Understanding Phylogeographic Histories in an Understudied Region: Historical DNA Coming to the Rescue

Blog written by Haw Chuan Lim. Featured image by Paul van Els. Read the full paper here.

Questions such as why tropical regions are so rich in biological diversity, and how historical and ecological factors shaped the origin and distribution of tropical species have intrigued scientists for generations. Thankfully, exciting improvements in molecular genetics and analytical tools over the last few decades have allowed us to progressively peel back the layers. For example, we now the know the roles large Amazonian rivers and the Andes play in terms of initiating and maintaining species divergence in South America (Naka & Brumfield, 2018).

Image by Paul van Els

Interest in the biogeography and evolutionary history of Southeast Asian plants and animals dates back to Alfred Russel Wallace and earlier. Although researchers have made great strides, especially in the last decade or so (Sheldon, Lim, & Moyle, 2015), it remains a challenge to conduct phylogeographic studies in Southeast Asia. Many areas in Southeast Asia, which is made up of biogeographic subregions such as Indochina, Sundaland and the Philippines, have not been systematically sampled because of logistic and administrative challenges. Further, the region is “feature-packed” when it comes to the diversity of biogeographic processes. In a relatively small area, Southeast Asia contains everything from oceanic archipelagos to continental areas dissected by rivers, mountain ranges and diverse habitat types. Thus, dense sampling is required to produce comprehensive understanding of the historical and geographic drivers of population divergence and speciation.

Grey-throated babbler by Dibyedu Ash, CC3.0

Because of these challenges, past studies have largely taken a piecemeal approach to phylogeographic studies. For example, work in Borneo showed that drier habitats that appeared during past glacial maxima likely caused lowland rainforest species to split into eastern and western forms (Lim et al., 2017). Some studies have shown that the Isthmus of Kra, the narrow land bridge in southern Thailand that connects Sundaland and Indochina also separates sister species or closely related populations (Manawatthana, Laosinchai, Onparn, Brockelman, & Round, 2017).

Black-headed Bubul, by Doug Janson CC3.0

In this study, we used techniques that allow us to sequence thousands of genetic markers using DNA extracted from old (from late 1800’s onwards) museum study skins to investigate phylogeography of five species of rainforest-associated passerine birds that co-occur across much of Indochina and Sundaland. While technically challenging, this approach let us achieve comprehensive and relatively even geographic sampling for each of the five species. The massive amount of genetic data generated enable high-resolution studies of population structure and historical demographic processes, thus providing insights that were previously unavailable.

Large Niltava by Ajit Hota, CC4.0

We discovered that the phylogeographic patterns of the study species largely agree with their ecological characteristics. The Black-headed Bulbul, a frugivore/insectivore species that often uses forest edges, shows little population genetic structure across the entire Sundaland and parts of western Indochina. In contrast, the Little Spiderhunter and Asian Fairy-Bluebird possess highly distinct populations in peripheral Sunda islands (Java and/or Palawan) and India. This is probably due to their intermediate dispersal abilities, which allowed them to colonize new areas, and then remain largely isolated subsequently. Such dispersal events could occur during periods of low global sea-level, which exposed land bridges. A north-south population break across the Isthmus of Kra is shared only by the two species (Gray-throated Babbler and Large Niltava) that live in hill/submontane habitats. This suggests that the low elevation of the Isthmus of Kra had contributed to population splitting or the maintenance of population separation in the two species.

Little Spiderhunter by Lip Yee Kap, CC2.0

Interestingly, the Black-headed Bulbul and Gray-throated Babbler, two species with different ecological characteristics, show an east-west break in Indochina. This break is associated with the central mountain (Tennasserim) range of Indochina or the dry Irrawaddy plains of central Myanmar. Without the use of DNA from old museum skins, the discovery of genetic breaks in this region will be very difficult because it has rarely been visited by museum scientists in recent years. In each of the five species, the deepest split dates back to 1-1.5 million years ago. This coincidence in timing suggests that region-wide environmental upheavals –likely those associated with glacial cycles – played important roles in splitting populations and structuring genetic diversity.

Asian Fairy-Bluebird by Tony Castro, CC4.0

With the accelerating loss of forest habitats across Southeast Asia, it is imperative that we improve our understanding of what makes up significant evolutionary units within species, and what historical, environmental and geographic factors caused these units to form and persist. Advances in phylogeographic studies in Southeast Asia, a biologically rich region composed of multiple biodiversity hotspots, will depend on broad geographic sampling and the use of increasingly sophisticated molecular genetics and analytical techniques.

Picture by Haw Chuan Lim

Lim, H. C., Gawin, D. F., Shakya, S. B., Harvey, M. G., Rahman, M. A., & Sheldon, F. H. (2017). 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(10), 2259-2271. doi:10.1111/jbi.13031

Manawatthana, S., Laosinchai, P., Onparn, N., Brockelman, W. Y., & Round, P. D. (2017). Phylogeography of bulbuls in the genus Iole (Aves: Pycnonotidae). Biological Journal of the Linnean Society, 120(4), 931-944.

Naka, L. N., & Brumfield, R. T. (2018). The dual role of Amazonian rivers in the generation and maintenance of avian diversity. Science Advances, 4(8), eaar8575. doi:10.1126/sciadv.aar8575

Sheldon, F., Lim, H. C., & Moyle, R. (2015). Return to the Malay Archipelago: the biogeography of Sundaic rainforest birds. Journal of Ornithology, 156 (Supplemental 1), 91-113.

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