Hi, I'm Heru Handika
Postdoctoral Researcher · AI Biodiversity Informatics , Florida Museum of Natural History, University of Florida
You can call me Heru or Hez. I'm an evolutionary biologist working at the intersection of field biology, genomics, phenomics, on-device deep learning, and cross-platform software. I study how geographic isolation shapes genomic divergence, ecological interactions, and phenotypic evolution in island small mammals, and build open-source tools so these questions can be tested at scale.
Research highlights
From Specimens to Scalable Biodiversity Science
Island speciation
An island of islands
My main system is the Bunomys rats of Sulawesi, where paleo-islands, tectonic plate movements, and mountain formation drove an in situ radiation. Through collaborations, I also support work on island shrews and other rodents.
24+ mammal species described or revised with collaborators
Received the 2023 Murie Family Conservation Award (ASM) for conserving mammals and their habitats
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AI phenomics
Reading evolution from specimen images
I use image embeddings to study coloration phenotypes from digitized specimens and test evolutionary hypotheses at scale.
619,739 specimen images across 9,342 species
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Fieldwork & collections
13 years in remote mountains
Collaborative expeditions across more than 20 mountain systems in Southeast Asia, building the specimen records and field experience that underly my research and software development.
8,000+ voucher specimens and 30,000+ specimen parts
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Open software
From phones to HPC clusters
SEGUL, NAHPU, ULLAR, and the MDD app make genomic analysis and biodiversity data management efficient and accessible through user-friendly applications and command-line tools.
3.6M lines of code added across public repositories
SEGUL received the 2024 Ernst Mayr Award (SSB)
Explore →Leadership & mentorship
On the cold mountains and the computer terminal
I've been lucky to work with amazing collaborators and local communities, and to mentor biology and computer science students. Together, we haul over 800 kg of supplies up barely visible trails to unsurveyed mountains, and build software that works for everyone across changing hardware and operating systems to answer new scientific questions.
Research questions
- How do paleo-islands, tectonic plate movements, and mountain formation drive speciation? My genomic work on Sulawesi’s endemic Bunomys rodents, many of which are restricted to individual mountains, reveals in situ diversification but mixed support for the island’s classic areas of endemism. Next, I plan to test whether their parasites diversify with them or switch hosts, and how they shape infection down to the level of individual host cells.
- How do complex phenotypes evolve across species? Using deep learning, I extract image embeddings from digitized butterfly specimens to map wing-pattern morphospace and identify known mimics among visually similar species, establishing a framework I aim to extend to study color evolution in island rodents.
- How can biodiversity data be collected and analyzed on any device, by anyone? Free, open-source tools that run on anything from a phone to a computing cluster and install in one click or a single command, from NAHPU in the field to SEGUL for phylogenomic data, and beyond.