Research Projects

My research integrates fieldwork, natural history collections, genomics, and the development of digital tools to address speciation, biogeography, and conservation questions. In particular, it centers on identifying patterns of small mammal diversity and understanding speciation processes within and across islands in the Indo-Australian Archipelago. I have also engaged in projects focusing on other taxa and in different regions. Most of the tools I develop are taxon-agnostic. My collaborative work involves more than a dozen people in some projects. I strive to make research using natural history collections and genomic data accessible to students and researchers with limited technical knowledge and access to computing resources.

Small Mammal Diversity & Speciation

Understanding patterns that generate species diversity within a complex island system

Lenomys meyeri

This project studies small mammal diversity and speciation in Sulawesi and islands on the Sunda Shelf, Southeast Asia. During the Pleistocene, the islands on the Sunda Shelf—such as Sumatra, Java, and Borneo— were connected as a continuous landmass. In contrast, Sulawesi were formed from separate islands. The isolated mountains on these islands promote other opportunities for speciation. We conduct extensive fieldwork, perform genomic studies, and describe undocumented species as necessary.

My dissertation focuses on the in-situ diversification of hill rats (the Bunomys species group) in Sulawesi. I aim to improve phylogenetic resolution and understand how the island's geological history has shaped the group's diversity. Ultimately, I aim to deepen our understanding of speciation on a large, isolated island like Sulawesi and aid conservation efforts by improving our knowledge of species diversity and endemism.

Publications:
Handika et. al. ( , )
Demos et. al. ( , )
Esselstyn et. al. ( , , )
Giarla et. al. ( )
Nations et. al. ( )

Inclusive, Open, and Accessible Software

Developing digital tools empowering new learners in evolutionary studies

SEGUL app preview

My goal for this project is to promote efficient, integrative, and inclusive collection-based evolutionary studies through high-performance computing and innovative data management and data-sharing approaches. Additionally, I aim to facilitate low-cost computing practices in genomic studies, which will reduce the ecological footprint of evolutionary studies while allowing underfunded labs to benefit from the decreasing cost of genomic sequencing. I create user-friendly, memory-efficient, cross-platform apps to achieve my objectives. The development of the apps leverages emerging technologies in software development (e.g., Rust, Flutter, and CI/CD ). Furthermore, I take advantage of advancements in CPU technology and heterogenous computing to accelerate data processing and minimize reliance on expensive and power-hungry High-Performance Computing Clusters.

I developed three apps under this project: NAHPU, SEGUL, and ULLAR. NAHPU is a digital field catalog that simplifies data acquisition and management for increasingly complex collection-based evolutionary studies. The app integrates specimen, tissue, and derivative data, such as specimen photographs and audio recordings. It streamlines data management from fieldwork to the museum database, eliminating typical secondary data entry required for conventional paper-based field catalogs. SEGUL is a high-performance, memory-efficient tool for genomic studies. It is a proof of concept for a genomic tool that runs from mobile devices and personal computers to high-performance computing clusters. It enables teaching genomic analyses in environments with limited access to computing power. ULLAR is currently in the early development stage. I develop the app to minimize dependencies and simplify phylogenomic data analyses.

Publications:
Handika et al. ( )
Handika and Esselstyn ( )

GPU-Agnostic, Low-cost Machine Learning Approaches

Developing on-devices, cross-platform machine-learning methods to improve biodiversity research

Coming soon as a part of my postdoc project at Porto's lab, the University of Florida.
Herbarium Universitas Andalas

Other Projects

Projects on other taxa and regions

Specimen Digitization

This project is led by Dr. Nurainas at the Herbarium Universitas Andalas (ANDA) funded through the collection and data mobilization grant provided by the Global Biodiversity Information Facility (GBIF). We aim to digitize >65,000 sheets of the herbarium specimens at ANDA and make the data accessible through the GBIF portal.

Published datasets:
Nurainas et. al. ( , , )

Genomics and Systematics of Antbirds in the Neotropics

I am involved in two projects led by Marky Mutchler (the University of Chicago) and Ryan Zucker (Cornell University). Both students are under the supervision of Dr. Glaucia Del-Rio, the University of Florida. We aim to understand the genomic basis of speciation and systematics of antbirds in the Neotropics.