Research / 01Four chapters · one question

Evolutionary novelties: from genotype to morphotype.

Evolution has produced remarkable structures — from the fused tail rod that lets frogs jump to the broad pelvis that lets humans walk upright. These are evolutionary novelties: structures that appear in one group of animals but have no clear counterpart in their ancestors.

My research tackles this question by combining classical approaches like comparative anatomy and embryology with cutting-edge tools such as single-cell multiomics, spatial transcriptomics, and genome-wide regulatory profiling. During my PhD, I investigated the frog urostyle — a novel skeletal element that appeared nearly 200 million years ago — uncovering how it develops and identifying the genes and regulatory networks that build it. As a postdoctoral fellow at Harvard, I turned to a structure closer to home: the human ilium, revealing the developmental shifts in the pelvis that made bipedal walking possible.

As I establish my own lab, I will continue to bridge deep evolutionary questions with modern genomic and developmental approaches.

Chapter 01Postdoc · Harvard · 2021 — present

Evolution of human bipedalismand the pelvic girdle

A multifaceted study — histology, comparative genomics, and spatial transcriptomics across 100+ embryonic tissue samples from humans and ~24 primate species — uncovering the developmental basis of the uniquely human pelvis.

Heterotopy: A 90° rotation of the cartilage growth plate produced a wide ilium instead of the tall, narrow blade seen in other primates.
Heterochrony: A shift in the timing and location of bone formation (ossification) reorganised how the ilium ossifies during development.
Genes: 300+ genes drive these changes. SOX9 and PTH1R control growth-plate reorientation; RUNX2 regulates the ossification shift.
When: The shifts likely began 5–8 million years ago, around our split from the African apes — enabling bipedal locomotion.

Senevirathne et al. 2025 — NaturePelvis

Comparative primate ilium · histology

Spatial transcriptomics — Visium spots

Marker genes · COL9A2 · THBS2

Chapter 02Postdoc · Harvard · 2025 — present

Evo-devo of bipedal jointship & knee · in prep

Two clinically critical synovial joints — the hip and the knee — examined through scRNA-seq, scATAC-seq, and high-resolution spatial transcriptomics (with Spatial HD optimised for human tissues) to map joint-specific cellular and regulatory atlases.

Atlases: Joint-specific cellular and regulatory atlases identifying conserved versus joint-specific transcriptional and chromatin networks.
Crosstalk: Cell–cell communication analyses across chondrocytes, osteoblasts, synovial fibroblasts, vasculature, and immune populations.
Disease: Single-cell regulatory networks intersected with hip and knee osteoarthritis GWAS to pinpoint the cell types and elements through which risk variants act.

Manuscripts in prepHip · Knee

UMAP · joint cell populations

Cells from developing hip and knee resolve into chondrocytes, osteoblasts, synovial fibroblasts, vasculature, and immune populations.

Xenopus tropicalis · cleared & stained (Stage 64)

Chapter 03PhD · UChicago · 2016 — 2021

Developmental origins of the anuran urostylea 200-million-year-old novelty

The urostyle — a fused bony rod at the end of the frog vertebral column — is an evolutionary novelty that arose nearly 200 million years ago. Its developmental origins had long been poorly understood.

Two parts: The urostyle comprises a mesodermal coccyx and an endodermal hypochord — two components with distinct germ-layer origins, resolving a longstanding debate.
How it forms: Neuromusculature, programmed cell death, and proliferation together drive its formation during metamorphosis.
Regulation: LCM + RNA-seq + ATAC-seq in Xenopus tropicalis tadpoles uncovered the gene-regulatory networks that distinguish the coccyx from the hypochord and drive its ossification.

Senevirathne et al. 2020 · 2024 — PNAS · Open BiologyFrog · Urostyle

Chapter 04Undergrad / MPhil · Sri Lanka · 2009 — 2014

Amphibian natural history & diversificationSri Lanka · India

Where my research journey began — natural history, systematics, and diversification of amphibians in one of the world's great biodiversity hotspots.

Discovery: Contributed to the description of the previously unknown fossorial tadpoles of the Indian dancing frog family Micrixalidae — eel-like, sand-burrowing larvae whose identity had eluded biologists for over 125 years.
Metamorphosis: Documented the dramatic skeletal transformation of the Indian purple frog (Nasikabatrachus sahyadrensis) — torrent-clinging tadpoles becoming fossorial adults.
Diversity: Molecular phylogenetics of Sri Lankan shrub frogs (Pseudophilautus) — how geography, historical climate, and allopatric isolation shaped an island's frog diversity.

Multiple publicationsAmphibians