Robb Brumfield - US grants

The development of new biotechnologies such as the polymerase chain reaction (PCR) and automated DNA sequencing have greatly facilitated the ability of basic researchers to study genetic variation. New genetic markers of potentially great relevance to biologists are known as single nucleotide polymorphisms (SNPs). To put them to the test, Robb Brumfield, in his NSF Research Starter Grant, proposes to use SNPs (pronounced "snips") to understand the evolutionary history of a group of brilliantly plumaged birds known as manakins that inhabit the rainforests of the New World Tropics. Previous studies of these birds have found that hybridization and sexual selection have both played important roles in their speciation. SNPs should provide the needed resolution to determine which process has played the more important role.

Brumfield's results will provide insights into the evolution of secondary sexual traits (i.e. traits that evolve because females prefer them but which are not necessarily in the best interest of the male for survival; a male peacock's tail is a good example). Because secondary sexual traits could evolve directly by female's desiring those traits or indirectly through hybridization with a closely related species that has a desirable trait, disentangling the relative importance of those processes is critical for a detailed understanding of their evolution. Brumfield's results should also help other biologists determine whether SNPs represent the best type of genetic marker for their own evolutionary studies of natural populations.

This award provides support for acquisition of a modern capillary DNA sequencing instrument capable of determining nearly 200,000 bases a day at 98.5% accuracy, and also capable of high throughput fragment analysis including that of microsatellites and single nucleotide polymorphisms. The instrument will be used in a number of ongoing projects, including an NSF-funded Tree of Life sequencing project aimed at producing a molecular phylogeny of all birds. The instrument will be used. In addition to its role in research, the instrument will be used for training at the high school, undergraduate, graduate, and post-doctoral levels. The instrument will replace an existing slab-gel instrument that has been heavily used for studies of population genetics and evolutionary genomics of avian systems, co-evolutionary genetics of mammals and their parasitic lice, and evolutionary genetics of reptiles and amphibians. The new instrument will provide a several-fold increase in the sequencing capacity that can be brought to bear on these and other projects at the Museum of Natural History.

Darwin's finches of the Galapagos Islands stand as one of the most impressive examples of evolution. After colonizing the islands, a single ancestral finch species eventually diversified into 13 species of different sizes, bill shapes, and ecologies. Imagine if the distribution of that ancestral species was not limited to a small set of islands, but instead had the entire continent of South America in which to diversify! That is exactly what happened with a group of birds known commonly as the ovenbirds and woodcreepers (family Furnariidae). From a single ancestral species, there are now 326 species that differ wildly in body shape and size, feeding behavior, and nest architecture. The primary goal of the project is to use DNA sequences to reconstruct the evolutionary history of all 326 species of ovenbirds and woodcreepers. Over 97% of the ovenbird and woodcreeper species are found within South America so that an evolutionary tree of all 326 species will permit a detailed understanding of the historical processes that led to the impressive radiation.


A vital component of this collaborative project between U.S., Brazilian, and Venezulean scientists is the research training it will provide. With fieldwork planned in Bolivia, Brazil, Chile, Colombia, Peru, Suriname, and Venezuela, young scientists from North and South America will be exposed not only to a diversity of natural environments but will also interact and forge relationships with their international peers. By working together to reconstruct perhaps the most spectacular evolutionary radiations of birds in the world, the researchers will learn how evolution works on a continental scale while training a new generation of scientists. This project has been partially supported by the Office of International Science and Engineering at NSF.

Studies of hybridization between model organisms have been extremely important to our understanding of the formation of new species, but are unlikely to fully capture how speciation and hybridization proceed in natural systems. In the proposed project, the researchers investigate the genetic basis of reproductive isolation between Indigo (Passerina cyanea) and Lazuli (P. amoena) buntings (Aves: Cardinalidae), which form a hybrid zone where their breeding ranges overlap. Preliminary data suggest that different genetic loci (mitochondrial, nuclear autosomal, nuclear Z-linked) exhibit differential introgression across the hybrid zone and implicate the Z-chromosome as having a relatively large impact on avian speciation. Here, patterns of genetic introgression of multiple Z-linked loci will be combined with theoretical predictions to test hypotheses aimed at identifying genes contributing to reproductive isolation between these species.

Beyond the impact the research will have on our understanding of the evolution of reproductive isolation between closely related species, the data collected will also allow for assessments of range expansion in P. cyanea. Observational data suggests the breeding range of P. cyanea is expanding westward, perhaps at the expense of P. amoena, such that an accurate knowledge of the patterns of hybridization between them may be important for conservation purposes.

Why is biological diversity so rich in the tropics? One piece of this puzzle may be found in patterns of bird distributions. In South America, the ranges of many lowland bird species are delimited by rivers and large mountain chains. For example, a birdwatcher on the east bank of the Negro River may observe the White-throated Toucan but, if they crossed to the west bank, they would instead find Cuvier's Toucan. A similar species turnover is noticed when crossing from the lowland rainforests west of the Andes to those east of the Andes. These distribution patterns suggest that the formation of rivers and mountains may have played pivotal roles in isolating populations of birds and driving evolutionary diversification in the tropics. This research will analyze genetic data from 125 tropical bird species to examine how rivers and mountains affected species formation and diversity.

A vital component of this collaborative project is the research training it will provide to scientists in developing countries. With labwork and fieldwork planned in Brazil, Colombia, and Venezuela, scientists from North and South America will be exposed to a diversity of natural environments and techniques. The collaborations will result in increased knowledge of how tropical diversity arises and is maintained, and how habitats should be preserved to maximize diversity.

The humid forests that cover the tropical mountains of South America sustain one of the highest diversity of bird species in the world. This huge avifauna is packed in different elevation zones and stretches along the narrow strip of cloud forest of the Andes, from Bolivia to Venezuela. The geographic distributions of the birds from this habitat are fragmented by low-elevation dry valleys, which function as barriers to interbreeding between populations. The isolation imposed by these valleys has the potential to promote the genetic and phenotypic divergence of bird populations, and may ultimately result in the formation of new species. This diversification could have been intensified during the forest movements up and down the mountain slopes that resulted from climatic changes in the glacial age. For example, in the coldest periods of the glaciations, montane forests moved downslope several hundred meters bridging the gap across valley barriers and facilitating the contact of formerly isolated populations. These ideas are addressed by means of a large-scale comparative analysis of the genetics of population divergence. Approximately 250 species of birds will be studied in the slopes of two large valleys in the Andes. Five species will be the subjects of a more intensive genetic analysis to infer historical factors associated with habitat movements.

This investigation not only will provide new insights into the mechanisms driving diversification, but also will increase our knowledge of biodiversity for its conservation. Furthermore it will enhance training in biology to undergraduate female students in Colombia and Venezuela. The graduate student is mentoring two student theses and has made presentations to university and national park staff.

"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)."

In the 37 years since the DNA sequence of a gene was first identified, biologists have benefited from several waves of technological advancement in sequencing technologies. The latest of these, sequence-by-synthesis, offers dramatic improvements to both the amount and quality of data collected, and allows biologists to generate genomic data in non-model organisms for the first time. The greatest impediment to the adoption of the novel technology is computational; particularly software for post-run bioinformatics processing. This proposal will develop software that facilitates investigations into the genetic diversity within and between species. Software will be tested on next-generation sequence data collected to augment existing projects in the labs of the principal investigators; these projects seek to understand the process of speciation in organisms from North and South America.

This research will serve as a catalyst for the adoption of next-generation sequence data in phylogeography and will also benefit evolutionary biology, ecology, and conservation biology. The proposed research will provide training and valuable experience for a female bioinformatics graduate student, and will enable other researchers to utilize next-generation sequencing technologies.

The fundamental research goal of this project is to understand the relative roles of evolutionary history, geography, and ecology in producing the morphological and behavioral diversity of the antbirds (Thamnophilidae), a species-rich group of birds that inhabit lowland tropical forests of South and Central America. The integration of genetic data with morphological, behavioral, ecological, geographic, and environmental data for every species in the group will allow increased understanding of differences in vocalizations, shapes, sizes, and species numbers within the antbirds.

Understanding why some groups of organisms are more diverse than others, and why some groups exhibit more behavioral and morphological variation, is a central goal of evolutionary biology. It is well known that diversity does not evolve uniformly over time, and that differences in morphological and behavioral diversity are often correlated with the number of species in the group. It remains unclear, however, to what extent the evolution of behavioral and morphological diversity promotes the creation of new species. The integration of genetic, geographic, ecological, behavioral and morphological information, along with cutting-edge analytical approaches, in this project will allow insights into the mechanisms that generate and maintain biological diversity in the Neotropics.

The two species of marsh birds being studied live along the Gulf and Atlantic coasts. King Rails breed in freshwater marshes, while the very similar Clapper Rail breeds in saltmarshes, and the two hybridize in intermediate brackish marshes. The researchers collected and genetically analyzed birds distributed along the transition from freshwater to saltwater in Louisiana, and found evidence that adaptation to the environment may be keeping the two species from fusing into one. The goal of the funded NSF project is to find the genes underlying this adaptation and analyze them for the samples collected across the transition. The researchers will use next-generation sequencing technologies to gather large amounts of genetic data on samples already collected, and try to understand adaptation in the context of this hybrid zone.
The overall goal of the research is to better understand the process of speciation. The researchers are interested in using closely related species that are hybridizing to understand the forces maintaining the distinct species. Their long-term goal with the rails is to understand genetic differences between the two species that underlie adaptations to different salinities. The results of this study will provide the most detailed population genetic analysis of two closely related, hybridizing species of birds to date. Additionally, this will be the first genetic characterization of the avian salt gland, a specialized salt-excreting organ found in some birds. Finally, the results will provide a foundation for a multitude of future research studies of this system.

Darwin's finches of the Galápagos Islands stand as one of the most impressive examples of evolution. After colonizing the islands, a single ancestral finch species eventually diversified into 13 species of different sizes, bill shapes, and ecologies. The suboscine passerine birds exhibit a similar history, but their diversification was not limited to a small set of islands; instead they are found throughout South America, Central America, North America, and parts of the Old World. There are now 1,300 species that differ dramatically in body shape and size, feeding behavior, and nest architecture. The primary goal of this project is to use DNA sequences to reconstruct the evolutionary history of these species, and to use this model system to investigate why the tropics are so biologically diverse.

A vital component of this collaborative project between U.S. and Brazilian scientists is the research training it will provide. With fieldwork planned in Argentina, Chile, Costa Rica, Malaysia, Venezuela, and Viet Nam, young scientists from a diversity of countries will be exposed not only to a diversity of natural environments but will also interact and forge relationships with their international peers. By working together to reconstruct perhaps the most spectacular evolutionary radiations of birds in the world, the researchers will learn how evolution works on a continental scale while training a new generation of scientists.

The production of species diversity is of fundamental interest, but the factors that cause diversification are poorly understood. Diversification is known to occur at different rates depending on the species or group of species involved, and comparative study of this variation can reveal the processes that promote diversity. Comparative phylogeography is the study of diversification at the population level within different species, and it allows us to observe differences in diversification at the point where speciation occurs. The goals of this study are to use comparative phylogeography and novel methods of generating data to detect differences in diversification across species, and to analyze the factors that promote faster diversification in some species than in others. Phylogeography will be compared across sixteen Amazonian bird species with similar distributions. A new set of genetic markers scattered across the genome will be used to generate data from 24 individuals of each species. These genetic sequences will be extracted from museum tissue samples using a new method of enriching genomic DNA for sequences of interest, and then sequenced on a next-generation sequencing instrument. New analytical tools for testing models will allow us to measure the processes that are most important in driving the diversification of a given species. The massive amount of data generated by this method will allow for analysis of more complex models than could ever be analyzed previously, giving us new insight into the processes promoting species diversity.

This project provides research opportunities for undergraduate students in Louisiana and the geographic scope of the project fosters inter-institutional and international collaborations. The research provides a test of next-generation sequencing methods and a new genomic marker set, and our results will aid in the application of these methods to other study systems. New biogeographic and geographic genetic data from our work support conservation efforts in the Amazon. All specimens, audio recordings, and observational data from our fieldwork and genetic data from our lab work are deposited in publicly accessible collection and databases. We consider these resources invaluable for current and future, pure and applied research on Amazonian birds and other systems.

Determining the how species are created is key to understanding the origins and maintenance of biodiversity across the planet. This project tackles this issue by focusing on a small set of very similar tropical birds called "spinetails", which are unusual because they appear to have developed new species at an incredibly fast rate. If this rapid speciation is indeed the case, study of spinetails will likely reveal novel insights about how new species come about. Investigators will use genetic techniques and cutting-edge statistical analyses to determine the evolutionary history of spinetails. The study will foster international partnerships through sharing of genetic samples and collaborating on complicated analyses of huge genetic datasets. The study will also provide research opportunities for undergraduates interested in learning how to apply bioinformatics and statistical programming to answer fundamental questions in ecology and evolutionary biology. Results of this study will help resolve long-standing taxonomic confusion about spinetails and provide a clearer picture of South American biodiversity -- a goal of both science and conservation.

Specifically, the investigators will test two alternative hypotheses of speciation. Both hypotheses rely on geographic isolation as a key requirement and explore the ecological context in which populations become isolated. On the one hand, if two populations of the same species occur in different environments it may cause to them to diverge ecologically due to local adaptation. Alternatively, small environmental differences may exist within a species' distribution due to conserved ecological preferences. If this distribution is divided by a region outside the species' ecological preference, such as mountains for a lowland species, dispersal will be greatly restricted. These hypotheses will be tested at multiple evolutionary scales. Across Furnariidae, there is a positive relationship between the rate of ecological divergence and speciation. Importantly, the arboreal spinetails (genus Cranioleuca) exhibit rates of ecological divergence and speciation far exceeding those found in other groups in the family. Both observations support the hypothesis that ecological divergence is associated with speciation, but to test these hypotheses a densely sampled phylogeny is needed. This study will reconstruct the evolutionary relationships of the arboreal spinetails using genomic scale genetic datasets. Investigators will then employ detailed comparative analyses to determine if speciation in this group is associated with ecological divergence or conservatism.

There are over 10,000 species of birds and they are found in nearly every terrestrial environment. This remarkable diversity has served as a critical component of enhancing public engagement with science and nature, as evidenced by the multi-billion dollar output generated by bird-watching activities in the US economy. Birds exhibit complex behaviors, elaborate physical characteristics, and impressive adaptations, which has made them a major focus of modern scientific research. In current research, birds are a model system for comparative studies on a range of fundamental topics in biology. However, the missing piece of this otherwise powerful comparative biology toolkit is an accurate and complete description of the evolutionary relationships (phylogeny) among all bird species, i.e., an avian tree of life. This project will collect DNA data to fill this gap by producing a complete tree of life for all bird species in order to test hypotheses regarding the origins, diversification, and dispersal of birds around the planet. A complete tree will be transformative to fields like ornithology and evolutionary biology. This project will help prepare the next-generation of biodiversity scientists by training undergraduate, graduate, and post-doctoral scientists, and also will include numerous public outreach components including exhibits and videos. Developing learning modules and working with teachers will help bring the research into the classroom, reaching a diversity of students in several states. Finally, the researchers will make all data collected from each bird immediately available to the scientific community and the public to enable broad-scale comparative analyses and integration with other avian data sets.

"Big trees" - comprehensive species-level phylogenies - are revolutionizing the field of evolutionary biology. This project will generate genome-wide markers for 8,000 species of birds and leverage data products from other NSF-supported studies to produce a phylogenetic hypothesis for all 10,560 bird species. A well-resolved, complete, time-calibrated, species-level phylogeny of birds will allow numerous challenging hypotheses to be tested, provide the conceptual foundation for a phylogenetic revision of bird taxonomy, and permit transformative analyses aimed at elucidating the processes that generate biological diversity. Specific hypotheses to be tested using phylogenies generated by this project include 1) Neoaves underwent a rapid radiation after the K-Pg mass extinction, 2) avian diversification has been shaped by the history of intercontinental dispersal, and 3) species tree methods outperform concatenation in phylogenetic analyses of genome-scale data.

The Neotropical region includes Central and South America and the Caribbean and contains the highest diversity of birds of any region on the planet. Roughly one in three birds in the Neotropics is from a group called the suboscine passerines. The suboscines are diverse in form and function and are an important component of the bird life in habitats ranging from tropical rainforests to alpine grasslands and rocky coastlines. The origins of this diversity – the tempo and mode of species formation – have been studied through prior NSF-funded work. However, this work did not contain sufficient sampling to capture the most recent and ongoing speciation events. These recent speciation events are the most critical for evolutionary research because they tell us about where and why new species are forming currently. High-resolution sampling also provides the information necessary to identify new species and revise species classification. In this project, the investigators are completely sampling suboscine diversity, obtaining new vouchered samples and adding genomic data from 1,548 missing populations in order to resolve the species limits in the group and provide a comprehensive framework for research on diversification. This work integrates a concerted program for recruiting and retaining underrepresented students in biodiversity science in three underserved geographic areas: Appalachian Tennessee, Louisiana, and majority Hispanic communities in west Texas. It involves a new program on avian diversity at the K–12 level, development of a dedicated module on biodiversity genetics for undergraduate Genetics students, and support for graduate and post-graduate researchers to conduct research.

The unifying principle of this project is that a completely sampled phylogeny of all suboscine evolutionary units is needed to provide the foundation for systematic revision as well as improved capacity for research on speciation and evolution in the group. The researchers are leveraging the well-sampled suboscine passerine radiation (1,323 currently recognized species, plus 1,875 subspecies) to complete two primary aims. First, they are using field work, existing genomic resources, and historical DNA approaches to obtain genomic data from all 1,548 unsampled taxa, including all subspecies, in the group and estimate a complete, time-calibrated phylogeny. Second, they are using this phylogeny to conduct a re-assessment and revision of suboscine systematics at the genus, species, and subspecies levels within a hypothesis-testing framework. Because the phylogeny contains information on all lineage divergences in suboscines even those between the youngest taxa, it provides an invaluable resource for researchers interested in detailed diversification dynamics, modes of speciation, avian evolution at a range of timescales, molecular evolution, and species concepts and delimitation. The new specimens, genetic samples, and genomic data being obtained are also invaluable. Together, this work and its results are providing a high-resolution picture of how diversity has evolved in a species-rich tropical group that contributes to one of the major biodiversity hotspots on the planet.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.