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To reliably identify taxa that require attention, and to evaluate progress and/or effectiveness of conservation actions, accurate status assessments are required. Genetic research is needed for a variety of conservation targets, including guidance for breeding programmes to avoid inbreeding between closely related individuals, identification of pure (non-introgressed) individuals for breeding programmes, and identification of genetically distinct lineages deserving of protection as separate conservation units.

Javan Jungle Flycatcher (1) - Mohammad I

Cyornis banyumas / ©Mohammad Irham 

Genomic analysis of the White-rumped Shama

A recent conservation-genomic study on the White-rumped Shama (Copsychus malabaricus) (Ng et al. 2017) looked into the provenance of Singapore’s modern population of this species, which is one of the most secure populations within the range of the threatened subspecies tricolor. The data revealed that the main island of Singapore is largely inhabited by non-native individuals that were either released or escaped from the bird trade. Individuals from the north-eastern satellite islands of Singapore (Pulau Ubin and Pulau Tekong), in contrast, were shown to be genetically native.

Despite its non-native provenance, the population on the main island of Singapore is beneficial for local conservation, as the population of origin is extremely closely related genomically. This study underscored the importance of genomic techniques in determining population origins and further corroborated previous findings that the population on Sarawak (suavis) is genomically unusually distinct.

We are currently engaging in follow-up research to look into the distinctness of various small-island taxa of Shama in the West Sumatran Island chain, some of which have recently gone extinct in the wild and require urgent ex-situ breeding attention if they are to persist into the future.

The original study can be found here (under 2017):

Contact: Frank Rheindt - dbsrfe [at]

White-rumped Shama - Sin Yong Chee Keita

Copsychus malabaricus / ©Sin Yong Chee Keita 

Conservation genomic framework for Rufous-fronted Laughingthrush

Rufous-fronted Laughingthrush (Garrulax

Garrulax rufifrons / ©Jonathan Beilby

The Rufous-fronted Laughingthrush (Garrulax rufifrons), also known as Javan Laughingthrush, is endemic to the island of Java, where it is the only representative of its family. Unfortunately, the species has been targeted for its great vocal abilities and comes under heavy pressure from illegal wildlife traffickers. The species is now listed as Critically Endangered by IUCN, with the only well-known wild population consisting of a dozen or so individuals in Gunung Gede Pangrango National Park. Much of its continued survival therefore hinges on the success of an ex-situ conservation breeding program. With less than twenty individuals available globally for such a crucial effort, a main focal point of the ASTSG Genetic Research Group has been towards implementing a conservation genomic framework for the remaining captive individuals in the breeding program. Our work uses genome-wide DNA sequencing to ascertain kin relationships across founder individuals in order to prevent unwitting incestuous mating.

This comprehensive dataset also allows us to calculate optimal breeding pair combinations that seek to stave off the loss of genetic diversity which is often observed in small captive breeding schemes. In doing so, we have also been able to simulate future generations of laughingthrushes, allowing a glimpse into the likely future population-genomic outlook of the captive population. Finally, we are in the process of addressing whether the intentional interbreeding of the two existing Rufous-fronted Laughingthrush subspecies should be undertaken seriously as a form of genetic rescue for the nominate subspecies - and indeed the species as a whole.

Contact: Frank Rheindt - dbsrfe [at]

Javan Jungle Flycatcher –

the latest addition to Java’s threatened birds

Using bioacoustic and genetic approaches, we recently re-assessed the taxonomy of various tropical Asian jungle-flycatcher complexes (Gwee et al. 2019), leading to a separation of the Hill Blue-Flycatcher (Cyornis banyumas) into as many as five species. One of these, the newly-defined Javan Jungle Flycatcher (Cyornis banyumas), is threatened by the trade and has become widely extirpated throughout its known range. It will now be important for bird taxonomic authorities to catch up with this revised taxonomic treatment, allowing the Javan Jungle Flycatcher to be assessed according to IUCN criteria. Any delay in implementing these taxonomic changes will lead to a continuation of the present situation, in which the Javan Jungle Flycatcher is considered part of a larger species and not afforded a separate conservation status. 

The original study on these flycatchers can be found here
(under 2019):

Contact: Frank Rheindt - dbsrfe [at]

Javan Jungle Flycatcher (2) - Mohammad I

Cyornis banyumas / ©Mohammad Irham 

A reorganisation of the confused taxonomy of White-eyes

Sangkar White-eye - Sin Yong Chee Keita.

Zosterops melanurus / ©Sin Yong Chee Keita 

In a recent phylogenomic analysis (Lim et al. 2019), we revised the classification of multiple complicated Asian white-eye (Zosterops) complexes, leading – amongst many others – to the recognition of a newly-delimited white-eye species endemic to Java and Bali, the Sangkar White-eye (Zosterops melanurus). This species, which was previously misdiagnosed as a mere group of subspecies of the widespread Oriental White-eye (Zosterops palpebrosus), turns out to be the most heavily traded bird on earth, with easily hundreds of thousands in the trade in Java. Our study underscores the importance of correct taxonomic insights for preserving the endemic fauna of Java and other Indonesian islands heavily affected by the bird trade. 

The original study can be found here (under 2019):

Contact: Frank Rheindt - dbsrfe [at]

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