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Kuo HC, Schoneman T, Gao LM, Gruezo WS, Amoroso VB, Yang Y, Yang KC, Chien CT, Möller M, Wang CN. A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines. Front Genet 2024; 15:1372309. [PMID: 38756448 PMCID: PMC11096487 DOI: 10.3389/fgene.2024.1372309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.
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Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Travis Schoneman
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - William Sm. Gruezo
- Plant Biology Division, College of Arts and Sciences, Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Victor B. Amoroso
- Center for Biodiversity Research and Extension in Mindanao (CEBREM), Central Mindanao University, Mindanao, Philippines
| | - Yang Yang
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan, Taiwan
| | - Kuo-Cheng Yang
- General Education Center, Providence University, Taichung, Taiwan
| | - Ching-Te Chien
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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Wei S, Zhang Q, Tang S, Liao W. Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida. BMC PLANT BIOLOGY 2023; 23:154. [PMID: 36944951 PMCID: PMC10031943 DOI: 10.1186/s12870-023-04164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hybridization is generally considered an important creative evolutionary force, yet this evolutionary process is still poorly characterized in karst plants. In this study, we focus on natural hybridization in yellow Camellia species, a group of habitat specialists confined to karst/non-karst habitats in southwestern China. RESULTS Based on population genome data obtain from double digest restriction-site associated DNA (ddRAD) sequencing, we found evidence for natural hybridization and introgression between C. micrantha and C. flavida, and specifically confirmed their hybrid population, C. "ptilosperma". Ecophysiological results suggested that extreme hydraulic traits were fixed in C. "ptilosperma", these being consistent with its distinct ecological niche, which lies outside its parental ranges. CONCLUSION The identified hybridization event is expected to have played a role in generating novel variation during, in which the hybrid population displays different phenological characteristics and novel ecophysiological traits associated with the colonization of a new niche in limestone karst.
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Affiliation(s)
- Sujuan Wei
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China.
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Chornelia A, Hughes AC. The evolutionary history and ancestral biogeographic range estimation of old-world Rhinolophidae and Hipposideridae (Chiroptera). BMC Ecol Evol 2022; 22:112. [PMID: 36192699 PMCID: PMC9528145 DOI: 10.1186/s12862-022-02066-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/15/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia-Oriental-Oceania (AOO) and Afrotropical-Madagascar-Palearctic (AMP)]. RESULT Our result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene. CONCLUSION Overall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.
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Affiliation(s)
- Ada Chornelia
- grid.9227.e0000000119573309Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden (XTBG), Chinese Academy of Sciences, Yunnan, People’s Republic of China ,grid.410726.60000 0004 1797 8419International College, University of Chinese Academy of Sciences (UCAS), Huairou, Beijing, People’s Republic of China ,grid.194645.b0000000121742757School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR People’s Republic of China
| | - Alice Catherine Hughes
- grid.194645.b0000000121742757School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR People’s Republic of China
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Kono Y, Peng CI, Oginuma K, Rubite RR, Yang HA, Chung KF. Cytological Study of <i>Begonia</i> Sections <i>Petermannia</i> and <i>Haagea</i> (Begoniaceae): Chromosome Evolution for 2<i>n</i>=30. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoshiko Kono
- The Community Center for the Advancement of Education and Research at the University of Kochi
| | - Ching-I Peng
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
| | - Kazuo Oginuma
- The Community Center for the Advancement of Education and Research at the University of Kochi
| | - Rosario R. Rubite
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila
| | - Hsun-An Yang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
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Kono Y, Peng CI, Oginuma K, Rubite RR, Tseng YH, Yang HA, Chung KF. Cytological Study of Begonia Sect. Baryandra (Begoniaceae). CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoshiko Kono
- The Community Center for the Advancement of Education and Research at the University of Kochi
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
| | - Ching-I Peng
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
| | - Kazuo Oginuma
- The Community Center for the Advancement of Education and Research at the University of Kochi
| | - Rosario R. Rubite
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila
| | - Yu-Hsin Tseng
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
| | - Hsun-An Yang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica
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Chung KF. In memoriam Ching-I Peng (1950-2018)-an outstanding scientist and mentor with a remarkable legacy. BOTANICAL STUDIES 2020; 61:14. [PMID: 32333228 PMCID: PMC7182648 DOI: 10.1186/s40529-020-00291-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
Ching-I Peng, the most prolific and internationally recognized Taiwanese plant taxonomist of his generation, passed away on May 1, 2018. Dr. Peng was an eminent worker on the taxonomy of East Asian plants and the genus Ludwigia, and the foremost expert on Asian Begonia. He served as associate editor, co-editor in chief, and editor-in-chief of Botanical Studies and its predecessor Botanical Bulletin of Academia Sinica during the period 1992-2016. He gathered over 25,000 plant specimens, name 121 plant taxa, and has left a remarkable legacy of literature, collaborations and collections. This article summarizes Dr. Peng's academic career and commemorates his enduring contribution.
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Affiliation(s)
- Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species. PLoS One 2018; 13:e0194877. [PMID: 29718922 PMCID: PMC5931476 DOI: 10.1371/journal.pone.0194877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/11/2018] [Indexed: 11/19/2022] Open
Abstract
The Philippine island of Palawan is highly biodiverse. During fieldwork there in 2011 & 2014 we found five unknown species in the large genus Begonia. The species are similar in their rhizomatous stems, four-tepaled flowers, inferior two- or three-locular ovaries with bilamellate placentas, and are assignable to Begonia sect. Baryandra. Our observations support the recognition of these as five new species endemic to Palawan: B. elnidoensis, B. gironellae, B. quinquealata, B. tabonensis and B. tenuibracteata which are described here. The five new species were added to phylogenies based Bayesian analysis of nrDNA (ITS) and chloroplast DNA (ndhA, ndhF-rpl32, rpl32-trnL, trnC-trnD), along with 45 other allied ingroup species. A majority of the species show incongruent positions in the two phylogenies, with evidence of prevalent chloroplast capture. Models show chloroplast capture is more likely in plant populations with high levels of inbreeding following a reduction in selfing rate after hybridisation; we suggest that this is a possible explanation for the massive amount of chloroplast exchange seen in our phylogeny, as Begonia species often exist as small isolated populations and may be prone to inbreeding depression. Our data also indicate a level of nuclear genetic exchange between species. The high prevalence of hybrid events in Begonia is potentially an important factor in driving genomic change and species evolution in this mega-diverse genus.
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Peng CI, Rubite RR, Lin CW, Hughes M, Kono Y, Chung KF. Three new species of Begonia sect. Baryandra from Panay Island, Philippines. BOTANICAL STUDIES 2017; 58:28. [PMID: 28664395 PMCID: PMC5491425 DOI: 10.1186/s40529-017-0182-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia species and compared them with potentially allied species. RESULTS The three species are clearly assignable to Begonia sect. Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, B. merrilliana, and B. sykakiengii. Somatic chromosomes at metaphase were determined to be 2n = 30 for B. culasiensis and 2n = 28 for both B. merrilliana and B. sykakiengii, congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene and B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. CONCLUSION The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex situ conservation collections and raising awareness with community groups.
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Affiliation(s)
- Ching-I Peng
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Nangang, Taipei, 11529 Taiwan
| | - Rosario Rivera Rubite
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Padre Faura, 1000 Manila, Philippines
| | - Che-Wei Lin
- Herbarium of Taiwan Forestry Research Institute (TAIF), Taiwan Forestry Research Institute, Taipei, 10066 Taiwan
| | - Mark Hughes
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR Scotland UK
| | - Yoshiko Kono
- The Community Center for the Advancement of Education and Research at the University of Kochi, 5-15 Eikokuji-cho, Kochi, 780-8515 Japan
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Nangang, Taipei, 11529 Taiwan
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Banag CI, Mouly A, Alejandro GJD, Bremer B, Meve U, Grimm GW, Liede-Schumann S. Ixora (Rubiaceae) on the Philippines - crossroad or cradle? BMC Evol Biol 2017; 17:131. [PMID: 28592249 PMCID: PMC5463362 DOI: 10.1186/s12862-017-0974-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora. RESULTS The complex plastid and nuclear divergence patterns in Philippine Ixora, documented using tree and network approaches, reveal a highly dynamic evolution in Ixora, involving several phases of radiation and recolonization. Philippine Ixora comprises at least five lineages, of which one is most closely related to species from Wallacea, and the remaining four to species from Asia. CONCLUSIONS Our study highlights the importance of Philippine species for understanding phytogeographic patterns in the Indomalayan-Australasian eco-region. The overall genetic differentiation, as well as the incongruence between genealogies based on the biparentally inherited nucleome and the maternally inherited plastome in Ixora, reflect the complex tectonic history of the Philippine archipelago. The Ixora lineage related to Wallacean species supports the delimitation of different ecozones along Huxley's line, because it is absent from Palawan. The remaining four lineages are all allied with Asian taxa, reflecting several waves of colonization. Close relationships between some widespread Philippine species and locally adapted narrow endemics suggest that the widespread, genetically diverse species act as pools for the formation of new species in a process of ongoing speciation. Our results suggest that the species concepts of some of the more widespread taxa need to be revised.
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Affiliation(s)
- Cecilia I. Banag
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
| | - Arnaud Mouly
- UMR CNRS 6249 Chrono-environnement, Université Bourgogne - Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France
| | - Grecebio Jonathan D. Alejandro
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Boulevard, 1015 Manila, Philippines
| | - Birgitta Bremer
- Bergius Botanic Garden, Stockholm University, 106 91 Stockholm, Sweden
| | - Ulrich Meve
- Department of Plant Systematics, University of Bayreuth, Universitätstraße 30, 95440 Bayreuth, Germany
| | | | - Sigrid Liede-Schumann
- Department of Plant Systematics, University of Bayreuth, Universitätstraße 30, 95440 Bayreuth, Germany
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Rubite RR, Hughes M, Blanc P, Chung KF, Yang HA, Kono Y, Alejandro GJD, De Layola LB, Virata AGN, Peng CI. Three new species of Begonia endemic to the Puerto Princesa Subterranean River National Park, Palawan. BOTANICAL STUDIES 2015; 56:19. [PMID: 28510828 PMCID: PMC5432911 DOI: 10.1186/s40529-015-0099-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/01/2015] [Indexed: 06/07/2023]
Abstract
BACKGROUND Begonia is a mega-diverse genus of flowering plants prone to generating micro-endemic species, especially on limestone habitats. During fieldwork in the Puerto Princesa Subterranean River National Park, Palawan (Philippines), three species were encountered which did not match any previously described from the region. RESULTS Following morphological, anatomical, molecular phylogenetic and cytological investigation a hypothesis of three new species is supported. The three new species belong to a clade endemic to Palawan and Borneo. CONCLUSIONS The limestone habitats in the Puerto Princesa Subterranean River National Park environs support a unique flora. The description of three new species from a small area within the park demonstrates how much remains to be discovered there, and the importance of its continued protection.
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Affiliation(s)
- Rosario Rivera Rubite
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Padre Faura, Manila, 1000 Philippines
| | - Mark Hughes
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK
| | | | - Kuo-Fang Chung
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 106 Taiwan
| | - Hsun-An Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Yoshiko Kono
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Grecebio J D Alejandro
- College of Science and Research Centre for the Natural and Applied Sciences, University of Santo Tomas, España, Manila, 1015 Philippines
| | - Llogene B De Layola
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Padre Faura, Manila, 1000 Philippines
| | - Arthur Gregory N Virata
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Padre Faura, Manila, 1000 Philippines
| | - Ching-I Peng
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
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