Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

Acknowledgements Y.W.L. was supported by a postgraduate scholarship research grant from the Ministry of National Development, Singapore awarded through the National Parks Board, Singapore (NParks; NParks’ Garden City Fund). Principal research funding from NParks and the School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, is acknowledged. We thank Peter Preiser, Associate Vice President for Biomedical and Life Sciences, for facilitating NTU support, and Kenneth Er, CEO of NParks, for facilitating research funding through that organisation. V.A.A. and C.L. were funded by SBS, NTU for a one-year research leave. V.A.A. and C.L. also acknowledge support from the United States National Science Foundation (grants 2030871 and 1854550, respectively). S.R. was supported by a postdoctoral research fellowship under the NTU Strategic Plant Programme. S.R. and N.R.W.C. acknowledge funding from NTU start-up and the Academy of Finland (decisions 318288, 319947) grants to J.S. Fieldwork conducted by Y.W.L. was supported by an Indonesian Government RISTEK research permit (Application ID: 1517217008) and an Access License from the Sabah State government [JKM/MBS.1000-2/2JLD.7(84)]. T.N.C.V. is grateful to the Assemblée de la Province Nord and Assemblée de la Province Sud (New Caledonia) for facilitating relevant collection permits. A.N. was partly supported by the Research Project Promotion Grant (Strategic Research Grant No. 17SP01302) from the University of the Ryukyus, and partly by the Environment Research and Technology Development Fund (JPMEERF20204003) from the Environmental Restoration and Conservation Agency of Japan. Fieldwork in Fiji conducted by R.B. was hosted and facilitated by Elina Nabubuniyaka-Young (The Pacific Community’s Centre for Pacific Crops and Trees, Fiji). We thank the NTU-Smithsonian Partnership for tree data obtained for the Bukit Timah Nature Reserve (BTNR) long-term forest dynamics plots. Administrative support provided by Mui Hwang Khoo-Woon and Peter Ang at the molecular laboratory of the Singapore Botanic Gardens (SBG) is acknowledged. Rosie Woods and Imalka Kahandawala (DNA and Tissue Bank, Royal Botanic Gardens, Kew) facilitated additional DNA samples. Daniel Thomas (SBG) and Yan Yu (Sichuan University) commented on biogeographical analyses. NovogeneAIT in Singapore is acknowledged for personalised sequencing service.Peer reviewedPublisher PD

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.Peer reviewe

Anoxia reduces whole cell permeability in cortical neurons of the anoxia tolerant turtle, Chrysemys picta belli

grantor: University of TorontoThe western painted turtle, 'Chrysemys picta belli,' is one of the most anoxia tolerant species presently known. It has been postulated that anoxia tolerant species can acutely reduce membrane ion permeability (Channel Arrest) as a means of reducing energy requirements during anoxia. To test this, whole cell conductance (Gw) was measured in turtle neurons using a whole cell patch clamp technique. Perfusion of cortical sheets with control (normoxic) saline did not result in any significant changes in Gw. However, anoxic and adenosine (200[mu]M) perfusions significantly reduced Gw, an effect which was inhibited with the inclusion of EGTA (5mM) in the recording electrode. Additionally, perfusion of cortical sheets with high levels of extracellular calcium (4,8mM) also reduced G w. To determine if the observed changes in Gw can be attributed to changes in gap junction permeability, a whole cell patch clamp technique was employed to measure changes in whole cell capacitance (Cw) during normoxic, anoxic, high adenosine (200[mu]M and high calcium (4mM) perfusions. Whole cell capacitance values calculated under these conditions did not change significantly when compared to control values. Additionally, injection of lucifer yellow into turtle brain neurons did not show dye propagation to neighbouring cells during either normoxic or anoxic perfusion. These data suggest that whole-cell conductance does decrease with the transition to anoxia in turtle brain and that the response is not entirely intrinsic to the tissue but may be systemic. Furthermore, the lack of dye propagation during conditions that decrease Gw suggests that gap junctions are not involved in the observed anoxia-mediated changes in Gw.M.Sc

Simulation of high-impact tropical weather events: Comparative analysis of three heavy rainfall events

Episodes of heavy rainfall, although relatively rare, significantly contribute to the hydrological cycle due to the large quantum of rainfall in a short span of time. Accurate simulation of such heavy or extreme rainfall events therefore is an important benchmark for a model. Here, we consider the simulation of three heavy rainfall events (Mumbai, Bangalore and Chennai) that occurred over the Indian monsoon region in different geographical locations and seasons during 2005, using a mesoscale meteorological model, namely MM5V3. Simulations have been carried out at high resolution (2 km) to resolve orographic features and land-ocean gradients over the event locations with a 3-nest, 2-way configuration. The primary objective of this study is to carry out a multi-event, multi-location evaluation of the model configuration for simulating a class of heavy rainfall events and to compare some important meteorological features of the events. Our results have shown that a very high relative humidity, low-level convergence, convective instability in terms of equivalent potential temperature, high vertical velocity, smaller mixing ratio at low level and higher mixing ratio at upper level essentially dominated and sustained the convective dynamics in all the three events. It was also found that the latent heat flux (LHF) dominated coastal events (Mumbai and Chennai) with relatively much higher values compared to sensible heat flux (SHF) throughout the event life cycle. In the case of the Bangalore event, both LHF and SHF are comparable during the event life cycle. © 2012 Springer Science+Business Media Dordrecht

Simulation of extreme temperature over Odisha during May 2015

An extreme temperature event (heat wave) over the state of Odisha was unique as it lasted for about 2 weeks in the 3rd and 4th weeks of May 2015. There was a similar severe heat wave in western and central Odisha in the month of April 1998. The interesting feature of the recent episodic heat wave is that it prevailed in the late pre-monsoon season with wider spread in the state of Odisha. Around 12–15 cities experienced a daily maximum temperature of over 45 °C during the strong heat wave period, and 25th −27th May was declared as the red box zone. In this study, we first analysed the intense summer temperature of 2015 May using India Meteorological Department observations of daily maximum temperature. The observed heat wave phenomenon was then simulated using the Weather Research and Forecast Model (WRFV3) at 2-km horizontal resolution to assess its ability to forecast such a rare event. The observational analysis clearly indicated that this episodic event was unique both in terms of intensity, geographical spread and duration. An optimized configuration of the WRF model is proposed and implemented for the simulation of the episodic heat wave phenomenon (daily maximum temperature) over the state of Odisha. The time-ensemble simulation of the temperature is shown to be in close agreement with the station-scale observations