Haw Chuan Lim

Responses of avian guilds to urbanisation in a tropical city

Avian ecology in tropical urban area is poorly understood. We determined, through surveys in 29 sites, how birds with different dietary and nesting requirements responded in terms of guild richness and abundance to various facets of urbanisation in Singapore. The sites selected were representative of the full range of urbanisation outside of the undisturbed native forests. Among the dietary guilds, we found that insectivores and carnivores were adversely affected by increased urbanisation. Frugivores were favoured by low-density housing, probably because more fruit-bearing ornamental plants were planted in such estates. Richness and abundance of shrub and shrub/tree nesters, and primary cavity excavators declined with increased urbanisation. We believe that the availability of nesting sites was an important factor in their decline. Exotic species accounted for only 13% of the total species richness detected in our surveys but they were numerically dominant (accounting for 61% of overall bird abundance). Abundance of native resident birds declined monotonically with increasing amount of built-up environment while birds of exotic species appeared to be more abundant in sites with intermediate amount of built-up environment. While urban greenery serves architectural and other functions, it has little effect on overall bird community assembly. The preponderance of exotic species in Singapore city suggests that birds of tropical rainforests are poor colonisers of this relatively novel environment. Many of the native urban species originated from mangrove and coastal scrub forests, so the maintenance of rainforests is necessary for the preservation of many native bird species.

REVISITING WALLACE'S HAUNT: COALESCENT SIMULATIONS AND COMPARATIVE NICHE MODELING REVEAL HISTORICAL MECHANISMS THAT PROMOTED AVIAN POPULATION DIVERGENCE IN THE MALAY ARCHIPELAGO.

Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long‐standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea‐levels during the Last Glacial Maximum (LGM) exposed land‐bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo‐riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.

Undesirable aliens: factors determining the distribution of three invasive bird species in Singapore

Biological invasions are a major environmental concern due to their negative impacts on biodiversity and economics. We determined the population sizes and habitat-abundance relationships of the three most successful invasive bird species in Singapore: the house crow Corvus splendens, white-vented myna Acridotheres javanicus and common myna A. tristis. Estimated population sizes of the three species between February 2000 and February 2001 were between 106 000-176 000, 122 000-155 000 and 20 000-29 000, respectively. Population size of the house crow grew dramatically (>30-fold) in the last 15-16 y while that of the white-vented and common myna declined. Habitat-abundance relationships suggest that house crows are highly dependent on anthropogenic food. Their abundance was also positively related to proximity to coast. The common myna associated closely with agricultural areas while the white-vented myna probably preferred urban greenery among residential buildings. Our study shows that the three invasive bird species associated with different aspects of human-modified environment.

Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia.

Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co‐distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now‐submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross‐shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post‐divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid‐Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630–690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.

Abundance and projected control of invasive house crows in Singapore

The Indian house crow (Corvus splendens) has successfully invaded tropical and subtropical regions well beyond its native range, reaching pest proportions in many areas. The invasive population of house crows in Singapore (Southeast Asia) has increased at least 30-fold since 1985 and now numbers in excess of 130,000 birds. To understand the population ecology and behavior of the house crow in Singapore, we undertook regular population size and roost surveys, dissections of birds shot (to provide age structure and breeding status), detailed nestsite observations, and monitoring of coastal dispersal. Using a discrete-time, density-dependent population model to synthesize this information, we demonstrated that at least 41,000 crows will need to be culled in the first year of a control program, and equivalent effort committed each year thereafter, to be confident of suppressing the Singapore population from its 2001 density of 190 birds/km(2) to the management target of <10 birds/km(2) within a 10-year period. This figure drops to 32,000 if culling is combined with other management strategies such as resource limitation and nest destruction. Complete eradication of the house crow from Singapore may be an unrealistic goal due to potential difficulties in detecting crows at IOW population densities and influx of migrants from neighboring Malaysia. Our study has implications for pest-bird management in other cities in Asia, Africa, and the Middle East, and presents it surrogate population-dynamics management tool for use in regions where the house crow has become established as a pest species, but where limited local field data is available.

Molecular phylogeny and insular biogeography of the lowland tailorbirds of Southeast Asia (Cisticolidae: Orthotomus)

The lowland tailorbirds of Southeast Asia (Orthotomus) offer an excellent opportunity for comparative biogeography because of their diversity in the Greater Sunda and Philippine islands. We reconstructed the phylogeny of all species in the genus using maximum likelihood, Bayesian, and coalescent methods on DNA sequences of three gene segments: an autosomal intron (TGF), a Z-linked intron (MUSK), and a mitochondrial coding gene (ND2). Although resolution is low in parts of the phylogeny, several well defined clades emerge. When considered in light of distribution, these clades indicate that the Greater Sunda and Philippine islands were occupied early in Orthotomus history by the ancestors of O. sericeus in the Greater Sundas and O. frontalis in the Philippines. Subsequently, tailorbirds diversified further in each island group: O. atrogularis, O. ruficeps, and O. sepium arose in the Greater Sundas, and O. castaneiceps castaneiceps, O. c. chloronotus, O. derbianus, O. samarensis, O. nigriceps, and O. cinereiceps in the Philippines. Among the continental taxa (including Sundaic birds), the older lineages (O. sutorius and O. sericeus) are habitat generalists and the recently evolved taxa are more specialized. In the Philippines, several taxa once considered conspecific with O. atrogularis turn out to be highly divergent species (>9% in ND2). Indeed, all Philippine allospecies are well diverged from one another. This finding supports the recent assertion of higher-than-appreciated bird endemicity in the Philippines.

DIVERSIFICATION OF AN ENDEMIC SOUTHEAST ASIAN GENUS: PHYLOGENETIC RELATIONSHIPS OF THE SPIDERHUNTERS (NECTARINIIDAE: ARACHNOTHERA)

ABSTRACT. The phylogeny of spiderhunters (Nectariniidae: Arachnothera) was reconstructed by comparing mitochondrial and nuclear DNA sequences of all currently recognized species and with broad geographic sampling of two particularly variable species complexes, the Little Spiderhunter (Arachnothera longirostra) and the streaky spiderhunters (A. modesta and A. affinis). It appears to be a relatively old group, whose diversification was not caused by recent sea-level changes. However, the modern, highly sympatric distribution of the large species in the Sunda lowlands was probably a result of dispersal via recent land bridges. Within the highly variable A. longirostra group, there are substantially diverged taxa in the Philippines that should be considered different species. Within the A. affinis—modesta complex, there are three distinct species and a closely related fourth, which describe a clear allopatric distribution: A. affinis in Java, A. modesta in the rest of the Sunda lowlands (except Sabah), A. magna in the Malayan highlands and mainland Southeast Asia, and A. everetti in the Bornean highlands and Sabah. Depending on whether mitochondrial or nuclear genes were compared, monophyly of the genus was disrupted by a single outgroup sunbird (Hypogramma hypogrammicum) or by all outgroup sunbirds included in the study. The discrepancy between nuclear and mitochondrial results is probably a case of deep coalescence and will require additional markers for resolution.

Phylogeny and biogeography of the Asian trogons (Aves: Trogoniformes) inferred from nuclear and mitochondrial DNA sequences.

We present the first species-level molecular phylogenetic hypothesis for the Asian trogons, using DNA sequences of multiple mitochondrial and nuclear loci, and Bayesian and maximum likelihood tree reconstruction methods. The two genera of Asian trogons, Harpactes and Apalharpactes, are distantly related to each other. Within the widespread Southeast Asian genus Harpactes, we recovered three species groups: (1) H. oreskios; (2) H. orrhophaeus and H. duvaucelii; and (3) a clade of the seven large-bodied species. Short internal branch lengths link species in the large-bodied group, suggesting rapid diversification. Apalharpactes, which is currently restricted to the montane forests of Sumatra and Java, appears to be a relictual lineage distantly related to all other trogons. Bayesian and maximum likelihood analyses indicate Apalharpactes is sister to the African genus Apaloderma, although this result was not strongly supported. Overall, the extant Asian trogon species appear to have diversified prior to the Pleistocene, based on large pair-wise mitochondrial divergences between taxa.

Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae)

ABSTRACT The Mountain Black-eye (Chlorocharis emiliae) is an endemic white-eye (Zosteropidae) of Borneo with a unique “sky island” distribution. We compared mitochondrial ND2, ND3, Cytb, and control region DNA sequences (2,194 nucleotides) to study the phylogeographic relationships of five populations of this species that span its range: Mounts Kinabalu, Trus Madi, Murud, Mulu, and Pueh. These comparisons showed that black-eyes are divided into two main clades that correspond generally to subspecific morphological groups: one in Sabah, Malaysia (Kinabalu and Trus Madi), and one in Sarawak, Malaysia (Murud, Mulu, and Pueh). The genetic and morphologic subdivision of black-eyes disputes the expected merging of populations during the Last Glacial Maximum (LGM), when montane forest presumably expanded and provided the opportunity for currently isolated populations to intermingle. Instead the genetic aging of black-eye populations indicates they diversified long before the LGM, and either did not expand sufficiently in range during the LGM to reach one another, or were reproductively isolated by the time of the LGM and thus prevented from interbreeding. Moreover, the subdivision between black-eyes in Sabah and Sarawak means that this species (and probably several other montane species) has a phylogeographic structure remarkably similar to Borneos lowland bird populations, which are presumed to have evolved under different paleo-geographic conditions. The similar phylogeographic pattern found in both montane and lowland species requires that we rethink the causes of bird population diversification on the island of Borneo.

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

ABSTRACT The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively during Quaternary glacio-eustatic land connections, whereas the Bornean and Palawan populations did not. Unlike the other Greater Sunda Islands, Palawan has not been attached by a land bridge to the rest of Sundaland for at least one million years, and its relative isolation has prevented extensive intermixing between Palawans and other Sunda populations. Thus, the Palawan population appears to be on its own evolutionary trajectory. The ability to demonstrate extensive interbreeding among some Sunda island populations, but not others, illustrates the practicality of testing Gills (2014) “null hypothesis” that morphologically distinct populations on different islands are different species unless a compelling argument can be made to the contrary. In this case, Rufous-tailed Tailorbird morphology provided little or misleading evidence of the extent of interbreeding, whereas modern genetic analysis provided a clear view.