The KU Biodiversity Institute is hiring a postdoctoral researcher in comparative phylogenomics of Philippine amphibians and reptiles.
The successful candidate will conduct scientific analyses focused on comparative phylogenomics of diversification in co-distributed land vertebrates of the Philippine archipelago. These studies will draw on a very large collection of genetic resources (primarily amphibians and reptiles) from the Philippines and will consider patterns of speciation in numerous groups, focusing in particular on endemic archipelago-wide clades, and species pairs spanning geographical barriers of variable permeability (marine channels, ephemeral land bridges, landscape features, and ecological gradients). The successful candidate will interact primarily with KU’s Herpetology Division (its curators, collections manager, another postdoctoral researcher, and graduate students) as appropriate during the analysis of data and composition of scientific publications.
- Ph.D. in biological sciences from an accredited university.
- Extensive experience in the collection of genomic data collection and downstream bioinformatics analysis.
- Demonstrated publication record in genomic sciences.
- Demonstrated record of presenting and communicating research findings at international and national meetings.
Application and Additional information are available on the KU employment website.
Complete applications will consist of a CV, a 2-page research statement, and two recommendation letters. Review of applications will begin 30 August 2016. Anticipated start-date: 1 January 2017.
The University of Kansas prohibits discrimination on the basis of race, color, ethnicity, religion, sex, national origin, age, ancestry, disability status as a veteran, sexual orientation, marital status, parental status, gender identity, gender expression, and genetic information in the university’s programs and activities.
Herpetologist Rich Glor was on KCUR to discuss how anoles branch into various species and his research on what defines a species. Listen to the broadcast here.
LAWRENCE — For about 60 million years during the Eocene epoch, the Indian subcontinent was a huge island. Having broken off from the ancient continent of Gondwanaland, the Indian Tectonic Plate drifted toward Eurasia.
During that gradual voyage, the subcontinent saw a blossoming of exceptional wildlife, and when the trove of unique biodiversity finally made contact with bigger Eurasia, the exchange of animals and plants between these areas laid the foundations for countless modern species.
“Today, mainland Asia and India have all this unique biodiversity — but did the mainland Asian biodiversity come from India, or did the Indian biodiversity come from other regions of Asia?” asked Jesse Grismer, doctoral candidate with the Biodiversity Institute at the University of Kansas.
Grismer claims the answer depends on the organism in question.
“If you picked Asian freshwater crabs, you’d see they started in India and made their way to Asia, but if you picked dragon lizards you’d get the opposite answer,” he said. “The opposing distribution patterns created a lot of conflict for a while. You’d see papers saying, ‘Everything came from India,’ and others saying, ‘No, everything came from Indochina and Southeast Asia.’ But they were looking at opposite ends of the same pattern, just with different animals.”
Now, Grismer has authored research appearing in the journal BMC Evolutionary Biology showing that before the final collision of Eurasia and the Indian subcontinent, land bridges between the landmasses may have served as “freeways” of biodiversity exchange that flowed in both directions.
“Our paper shows that as India was approaching Eurasia, it was connecting by ephemeral land bridges,” Grismer said. “It was these land bridges that allowed for dispersal and exchange of all these species. There were two areas of suitable habitat separated by unsuitable oceans. But once that new area was exposed, species were allowed to disperse into mainland Asia or India, respectively, areas that these species had not been able to previously exploit.”
To arrive at their conclusion, Grismer and his co-authors performed a phylogenomic analysis of Indian Dragon Lizards, revealing multiple origins in Southeast Asia. The researchers included Alana Alexander, Phillip Wagner, Scott L. Travers, Matt D. Buehler, Luke J. Welton and Rafe M. Brown from KU and James A. Schulte II from Clarkson University. Grismer also credits his KU lab mates Chan Kin Onn, Robin Abraham and Carl Hutter with help on the research via “a lot of fruitful discussion.”
Importantly, the team showed that two land bridges connected the Indian subcontinent to Eurasia at two different times during the early to middle Eocene, some 35 to 40 million years ago.
“This hypothesis is based on evolutionary relationships between the species used in this study,” he said. Grismer added that his team blended new genomic data with previous studies and combined that analysis with new geologic studies about Eocene geology.
The KU researcher said Indian Dragon Lizards, or the Draconinae subfamily of the lizard family Agamidae, are an ideal species to study in order to piece together a picture of the exchange of biodiversity that took place due to the land bridges.
“Dragon lizards added new light because of the previous work that has been done on them, plus our new samples,” Grismer said. “They’re quite diverse as a group, distributed equally, and so they’re great study system for testing a new hypotheses.”
He added that conservation of certain species of Dragon Lizards and keeping them out of the international pet trade would help make possible more opportunities for understanding the history of this unique group of family of lizards.
“We were only able to do this because we had all these species to work with, and a future study with more data and new species could find a new result to this question ” he said. “Animals in general tell us a lot about our world and how we fit into it. I think protecting them is just as important as anything else we do.”
Top photo: Jesse Grismer, doctoral candidate with the Biodiversity Institute at the University of Kansas, recently published research in the journal BMC Evolutionary Biology. Photo by Meg Kumin, KU Marketing Communications.
Top right image: A map shows the distribution of Draconinae and the four biogeographic area (differently colored borders) used in ancestral range reconstructions. Image courtesy Jesse Grismer.
Bottom right image: b Hypothesized position of the ISC and an early Eocene land bridge allowing for the first inferred dispersal event (D#1 in a) from Eurasia into India, 50–55 MYA. c. Hypothesized position of the ISC and a middle-late Eocene land bridge allowing for the second first inferred dispersal event (D#2 in a) from Eurasia into India between 35–50 MYA (paleomaps modified from Klaus et al.) Image courtesy Jesse Grismer.
-Brendan M. Lynch
A Hispaniolan trunk anole photographed at La Palma, Dominican Republic. Photo credit: Rich Glor
With a recent four-year, $600,000 grant from the National Science Foundation, a University of Kansas researcher is undertaking the most-detailed analysis ever carried out of how reptiles branch into various species.
In doing so, Richard Glor, associate professor of ecology and evolutionary biology at KU and associate curator of herpetology at KU’s Biodiversity Institute, is questioning some of the very methods scientists use to define species.
Further, by combining laboratory studies with fieldwork and genomic sequence data, Glor and his team hope to determine the genetic basis for species differences and why these species diverged in the first place.
Glor said biologists traditionally employ the idea of “reproductive isolation,” or the inability of one kind of animal to fruitfully breed with another, to determine boundaries defining individual species.
“Every student in biology has learned the philosophy of what a species is — something that can’t reproduce with other species,” Glor said. “So when someone describes a new species, you’d think they’ve done a bunch of crossing experiments [to see if a species can reproduce with another], but the answer is that nobody ever does that.”
He said more laboratory studies should be conducted to verify assumptions about boundaries between species and less reliance should rest on how animals look to the eye. His new grant is based on the idea that conventional methods have overlooked recent and ongoing speciation events.
“Traditional taxonomists say that if species exhibit differences in their appearance — this one is green, and this one is red — they likely aren't reproducing with one another,” Glor said. “I saw that as an understudied area in speciation research. We always talk about reproductive isolation, but we never test it.”
Glor has revealed this shortcoming in part by conducting crossing experiments on a group of lizards called bark anoles found on Hispaniola, the Caribbean island shared by Haiti and the Dominican Republic. These lizards are notable for the remarkable variation of their “dewlap,” or flap of skin along the throat, that can be found in different colors and patterns.
“The dewlap is colorful, kind of like a fancy car or jewelry in the human population,” Glor said. “It shows the female you’re attractive and helps her recognize her own species, so it’s critical to sexual selection. The group that I study is particularly noteworthy because a single species exhibits very different dewlap colors and patterns (i.e., some populations are yellow, while others are red). Most anole species exhibit only a single color.”
Previous biologists have relied on variation in dewlaps to separate bark anoles into different subspecies.
“When herpetologists drove across Haiti's mountainous Tiburon Peninsula more than 50 years ago, they saw bark anoles with pale yellow dewlaps at the beginning of their journey, bark anoles with orange and then wine red dewlaps further along, and then started seeing bark anoles with pale yellow dewlaps again by the time they reached the far tip of the peninsula,” Glor said. “As a result, they described these populations with different dewlap colors as distinct subspecies.”
But as Glor and his colleagues obtained genomic data from the lizards, they found dewlap colors weren’t a trustworthy sign of the underlying genetic differences scientists expect to find in distinct species.
“These populations don’t seem to be genomically differentiated,” he said. “Some of those taxa that traditional methods show to be different species probably aren’t different species. Natural selection is driving them to have different dewlap color and appearance for reasons not related to them being different species.”
In other cases, Glor said traditional methods missed species that appear to be strongly differentiated genetically because they are nearly impossible to distinguish externally.
Glor’s work represents the most detailed and integrated analysis ever performed on squamate reptiles — a group of almost 10,000 species, including all lizards and snakes. The research will result in the establishment of a new laboratory model organism, the first squamate genome assembled through linkage mapping and the first “estimates of heritability and the genomic basis for phenotypic traits” vital to systematically studying reptiles in general.
Further, the research has resulted in a public exhibit now on display at the KU Museum of Natural History.
Ultimately, however, Glor said that evolution in species is an unending and fluid process that biologists might always struggle to catalogue and measure.
“All of these ideas like reproductive isolation or morphological divergence are all just benchmarks that occur as new species are forming,” he said. “It could be that some species exhibit all these benchmarks, and some display only one or two. The problem identifying species is that we're trying to put discrete start and stop points on a process we know is continuous.”
- Brendan Lynch, KU News
Note: Live animal display hours at the Oread have changed to be 8:30am-6 pm daily during the confernce, Friday, Saturday and Sunday.
The KU Biodiversity Institute will celebrate 100 years of amphibian and reptile research this month with an international herpetology conference, exhibitions and a variety of educational public events.
KU will host more than 425 scientists and students for the 58th annual meeting of the Society for the Study of Amphibians and Reptiles from July 30–Aug. 2. Single-day and full-conference registration and program information are available on the Biodiversity Institute’s SSAR 2015 meeting website.
Conference highlights include talks by world-famous biologists, including KU alumnus and National Academy of Sciences member David Hillis of the University of Texas at Austin, renowned snake expert Harry Greene of Cornell University, Madagascar explorer Miguel Vences of Technical University of Braunschweig in Germany, and amphibian conservation advocate Tyrone Hayes of the University of California, Berkeley. There are academic sessions and symposia, a reception honoring distinguished senior herpetologists, a live auction of historical herpetological memorabilia, and tours of the Fitch Reservation at the KU Biological Field Station and herpetological collections of the Natural History Museum.
The conference also offers two events for the community to explore herpetology. One is a live animal exhibition at the Oread Hotel that includes the majority of Kansas’ non-venomous reptile and amphibian species. The exhibit is a Sternberg and Kansas Herpetological Society event presented in conjunction with the SSAR meeting. It will be open to the public daily in Gathering Room 1 during the conference.
Another event consists of two multimedia presentations featuring spectacular wildlife photography and music. The presentations will be offered 9:30-11 p.m. July 31 and 8-9:30 p.m. Aug. 2 at the Woodruff Auditorium in the Kansas Union. Both presentations will feature the renowned herpetological imagery of David Dennis and Eric Juterbock. In one show, viewers will explore the “Amphibians of the Appalachians” through stunning photographs of the region’s spectacular frogs and salamanders. The second show, “Herpetologists Past and Present,” will take readers on a colorful and informative journey through the lives of herpetologists. Both shows are free and open to the public.
Beyond the conference, the Biodiversity Institute will encourage local residents to learn more about and celebrate the ecological role of amphibians and reptiles in Kansas. In that spirit, the Lawrence City Commission’s agenda for July 28 includes a proclamation declaring the week of July 27–Aug. 2 International Amphibian and Reptile Week.
This month the Society for the Study of Reptiles and Amphibians will publish “Herpetology at Kansas: A Centennial History,” by William Duellman, professor emeritus and a former curator of herpetology at KU.
Two new herpetology-focused exhibitions are now on view at the KU Natural History Museum. One is a new live animal display of lizards focused on anole lizards and their ecology. Another recently completed exhibition features student wildlife photography, field journals and maps describing a 2014 Kansas herpetology field course.
Scientists at KU have been studying amphibians and reptiles for more than 100 years. Alumnus Edward Taylor, who first published his research in 1915, helped begin what is now the fifth-largest amphibian and reptile collection in the world at KU. Today the collection includes 340,000 specimens representing 5,000 species from 156 countries, and it includes the largest collection of Kansas specimens in the state. KU herpetology curators and graduate students conduct collections-based research throughout the world, from across Southeast Asia to Africa to Latin America to Kansas.
The Philippine site Mongabay.com published the news of a species discovered through an unconventional approach. "Searching the globe for undiscovered species takes biologists to far and remote locations, trekking through exotic locales that may yield a new discovery. However, exploring the black market can also produce results. And this is just the case for Rafe Brown, curator of the University Of Kansas (KU) Biodiversity Institute, during a recent visit to the Philippines. In a black market in Manila, Brown and his colleagues discovered two new species of water monitor lizard for sale..."
Link published on Mongabay.com.
LAWRENCE — It’s not a monkey. It’s not a lemur. It’s not an African Bush Baby or even a Madagascan Mouse. Meet the Philippine tarsier: a tiny, adorable and downright “cool” primate from Southeast Asia.
“It’s really not like any animals that Americans are familiar with,” said Rafe Brown, curator-in-charge at the University of Kansas’ Biodiversity Institute. “A tarsier has giant eyes and ears; an extremely cute, furry body; a long tail with a furry tuft at the end; and interesting expanded fingers and toe tips that look a bit like the disks on the digits of tree frogs.”
Brown said the tarsier (tar-SEER) has become the “flagship” iconic species for promoting environmental stewardship and ecotourism in the Philippines, a nation suffering from large-scale destruction of natural habitat.
“They’re threatened with habitat loss due to development, mining and deforestation from the timber industry,” Brown said. “On Bohol, where they are a big part of the tourist economy, literally thousands of animals are taken out of the wild, essentially harassed by tourists, and die in captivity due to the stress and inability of their captors to feed them an appropriate diet of live small animals. Tarsiers must eat an enormous amount every night to fuel their high metabolism.”
Because of threats to the tarsier, conservation efforts are mounting for the charismatic animal. But these have been thwarted by a lack of research: Too little has been known about the tarsier’s taxonomic diversity; there have been too few field studies; and a scarcity of genetic samples and voucher specimens in biodiversity repositories has left advocates of the tarsier in the dark. In short, to save the tarsier, experts have needed to know much more about the species.
“Basically, we can not legally protect something if we do not know that it exists,” Brown said.
Today, research by Brown and colleagues published by the journal PLOS ONE will shed new light on the animal’s genetic diversity and distribution. Additionally, the KU researchers have verified the presence of a new variety of tarsier, one heretofore only suspected to exist — the Dinagat-Caraga tarsier.
“Previously tarsiers were one species, divided into three named subspecies,” Brown said. “Our data disagree with that subspecies arrangement and instead demonstrate that the Philippine tarsiers are divided into three genetic units — but these units are from different localities than the named taxa. So our data provide an objective way to restructure conservation efforts and point the resources where they need to go, in order to really have an effective impact on preserving genetic diversity in the group.”
Brown’s student Anthony Barley performed genetic sequencing of the tarsiers’ mitochondrial DNA at KU, while fellow student Karen Olsen characterized the nuclear microsatellite loci variation of the animals.
According to Brown, the results “tell us that we need a protected area — such as a national park — in the ranges of each of the genetic units if our goal is to maximally preserve the genetic underpinnings of that biodiversity. Currently, the newly discovered entity, the Dinagat-Caraga tarsier, has no protection. It is known from a small island that is being extremely heavily mined. Thus, it emerges as a new lineage — and a new major conservation urgency.”
They question of just how many Philippine tarsiers exist has been “left sort of hanging” for 25 years until now, according to the researcher. The newly discovered Dinagat Island and Caraga Region tarsier was first recognized as possibly distinct by the Filipino biologist Dioscoro Rabor in the 1970s, and now is confirmed by the KU genetic analysis.
“The confirmation of Rabor’s early suspicions about the Dinagat Island tarsier population was extremely exciting, and it was very satisfying to affirm his very perceptive early observations,” Brown said. “He commented that it looked larger to him and had different shaped fingers and toes. I’m just glad we were able to bring new, modern tools to this problem and identify the Dinagat-Caraga tarsier as a real conservation priority.”
Brown and Filipino colleagues have called for the establishment of separate tarsier sanctuaries and protection programs within the range of “at least” the three genetic entities established by the research at the Biodiversity Institute. Each, he said, merits unique strategies and programs, along with identification and remediation of conservation threats — for instance “mining in Dinagat versus unregulated tourist industry on Bohol,” he said.
To do less, Brown said, would harm the tarsier’s long-term prospects, potentially depriving the Philippines and the rest of the world of one of nature’s most charming and curious mammals.
“They move very rapidly and jump from tree trunk to tree trunk with ‘ricochet locomotion,'” Brown said. “They bounce from small sapling trunk to trunk, then leap down to pounce on their prey. They’re completely carnivorous. This is relatively unique among primates. The tarsier is famous for not eating any vegetable material of any kind. They eat insects, small snakes, lizards, small mammals and birds. They communicate with ultrasonic calls outside the range of human hearing. The tarsier is so cool!”
The National Geographic Society's Committee for Research and Exploration and the National Science Foundation supported the research. -Brendan Lynch, KU News service
LAWRENCE — Recently, Malaysian herpetologist Juliana Senawi puzzled over an unfamiliar orange-striped, yellow-speckled frog she’d live-caught in swampland on the Malay Peninsula.
She showed the frog to Chan Kin Onn, a fellow herpetologist pursuing his doctorate at the University of Kansas. They wondered — was this striking frog with an appearance unlike others nearby in the central peninsula an unidentified species?
Poring over records to find out, the researchers saw that a comparable frog had been collected in the area 10 years earlier, but it was written off then as a species from an Indonesian island about 450 miles to the west. The distance and geography between the two habitats made them suspect their frog might have been formerly misidentified.
“The frog was originally confused with the Siberut Island Frog, which is a species that occurs on Siberut Island off the western coast of Sumatra, Indonesia, due to their similar appearance in color-pattern,” Chan said.
They wondered if genetic code from the exact same frog species could have jumped eastward from a remote island across 150 miles of Indian Ocean — then over the whole of Sumatra — then across the Strait of Malacca into the Malaysian interior?
“Despite their similarities, we had a strong suspicion that the frog from Malaysia wasn’t the Siberut Island Frog,” Chan said.
Later, extensive genetic analysis performed in the lab of Rafe Brown, curator of herpetology at KU’s Biodiversity Institute, would determine whether the Malaysian frog was indeed new to science — genetically distinct from its doppelgänger on Siberut Island.
“The lab is very high-tech and is able to run a number of different types of genetic analyses,” Chan said. “It’s also able to run the latest in cutting-edge genetic analysis called Next Generation Sequencing, which a lot of researchers are currently utilizing. We also have a very powerful bioinformatics lab that can analyze extremely large and computationally expensive datasets. The great thing about the lab is that we have the equipment and expertise to run everything from initial DNA extractions to the final data analyses without having to rely on any outsourcing.”
When testing was complete, the first hunch of the Malaysian team proved right: “Sure enough, results from Rafe’s genetic analysis showed that the frog from Peninsular Malaysia was genetically too distant from the Siberut Island Frog to be considered the same species, so we decided to describe it as a new species.”
As lead author, Chan published the team’s findings in a recent issue of the journal Herpetologica.
“We decided to call it ‘Hylarana centropeninsularis’ because it’s currently only known from central Peninsular Malaysia,” he said. “The name is constructed from the Latin word ‘centro’ that means center and ‘peninsularis,’ in reference to Peninsular Malaysia.”
To date, Chan has described seven species of frogs and three species of lizards, all from Peninsular Malaysia, that are new to science.
Born and raised in Malaysia, Chan took interest in nature as a child, interacting with jungle plants and animals — then keeping snakes and lizards as pets.
“At one point, I had as many as 25 species of pet snakes in my room,” said the KU researcher.
At the National University of Malaysia, Chan found himself under the tutelage of herpetologist Norhayati Ahmad and Lee Grismer of La Sierra University, California, a world-renowned herpetologist with research interests in Malaysia.
“I knew about Rafe Brown and KU through their research and publications and first met him at a conference in Borneo,” Chan said. “My research interests aligned well with Rafe — we both work on frogs in Southeast Asia and are generally interested in answering the same type of questions.”
For would-be herpetologists looking to follow in Chan's species-finding footsteps, the KU researcher had words of advice: “Do it the old-fashioned way. Wade through the mud and get dirty!” - Brendan Lynch, KU News Service
KU Herpetology has launched a new Flickr group that will contain images taken by members of the division and their associates. The group already hosts more than 750 images. Visit the group's page and sign up for Flickr if you want to become a contributor.
In the Summer of 2015, KU Herpetology will host the annual meeting of the Society for the Study of Amphibians and Reptiles. The meeting will take place in the Kansas Memorial Union, which is located adjacent to KU Herpetology headquarters in the KU Natural History Museum. Some social events will be hosted just down the road at the Oread Hotel. Preliminary details can be found in an announcement published in Herpetological Review. Stay tuned for more details.