Graduate student Sarah Cowles (Al Uy Lab) receives a grant from the Society of Integrative and Comparative Biology to work hybridization in Solomon Island white-eyes


Sarah Cowles, a Ph.D. graduate student in the (Al) Uy Lab, has received a 2017 Grants-in-Aid of Research Award from the Society for Integrative and Comparative Biology. This award will help cover the costs of her 2017 field season on Kolombangara Island in the New Georgia Province of the Solomon Archipelago.

On the small 15-km wide island of Kolombangara, two species of White-eye birds in the rapidly-speciating Zosterops genus have come into secondary contact. As part of her dissertation, Sarah is using two replicate elevational transects to examine the levels of gene flow, morphological divergence, and species recognition in areas of overlap and non-overlap between the two species.


Graduate student, Karla Rivera-Caceres, and Maytag Professor Bill Searcy characterizes the mechanisms that underly complex duets between Neotropical wrens

‌‌‌‌‌‌‌‌From UM's Press Release:

Karla Rivera-Cáceres, a University of Miami biology graduate student, plays a harmonious duet of singing wrens from a recording she captured out in the field during a recent trip to Costa Rica.

"The song sounds like one bird but if you listen closely, it’s a male and female wren singing a duet in perfect unison,” said Rivera-Cáceres.

Along with songbirds, many animal species perform duets, an uncommon vocal interaction that can occur between mated or unmated species, such as frogs and crickets. But the coupled wrens Rivera-Cáceres recorded in Costa Rica sing alternating phrases, or parts, of the song so smoothly and with such complexity and fast tempo that the untrained ear may hear just a single bird. 

For years, Rivera-Cáceres studied the “duet codes” (non-random association of song types) of paired wrens and wondered if the ability to perform their complex and seamless music was a skill the birds were born with or learned during juvenile or adult stages of life. Now, after two months of intense listening in Costa Rica, she knows that they can learn new songs with new partners, even as adults. She says the newly learned songs are akin to prenuptial agreements.

“It’s like the birds think: If you’re willing to invest the time and energy to learn a new duet code, then I am sure you are not going to leave me because if you do, you would lose a big investment and would need to learn a whole new duet code with another partner,” she said.

For the rest of the press‌ release: Hitting the Right Notes

Link to paper: Neotropical wrens learn new duets as adults


The  Collins lab identifies the signals that drive distinct active and inactive reproductive behavior states in nematode worms

‌‌‌‌‌‌‌‌The complexity of the human brain, with its 80 billion neurons, presents a tremendous challenge to understanding how it works. Fortunately, the nervous system is organized into small functional units called neural circuits with just a few neurons that communicate with each other to control a simple outcome, such as one behavior. As yet there is no neural circuit in any organism for which we understand how the dynamic pattern of electrical activity drives chemical signals between the neurons to drive behavior.

In a new research study published in eLife, the Collins lab characterized in depth perhaps the simplest neural circuit in the nematode worm Caenorhabditis elegans, the egg-laying behavior circuit.  Using cutting-edge ontogenetic approaches to record the patterns of activity of each cell in the circuit, manipulating activity of the cells and their ability to signal to each other, the Collins lab hopes to understand how these cells together produce the worm’s egg-laying behavior.

They found the C. elegans circuit has “command neurons” that release serotonin to increase excitability of the rest of the circuit. The circuit is then able to respond to rhythmic pulses of excitation from a “central pattern generator” to coordinate egg laying with other behaviors like locomotion. The circuit also contains cells activated only when an egg is laid, releasing a signal to turn off circuit activity. These features that turn on circuit activity, generate a pattern of activity when the circuit is on, and then turn off the circuit when it has completed its function, are general features of many neural circuits.

The C. elegans model system allows a powerful combination of genetic and optical manipulations of specific neurons so that details of all the signaling events among cells of a neural circuit can be delineated, promising that further studies will allow unprecedented mechanistic insights into how a neural circuit works.

Link to paper: Activity of the C. elegans egg-laying behavior circuit is controlled by competing activation and feedback inhibition

Link to UM's e-veritas article covering the Collins Lab: Mapping the Minds of Worms

Figure Caption (left):  A genetically encoded calcium reporter was used to record changes in cellular activity in the 6 VC motoneurons during egg-laying behavior.  Red indicates high levels of intracellular calcium.  Each adult worm is only 1 mm long, has exactly 959 somatic cells, and will produce >300 progeny during its ~2 week lifespan.

The  McCracken Lab identifies unique adaptations that help ducks thrive in the Andes

‌‌‌‌From UM's Press Release:

A diving bird, the torrent duck is like a seal or penguin. Not in looks, of course, but in physiology. Like emperor penguins or Weddell seals, University of Miami researchers discovered, torrent ducks have among the highest concentrations of myoglobin, the protein that holds oxygen in muscle tissue.
That’s partly how this tiny waterbird species, averaging less than a pound, expertly dives in high-altitude rivers in the Peruvian Andes and has managed to survive for close to a million years in permanent states of hypoxia, or lack of oxygen. Travelers can see the ducks in the surging whitewater on the train ride to Machu Picchu.

“In most environments where you encounter hypoxia, it’s usually where animals will be able to escape it at some point,” said Neal Dawson, a postdoctoral biology researcher at the UM College of Arts and Sciences and McMaster University in Ontario, Canada, who with fellow UM biologists Kevin McCracken and Luis Alza discovered this adaptive trait on a July 2015 expedition. “In high altitudes, there’s no escaping it. These territorial ducks are stuck year-round with this hypoxia environment.”

‌For more see:  Unique Adaptations Help Ducks Thrive in Andes

The Uy lab publishes a paper on the genetic basis of beak size in Darwin's Finches


‌‌‌‌‌‌‌From the News & Views piece by Prof Nick Mundy:

“Darwin's finches are an iconic case of adaptive radiation. The size and shape of their beaks are key adaptive traits related to trophic niche that vary among species and evolve rapidly when the food supply changes. Building on recent studies, a paper in this issue of Molecular Ecology (Chaves et al. 2016) investigates the genomic basis of beak size variation in sympatric populations of three species of ground finch (Geospiza) by performing a Genome-wide association study using RAD-seq data. The authors find that variation in a small number of markers can explain a substantial proportion of variation in beak size. Some of these markers are in genomic regions that have previously been implicated in beak size variation in Darwin's finches, whereas other markers have not, suggesting both conservation and divergence in the genetic basis of morphological evolution. Overall, the study confirms that loci of large effect are involved in beak size variation, which helps to explain the high heritability and rapid response to selection of this trait. The independent identification of regions containing HMGA2 and DLK1 loci in a GWAS makes them prime targets for functional studies. The study also shows that under the right conditions, RAD-seq can be a viable alternative to genome sequencing for GWAS in wild vertebrate populations.”

This work was led by former postdocs Jaime Chaves & Liz Cooper and Aresty Professor Al Uy, in close collaboration with colleagues from UMass Amherst, McGill University and the Smithsonian Tropical Research Institute.

Link to the full News & Views Piece: Population genomics fits the bill: genetics of adaptive beak variation in Darwin's finches

Link to paper: Genomic variation at the tips of the adaptive radiation of Darwin's finches


The Afkhami lab finds that microbial “hidden players” promote biodiversity by suppressing an invasive species

‌‌‌‌‌‌‌Understanding community dynamics and processes – such as what factors generate and maintain biodiversity and those that affect invasion susceptibility – is a central goal of ecology and evolution. While most studies of how species interactions affect communities have focused on highly visible macro-organisms, in a recent paper published in the journal Ecology, Assistant Professor Michelle Afkhami and a collaborator investigated the impact of a microbial “hidden player” on communities.  They found for the first time that, despite minute size, micro-fungal endophytes dramatically increased the diversity of plant communities by suppressing a dominant invasive grass, Bromus diandrus, across ecologically diverse habitats. This research demonstrated that mutualistic microbes, while often hidden players, can have unexpectedly large ecological impacts and may be important for promoting diverse communities and ecosystems.

Link to the paper: Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales

Image caption: Micro-fungal endophyte hyphae (dark blue lines indicated by black arrow) living between cells of its native plant host. Stained plant tissue under 200x magnification.

The Afkhami Lab publishes paper on consequences of mutualist diversity for genomewide expression in tripartite plant-microbe mutualism

‌‌‌‌‌‌Mutualisms, species interactions in which all participants benefit, are extremely common in nature, so much so that organisms interact with many different mutualists throughout their lives. While essentially all species interact with multiple mutualists and these complex interactions play critical roles in providing ecosystem services and supporting biodiversity, in most cases our understanding of their biological consequences is lacking.

‌Building on a previous synthesis (Afkhami et al. Ecology 2014), Assistant Professor Michelle Afkhami and a collaborator investigated the molecular basis of these complex multiple mutualist interactions in a recently published paper in the journal Molecular Ecology. Their work combined manipulative experiments and genomewide expression analysis to examine phenotypic and transcriptomic responses of a model legume Medicago truncatula to its interaction with nitrogen-fixing bacteria and mycorrhizal fungi. They found diverse molecular mechanisms and transcriptional responses associated with the synergistic benefits of multiple mutualists on plant growth, including genomewide signatures of mutualists and multiple mutualists on expression as well as surprising, nonadditive effects on some genes with important functions such as nutrient metabolism. For example, interacting with multiple mutualists even led to reversals in the direction of expression compared to interacting with single mutualists. Their results suggest possible biochemical mechanisms for how organisms balance these complex interactions and possible genetic targets for improvement of crop and forage plants.

Link to the paper: Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi

Image caption:

(A)    M. truncatula plants at 2.5 weeks. Left is a plant grown with both rhizobia and mycorrhizal fungi (M+R+) and right is a plant grown with neither (M-R-).
(B)    Principal components analysis of the M. truncatula genomewide expression profiles. The strong pattern of clustering by microbial treatment combination indicates that both mycorrhizal fungi (M+/-) and rhizobia (R+/-) have effects on expression across the genome. Each point indicates the transcriptome profile of an individual plant, and differences in the shapes/colors of points indicate different treatment combinations.

The Uy Lab publishes a paper on the genetic basis of convergent plumage color in island flycatchers

‌‌‌‌‌‌In a paper published in the Proceedings of Royal Society of London, Aresty Professor Al Uy with students, postdocs and collaborators show that different genetic mechanisms create the same plumage color in flycatchers from different islands in the Solomon Archipelago. In one island , a mutation in the Melanocortin-1 Receptor creates entirely black (melanic) birds, while over 100km away on a separate island, a mutation in the Agouti Signaling Protein creates the same melanic coloration (see picture to the right). In essence, evolution has found two different solutions to solve a single problem!

Link to the paper: Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers

These results are also featured in Islands of Creation, a documentary by the Smithsonian Channel.

Maytag Professor Bill Searcy is elected as the President of the Animal Behaviour Society

‌‌‌‌‌Congratulations to Maytag Professor Bill Searcy for being elected as President of the Animal Behaviour Society. Established in 1964,  the Animal Behaviour Society is a "professional organization dedicated to promote and encourage the biological study of animal behavior in the broadest sense, including studies at all levels of organization using both descriptive and experimental methods under natural and controlled conditions. Both research studies and the dissemination of knowledge about animal behavior through publications, educational programs, and activities shall be encouraged."



Dan Baldassarre, former postdoc in the Uy Lab, receives the Cooper Ornithological Society’s Young Professional Award

‌‌‌Congratulations to Dan Baldassarre, former postdoc in the A. Uy Lab, for receiving the Cooper Ornithological Society’s Young Professional Award!! As a National Science Foundation postdoctoral fellow from 2014 to 2016, Dan worked on the evolution of blood feeding in Darwin’s Finches. Stay tuned for results from this exciting work – but, in the mean time, here’s a link to the synopsis of his prestigious award:

The Cooper Ornithological Society’s Young Professional Award



Graduate student Luis Vargas-Castro of the Searcy Lab receives the 2016 Dean’s  Dissertation Fellowship and the 2016 Academic Excellence, Leadership and Service Award from the Graduate Student Association

‌‌‌‌Luis Vargas-Castro was selected to receive the 2016 Dean’s Academic Year Dissertation Award from the College of Arts & Sciences and the 2016 Academic Excellence, Leadership and Service Award from the Graduate Student Association. His dissertation focuses on the ecology and evolution of soft song, a complex behavior, in the avian genus Turdus. Soft vocalizations have been less studied than broadcast vocalizations because these are inconspicuous behaviors by nature and thus difficult to observe and record. However, soft singing is a widespread behavior among different animal taxa for which still little is known in animal communication. Luis’ work integrates behavioral, ecological and evolutionary processes, by analyzing the effects of ecological and morphological factors that shape animal signals. After doing fieldwork in Costa Rica and working with worldwide acoustic libraries, his research will provide experimental tests of important hypotheses that explain the properties of animal sounds and new insights on the evolution of complex behavioral traits.

Luis is currently a graduate student in William Searcy’s lab. His research has been supported by the Kushlan Graduate Research Fund, Savage Graduate Research Fund and a Research Fellowship from the Organization for Tropical Studies.

More about his research work can be found on his website.

Luis recording birds songs in his field site in Costa Rica.


Graduate students Jason Presnell and Kaitlyn Warren publish a paper in Current Biology

Ctenophores have historically been described as having a blind, sac-like gut. Using live imaging of ctenophore digestion in their report, Presnell et al. demonstrate that ctenophores possess a functionally tripartite through-gut, challenging the current paradigm that assumes that the through-gut originated within Bilateria.

Link to the paper: The Presence of a Functionally Tripartite Through-gut in Ctenophora Has Implications for Metazoan Character Trait Evolution


Dallman lab publishes a new article on neurological disorders in the journal Frontiers of Molecular Neuroscience

‌‌The Dallman Lab with first author Rob Kozol and contributions from Alex Abrams, David James, Qing Yan, and Elena Buglo publish a solicited review "Function over form: Modeling groups of inherited neurological disorders in zebrafish" in a special issue of the journal Frontiers in Molecular Neuroscience.

Link to the paper: Function over form: Modeling groups of inherited neurological disorders in zebrafish


News from the McCracken Lab


Philip Lavretsky, postdoctoral researcher in Kushlan Chair Kevin McCracken’s lab, will begin a tenure-track faculty position at the University of Texas El Paso on 1 August 2016.

Postdoc Neal Dawson has received a prestigious two-year NSERC fellowship from the Government of Canada to his work on high-altitude hypoxia resistance.

Congratulations to Philip and Neal!


The Association for the Study of the Cuban Economy Awards Biology and Engineering Undergraduate Students 1st Place for their Collaborative Research

‌‌From the College of Arts and Science’s press release:

Research suggest ways to improve Havana’s wastewater issues and earns top honors in national competition

Suggesting improvements to Cuba’s dilapidated wastewater infrastructure is at the core of University of Miami biology and engineering students Nayara Sabrina and Alexandra Westbrook’s award-winning research paper entitled, “Havana’s Wastewater Treatment Plants: Changes Over Time and Estimate of Replacement Cost.”

The paper earned Sabrina and Westbrook first place prize in the undergraduate student category from the Association for the Study of the Cuban Economy (ASCE) 2016 Jorge Perez-Lopez Graduate and Undergraduate Student Award Competition.

“I am super happy for this great opportunity. We did not expect to win the first place in the competition,” said Sabrina. “We wrote this paper because we had a lot of new information about Havana´s wastewater system, so we wanted to publish it to contribute to this area of research.”

Follow this link to read the full article: Link


Sarah Cowles, graduate student in the Uy Lab, receives a grant from the Lewis & Clark Fund

Graduate student Sarah Cowles (JAC Uy Lab) received a grant from the Lewis & Clark Fund for Exploration and Field Research to help support her dissertation research on white-eyes of Solomon Islands. Sarah is combining long-term field research with cutting-edge next generation sequencing approach to explore hybridization between two species of white-eyes that have come into contact in Kolombangara Island in the Western Province of the Solomons (see picture to the left). Her ultimate goal is to understand the interplay between gene flow and isolation in mediating the evolution of new species.


Catalina Vasquez, graduate student in the Sullivan Sealy Lab, receives a grant from the National Geographic Society for a field expedition in Colombia

Catalina Vasquez, Doctoral Student from the Sullivan Sealey Lab (UM Biology), received funding from the National Geographic Society  for a 45-day field expedition of the La Guajira peninsula in Colombia. She will run a rapid coastal assessments of the unique seagrass environments critical to juvenile green turtles. La Guajira coastal environs are unusual in the tropical western Atlantic for  supporting upwelling, and high productivity of marine plants, and invertebrates in the robust ecosystem supporting rapid growth of juvenile sea turtles. La Guajira, a hot, dry environment, has a sparse human population. Scattered settlements of the Wayuu tribe in Uribia region of La Guijira, Colombia has self-government of the clans, but many members live in poverty and fish in small boats from ports and embayments  along the long rocky shore.  The expedition creates partnership with the University of Miami, INVEMAR, Conservation International and the Wayuu Sea Turtle Stewards (based in Bahia Hondita). The expedition will build a long-term collaboration for resource management and bring attention to threats to juvenile green turtles.

La Guijira is remote with few opportunities for researchers to visit. The peninsula represents a point of exchange between sea turtle population in the western Caribbean, and eastern tropical Atlantic. Conditions in this ecosystem could support high growth rates in juvenile turtles, and thus be key in the regional production and survival of green sea turtles. The extent of impacts on both turtles and the benthic environments from petroleum pollution (from Lago Maracaibo), solid waste, and fishing are unknown.  This expedition will produce a preliminary threats assessment, and initiate longer-term partnerships with the Wayuu for resource stewardship. The expedition runs from 4 July to 19 August, 2016, with the field work headed by Catalina and assisted by Associate Professor Kathleen Sullivan Sealey and Mr. Jacob Patus from the Coastal Ecology Laboratory (Biology, UM). Ms. Manuela Pelaez, a UM alumnus (2013) of the Abess Center for Ecosystem Science and Policy, and director to the Fundacion Pez Leon in Colombia, will head the fishermen interview component.


The journal Ecological Modelling  dedicates an entire issue to Research Professor Don DeAngelis to honor his prominent contributions to the field

From the Press Release:

A special edition of the journal Ecological Modelling has been dedicated to Donald DeAngelis, US Geological Survey Research Ecologist, in honor of his 70th birthday. A prominent contributor to the journal, DeAngelis has played a decisive role in the progression of ecological and mathematical modelling, specifically related to individual-based approaches.

“Don’s contributions to Ecological Modelling – and the field of modelling – over the last four decades are invaluable,” said Volker Grimm, a professor at the Helmholtz Center for Environmental Research - UFZ, and co-editor of the special edition. “The current state of the art wouldn’t be where it is without his work.”

To read the rest of the article, follow this link:

Special Issue of Ecological Modeling


Dept of Biology and UGalapagos Alumnus Devika Kaul receives a competitive Fulbright Research Grant to develop waste management in the Galápagos Islands

Devika Kaul, an alumnus of the UGalapagos program, has received a Fulbright research grant in the field of Environmental Studies. She will spend 10 months on the Galápagos Islands conducting a comprehensive study of waste management.

Solid waste management is one of the many conservation challenges the islands face, affecting both public health and the fragile ecosystem of the Galápagos. While efforts have been made to implement waste management and recycling programs, electronic waste (e-waste) disposal is a growing concern that has not yet been addressed. Devika will examine e-waste disposal practices across the Galápagos and quantify the associated ecological impacts. She hopes to gain insight on developing long term, sustainable e-waste management solutions that are both economically and environmentally favorable for the Galapagos archipelago. She will also work to engage the community in her project and promote awareness among residents on issues of environmental preservation.

Devika believes this research can be used to support the development of environmental policies, public health initiatives, education efforts and conservation programs related to e-waste management throughout Ecuador.


BiologyBiology undergrads, Rowanne Ali, Layla Nassar, and Grace Jean, receive an award to develop outreach tools to inspire young women for STEM careers  at the Clinton Global Initiative  2016

Biology undergraduate students (from left to right in the picture below), Layla Nassar, Rowanne Ali and Grace Jean received an award from the Resolution Social Venture Challenge hosted at the Clinton Global Initiative 2016 to develop a program to inspire  young women for careers in STEM. Women in Next Generation Sciences (WINGS) strives to spark an interest in STEM disciplines in early adolescent women of the greater Miami area. WINGS has developed an after school program to be hosted at local middle schools that will expose students to interactive physics curricula, foster team-building and creativity via robotics, and advance personal development through mentorship-based support networks. Together, these initiatives will empower and prepare young women for further study in applied sciences.


Graduate student Natalia Borrego and Professor Michael Gaines' work on the evolution of intelligence in big cats is featured in a news piece in ScienceNow

From the News Piece:

‌Good Social Skills Make Animals Smarter

by Virginia Morell

Using tools doesn’t make humans, dolphins, and crows smart. Rather, it’s the stress and challenge of living with others—recognizing friend from foe, calculating who to deceive and who to befriend—that led these and other social creatures to evolve their cognitive skills. That’s the gist of the social intelligence hypothesis, an idea that’s been around since 1966. But does having to remember whose lice need picking actually improve other mental abilities, like figuring out how to open a locked box with a hunk of meat inside? A new study of four carnivores—two social and two solitary species—suggests that it does.

“They’ve taken an important issue and tested it in a simple but novel way,” says Richard Byrne, an evolutionary psychologist at The University of St. Andrews in the United Kingdom, who was not involved in the study. “The results are clear: The cognitive benefit from being a social carnivore does transfer” to a mental ability that has nothing to do with being social, he says.

To read the rest of the article, follow this link:

Good Social Skills Make Animals Smarter


Graduate student Jason Sardell and Aresty Professor Al Uy publish a paper characterizing hybridization between two birds species in the journal Evolution

‌Although it is frequently assumed that individuals of different species do not interbreed, hybridization is known to occur naturally in many taxa, which can have important consequences for the evolution of species. In a manuscript featured on the cover of the February issue of Evolution (left), graduate student Jason Sardell and Aresty Professor Al Uy investigate the consequences of recent contact between two bird species, the Myzomela honeyeaters of the Solomon Islands. The study confirms that the two species continue to hybridize more than a century after the red-and-black Cardinal Myzomela colonized the range of the all-black Sooty Myzomela, even though the species diverged millions of years ago. Genetic sequencing revealed that all successful hybridization involved pairings of female Cardinal Myzomela with male Sooty Myzomela, resulting in introgression of black plumage color into the former species. This resulted in the creation of “cryptic hybrids”: all black females that are genotypically more closely related to the Cardinal Myzomela. In addition, Jason published a paper in Pacific Science, in which he used observations of recent range expansions among Solomon Islands birds to identify routes by which species colonize new islands. Together, these two manuscripts provide insights into the dynamics and consequences of contact between previously-isolated species, an important, but poorly-understood stage in the evolution of biodiversity.

Sardell, J.M. and J.A.C. Uy. (2016) Hybridization following recent secondary contact results in asymmetric genotypic and phenotypic introgression between island species of Myzomela honeyeaters. Evolution 70(2): 257-269 Link

Sardell, J.M. (2016) Recent dispersal events among Solomon Islands bird species reveal differing potential routes of island colonization. Pacific Science 70(2).Link


Graduate student Natalia Borrego and Professor Michael Gaines publish a paper in Animal Behaviour exploring cognition in large cats

‌A chapter from Natalia Borrego's dissertation research was published in the journal Animal Behaviour.  Natalia's research was the first to experimentally compare innovation in closely related social and nonsocial species.  Their findings support the Social Intelligence Hypothesis and an evolutionary link between cognitive complexity and social complexity, even in solving ecological challenges.

Link to Social Carnivores Outperform Asocial Carnivores on an Innovative Problem