed that most of these specimens were not, in fact, Lutjanus campechinus - they were often understudied and probably rare relatives, or in some cases not snapper at all. The conservation implications from this study were huge, and a number of papers have followed suit, looking at a variety of similar systems. If you aren't interested in adding to your list of papers to read, check out the short film based on work done in Steve Palumbi's lab that documents their work to identify shark fins.

In a paper by Lowenstein et al., published last week in PLoS ONE, the focus was on sushi, specifically tuna. The common labeling errors were caught again: there were mismatches between what restaurants called the fish, and what was actually being offered. In some cases, very phylo-distant species are being sold as "tuna", and these species can actually make consumers ill. The story is an interesting one of how fraud develops in samples of organisms that can no longer be visually tied to the species they came from, and the difficulties in protecting consumers from fraud under current regulations. Obviously, the perils of overfishing are becoming quite clear and interested readers should carry their Monterey Bay Aquarium seafood guides or similar (there's even an iPhone app for that!) with them before ordering at restaurants.

A particularly interesting advance in this study was taking the barcoding approach beyond the visual appeal of tree-building and similarity with databased sequence data. One concern about barcoding has been that even when a new clade appears in a phylogeny, taxonomy cannot be updated without some sort of diagnostic characters. It is uncommon for new species (especially of animals) to be described based on DNA sequence data alone, but it is nevertheless the norm to define the character states that uniquely define a species from its relatives. In Lowenstein et al.'s paper, they identified 14 diagnostic DNA substitutions that could be used to uniquely identify all species of Thunnus and suggested that focusing on particular characters within the "barcode gene" (mitochondrial cytochrome oxidase I) will also be necessary for new technologies to accelerate in-the-field identification.

This latter step is of interest for anybody interested in cryptic species, or identifications when other reference material is not available. I hassled one of my former Ph.D. students endlessly as she revised her dissertation because we had been comfortably using a phylogenetic tree to assign unknown individuals to one of three cryptic taxa (in the isopod genus Idotea), but prior to publication we knew that diagnostic characters would be necessary for subsequent work to be readily comparable. And, since the undergraduate evolution lab at the University of Georgia repeats Marko's work on red snapper every few years (the local Kroger now knows not to advertise their special on "red snapper from Indonesia"), perhaps the lab can be extended by having the students generate these characters for the genus Lutjanus as well. I don't seem to have any problem convincing students to do their homework when it involves going out for sushi.