The Mexican National Institute for Anthropology and History (NIAH) has awarded the Antonio Garcia Cubas 2016 prize in the “scientific works” category to a book authored by three KU affiliated ornithologists. KU Ornithology Research Associate Adolfo Navarro, Professor Town Peterson, as well as former KU Ornithology postdoc Luis Sanchez-Gonzalez, contributed significant portions of Volume 13 (Ornithology) of the series of books entitled La Real Expedición Botánica a Nueva España [The Royal Botanical Expedition to New Spain]. Their work on the ornithology of the Mociño expeditions in the late 1700s has spanned more than 15 years, documenting a significant early documentation of Mexican avifaunas. When the work was written (but not published), more than half of the species treated in the summary were not yet described scientifically.
The Solomon Islands in the Southwest Pacific are best known as a locale for some of the most intense fighting of the Second World War, including the bloody Battle of Guadalcanal. But for nearly a century, the rich biodiversity of the islands has been instrumental to the study of evolution, including research by noted scientists Ernst Mayr and Jared Diamond.
“Leading ideas of how speciation happens and evolution occurs were formed based on birds and frogs in this region,” said Rob Moyle, associate curator at the University of Kansas’ Biodiversity Institute, who specializes in the evolution of birds. “The islands are incredibly beautiful places but also at times incredibly inhospitable, very hot with really rough terrain and torrential downpours.”
Today, Moyle is leading a major research effort in the region supported by $1.3 million from the National Science Foundation to conduct fieldwork, collect museum specimens, record bioacoustics and sequence DNA of birds, reptiles, amphibians and mammals.
“We want to go back to test hypotheses, fill in gaps in the data and revisit this with much more modern methods than they were using decades ago,” Moyle said. “Some of the problems doing this work today are permitting issues and national boundaries. In the past, researchers just went island to island and collected what they wanted. It’s difficult to do the same thing today, but that’s what we’re hoping to do.”
The grant includes fieldwork spread across three nations — the Solomon Islands, New Guinea and Vanuatu. Many islands in the region are remote and isolated, making travel difficult for the researchers hoping to follow up on work performed by earlier biologists.
“Getting there isn’t simple,” Moyle said. “From the U.S., you have to go through Australia and fly back several hours to get to the Solomons. Very few airlines go there, but the main islands have little airstrips you get to on a little Twin Otter prop plane. To get to most small islands, you take small outboard boats. That can be iffy, because you go across some pretty open ocean crossings. Then, sometimes we take a boat up the river — a year ago we took a helicopter to a site in Guadalcanal.”
Moyle’s colleagues include KU’s Rafe Brown, who is in charge of amphibian and reptile work; Chris Filardi, senior scientist at Conservation International; Michael Andersen of the University of New Mexico; Tyrone Lavery of the University of Queensland, Australia; Jonathan Richmond of the U.S. Geological Survey; and many participants and collaborators in the Solomon Islands, including David Boseto, co-director of Ecological Solutions Solomon Islands, a group dedicated to environmental research and conservation.
In the field, biologists will camp in teams ranging from two to 20 people, performing their work in shifts that depend on the animals of interest.
“If you’re studying birds, you’re up early,” Moyle said. “Our day starts before dawn, getting up, getting ready, getting tape recorders ready for vocalizations, getting nets ready — that goes through mid-morning, then we have work back at camp to preserve and prepare specimens. If you study frogs, you go herping at night. Sometimes we overlap, the herpetologists get back late, and the bird people are getting up.”
The teams will include many graduate and undergraduate students from KU and partner institutions.
“Graduate students will be heavily involved in fieldwork, lab work and publishing papers,” Moyle said. “We’ll also bring undergrads from the U.S. over to the Solomon Islands. They’ll be paired with undergraduates from the Solomons to work on research projects — so there’s both an international cultural experience as well as a scientific project.”
Back at KU’s specialized labs, researchers will conduct genomic sequencing of samples from the field to establish relationships between species and determine when separate species may have branched off from each other.
“Traditionally, scientists would collect bird specimens and their insights into what went on in a region came from looking at plumage color, the size and shape of the animal, and looking at maps of where they occurred on islands, but physical appearance can be very misleading,” Moyle said. “Genomic sequencing opened up new realm of inquiry, not just for figuring out if specimens A and B are related, or if A is more closely related to C, but also figuring out how quickly they diversified or how long ago they arrived in the archipelago.”
Moyle and his colleagues will use a process called “high-throughput sequencing” to trace how gene flow occurs between populations separated on isolated islands.
“Sometimes, we see there are populations on different islands that look or sound very different, and, so far, we actually can’t tell them apart genetically,” Moyle said. “We know there are differences in there, but it shows how little change there has to be in the genome to get something that sounds and looks very different. With some of this work, we’re able to identify the specific genes for differences we’re seeing among the species.”
Moreover, the scientists are likely to identify species that are unknown to science and describe them for the first time.
In addition to the scientific value of the research, work performed under the grant will inform policymakers and conservationists looking to protect biodiversity in the region.
“These islands are under great threat from a variety of sources,” Moyle said. “The most prominent threat is logging, but there are also some very aggressive resource extractions like gold, nickel, and bauxite mines and oil drilling. Some of these islands aren’t that large, and there’s not much forest left, so figuring out where species are and what’s left of them can give conservationists and governments some data to work with to make informed decisions.” - Brendan Lynch, KU News
Photos, from top:
The Solomon Island Palm Frog (Cornufer heffernani) is uncommon and found only in pristine rainforest. Its chirping call is often heard after heavy rains. Credit: Scott Travers
Mark Robbins, collection manager of birds in the KU Biodiversity Institute, examines bird specimens during a 2014 expedition to Choiseul Island while local guides from the Lauru Land Tribal Community look on. Credit: Scott Travers
The Solomon Island Eyelash Frog (Cornufer guentheri) is widely distributed in the archipelago and is an example of direct development – they skip the tadpole phase and hatch from eggs as tiny but fully developed frogs. Credit: Scott Travers
The field team at Nunubala camp, West Kwaio Region of Malaita Island during a 2015 expedition, including KU graduate students, local guides and Solomon Islands researchers. Credit: Scott Travers
The Collared Kingfisher (Todiramphus chloris) is ubiquitous in the region. Like most Old World kingfishers, this species is not a fisher but instead inhabits forest and open country, feeding on insects and small vertebrates. Credit: Rob Moyle.
While it is widely accepted that songbirds originated from the Australian continent, how and when they diversified and colonized the rest of the globe has remained a mystery.
Researchers from the University of Kansas, Louisiana State University and three other institutions reconstructed the evolutionary history of songbirds using thousands of DNA sequences from majority songbird lineages and information from the fossil record to provide answers to these questions. They found that songbirds began diversifying about 33 million years ago and underwent extensive diversification in Australia. Furthermore, the researchers also found that songbirds first dispersed out of Australia about 23 million years ago through early islands in the Indonesian archipelago into Asia and subsequently the entire globe.
This new research will be published in Nature Communications on Aug. 30.
“One of the challenges with deciphering songbird evolutionary history is that they diversified so rapidly that previous studies had a difficult time estimating the branching pattern of the songbird family tree,” said lead author Rob Moyle, KU professor of ecology and evolutionary biology and curator of ornithology at the KU Biodiversity Institute. “With advances in DNA sequencing technology, we were able to collect an unprecedented amount of DNA sequence data that helped clarify songbird relationships.”
Songbirds comprise the largest group of birds, with about 5,000 species, accounting for nearly half of avian diversity. They are found on almost all corners of the globe, with the exception of Antarctica, and include the familiar crows and sparrows, as well as elaborate singers like mockingbirds and lyrebirds.
With a better understanding of the songbird family tree, Moyle and his colleagues were able to infer the colonization history undertaken by songbird ancestors.
The dispersal of songbirds from Australia through Indonesia, Moyle said, seems like an obvious explanation to anyone who knows world geography; but one has to bear in mind that tens of millions of years ago, world geography looked a lot different because of the Earth’s constant process of plate tectonic movements.
“Thirty-three million years ago, Australia was thousands of kilometers away from any continent, and New Guinea barely existed,” Moyle said.
Another issue confounding our understanding of songbird evolution is the estimated age of the group, said co-lead author Carl Oliveros, a postdoctoral researcher at Louisiana State University.
“Our estimate for the age of songbirds is about half of most previous estimates, placing songbird evolution in a very different geological landscape than previously thought,” said Oliveros, who earned his doctorate in ecology and evolutionary biology at KU.
“Thus the previous hypothesis of long-distance dispersal by songbirds from Australia to Africa via Indian Ocean landmasses are put into question because these Indian Ocean islands were submerged by the time we think songbirds diversified.”
Oliveros’ and his colleagues’ work also provides an alternative explanation to the high diversity of songbirds that are presently found only in New Guinea. Previous research suggested that songbirds diversified extensively in proto-islands of New Guinea before colonizing adjacent areas.
However, Oliveros and his colleagues believe that songbirds underwent extensive diversification in Australia and subsequently colonized New Guinea after the formation of the New Guinea landmass. They suggest that the aridification of Australia caused the extinction of forest-adapted songbird lineages in the continent, which left relicts of the first colonizers as sole surviving lineages in New Guinea. According to the researchers, this idea is supported by the presence of fossils in Australia of plants and mammals that are currently only found in New Guinea.
The study used tissue samples of birds deposited at the KU Biodiversity Institute collected from expeditions to 25 countries within the past 25 years. This research is supported by funds from the National Science Foundation, KU and Louisiana State.
By Brendan Lynch
Photo: This yellow-breasted satinbird (Loboparadisea sericea) is among the songbirds research shows first dispersed out of Australia about 23 million years ago through early islands in the Indonesian archipelago into Asia and subsequently the entire globe. Image credit: Brett Benz, American Museum of Natural History
LAWRENCE — The University of Kansas has been at the forefront of the open-access movement, an international effort aiming to ensure that peer-reviewed journal articles are available to all, not just those who can afford subscriptions. Three KU authors have published a new article and provided early comments on a white paper calling for the end of “parasitic models” of publishing and describing a phased approach toward a practical dissemination model that would make scholarship open and free.
Traditionally, the cost of accessing academic journals has fallen to the universities in the form of subscription fees. With growing interest in models of scholarly publishing where the contents are “open” without subscriptions, open-access journal publishing is beginning to demonstrate its viability as a model, with different business models supporting it. While those subscription fees still exist for traditional journals, the new costs of running an open-access publishing system are shifting increasingly to authors, who are often required to pay up to $3,000 or more to publish in the most prestigious open-access journals. Town Peterson, Distinguished Professor of Ecology and Evolutionary Biology; Ada Emmett, associate librarian for scholarly communication; and Marc Greenberg, professor of Slavic languages and literatures, are among the leaders of a shift to a truly open-access system, where scholarship is open to anyone who wants to access it, not just those with money or subscriptions.
“The future is open access. But how that gets played out is in question,” Emmett said. “There is an attempt to shift the cost of publishing from the reader to the author. That’s inadequate for many reasons. We don’t want to right one wrong by creating another wrong.”
The authors published their study in the Journal of Librarianship and Scholarly Communication (available openly from the publisher here). The article grew out of an ongoing conversation among the three about how they could best apply their efforts, as an interdisciplinary group of scholars, to advancing open access in scholarly communication. For their most recent project, they decided to assemble a group of colleagues from around the world to contemplate barriers to open access in their countries and academic systems. They discovered that while author fees were the largest obstacle, there were additional hurdles. Psychological barriers to publishing in open-access journals were relevant as well. Some scholars from less wealthy countries or institutions, knowing they would have to apply for a publication fee waiver, which carries with it some degree of indignity, didn’t submit their manuscripts.
The researchers also documented experiences where colleagues had to travel to other countries at their own time and expense to access facilities and resources published in traditional and closed-access journals to perform their research. Others reported that while some journals claim they will waive fees for authors from certain countries, they had applied and been given only a 10 percent discount.
The issue of money can’t be ignored, however. Peterson cited a colleague working in Cuba who earns less than $1,000 a year, less than the average cost of an author processing charge for publishing in open access journals that leverage such fees. Some scholars in other countries only earn per month about 25 percent of the cost of publishing one article in a for-profit open-access journal, whose fees for open access can run to $3,000. Compounding the problem, some nations require their faculty members to publish in the so-called “elite” or “top 10” journals to receive promotion or tenure. Those elite journals may be closed access — therefore with limited readership — or open access, but with high author fees. Some universities such as KU have funds to help authors defray such costs, but many more, including small schools and those not located in wealthy nations, do not.
Greenberg, Peterson and Emmett argue that, just as Ivy Leagues and elite universities should not have exclusive control of scholarship, neither should a select few institutions control how open access is developed and instituted in the future. That goal has led them to seek input from researchers across the country and globe.
“We’ve found that there are all sorts of bottlenecks in the system. We’re hoping to help level the playing field for all,” Greenberg said.
The KU authors’ concerns and efforts tie into national efforts to design a funding model for openly accessible scholarship where neither readers nor authors need to pay. A white paper, available online, is under development that describes the need and a framework for the establishment of a universal fund to help implement true open access for scholarship, with an initial focus on the humanities and social sciences, disciplines that have had greater difficulty adopting open-access practices in their publishing venues. The group behind the white paper has organized a board of directors, on which KU’s Dean of Libraries, Lorraine Haricombe, also a strong national and internationally known advocate for open access, serves as chair. The fund would start with scalable payments from universities predominantly from the U.S. and Europe. While the payments would be relatively small, taken together, they could create a sizable fund that could cover costs associated with scholarly journal publishing.
“The payment is modest relative to the overall budget of most institutions, but, when spread broadly across all institutions, results in a sum substantial enough to sustain a vibrant and open scholarly communication environment,” the authors wrote.
Such a fund would help transition to an open-access system that is not driven by profits for publishers and does not require wealth to participate. The current system allows commercial publishers that offer “hybrid” open access to “double dip” by both charging universities for subscriptions and charging authors to be able to publish their one article as “open" in an otherwise subscription-only access journal. Add to this the free services that commercial publishers get from faculty volunteers in terms of time spent as editors and reviewers. In addition, public money is often part of funding for research projects, access to which can be blocked by exorbitant costs.
“That is a huge discredit to the rather noble idea that research and knowledge should be open and available for all,” Peterson said.
While publishers often argue that switching to open access would put them out of business, the KU authors argue that even in the face of the National Institutes of Health’s open access policy, there is no evidence that any for-profit journals have had to cease operation. Peterson likens the situation to Lawrence, Kansas, restaurant and bar owners who fought bitterly against smoking bans. Many argued that they would be harmed financially if they weren’t able to allow smoking, but after bans passed none have proven that a ban was a reason they closed.
KU was the first public institution to enact a policy (http://policy.ku.edu/governance/open-access-policy) that all faculty-produced journal articles should be available in an open access repository. KU faculty and librarians also helped to lead the formation of the Coalition of Open Access Policy Institutions, which started with more than 20 universities, including Harvard University, Duke University and Concordia University in Montreal. It has since grown to include 62 North American institutions. Haricombe serves on several national and international boards and advisory committees related to open-access efforts, and she is chair of the steering committee for SPARC, the Scholarly Publishing and Academic Resources Coalition.
A recent editorial in The Chronicle of Higher Education described the open-access movement, and the COAPI group in particular, as “termite change.” The term refers to change that proceeds almost undetected from without, but fundamentally transforms the system from within. As William Allen White famously said, “When anything is going to happen in this country, it happens first in Kansas.”
Mike Andersen, former student of Rob Moyle, Division of Ornithology, has been offered a tenure track job at the University of New Mexico in the Department of Biology.
Graduate students from the Department of Ecology and Evolutionary Biology, Joe Manthey and Andres Lira, recently published a paper in the journal Evolution. A link to the paper's abstract is here:
Birds are subjects of great interest to many people. They are often easy-to-spot, charismatic and beautiful. Because of this interest, birds tend to be well-studied, and most years see only a handful of new bird species discovered and described in scientific journals. However, this past year has seen 23 new birds described so far.
Remarkably, three of those new birds have been introduced to science by researchers at the University of Kansas' Biodiversity Institute. And a KU graduate student in ecology and evolutionary biology, Pete Hosner, has co-authored two of those.
"I think these discoveries reflect the opportunities I've had to work in tropical forests, where most new bird species are found," said Hosner. "Since I began my doctorate in 2007, KU ornithology has had active field research in Central and South America, Africa, Asia, Australia and Oceania. Even though undescribed bird species are a rare find, with such a broad search radius, new things are bound to turn up."
The KU researcher's most recent find is dubbed the Sierra Madre Ground-Warbler, a ground-dwelling forest bird that lives on Luzon Island of the Philippine archipelago. Its description is published in the August issue of The Condor, a scientific journal of the Cooper Ornithological Society.
"The ground-warblers are very unique birds," said Hosner. "They're only known from the northern Philippines, and they have no close relatives. As the name suggests, they're ground-walking songbirds - rotund, with strong legs and weak wings - and it appears that they can barely fly. They tend to inhabit dense forest understory, where they feed on insects. Their song is extremely high in pitch, and ventriloquial - it's almost impossible to locate the source of the sound in the forest - they always sound like they are far away, even when they are almost at your feet."
Hosner said the new species of ground-warbler looks similar to the other two species of ground-warblers in the Philippines, so it wasn't recognized as an independent species at first.
"The three species of ground-warblers now recognized are essentially identical in size, shape and juvenile plumage coloration held in their first year of life, but they differ from one another in adult plumage coloration," he said. "The reason that this new species remained undescribed for so long was that the adult plumage of the very first ground-warbler to be described was unknown. That species, Cordilleran Ground-Warbler, was documented only from a single juvenile until our recent fieldwork. As a result, the 'discovery moment' was when we saw an adult individual of the known species."
Examination of its DNA was key to differentiating the new ground-warbler once it was spotted in the field. The DNA sequence data was collected in KU Biodiversity Institute's Molecular Phylogenetics Laboratory, which was recently renovated with investment from the National Science Foundation, the state of Kansas and KU.
"When we noted the different plumage coloration between adult birds in the Cordillera and the Sierra Madre in northern Luzon, we sequenced DNA to determine if the plumage differences were individual variation within a species, or if the two plumage forms were also genetically diagnosable," Hosner said. "We found that Cordillera and Sierra Madre birds were highly divergent in their DNA, almost as different as the distinctive Bicol Ground-Warbler in southern Luzon."
However, it was the basic legwork of searching in the field for new birds that ultimately brought the Sierra Madre Ground-Warbler to the attention of the world.
"Most of the authors participated in fieldwork in the Philippines," Hosner said. "Working in the Philippines is awesome. We hike out into the forests and establish field camps - usually about two weeks per site -where we survey the birds and other organisms. No electricity, no road noise, just the forest. Usually it's hot, sweaty and dirty work, but we always camp near a stream for a water source, which helps. Sometimes our visits coincide with typhoons, which adds some excitement, especially when you are trying to keep your tent dry. One of the sites where we found the Sierra Madre Ground-Warbler, Mount Cagua, is an active volcano with thermal vents and mud pots."
The new bird species' scientific name honors Max Thompson, a retired professor from Southwestern College in Winfield and a research associate in the KU Biodiversity Institute.
"He received his master's degree from KU in the '60s for his studies on the birds of Borneo, and he has conducted avian research on every continent," Hosner said. "When Max retired a few years ago, his extensive research collection came to the KU Biodiversity Institute. We wanted to name the bird after Max for his decades of avian research around the world and thank him for his contributions to KU ornithology."
Hosner's co-authors are Nikki C. Boggess, Carl H. Oliveros and Robert G. Moyle from KU's Biodiversity Institute and Department of Ecology and Evolutionary Biology; Luis Sanchez-Gonzalez from KU's Biodiversity Institute and the Universidad Nacional Autónoma de Mexico; Phillip Alviola from the University of the Philippines Los Baños; and Rolly Urriza from the Philippine National Museum.
A five-year Biotic Surveys and Inventories Grant from the National Science Foundation, headed by KU herpetologist Rafe Brown, funded the field research. As of this year, the grant has funded 22 expeditions to the Philippines, and data collected on these expeditions has contributed to more than 120 scientific publications.
Once, during a night time trek through a remote patch of Philippine rainforest to record frogs and collect their eggs for his doctoral dissertation, University of Kansas researcher Rafe Brown found himself alone, far ahead of his colleagues on the trail.
That’s when his headlamp died.
“I had to sit on a log for an hour in the dark,” Brown recalled. “Already, I’d spent a couple of hours trying to record all the frogs in the area, and I was pretty sure there were just three species. But when forced to just sit there and listen to them, I found that there were seven or eight different calls in the area.”
Such is the importance of sound to biologists and naturalists: It can help distinguish one species of animal from another, even when two species might look nearly identical.
That’s one reason why scientists for generations have lugged recording gear into the field, capturing all manner of animal signal, from croaking frogs to chirping insects to singing birds. Unfortunately, over the years, many hard-won recordings have moldered on back shelves of museums and offices, often in outdated audio formats, such as reel-to-reel tape.
Today, Brown is an associate professor of ecology and evolutionary biology and curator-in-charge of the herpetology division of the KU Biodiversity Institute. In that role, he is helping to lead a new, $200,000 effort, funded by the National Science Foundation, to digitize, archive and make available thousands of field recordings of animal sounds at KU, and tie them with the voucher specimens that were recorded.
“In the past, if someone wanted to get a call of a recording of a species of frog from Central America that was recorded 30 years ago, it was a complicated process,” said Brown. “They’d have to contact us, and one of us would have to go back and try to sift through all the material to try and find the tape and the segment of the tape with the frog, and then record it to a cassette tape and send it to them.”
The KU researcher said the new grant would upgrade data accessibility for the Internet era.
“The idea is to take all off this ancillary material and put it online,” said Brown. “You’ll go look at the record for the frog, and you’ll see there are digital photos of it and its habitat, and then you can click on a link and instantly hear the sound that it made.”
KU is one of a consortium of 11 research institutions to digitize audio recordings through this effort. Other major contributors include the Smithsonian, Louisiana State University’s Museum of Natural Science and the Texas Natural Science Center at the University of Texas at Austin. The work at KU’s Biodiversity Institute will focus on the strength of its herpetology and ornithology collections, the latter of which is curated by co-investigator Mark Robbins.
Ultimately, Brown said the grant would speed the process of discovering, cataloging and naming species for academic researchers and naturalists. Also, many of the animal sounds will be made available to the public, helping to underscore the importance of sound to biology — and conveying the mysteries of animal communication.
“Species are making sounds to mark their territory, to attract mates, to scare away predators, to call to their offspring, and even in some cases to send signals to other species,” Brown said. “And there are things that people still debate. Why do birds sing at dawn? Are they marking their territory? Are they happy that the sun is up and making noise because they can? There still are questions about why organisms make sounds, sometimes in a context that we can’t really understand.”
The project, which will fund several new positions for graduate students and postdoctoral researchers, should run through 2017.
Carl Oliveros, a KU Ph.D ecology and evolutionary biology student, has learned that his DIGG proposal has been recommended for funding. The title of the project is "Disentangling phylogenetic relationships in an explosive bird radiation." Oliveros, who is mentored by Rob Moyle, will be using next-generation DNA sequencing to generate hundreds of markers for phylogenetic analysis of the bird family Zosteropidae. This family has one of the fastest diversification rates among terrestrial vertebrates, and standard DNA sequencing has proven insufficient to decipher relationships in this group.
A. Townsend Peterson, curator of ornithology, and Mark Robbins, collection manager of ornithology, have received a grant of $25,000 from the National Geographic Society. The society's Committee for Research and Exploration awarded the grant for a project entitled, "Survey of Vertebrate Diversity of an Isolated Sub-Himalayan Site in Northern Vietnam."