Mark Holder, Ph.D. - US grants

In this project, a team of investigators will develop new algorithms and software to simultaneously align DNA sequences and reconstruct phylogenetic trees. This methods and theory-oriented project addresses an important problem in phylogenetic reconstruction: relatively poor performance of existing tools in the face of insertions, deletions, and duplications in large datasets. This project will develop a simultaneous approach to DNA sequence alignment and phylogenetic analysis that will allow researchers to overcome these problems. Specific goals for the project will be to develop a portal and open-source software for simultaneous alignment and phylogenetic analysis, develop new simulators to model DNA sequence evolution, establish a working group on alignment methods with the Assembling the Tree of Life (AToL) community, and develop training programs in alignment and phylogeny estimation with outreach activities to minority institutions. The project includes many members of the Cyberinfrastructure for Phylogenetic Research (CIPRES) project and will provide significant new analytic capabilities for that data resource.

By making simultaneous alignment and phylogenetic analysis feasible for very large datasets, this project will provide software tools that will serve a broad community of researchers conducting phylogenetic analyses of DNA sequence data. These tools will enable consideration of DNA regions for phylogenetic analysis that cannot be aligned using existing tools. An open-source, portal interface will open multiple sequence alignment and tree-building to a broader range of users and engagement of existing AToL users will provide input and evaluation early in the software development process.

The Philippine Archipelago represents a natural model system for the study of the processes of diversification. The islands harbor one of the greatest concentrations of biodiversity in the world and have a dynamic, yet well-understood, geological history. During the last 500,000 years, sets of islands in the Philippines have been repeatedly connected and isolated by changing sea levels. The researchers will use molecular data from populations of six species (three lizards and three frogs) co-distributed across one such set of islands and novel analytical techniques to test hypotheses about how recent climate change and associated sea-level change has influenced diversification in this dynamic system.
This research will yield insights into the processes responsible for the formation of new species, and investigate the effect of climate and sea-level change on biodiversity. This information is vitally important for understanding the long-term effects that current climate change will have on global biodiversity. One of the analytical techniques developed for this research will represent an important tool for delimiting species in a way that is both biologically and statistically meaningful, which will have important implications for both basic and conservation research.

The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

Biological research of all kinds, including studies of ecological health, environmental change, and human disease, increasingly depends on knowing how species are related to each other. Yet there is no single resource that unites knowledge of the tree of life. Instead, only small parts of the tree are individually available, generally as printed figures in journal articles. This project will provide the global community of scientists who study the tree of life with a means to share and combine their results, and will enable large-scale studies of Earth's biodiversity. It will also create a resource where students, educators and citizens can go to explore and learn about life's evolutionary history.

Rapid evolutionary radiations allow tremendous insights into speciation and biogeographic history. However, reconstruction of evolutionary relationships in such radiations has often been challenging owing largely to short periods of time between lineage-splitting events. Preliminary simulations show that using DNA sequence data from hundreds of gene regions helps improve estimates of genealogical relationships between species in rapid radiations. This study aims to resolve relationships within the bird family Zosteropidae, a group characterized by the fastest speciation rate known among land vertebrates. Investigators will use next generation sequencing technology to collect DNA sequence data from hundreds of genomic regions to illuminate evolutionary relationships among members of the family.
Resolution of genealogic relationships within Zosteropidae is vital to opening novel research avenues in historical biogeography across several archipelagos in the Old World. More broadly, this research can provide methodological insights into paths toward resolving relationships in other rapid evolutionary radiations. This study provides an excellent training opportunity for undergraduate students supported by KU?s Office of Diversity in Science Training. Through this project the investigators will help prepare undergraduates from underrepresented groups for careers in science through mentoring in collecting and analyzing data, as well as in presenting and publishing research.

While a rich set of statistical models have been developed to study evolution using DNA sequence data, many biological questions require information from organisms which are only known from the fossil record. In this project, the investigators will build models that account for biases inherent in using trait data from fossil species. The models will be tested and evaluated using the exceptionally rich fossil record associated with two groups of trilobites. Existing statistical tools will be extended to take full advantage of the estimates of the age of fossils. The new methods will be incorporated into widely used, open source software. Online educational materials in the form of virtual labs will be developed and distributed on the web.

This project will improve the computational and statistical machinery required to integrate information from fossil species into studies of the evolutionary tree of life. This will allow researchers to study extinction and speciation with unprecedented precision. Understanding these processes is crucial to understanding how Earth's biota will respond to the current biodiversity crisis. The virtual labs will teach junior high school students what data from these beautifully preserved organisms teaches us about evolutionary processes.

Parasites are everywhere and many species have been with their hosts for a long evolutionary time and are extremely particular about the kinds of hosts they parasitize. Somewhat unexpectedly, recent research suggests that many parasite species do not necessarily share a similar evolutionary history with their hosts; rather other factors may be at play in shaping these parasitic associations. Yet, little is understood about which other factors, such as diet or geographic distribution, influence these relationships. This is largely because a method for assessing the importance of other factors is not currently available. This research will develop a method and will test it using a well-known and species-rich system consisted of the tapeworms of sharks and stingrays. This method will be widely applicable to other coevolutionary systems, helping to further our understanding not only of host-parasite systems in general, but also of other biological systems involving intimate associations. Close species associations are ubiquitous and better knowledge on the role of the environment in shaping species associations will be critical to forecasting biodiversity's response to climate change. The research will train postdoctoral researchers and graduate students in quantitative techniques in evolutionary biology.


This project moves towards a more mechanistic modeling of the biological influences involved in the coevolution between parasites and hosts. Phylogenies will be generated for a large number of cestode genera, time-calibrated phylogenies will be generated for their corresponding shark and ray (elasmobranch) hosts and robust parasite-host association data will be compiled. New methods and open-source software tools using approximate Bayesian computation will be developed to allow the estimation and testing of models for the evolution of parasite-host systems. The models for parasite evolution will be geographically explicit and will include factors such as cospeciation, environmentally driven extinction, geographic constraints on dispersal and host-switching, and some effects of intermediate hosts. These rich empirical data sets will allow the use of robust, cross-validation methods for hypothesis testing. The end result will be a methodological framework for assessing the contributions of multiple factors, in addition to cophylogeny, in structuring host associations and parasite evolution. The new software will be used to address three main research questions regarding factors that underlie parasite-host interactions including the relative roles various factors play in systems with different properties.