Historical Biogeography, Phylogenetics and SE Asian Birds

Indomalaya is biologically hyperdiverse. It contains many biodiversity hotspots, including Indo-Burma, South-Central China, the Philippines, Sundaland and Wallacea. Hotspots differ from each other with respect to their geographic settings and historical forces that drove speciation. By combining field collecting with phylogenetics analyses, we are just beginning to understand the various patterns of avian species diversification, and the biogeographic and ecology processes that underlie them.

Publications

Shakya, S. B., H. C. Lim, R. G. Moyle, M. A. Rahman, M. Lakim, and F. H. Sheldon. 2019. A cryptic new species of bulbul from Borneo. Bulletin of the British Ornithologists’ Club 139:46-55.

Sheldon, F.H., H.C. Lim and R.G. Moyle. 2015. Return to the Malay Archipelago: the biogeography of Sundaic rainforest birds. Journal of Ornithology (International Ornithological Congress Special Issue) 156:91-113

Peterson, A. T., R. G. Moyle, F. Lei, L. C. Campillo, P. A. Hosner, L. B. Klicka, H. C. Lim, A. S. Nyari, Y. QU, S. Reddy, F. H. Sheldon, and F. Zou. 2015. Avian evolution and speciation in the Southeast Asian tropics. Current Zoology 61:898-900.

Sheldon, F. H., C. H. Oliveros, S. S. Taylor, B. McKay, H. C. Lim, M. A. Rahman, H. Mays, and R. G. Moyle. 2012. Molecular phylogeny and insular biogeography of the lowland tailorbirds of Southeast Asia (Cisticolidae: Orthotomus). Molecular Phylogenetics and Evolution 65:54-63

Moyle, R.G., Taylor, S.S., Oliveros, C.H., Lim, H.C., Haines, C.L., Rahman, M.A. and Sheldon, F.H. 2011. Diversification of an insular Southeast Asian clade: Phylogenetic relationships of the Spiderhunters (Aves: Nectariniidae). Auk: 128:777-788

Hosner, P. A., F. H. Sheldon, H. C. Lim, and R. G. Moyle. 2010. Phylogeny and biogeography of the Asian trogons (Aves: Trogoniformes) inferred from nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 57:1219-1225

 Lim, H.C., F. Zou, B. D. Marks, et al. 2010. Biogeography of the magpie-robins and shamas (Aves: Turdidae: Copsychus and Trichixos): role of the Philippines and pre-Pleistocene events in the diversification of Southeast Asian forest birds. Journal of Biogeography 37:1894-1906.

 Sheldon, F.H., H.C. Lim, J. Nais, et al. 2009. Observations on the distribution, ecology, and urbanization of forest birds in Sabah, Malaysia.Raffles Bulletin of Zoology 57: 577-586.

Sheldon, F.H., D.J. Lohman, H.C. Lim, et al. 2009. Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier and unusual dispersal patterns in the Indian Ocean and Southeast Asia. Journal of Biogeography 36: 1070-1083

Navjot S. Sodhi, D. Astuti, A. C. Diesmos, et al. 2007. Barcoding Indo-Malayan birds. Raffles Bulletin of Zoology 55: 397-398

Zou, F., H. C. Lim, B. D. Marks, R. G. Moyle, and F. H. Sheldon. 2007. Molecular phylogenetic analysis of the gray-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: a case of remarkable genetic divergence in a “species”. Molecular Phylogenetics and Evolution 44:165-174 

Phylogeography, population genetics and speciation 

Studies are also done at the within-species level. Population genetics and genomics analyses are combined with other methods to understand how geography, historical processes and environmental variation structure genetic diversity of a species. In addition, the region also contains multiple suture zones (places where hybrid zones of different species pairs co-occur). Variation in suture zone characteristics and species-pair ages allows us to probe different dimensions of the speciation process and how it is shaped by different underlying drivers (e.g., divergent selection vs. allopatric speciation). Such studies increasingly rely on a variety of next generation techniques - historical DNA extraction, sequence capture, restriction fragment sequencing and whole genome sequencing to generate data. 

Publications

Parker, L. D., M. T. R. Hawkins, M. Camacho-Sanchez, et al. 2020. Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient. Mol. Ecol. 29:4074-4090.

Lim, H. C., S. B. Shakya, M. G. Harvey, R. G. Moyle, R. C. Fleischer, M. J. Braun, and F. H. Sheldon. 2020. Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA. Ecology and Evolution 10:3222-3247.

Lim, H. C., D. F. Gawin, S. B. Shakya, M. G. Harvey, M. A. Rahman, and F. H. Sheldon Sundaland’s east-west rain forest population structure: Variable manifestations in four polytypic bird species examined using RAD-Seq and plumage analyses. Journal of Biogeography 44:2259-2271.

Sundaland's east-west rainforest population structure: Variable manifestations in 4 polytypic bird species examined using RAD-Seq and plumage analysis. Poster presented at NAOC 2016 (Washington DC)

Phylogeographic analysis of  mitogenomes of  five tropical Asian bird species. Poster presented by Smithsonian Research Experiences for Undergraduates intern Elizabeth Reardon.

Lim, H.C. and M.J. Braun. 2016. High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements. Molecular Ecology Resources (Sequence Capture Special Issue) 16:1204-23

Lim, H.C., F. Zou, F.H. Sheldon. 2015. Genetic differentiation in two widespread, open-forest bird species of Southeast Asia (Copsychus saularis and Megalaima haemacephala): Insights from ecological niche modeling. Current Zoology (Special East Asian and SE Asian issue): 61:922-934.

Lim, H. C., V. L. Chua, et al. 2014. Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) of Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general. The Auk 131:629-642.

Lim, H.C. and F.H. Sheldon 2011. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Molecular Ecology 20: 3414-3438.

Lim, H. C., M. A. Rahman, S. L. H. Lim, R. G. Moyle, and F. H. Sheldon. 2011. Revisiting Wallace's haunt: Coalescent simulations and comparative niche modeling reveal historical mechanisms that promoted avian population divergence in the Malay archipelago. Evolution 65:321-334.

Lim, H. C., F. H. Sheldon, and R. G. Moyle. 2010. Extensive color polymorphism in the Southeast Asian Oriental dwarf kingfisher Ceyx erithaca: a result of gene flow during population divergence? Journal of Avian Biology 41:305-318.