I am interested in the fundamental rules of evolutionary processes, using biological evolution and language evolution as two study systems. Current research question is how changes at population level build up to patterns observed among lineages. This question links population genetics and phylogenetics, and links social linguistics and historical linguistics. In general, I develop models and methods in inferring evolutionary processes from different data types. I'm also collaborating on using chemical evolution to reconstruct the formation of the galaxy.
Available student projects are:
- New generation of molecular dating: molecular dating uses mutations in DNA to date the tree of life. Existing molecular dating only uses fossil to calibrate time. The new generation of molecular dating will use species traits to calibrate mutation rate.
- Deep coalescence problem: deep coalescence is when genes are not completely sorted before the speciation event. This causes conflicts between species divergence time and gene divergence time. The project will develop efficient method to solve deep coalescence problem.
- Identifying speciation genes: speciation genes are the genes that make two species not able to reproduce offspring. The project will use coalescent theory and birth death model to identify speciation genes from its evolutionaty history.
- Heterogeneous continuous-time random walks: model species dispersal over heterogeneous landscape, while allowing individuals to have different birth rate and death rate. The solution allows us to reconstruct species responses to past climate change.
- DE19: Developing methods to link microevolutionary rate to macroevolutionary pattern: understanding how fixation of mutations at population level leads to genetic distinctiveness among species and how the generation of new species leads to observed patterns in biodiversity over long timescale.
- DP19: Developing the fourth generation of methods for molecular dating: use allometry to inform variation in the rate of molecular evolution across lineages.
- Pilot study for DP21: Developing methods to simultaneously infer niche evolution and ancestral species distribution.
Room 4.80, Hanna Neumann Building 145
- Bromham, L, Dinnage, R, Skirgard, A et al. 2022, 'Global predictors of language endangerment and the future of linguistic diversity', Nature Ecology & Evolution, vol. 6, pp. 163-173.
- Hua, X, Meakins, F, Algy, C et al. 2022, 'Language change in multidimensional space: New methods for modelling linguistic coherence', Language Dynamics and Change, vol. 12, no. 1, pp. 78-123.
- Ivan, J, Moritz, C, Potter, S et al. 2021, 'Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks', Evolution, vol. 76, no. 2, pp. 252-261.
- Ritchie, A, Hua, X, Cardillo, M et al. 2021, 'Phylogenetic diversity metrics from molecular phylogenies: modelling expected degree of error under realistic rate variation', Diversity and Distributions, vol. 27, pp. 164-178.
- Bromham, L, Skeels, A, Schneemann, H et al. 2021, 'There is little evidence that spicy food in hot countries is an adaptation to reducing infection risk', Nature Human Behaviour, vol. 5, pp. 878-891.
- Hua, X & Bromham, L 2020, 'Modeling colonization rates over time: Generating null models and testing model adequacy in phylogenetic analyses of species assemblages', Evolution, vol. 74, no. 12, pp. 2605-2616.
- Bromham, L, Hua, X, Algy, C et al 2020, 'Language endangerment: a multidimensional analysis of risk factors', Journal of Language Evolution, vol. 5, no. 1, pp. 75-91.
- Bromham, L, Hua, X & Cardillo, M 2020, 'Macroevolutionary and macroecological approaches to understanding the evolution of stress tolerance in plants, Plant Cell and Environment, https://doi.org/10.1111/pce.13857
- Hua, X, Greenhill, S, Cardillo, M et al. 2019, 'The ecological drivers of variation in global language diversity', Nature Communications, vol. 10, no. 2047, pp. -.
- Meakins, F, Hua, X, Algy, C et al 2019, 'Birth of a contact language did not favor simplification', Language (Washington), vol. 95, no. 2, pp. 294-332.
- Bromham, L, Duchene, S, Hua, X et al 2018, 'Bayesian molecular dating: opening up the black box', Biological Reviews, vol. 93, pp. 1165-1191.
- Greenhill, S, Hua, X, Welsh, L et al 2018, 'Population size and the rate of language evolution: A test across indo-European, Austronesian, and Bantu Languages', Frontiers in Psychology, vol. 9, no. 576, pp. 1-18pp.
- Hua, X & Lanfear, R 2018, 'The influence of non-random species sampling on macroevolutionary and macroecological inference from phylogenies', Methods in Ecology and Evolution, vol. 9, no. 5, pp. 1353-1362pp.
- Bromham, L, Hua, X, Cardillo, M et al 2018, 'Parasites and politics: Why cross-cultural studies must control for relatedness, proximity and covariation', Royal Society Open Science, vol. 5, no. 8, pp. 1-22pp.
- Hua, X & Bromham, L 2017, 'Darwinism for the genomic age: Connecting mutation to diversification', Frontiers in Genetics, vol. 8, no. 12, pp. 12-12.
- Duchene Garzon, D, Hua, X & Bromham, L 2017, 'Phylogenetic estimates of diversification rate are affected by molecular rate variation', Journal of Evolutionary Biology, vol. 30, no. 10, pp. 1884-1897pp..
- Greenhill, S, Wu, C, Hua, X et al 2017, 'Evolutionary dynamics of language systems', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 42, pp. E8822-E8829.
- Lanfear, R, Hua, X & Warren, D 2016, 'Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses', Genome Biology and Evolution, vol. 8, no. 8, pp. 2319-2332pp.
- Bromham, L, Hua, X & Cardillo, M 2016, 'Detecting Macroevolutionary Self-Destruction from Phylogenies', Systematic Biology, vol. 65, no. 1, pp. 109-127.
- Day, E, Hua, X & Bromham, L 2016, 'Is specialization an evolutionary dead end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists', Journal of Evolutionary Biology, vol. 29, no. 6, pp. 1257-1267.
- Hua, X & Bromham, L 2016, 'PHYLOMETRICS: an R package for detecting macroevolutionary patterns, using phylogenetic metricsand backward tree simulation', Methods in Ecology and Evolution, vol. 7, no. 7, pp. 806-810pp.
- Hua, X 2016, 'The impact of seasonality on niche breadth, distribution range and species richness: A theoretical exploration of Janzen's hypothesis', Proceedings of the Royal Society of London Series B: Biological Sciences, vol. 283, no. 1835, pp. 20160349-20160349.
- Bromham, L, Dinnage, R & Hua, X 2016, 'Interdisciplinary research has consistently lower funding success', Nature, vol. 534, no. 7609, pp. 684-687.
- Saslis-Lagoudakis, H, Hua, X, Bui, E et al. 2015, 'Predicting species' tolerance to salinity and alkalinity using distribution data and geochemical modelling: a case study using Australian grasses', Annals of Botany, vol. 115, no. 3, pp. 343-351.
- Bromham, L, Hua, X, Fitzpatrick, T et al 2015, 'Rate of language evolution is affected by population size', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 7, pp. 2097-2102.
- Bromham, L, Hua, X, Lanfear, R et al 2015, 'Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants', The American Naturalist, vol. 185, no. 4, pp. 507-524.
- Moray, C, Hua, X & Bromham, L 2015, 'Salt tolerance is evolutionarily labile in a diverse set of angiosperm families', BMC Evolutionary Biology (now BMC Ecology and Evolution), vol. 15, no. 1, pp. 1-10.
- Hua, X, Cowman, P, Warren, D et al 2015, 'Longevity Is Linked to Mitochondrial Mutation Rates in Rockfish: A Test Using Poisson Regression', Molecular Biology and Evolution, vol. 32, no. 10, pp. 2633-2645.
- Cahill, A, Aiello-Lammens, M, Fisher-Reid, M et al 2014, 'Causes of warm-edge range limits: Systematic review, proximate factors and implications for climate change', Journal of Biogeography, vol. 41, no. 3, pp. 429-442.
- Cahill, A, Aiello-Lammens, M, Fisher-Reid, M et al 2013, 'How does climate change cause extinction?', Proceedings of the Royal Society of London Series B: Biological Sciences, vol. 280, no. 1750, pp. 20121890-20121890.
- Hua, X & Wiens, J 2013, 'How does climate influence speciation?', The American Naturalist, vol. 182, no. 1, pp. 1-12.
- Hua, X & Wiens, J 2010, 'Latitudinal variation in speciation mechanisms in frogs', Evolution, vol. 64, no. 2, pp. 429-443.
- Wiens, J, Kuczynski, C, Hua, X et al 2010, 'An expanded phylogeny of treefrogs (Hylidae) based on nuclear and mitochondrial sequence data', Molecular Phylogenetics and Evolution, vol. 55, no. 3, pp. 871-882.
- Li, J, He, Q, Hua, X et al 2009, 'Climate and history explain the species richness peak at mid-elevation for Schizothorax fishes (Cypriniformes: Cyprinidae) distributed in the Tibetan Plateau and its adjacent regions', Global Ecology and Biogeography, vol. 18, no. 2, pp. 264-272.
- Hua, X, Fu, C, Li, J et al 2009, 'A revised phylogeny of holarctic treefrogs (Genus Hyla) based on nuclear and mitochondrial DNA sequences', Herpetologica, vol. 65, no. 3, pp. 246-259.
- Hua, X, Wang, W, Yin, W et al 2009, 'Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north-western Pacific', Journal of Fish Biology, vol. 75, no. 2, pp. 354-367.
- Xie, J, Zhang, M, Zhou, T et al 2007, 'Sno/scaRNAbase: A curated database for small nucleolar RNAs and cajal body-specific RNAs', Nucleic Acids Research, vol. 35, no. SUPPL. 1, pp. D183-D187.
- Fu, C, Hua, X, Li, J et al 2006, 'Elevational patterns of frog species richness and endemic richness in the Hengduan Mountains, China: Geometric constraints, area and climate effects', Ecography, vol. 29, no. 6, pp. 919-927.