publications

2026

1. Persistent selection on size explains micro-and macroevolutionary alignments in fly wings

   Haoran Cai

   bioRxiv, 2026

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2. Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates

   Haoran Cai, and David L Des Marais

   Genome Biology and Evolution, 2026

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3. Highlight: Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals

   Haoran Cai

   Genome Biology and Evolution, Apr 2026

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2025

1. Disentangling variational bias: the roles of development, mutation, and selection

   Haoran Cai, Diogo Melo, and David L. Des Marais

   Trends in Genetics, Apr 2025

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   The extraordinary diversity and adaptive fit of organisms to their environment depends fundamentally on the availability of variation. While most population genetic frameworks assume that random mutations produce isotropic phenotypic variation, the distribution of variation available to natural selection is more restricted, as the distribution of phenotypic variation is affected by a range of factors in developmental systems. Here, we revisit the concept of developmental bias – the observation that the generation of phenotypic variation is biased due to the structure, character, composition, or dynamics of the developmental system – and argue that a more rigorous investigation into the role of developmental bias in the genotype-to-phenotype map will produce fundamental insights into evolutionary processes, with potentially important consequences on the relation between micro- and macro-evolution. We discuss the hierarchical relationships between different types of variational biases, including mutation bias and developmental bias, and their roles in shaping the realized phenotypic space. Furthermore, we highlight the challenges in studying variational bias and propose potential approaches to identify developmental bias using modern tools.

2. Highlight: How Life’s “Mistakes” Impact Adaptation

   Haoran Cai

   Molecular Biology and Evolution, Dec 2025

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2023

1. Revisiting regulatory coherence: accounting for temporal bias in plant gene co-expression analyses

   Haoran Cai, and David L. Des Marais

   New Phytologist, Dec 2023

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2. Dissecting genetic correlation and pleiotropy through a genetic cross

   Haoran Cai, Kerry Geiler-Samerotte, and David L Des Marais

   bioRxiv, Dec 2023

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3. Digest: Multivariate genetic variation constrains adaptation to environmental changes during range expansion

   Haoran Cai, and David Des Marais

   Evolution, Aug 2023

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   How do selection and standing genetic variation shape population divergence across landscapes?Henry and Stinchcombe (2023a) estimated selection gradients on traits in the ivy-leaved morning glory (Ipomoea hederacea) in the field and compared them with the G-matrix and population divergence for four populations in North America. The authors show that population divergence and genetic covariances are largely unaligned with the selection gradient at the species’ range edge. These findings raise the question of whether limited evolvability or multivariate genetic variation of populations at range edges prevent species from range expansion, which is important for understanding the role of genetic constraint in population divergence and predicting local adaptation in the face of climate change.

2021

1. Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium

   J Grey Monroe, Haoran Cai, and David L Des Marais

   G3, Aug 2021

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2018

1. Protective Role of Antioxidant Huskless Barley Extracts on TNF-α-Induced Endothelial Dysfunction in Human Vascular Endothelial Cells

   Zhanghua Liao, Haoran Cai, Zekun Xu, and 5 more authors

   Oxidative medicine and cellular longevity, Aug 2018

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2. Systems Biology Theory Clarification of a Controversy in Pancreatic Beta Cell Regeneration

   Haoran Cai, Runtan Cheng, Ruoshi Yuan, and 2 more authors

   bioRxiv, Aug 2018

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