12 Works

Multi-locus microsatellite genotypes of Pocillopora acuta (Scleractinia: Pocilloporidae) in the Bolinao-Anda Reef Complex, Philippines

Andrew Torres, Rachel Ravago-Gotanco & Zac Forsman
This repository contains genotype data and sampling metadata used for the manuscript "Shifts in coral clonality along a gradient of disturbance: insights on reproduction and dispersal of Pocillopora acuta". The dataset contains genotypes of 428 P. acuta colonies using 16 polymorphic microsatellite loci, colony sizes, in-transect locations of each coral, and geographic coordinates of reef sites. These were used to examine clonal richness and structure, population genetic differentiation, and demographic and genetic connectivity within the...

Data from: Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms

Marvin A. Altamia, Nicole Wood, Jennifer M. Fung, Sandra Dedrick, Eric W. Linton, Gisela P. Concepcion, Margo G. Haygood & Daniel L. Distel
Teredinibacter turnerae is a cultivable intracellular endosymbiont of xylotrophic (wood-feeding) bivalves of the Family Teredinidae (shipworms). Although T. turnerae has been isolated from many shipworm taxa collected in many locations, no systematic effort has been made to explore genetic diversity within this symbiont species across the taxonomic and geographical range of its hosts. The mode of symbiont transmission is unknown. Here, we examine sequence diversity in fragments of six genes (16S rRNA, gyrB, sseA, recA,...

Data from: DNA barcoding of the ichthyofauna of Taal Lake, Philippines

Sean Vincent L. Aquilino, Jazzlyn M. Tango, Ian Kendrich C. Fontanilla, Roberto C. Pagulayan, Zubaida U. Basiao, Perry S. Ong & Jonas P. Quilang
This study represents the first molecular survey of the ichthyofauna of Taal Lake and the first DNA barcoding attempt in Philippine fishes. Taal Lake, the third largest lake in the Philippines, is considered a very important fisheries resource and is home to the world’s only freshwater sardine, Sardinella tawilis. However, over-exploitation and introduction of exotic fishes have caused a massive decline in the diversity of native species as well as overall productivity of the lake....

Data from: The Kuroshio Current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides

Yuichi Nakajima, Yu Matsuki, Chunlan Lian, Miguel D. Fortes, Wilfredo H. Uy, Wilfredo L. Campos, Masahiro Nakaoka & Kazuo Nadaoka
Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The...

Revisiting the historical debris avalanche deposit at the footslopes of Iriga Volcano, Philippines

Engielle Mae Paguican, A. M. F. Lagmay, B. van Wyk de Vries & G. Quina

Data from: Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate

Rafe M. Brown, Jennifer A. Weghorst, Karen V. Olson, Mariano R. M. Duya, Anthony J. Barley, Melizar V. Duya, Myron Shekelle, Irene Neri-Arboleda, Jacob A. Esselstyn, Nathaniel J. Dominy, Perry S. Ong, Gillian L. Moritz, Adrian Luczon, Mae Lowe L. Diesmos, Arvin C. Diesmos & Cameron D. Siler
Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies,...

Data from: Opsin genes of select treeshrews resolve ancestral character states within Scandentia

Gwen Duytschaever, Mareike C. Janiak, Perry S. Ong, Konstans Wells, Nathaniel J. Dominy & Amanda D. Melin
Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed treeshrew (Dendrogale melanura). The...

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea

Michael John Mendiola & Rachel Ravago-Gotanco
Connectivity of marine populations is shaped by complex interactions of biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications to the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained...

Data from: Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

Rachel June Ravago-Gotanco, Talna Lorena De La Cruz, Ma. Josefa Pante, Philippe Borsa & Rachel Ravago-Gotanco
The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade...

Data from: Establishing rates of carbon sequestration in mangroves from an earthquake uplift event

Severino G. Salmo, Vanessa Malapit, Maria Carmela A. Garcia & Homer M. Pagkalinawan
We assessed the carbon stocks (CS) in mangroves that developed after a Magnitude 7.1 earthquake in Silonay, Oriental Mindoro, south Luzon, Philippines in November 1994. The earthquake resulted in a 50 cm uplift of sediment that provided new habitat within the upper intertidal zone which mangroves colonized (from < 2 ha pre-earthquake to the current 45 ha, 23 yrs post-earthquake). The site provided opportunity for a novel assessment of the rate of carbon sequestration in...

Data from: Functional preservation and variation in the cone opsin genes of nocturnal tarsiers

Gillian L. Moritz, Perry S. Ong, George H. Perry & Nathaniel J. Dominy
The short-wavelength sensitive (S-) opsin gene OPN1SW is pseudogenized in some nocturnal primates and retained in others, enabling dichromatic colour vision. Debate on the functional significance of this variation has focused on dark conditions, yet many nocturnal species initiate activity under dim (mesopic) light levels that can support colour vision. Tarsiers are nocturnal, twilight-active primates and exemplary visual predators; they also express different colour vision phenotypes, raising the possibility of discrete adaptations to mesopic conditions....

River channel migration and characteristics from 1988 to 2019 at 74 bridges in the Philippines

R.J. Boothroyd, R.D. Williams, T.B. Hoey, P.L.M. Tolentino & X. Yang
The data set contains the Philippines bridge inventory, river migration geodatabase and source code to assess active river channel change (i.e. planform adjustments) using Landsat 5, 7 and 8 products in Google Earth Engine. The data set contains hydro-morphological and bridge characteristics for 74 bridges (> 200 m deck length) in the Philippines from 1988 to 2019 and is available in .csv and .shp format. For a given region of interest (ROI), the code will...

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  • University of the Philippines Diliman
  • Dartmouth College
  • University of Kansas
  • National Museum
  • Oregon Health & Science University
  • University of Santo Tomas
  • Duke University
  • University of Glasgow
  • Tokyo Institute of Technology
  • Mindanao State University Naawan