FRANK RHEINDT

FRANK RHEINDT

FRANK RHEINDT

Associate Professor and Dean’s Chair

Contact Information:

Department of Biological Sciences
National University of Singapore
14 Science Drive 4
Singapore 117543

Lab: Avian Evolution Lab

6516 2853
6779 2486
dbsrfe@nus.edu.sg

Lab Information:

Members of the Rheindt Lab have in common a fascination for biodiversity and its underlying evolutionary processes. With the on-going biodiversity crisis on our planet, we are also interested in how knowledge of evolutionary processes can inform conservation.

Most of our research activities focus on the mechanisms that lead to – or sometimes act against – the build-up of biodiversity, such as genetic differentiation and introgression. Birds are our main model organism because their well-known distribution and life-history make them a suitable object for evolutionary studies. Pursuing a research project at my lab usually involves the application of a variety of laboratory approaches and contemporary computational tools, with a more recent focus on phylogenomic methods using Next-Generation sequencing approaches. Fieldwork is often, but not always, an important component of my students’ work.

Some of the projects the Rheindt Lab is involved in include:

(1) Genetic introgression: Genetic introgression is increasingly recognized as a pervasive phenomenon in evolutionary processes such as speciation and in the introduction of novelty into the gene pool. One of our main study foci is to examine the mechanisms of introgression. In particular, we are interested in the spatio-temporal patterns of introgression given different geographic and ecological conditions, and in whether selection or neutral processes are the main driver of introgression. We employ emerging technologies such as Next-Generation Sequencing in our introgression research.

One of the introgression models we have worked with is a clade of Neotropical tyrant-flycatchers (Zimmerius). Using a dataset of thousands of homologous markers from across the genomes of 12 flycatcher individuals, we have looked at signs of genetic introgression in a flycatcher population that is intermediate between two species. In the near future, we will be using similar approaches on a multitude of South-east Asian bird models.

(2) Complex radiations and leapfrog patterns: Advances in sequencing technology have opened up challenging new areas in evolutionary biology. We are about to analyze biogeographic leapfrog patterns and complicated explosive radiations in South-east Asian birds that are recent and therefore challenging to trace with traditional molecular markers. Using sequence data of genomic proportions and emerging analytical techniques, it will be possible to disentangle the evolutionary history of such complex radiations in unprecedented detail and explore the genomic landscape of differentiation and the neutral and selectional factors that may have shaped their diversification process.

(3) Biogeography in Wallacea: The Wallacean Region has had a major influence on our understanding of biogeography. Using his insights on animal distribution – especially birds – Alfred Russel Wallace delimited the area’s biogeographic regions along an improbable dividing line. Even so, the region’s avifauna remains virtually unexplored from a phylogenetic and population genetic perspective. This region has had a tumultuous earth-historic trajectory, involving impressive faunal turnover at localized as well as regional levels. Our aim is to use a thorough geographic sampling regime of birds coupled with modern phylogenomic methodology to illuminate regional biogeographic patterns against an earth-historic and paleo-climatic background of changing island connections. The results of this research will provide a solid foundation for understanding how biogeographic processes shape regional turnover.

Recent Publications (2019 – early 2021)

2021

  1. Rheindt FE, Ahyong ST, Azevedo-Santos VM, Bertling M, Bouchard P, Evenhuis N, Harvey M, Irham M, Krell F-T, Pape T, Peterson AT, Prawiradilaga DM, Pyle R, Rasmussen P, Welter-Schultes F, Winker K. 2021. Response to O’Connell et al. (2020): There are multiple ways to adapt taxonomy to conservation goals. Biodiversity and Conservation 30: 249-251.

  2. Ng DYJ, Švejcarová T, Sadanandan KR, Ferasyi TR, Lee JGH, Prawiradilaga DM, Ouhel T, Ng EYX, Rheindt FE*. 2021. Genomic and morphological data help uncover extinction-in-progress of an unsustainably traded hill myna radiation. Ibis 163: 38-51.

  3. Gwee CY, Lee QL, Mahood SP, Hung Le Manh, Tizard R, Krairat Eiamampai, Round PD, Rheindt FE*. 2021. The interplay of colour and bioacoustic traits in the differentiation of a Southeast Asian songbird complex. Molecular Ecology 30: 297-309.

2020

  1.  Gwee CY, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Irestedt M, Lei F, Bloch LM, Lee JGH, Irham M, Haryoko T, Soh MCK, Peh KS-H, Rowe KMC, Ferasyi TR, Wu S, Wogan GOU, Bowie RCK, Rheindt FE. 2020. Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity. eLife 9: e62765.

  2. Sadanandan KR, Low GW, Sridharan S, Gwee CY, Ng EYX, Yuda P, Prawiradilaga DM, Lee JGH, Tritto A, Rheindt FE. 2020. The conservation value of admixed phenotypes in a critically endangered species complex. Scientific Reports 10:15549.

  3. Wu MY, Low GW, Forcina G, van Grouw H, Lee BPY-H, Oh RRY, Rheindt FE. 2020. Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population. Evolutionary Applications 13: 2300-2315.

  4. Yue AY, Ng EYX, Eaton JA, Rheindt FE. 2020. Species limits in the Elegant Pitta (Pitta elegans) complex from Wallacea based on bioacoustic and morphometric analysis. Avian Research 11: 42.

  5. Cros E, Ng EYX, Oh RRY, Tang Q, Benedick S, Edwards DP, Tomassi S, Irestedt M, Ericson PGP, Rheindt FE*. 2020. Fine-scale barriers to connectivity across a fragmented South-East Asian landscape in six songbird species. Evolutionary Applications 13: 1026-1036.

  6. Shingate P, Ravi V, Prasad A, Tay B-H, Garg KM, Chattopadhyay B, Yap L-M, Rheindt FE, Venkatesh B. 2020. Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution. Nature Communications 11: 2322.

  7. Ng EYX, Yue AY, Eaton JA, Gwee CY, van Balen B, Rheindt FE. 2020. Integrative taxonomy reveals cryptic robin lineage in the Greater Sunda islands. Treubia 47: 39-52.

  8. Cros E, Chattopadhyay B, Garg KM, Ng NSR, Tomassi S, Benedick S, Edwards DP, Rheindt FE*. 2020. Quaternary land bridges have not been universal conduits of gene flow. Molecular Ecology 29: 2692-2706.

  9. Garg KM, Chattopadhyay B, Koane B, Sam K*, Rheindt FE*. 2020. Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea. BMC – Evol. Biol. 20: 82.

  10. Rheindt FE*, Gwee CY, Baveja P, Ferasyi TR, Nurza A, Rosa TS, Haminuddin. 2020. A taxonomic and conservation re-appraisal of all the birds on the island of Nias. Raffles Bulletin of Zoology 68: 496-528.

  11. O’Connell DP, Kelly DJ, Kelly SBA, Analuddin K, Karya A, Marples NM, Rheindt FE, Martin TE. 2020. An assessment of the avifauna of the Wakatobi Islands, South-east Sulawesi, Indonesia: species recorded and taxonomic considerations. Raffles Bulletin of Zoology 68: 574-587.

  12. Tan HZ*, Low GW, Sadanandan KR, Rheindt FE*. 2020. Population assessment of the house crow, Corvus splendens, in Singapore. Malayan Nature Journal 72: 133-142.

  13. Tang Q, Fung T, Rheindt FE*. 2020. ResDisMapper: An R package for fine-scale mapping of resistance to dispersal. Molecular Ecology Resources 20: 819-831.

  14. Verma M, Symes WS, Watson JEM, Jones KR, Allan JR, Venter O, Rheindt FE, Edwards DP, Carrasco LR. 2020. Severe human pressures in the Sundaland biodiversity hotspot. Conservation Science and Practice: e169. 

  15. Chattopadhyay B*, Garg KM, Ray R, Mendenhall IH, Rheindt FE*. 2020. Novel de novo genome of Cynopterus brachyotis reveals evolutionarily abrupt shifts in gene family composition across fruit bats. Genome Biology and Evolution 12: 259-272.

  16. Rheindt FE*, Prawiradilaga DM, Ashari H, Suparno, Gwee CY, Lee GWX, Wu MY, Ng NSR. 2020. A lost world in Wallacea: Description of a montane archipelagic avifauna. Science 367: 167-170.

  17. Irham M, Ashari H, Suparno, Trainor CR, Verbelen P, Wu MY, Rheindt FE*. 2020. A new Myzomela honeyeater (Meliphagidae) from the highlands of Alor Island, Indonesia. Journal of Ornithology 161: 313-324.

2019

  1. Rheindt FE, Baveja P, Ferasyi TR, Nurza A, Rosa TS, Haminuddin, Ramadhan R, Gwee CY. 2019. The extinction-in-progress in the wild of the Barusan Shama Copsychus [malabaricus] melanurus. Forktail 35: 30-37.

  2. Chiok WX, Miller AE, Pang SEH, Eaton JA, Rao M, Rheindt FE. 2019. Regional and local extirpation of a formerly common Sundaic passerine, the Straw-headed Bulbul Pycnonotus zeylanicus. Forktail 35: 3-11.

  3. Zhang D, Tang L, Cheng Y, Hao Y, Xiong Y, Song G, Qu Y, Rheindt FE, Alström P, Jia C, Lei F. 2019. ‘Ghost introgression’ as a cause of deep mitochondrial divergence in a bird species complex. Molecular Biology and Evolution 36: 2375-2386.

  4. Chattopadhyay B*, Garg KM, Ray R, Rheindt FE*. 2019. Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats’ genetic diversity. Proceedings of the Royal Society B 286: 20190304.

  5. Tan HZ, Ng EYX, Tang Q, Allport GA, Jansen JJFJ, Tomkovich PS, Rheindt FE*. 2019. Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitat types. Scientific Reports 9: 18172.

  6. Garg KM, Sam K, Chattopadhyay B, Sadanandan KR, Koane B, Ericson PGP, Rheindt FE*. 2019. Gene flow in the Müllerian mimicry ring of a poisonous Papuan songbird clade (Pitohui; Aves). Genome Biology and Evolution 11: 2332-2343.

  7. Chattopadhyay B, Garg KM, Mendenhall IH, Rheindt FE*. 2019. Historic DNA reveals Anthropocene threat to a tropical urban fruit bat. Current Biology 29: R1-R3.

  8. Ng EYX, Le Manh Hung, Wu S, Rheindt FE. 2019. First nest description and altitudinal range extension of the south Indochinese endemic Black-headed Parrotbill Psittiparus margaritae. BirdingASIA 31: 91-93.

  9. Rheindt FE, Eaton JA. 2019. The taxonomy of the Blood-breasted Flowerpecker Dicaeum sanguinolentum complex. BirdingASIA 31: 36-39.

  10. Çilingir FG*, Seah A, Horne BD, Som S, Bickford DP, Rheindt FE*. 2019. Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin. Ecology and Evolution 9: 9500-9510.

  11. Gwee CY, Eaton JA, Ng EYX, Rheindt FE*. 2019. Species delimitation within the Glaucidium brodiei owlet complex using bioacoustic tools. Avian Research 10: 36.

  12. Gwee CY, Eaton JA, Garg KM, Alström P, van Balen S, Hutchinson RO, Prawiradilaga DM, Manh Hung Le, Rheindt FE*. 2019. Cryptic diversity in Cyornis (Aves: Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches. Zoological Journal of the Linnean Society 186: 725-741.

  13. Sadanandan KR, Küpper C, Low GW, Yao C-T, Li Y, Xu T, Rheindt FE*, Wu S*. 2019. Population divergence and gene flow in two East Asian shorebirds on the verge of speciation. Scientific Reports 9: 8546.

  14. Ericson PGP, Qu Y, Rasmussen PC, Blom MPK, Rheindt FE, Irestedt M. 2019. Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex. BMC – Evolutionary Biology 19: 151.

  15. Chattopadhyay B, Garg KM, Soo YJ, Low GW, Frechette JL, Rheindt FE*. 2019. Conservation genomics in the fight to help the recovery of the critically endangered Siamese crocodile Crocodylus siamensis. Molecular Ecology 28: 936-950.

  16. Baveja P, Tang Q, Lee JGH, Rheindt FE*. 2019. Impact of genomic leakage on the conservation of the endangered Milky Stork. Biological Conservation 229: 59-66.

  17. Koh JJ-M, Rheindt FE, Ng EYX, Webb EL. 2019. Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state. Raffles Bulletin of Zoology 67: 14-31.

  18. Lim BTM, Sadanandan KR, Dingle C, Leung YY, Prawiradilaga DM, Irham M, Ashari H, Lee JGH, Rheindt FE*. 2019. Molecular evidence suggests radical revision of species limits in the great speciator white-eye genus Zosterops. Journal of Ornithology 160: 1-16.