Category: Genetics - My Life is Crap

I love working at a zoo!

9/10/2019

I have moved on from being a graduate student. Although I don't graduate until December, I have started a new position as a post doctoral scientist of conservation genetics at the Center for Conservation Research (CCR) at Omaha's Henry Doorly Zoo & Aquarium (OHDZA)! I will be working mostly on projects on lemurs and other species from Madagascar, throwing in the occasional elephant and big cat project to keep myself associated with main land Africa. I'm still settling in but it won't be too difficult a transition when I can see orangutans out the lab window and I get to take a daily safari walk to see all my favorite animals.

It will take only 15 minutes for me to get to these nuggets (born May 22nd) being introduced to the public today!

I, personally, don't get to do any snow leopard work but OHDZA is a dedicated member of the Snow Leopard Species Survival Plan (SSP), a program that works to maintain a genetically stable assurance population of Snow leopards in zoos. Our neighbors in the CCR in nutrition and reproductive physiology do research on these floofs to improve care and management around the world.

Being so close to the action I'll hopefully be able to get the inside scoop (like I did with the Indian rhino. The repro team showed us the birth video only hours after it happened!) and you know I'll be making regular visits to their enclosure to bask in the tail poof glory. I'd have to pass by sloth bears and tigers on the way there too. Darn.

It's getting crowded in here!

5/19/2016

Today I start my first stab at crowdfunding. My dissertation project has been selected to be a project in the Cat Challenge on the crowdfunding site Experiment.com. This site is different than most other crowdfunding sites in that it is strictly for research and all projects are vetted by a panel of professionals before being launched. On general crowdfunding sites, anyone can start a campaign so, really, anyone can claim they're doing research. On Experiment.com, every project is rigorously reviewed, provided feedback, and scientifically approved so you know, as a financial backer, you can be confident you are funding real research. And through their website, us researchers are able to easily keep our backers up to date on the progress of our research.

My profile can be found at Experiment.com/liondiversity
(Make sure to watch my promo video. It took me about 24 hours to write, research, film and edit!)

The Challenge is 2-fold:

Raise the full value of my GOAL by
getting lots of BACKERS (people like you) to support my research

The project with the most BACKERS will receive an extra $1,000 added to their GOAL.
Our GOAL is $5,000 and we must receive 100% of our GOAL to get any of the money donated by the BACKERS.

PLEASE HELP!

Go to Experiment.com/liondiversity and show some support by making a donation. Any little bit helps! The more people who make donations the better. You can also help by spreading the word.

The Challenge (# of BACKERS) runs from today to Friday, June 10 @ 6PM ET
The Campaign (100% of GOAL) runs from today to Saturday, June 18

Your support is much appreciated! THANKS!!!

A Lion Decision's Been Made

1/22/2016

If you haven’t heard yet, U.S. Fish and Wildlife Services (USFWS) has made a ruling to list the lion as two subspecies under the Endangered Species Act (ESA). Effective today, under the ESA (this is an important distinction), the lion will now be Panthera leo leo and Panthera leo melanchaita.

Panthera leo leo are the western and central populations of African lion and the Asiatic lion. These populations have approx. 1,400 lions with about 900 in 14 African populations and 523 in India. These populations have seen the most dramatic declines. USFWS claims newly available scientific information make these populations more genetically related and due to the severity of the threats to these populations, have decided to list them all as one subspecies which meet the definition of endangered under the ESA.

IUCN still recognizes Panthera leo leo as being all African lions

Panthera leo melanchaita, which consists of the rest of the populations in East and Southern Africa, however, is not listed as endangered. They claim this population consists of 17,000-19,000 lions (but this estimation comes from a study that acknowledges that their estimates are “intrinsically imprecise” and previous estimations range from 23,000-39,000 so the exact number is still a bit hazy). USFWS says “this subspecies is less vulnerable and is not currently in danger of extinction.”

Panthera leo melanchaita was previously considered to be the now extinct Cape Lion, which has also been proven not to be a genetically distinct subspecies but rather a difference in weather induced morphology.

The ruling also includes some new regulations on hunting permit requirements. Anyone convicted of or who has pled guilty to violations of wildlife laws will be denied a permit. They will also only allow the importation of sport-hunted trophies from countries with established conservation programs and well-managed lion populations to help support and strengthen the accountability of conservation programs in other nations.

This ruling seems fair but their use of previously and currently used subspecies names may get a little convoluted in the overall scheme of things. It seems as though USFWS is showing a genuine concern in looking after the best interest of the African lion but I think more research is still needed (and not just because I’m one of the ones doing it) to make decisions that will be beneficial for both the lions and the countries they live in.

I'm a Published Author!

12/16/2015

The manuscript I have been working so hard on for most of the year has finally been published!

My first publication, Mitochondrial Haplotype Diversity in Zambian Lions: Bridging a Gap in the Biogeography of an Iconic Species, was made live today, December 16th, 2015! I am now officially a published author!

Table 4. Molecular diversity indices and nucleotide composition.

The paper is about matrelineal gene flow and genetic diversity of lions in Zambia. We found that lions in Zambia have a high level of diversity but can be separated into two sub-populations with little to no matrelineal gene flow between the two. The separation could be historical but it more likely due to an expanse of cities and roads that inhibit modern day dispersal because, when put in context with the entire range of the African lion, Zambia acts as a bridge connecting Southern and Eastern lion populations. This is all based on analysis of mitochondrial genes and the discovery of 5 sets of DNA variations (haplotypes) thus far not seen anywhere else in Africa.

Fig 1. Map of Zambia showing the five main areas sampled: LV (Luangwa Valley); CO (Corridor); ZA (Lower Zambezi); KF (Kafue); and SI (Sioma Ngwezi).
Eastern region consists of LV, CO and ZA. Western region consists of KF and SI. More detailed location information for each sample is available in S1 Table.

Fig 2. Geographic location of lion samples and phylogenetic relationship of 12S-16S.
(A) Range-wide map of lions sampled. Circles indicate geographic locations for populations determined by Antunes et al. [13]. Zambia is denoted by a square. All locations aside from ZAM (Zambia) were established by Antunes et al. 2009: UGA (Uganda); KEN (Kenya); SER (Serengeti National Park, Tanzania); NGC (Ngorongoro Crater, Tanzania); KRU (Kruger National Park, South Africa); BOT-I (Southern Botswana and Kalahari, South Africa); BOT-II (Northern Botswana); NAM (Namibia); GIR (Gir Forest, India); ANG (Angola); ZBW (Zimbabwe); and MOR (Morocco). (B) Bayesian analysis with posterior probability values on the nodes. H1-H12 are haplotypes that were described by Antunes et al. 2009 and Z1-Z5 are novel haplotypes so far only found within Zambia.

Here's my official citation:

Curry CJ, White PA, Derr JN (2015) Mitochondrial Haplotype Diversity in Zambian Lions: Bridging a Gap in the Biogeography of an Iconic Species. PLoS ONE 10(12): e0143827. doi:10.1371/journal.pone.0143827

I am currently working on a press release for this paper and I have already started writing my next publication, hopefully with two others soon to follow after that. My goal is that by the time I finish my PhD I will have at least 5 publications. Let the fun begin!

Cheetah Genome Published!

12/10/2015

Big news on the cheetah front... CCF, in partnership with St. Petersburg State University, Russia and Bejing Genome Institute-Shenzhen in China has published a detailed analysis of the cheetah genome! The paper was published yesterday in Genome Biology.

“Sequencing the cheetah genome illuminates our understanding of this species’ evolutionary past and aids us in efforts to sustain and increase cheetah populations in their present and former range. By understanding the history of the cheetah’s migration, its population bottlenecks and lack of genetic diversity, scientists and conservationists can work together to develop informed strategies to protect the species.”

For the study, the genomes of six cheetahs were sequenced, including that of the lovable Chewbaaka (RIP). Results of the study uncovered information about the species' population bottleneck which resulted in the near identical genomes of present day cheetahs. Inbreeding, some of which occurred as long as 100,000 years ago, resulted in physiological and reproductive impairment in the species that is still evident today. They were also able to look at the migration of the cheetah from it's origin in North America (that's right people, cheetahs used to roam the Great Plains) to their present range throughout Africa and some in Iran.

Me with Chewbaaka, who is now part of the Genome Legacy!

That's your beef...

7/13/2015

Along with the ever so important work of its graduate students, the Derr lab is also a core lab providing sequencing services and a service lab which provides bovid DNA testing. And a few months ago, those services were put to the test when the Derr lab took part in some investigative reporting being done by a South Carolina news station involving some bison meat that was suspected to be falsely labeled. Floyd, our trusty lab manager & sequencing master, sequenced some meat for the news station which they obtained and sent to us from the vendor to test what kind of bovid the steaks being sold were. Turns out... they were just your basic beef from cattle, not bison! Busted!!! Check out the story below.

WBTV 3 News, Weather, Sports, and Traffic for Charlotte, NC

Test results show shoppers not getting what they paid for at local butcher shop

Click "Read More" to read the full article from WBTV - CHARLOTTE, NC

Reintroduction of Lions to Rwanda

6/29/2015

Lions went extinct in Rwanda 15 years ago after the 1994 genocide when the Akagera National Park went unmanaged and cattle herders poisoned many of the animal species. And this week, in a big conservation effort, seven lions, 5 females and 2 males, are being relocated from the South African province of KwaZulu Natal to repopulate Rwanda with lions. They are starting their journey from OR Tambo International Airport in Johannesburg to Rwanda today!

But are South African lions the best option for reintroduction to this area? Rwanda is part of eastern Africa, adjacent to Tanzania and closely residing to Kenya, one of the largest populations of lions in Africa.

This new Rwandan population is already going to have to deal with potential issues with inbreeding from the small size of its starting population and being isolated from its neighboring lion populations. But other issues could arise if/when the population is no longer isolated if the founding population is from the wrong stock.

There has been enough research done on lions to have determined that eastern and southern lions cluster separately phylogenetically, meaning they have enough genetic differences to show there is some sort of structure amongst them. There hasn’t been enough research, however, to determine if there are enough genetic differences to differentiate between the two entities, or if we can split them into what some people might refer to as subspecies. Part of the research I am conducting is to further establish whether lions can be classified as regionally distinct, or subspecies, and if translocating southern African lions into eastern African lion territories, and vice versa, would be detrimental or beneficial to the population.

Reintroduction through Translocation

beneficial if not subspecies – creates greater genetic diversity & increases adaptive abilities
detrimental if subspecies – can reduce fitness & decrease adaptive abilities (outbreeding depression)

Red: The lions' translocation route from South Africa to Rwanda
Green: Tanzania and Kenya

Part of the reason I want to look at the historic genetics and compare it to the modern is to determine if there is a recent or evolutionary background for regional markers. All the anthropogenic effects of the past 100 years could have had a lot of impact on the genetics of lions across the continent and we don't know in which direction, creating or destroying rationality. Hopefully more research and larger sample sizes (like it my study) will help answer these questions.

They say these animals were "selected based on future reproductive potential and their ability to contribute to social cohesion". They may have chosen lions originating so far from Rwanda because with translocations there is the issue of the animals trying to get back to their home but I still wonder why they didn't use lions from Tanzania or Kenya. Lions native to Rwanda probably would have been more closely related to them, cost of transport probably would have been less... I wonder what kind of politics I don't know about it behind this as well...

Update:
7/1/2015 - While doing a bit more research combing through article after article reading the same shpeal over and over I finally found something that somewhat confirmed my suspicion but with no real concrete evidence... there is political mumbo jumbo afoot....

The Christian Science Monitor (um, the what?) says that Kenya offered to donate eight lions to Rwanda last year but Kenya's wildlife conservation groups fiercely opposed the plan saying "Rwanda had not sufficiently addressed issues that resulted to the loss of its own lion population."

Off the List

6/26/2015

The eastern cougar, Puma concolor couguar, is officially being removed from the endangered species list. It is being declared extinct since an eastern cougar has not been seen since 1938. The decision is based on an extensive review by the US Fish and Wildlife Services which included "the best available scientific and historic information [which we now know from my lion research isn't the best scientific and historic information, just the best available of the resources accessible to us lowly wildlife researchers], queried 21 states and eastern Canadian provinces, and reviewed hundreds of reports from the public." It's not that there haven't been any cougars seen, it's just that they claim that any cougars seen in the east in the past 77 years are a result of dispersing animals from western populations or animals that have been released or escaped from captivity. These claims come from more than 100 reports dating back to 1900.

There isn't much genetic research on the puma (FYI: puma, cougar, mountain lion, catamount, panther... all the same thing, just depends on where you are and who you talk to). The scientific community seems to be quite torn about taxonomic assessment and there has been much debate around subspecies distinction, particularly in the case of using cougars in Texas to repopulate the Florida panther population. Some say they are distinct enough that they shouldn't be hybridized while others say they are the same so one can successfully repopulate the other. According to the Federal Register, "the best available information continues to support the assignment of the eastern taxon to Puma concolor couguar as distinct from other North American subspecies" based primarily on biology and life history.

The proposal to remove the eastern cougar from the endangered species list does not affect the status of the endangered Florida panther subspecies, a cluster of conservation genetics issues to discuss in more detail at another time. But, although the extinct animals will no longer be protected under the Endangered Species Act, which is intended to save animals and plants that still have a recorded population, it will also no longer be able to be used to protect similar animals, such as the Florida panther. Not sure if that matters since the Florida panther is already protected (and possibly diluted with Texas cougar) but its interesting nonetheless.

I Like Big Mutts

4/17/2015

Crazy but true! A hilarious and informative expose on dog "breeds". I am rather fond of my mutt but I was also rather fond of my pure breeds - although Leah, Golden Retriever, did get cancer and Tucker, Australian Shepherd, had mental issues.

Throwback Third Thursday - April 2015 (sorry it's late)

4/17/2015

This month's Throwback Third Thursday (#tbtt) is a day late (so I guess its actually a Flashback Friday) and only looks back one day but for good reason: I didn't have time! The past few days I have been busy with the Genetics Graduate Student Association (GGSA) Spring Symposium featuring keynote speakers Dr. Bruce Budowle and Dr. Jeffrey Bennetzen. As Vice-President of GGSA, I was in charge of planning the event and it went GREAT! Our only criticism was there wasn't enough time for poster judging (but that was more of a venue availability problem than anything else). And what I am most grateful for, there was a good number of people who were incredibly helpful with set up and clean up. Amazing!

Our speakers were INCREDIBLE! Dr. Jeffrey Bennetzen, University of Georgia, and Dr. Bruce Budowle, University of North Texas and a member of my graduate committee, couldn't be further apart on the genomics spectrum but their charisma and impeccable story telling abilities made for a very entertaining and educational evening for all. We learned about applied genomics in plant breeding and forensics, respectively, from world-renowned, highly sought after scientists who are experts in their fields. We were incredibly fortunate to have gotten two such wonderful speakers to agree to speak at our little symposium!

Dr. Bruce Budowle

Dr. Jeffrey Bennetzen

A Little Rarity

3/2/2015

A white lion cub, a very rare color morph, has been causing quite a stir amongst visitors a Kruger National Park in the Republic of South Africa (mostly because he's so darn cute). This little rarity is a member of the Satara Pride and is one of only 13 wild white lions. White lions are so rare that none were seen in the wild from the early 1990's until 2006. And since 2006, only 16 white lions have been born and in only 5 lion prides, all in the Kruger/Timbavati region.

Why are they so rare?

White lions are a result of leucism, or lack of pigment which results in light coat and eyes. In lions, leucism is caused by getting a copy of a gene which has a recessive mutation from both mom and dad. For two tawny lions (the typical brown/tan color) to have a white lion cub, both lions would have to be carriers of the recessive allele, meaning they have the recessive copy but they display the dominant one.

Where did all the white lions go for 13 years?

If we think of this as a simple Mendelian trait, when a carrier mates with a carrier they have a 25% chance of creating a white cub and a 50% chance of creating more carriers. When a carrier mates with a full tawny they have a 50% chance of carriers. So, for 13 years, the recessive allele was 'hiding.' Because the white lion didn't disappear completely, this means that the carriers either weren't breeding with other carriers or when they did, neither of them passed along the recessive allele to the same cub (the other 75%).

It is quite possible that the statistics are way more complicated and that there may even be more than one way to be 'white.' It has been speculated that light coat in white lions with yellow eyes may we caused by a different gene than in white lions with blue eyes (the TYR gene versus a gene similar to what creates white cats and white tigers). Genomic analysis of big cats is just beginning but don't you worry, we're getting to the bottom of it!

On Top of the World!

1/29/2015

2015 is turning out to be a pretty good year! I just got back from a long day at the College of Veterinary Medicine Graduate Student and Postdoctoral Symposium where I presented a poster on my preliminary results of the diversity and distribution of lions in Zambia and was the winner (that’s 1st place) for the graduate student poster presentations!!!!

As a graduate student, there will be times when you feel like a fraud. In an interdisciplinary program and a member of the college of veterinary medicine I am often surrounded by microbiologists, biochemists and veterinarians who’s use of medical jargon and super cellular hoopla puts my macro-brain into a tailspin. Today was such a day. I read many posters and listened to even more talks which exceeded my veterinary knowledge. So, I didn't think I was in the running to win an award. But, rather than let it get the best of me, I stayed for the entire symposium, listened and tried to broaden my scope.

I was literally shocked when I won and I feel incredibly honored. What I forget is how different my field, conservation genetics, is than medical based science. To others, my poster may have been just as confusing as fibroblastomas and hepatic lipidosis is to me. I was never really sure how my work compared and I sometimes worried my work wouldn't come across as being as impressive as others. This win was the confidence booster I needed to help me along and I am now SO ready to keep this streak going! Next… Big funding.

2015 CVM-GSA/PDA Poster and Platform Presentation Award Winners

New Year, New Endeavors (sort of)

1/9/2015

Tomorrow I am attending the International Plant and Animal Genome Conference XXIII (fondly referred to as PAG by those attending). And it's not only exciting because it's my first big conference and I will be there with a bunch of wonderful people from the Genetics program at Texas A&M but it is in San Diego and I am presenting my first graduate level poster! People are going to get their first official look at my research then I get to go home to mom and dad when I'm done. It's like the 1997 Greater San Diego Science & Engineering Fair all over again but instead of "The Color Attraction of Mice" I will be presenting on African lions in "Genetics and Genomics: Powerful Tools for Wildlife Conservation" (Oh how times have changed). It's a brand new year and I am starting it off with a bang. This poster represents the next big stage of my graduate career and the beginning of what I know is going to be a successful year. I am finished with my classes so now I can really focus on my research, prelims and making sure I don't get sick while doing it. I can't wait!

The Park is (almost) Open....

11/25/2014

My level of excitement cannot be measured by conventional means....

Genetic modification along with their recurring theme of de-extinction.... CAN'T WAIT!

Threatened

11/3/2014

Some interesting news on the African lion front.... On October 27, 2014, the US Fish and Wildlife Service (USFWS) proposed listing the lion as “threatened” under the Endangered Species Act – a similar listing to the current International Union of Conservation of Nature (IUCN) listing of “vulnerable”. The curious thing is that, for the most part, both sides, the activists and the hunting community, are considering this to be a win. The activists get some regulation but the hunters don’t get so much that they're banned. It will be interesting to see how it will all play out in the long run.

What being “threatened” means:

The lion is not “on the brink of extinction.”
It is “likely to become endangered in the foreseeable future.”
USFWS “will establish a permitting mechanism to allow importation of sport-hunted African lion trophies into the United States provided that they are established as originating from countries with a scientifically sound management plan for the African lion.”

A little background:
A couple years ago some organizations (primarily of the “animal rights” persuasion) submitted a petition to USFWS and the IUCN demanding the African lion to be listed as an endangered species. Their reasoning is based on a perceived decline in census size and an association that all hunting is the horrific practice of canned lion hunting, which it is not. In fact, with this decision USFWS said lion hunting is “not… a threat to the species at this time.”

Prior to this decision the lion wasn’t listed under the USFWS Endangered Species Act at all; meaning, there were no US government mandated regulations for the species. Interestingly enough, however, USFWS recognizes African lion sub-species, a designation debated by many scientists and policy makers (especially since the discovery that the distinguishable fluffy mane of the Cape lion, thought to be an extinct sub-species, is simply a morphological result of colder weather, i.e. any lion can become a fluffy Cape lion if it’s chilly). Over the years, scientists have given 23 different scientific names to the African lion. Currently the IUCN Red List recognizes only the African and Asiatic sub-species while the Catalog of Life recognizes eleven sub-species (listed below) and USFWS recognizes four. According to the USFWS website, the new “threatened” designation only applies to Panthera leo ssp. leo. Panthera leo persica, the Asiatic lion, has been “endangered” since 1970 but Panthera leo ssp. melanochaita and Panthera leo ssp senegalensis remain “not listed”. Panthera leo ssp. leo is considered to be all lions on the African continent by IUCN but is considered to be the extinct North African Barbary lion in other circles. In the case of USFWS, it could be that Panthera leo ssp. leo is simply a new distinction which will encompass all African lions, as it does for IUCN, and they just haven’t removed Panthera leo ssp. melanochaita and Panthera leo ssp senegalensis from their list yet. Either way, some kind of agreement across organizations needs to happen if we think any kind of international/interorganization regulation is going to happen.

Last week’s USFWS decision was based on what they claim to be “the best available science.” The very reason I am conducting my dissertation research is because the information available is, as you can see, quite inconsistent and inconsistent information compromises conservation decisions, some of which could have a profound impact on both the long-term security of the species as well as the African economy. There is very little genetic information available and genetic information is what is needed to provide some much needed population driven guidance.

Some Recognized Sub-species of Lion:

azandica – Congo lion: Northeast Congo
bleyenberghi – Katanga Lion: Southwest Africa (Namibia to Democratic Republic of the Congo to Zambia)
hollisteri – synonym for nubica
kamptzi – synonym for senegalensis
krugeri – Transvaal Lion: Southeastern Africa (South Africa)
leo – Barbary lion: North Africa (Morocco to Egypt)
massaica – synonym for nubica
melanochaita – Cape lion: Republic of South Africa only
nubica – Masai lion: East Africa (Ethiopia to Mozambique)
nyanzae – synonym for nubica
senegalensis – West African (Senegal to Central African Republic)
persica – Asiatic lion: India