Current research
Understanding and conserving biodiversity is the underlying theme of my research, which primarily involves: 1) documenting plant diversity, and 2) studying evolutionary processes that shape the current plant diversity in the tropics. I incorporate a range of activities in my research, from field to the lab (wet and dry labs), exploring, cataloguing, and analyzing plant diversity under phylogenetic framework. The specimens and data gathered from the field are utilized in updating taxonomic knowledge of the plant group using morphological and molecular tools.
An updated and rich natural history of the plant group leads me to pursue some of the fundamental questions in evolutionary biology such as: What factors determine plant distribution? Why are some groups of plants widespread, but others endemic to small areas and what evolutionary novelties (traits) are associated with each pattern? How are specific traits of plants correlated with specific ecological and climatic conditions? My study system is a taxonomically difficult and highly diverse plant group, the tribe Spermacoceae (ca. 1000 species) in the fourth largest family Rubiaceae (coffee family).
Understanding and conserving biodiversity is the underlying theme of my research, which primarily involves: 1) documenting plant diversity, and 2) studying evolutionary processes that shape the current plant diversity in the tropics. I incorporate a range of activities in my research, from field to the lab (wet and dry labs), exploring, cataloguing, and analyzing plant diversity under phylogenetic framework. The specimens and data gathered from the field are utilized in updating taxonomic knowledge of the plant group using morphological and molecular tools.
An updated and rich natural history of the plant group leads me to pursue some of the fundamental questions in evolutionary biology such as: What factors determine plant distribution? Why are some groups of plants widespread, but others endemic to small areas and what evolutionary novelties (traits) are associated with each pattern? How are specific traits of plants correlated with specific ecological and climatic conditions? My study system is a taxonomically difficult and highly diverse plant group, the tribe Spermacoceae (ca. 1000 species) in the fourth largest family Rubiaceae (coffee family).
Systematics of Coffee Family (Rubiaceae)
The tribe Spermacoceae is one of the most enigmatic groups in Rubiaceae due to its wide range of morphological diversity and the long-standing taxonomic complexity with conflicting generic delimitations. The taxonomic statuses of the many genera within the tribe and the delimitation of the tribe itself have experienced a tremendous modification over time since the time of Linneaus. This often leads to complications in taxonomic names and correct identification of the species. I have been collaborating with scientists from India, Thailand, China, Belgium, Netherlands, and Sweden to address taxonomic problems existing within this group. This project resulted in two studies (Wikström et al. 2013, Neupane et al. 2015) that helped resolve most of the taxonomic inconsistences existing in the Asia-Pacific taxa of the group. This collaborative project also allowed us to collect 150 specimens (80 species) of Spermacoceae from the under-collected biodiversity hotspots in Sri-Lanka, Thailand, India, Nepal, and China. Although, we now have a better understanding of the group in the Asia and the Pacific, there is still a big gap in our taxonomic knowledge in the members representing Africa and Americas. I plan to further expand my study of Spermacoceae systematics to these areas by collaborating with herbaria and taxonomists from these regions.
Phylogenomic Congruence
Finding a reliable phylogenetic tree can be challenging due to incongruence between data subsets resulting from stochastic error (e.g. sampling artifacts) or systematic error (e.g. deep coalescence and incomplete lineage sorting that is not accommodated by the model). With the availability of large-scale genomic DNA data from high-throughput sequencing methods, the issue of incongruence becomes even more severe in phylogeny reconstruction. Although, some efficient and promising species tree methods are forthcoming, it is always advisable to assess the discordance beforehand, if any, and identify its nature (stochastic or biological) to make a meaningful interpretation of estimated phylogeny from a multi-gene phylogeny. Currently, I am investigating the issues of DNA data combinability (e.g. of different gene regions from targeted sequencing, or next-gen methods), phylogenetic information content, effect of taxonomic sampling and missing data, and the resulting systematic and stochastic bias in the phylogenetic inference under Bayesian framework. I am particularly exploring the behavior of Bayes Factor (computed using marginal likelihood values) in detecting phylogenomic congruence (alternatively discordance) using simulations designed to create a spectrum of data sets ranging from low to high phylogenetic information content and and from complete topological concordance to extreme discordance (due to deep coalescence and subsequent incomplete lineage sorting). |
Evolution in Tropical Mountains
The tribe Spermacoceae is a group of primarily herbaceous and widespread weedy plants. However, we have found that some lineages in the group are woody and are found only on mountains and have narrow distributional ranges. We found that these woody clades gained their woodiness independently from one another and are secondarily derived (a special case of character reversal from herbaceousness. Also, while heterostyly is common in the tribe, there are also cases of gender polymorphism such as the presence of subdioecious or dioecious members among islands taxa (e.g. Kadua from the Hawaiian Islands and Nesohedyotis from St. Helena island). The presence of secondary wood evolution, disproportionate species diversity, endemism of different habit forms, and diverse reproductive strategies, make the pantropical Spermacoceae an ideal system to study the tempo and mode of ancient dispersal and diversification patterns in tropical mountains and island systems. My future goals in this area is to improving existing models/methods of macroevolutionary studies for the evolution of discrete and continuous traits. This will be used to explore the set of ecological correlates that might promote woodiness and speciation among the tropical lineages that are nested within otherwise predominantly herbaceous groups across angiosperm and expand these approaches to other study systems involving macroevolutionary studies.
The tribe Spermacoceae is a group of primarily herbaceous and widespread weedy plants. However, we have found that some lineages in the group are woody and are found only on mountains and have narrow distributional ranges. We found that these woody clades gained their woodiness independently from one another and are secondarily derived (a special case of character reversal from herbaceousness. Also, while heterostyly is common in the tribe, there are also cases of gender polymorphism such as the presence of subdioecious or dioecious members among islands taxa (e.g. Kadua from the Hawaiian Islands and Nesohedyotis from St. Helena island). The presence of secondary wood evolution, disproportionate species diversity, endemism of different habit forms, and diverse reproductive strategies, make the pantropical Spermacoceae an ideal system to study the tempo and mode of ancient dispersal and diversification patterns in tropical mountains and island systems. My future goals in this area is to improving existing models/methods of macroevolutionary studies for the evolution of discrete and continuous traits. This will be used to explore the set of ecological correlates that might promote woodiness and speciation among the tropical lineages that are nested within otherwise predominantly herbaceous groups across angiosperm and expand these approaches to other study systems involving macroevolutionary studies.