Native Fish of Conservation Concern in Hong Kong (Part 1)
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ML-DSP: Machine Learning with Digital Signal Processing for Ultrafast, Accurate, and Scalable Genome Classification at All Taxonomic Levels Gurjit S
Randhawa et al. BMC Genomics (2019) 20:267 https://doi.org/10.1186/s12864-019-5571-y SOFTWARE ARTICLE Open Access ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels Gurjit S. Randhawa1* , Kathleen A. Hill2 and Lila Kari3 Abstract Background: Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the intrinsic problems associated with classification. The need exists for an approach and software tool that addresses the limitations of existing alignment-based methods, as well as the challenges of recently proposed alignment-free methods. Results: We propose a novel combination of supervised Machine Learning with Digital Signal Processing, resulting in ML-DSP: an alignment-free software tool for ultrafast, accurate, and scalable genome classification at all taxonomic levels. We test ML-DSP by classifying 7396 full mitochondrial genomes at various taxonomic levels, from kingdom to genus, with an average classification accuracy of > 97%. A quantitative comparison with state-of-the-art classification software tools is performed, on two small benchmark datasets and one large 4322 vertebrate mtDNA genomes dataset. Our results show that ML-DSP overwhelmingly outperforms the alignment-based software MEGA7 (alignment with MUSCLE or CLUSTALW) in terms of processing time, while having comparable classification accuracies for small datasets and superior accuracies for the large dataset. Compared with the alignment-free software FFP (Feature Frequency Profile), ML-DSP has significantly better classification accuracy, and is overall faster. We also provide preliminary experiments indicating the potential of ML-DSP to be used for other datasets, by classifying 4271 complete dengue virus genomes into subtypes with 100% accuracy, and 4,710 bacterial genomes into phyla with 95.5% accuracy. -
Taxonomic Research of the Gobioid Fishes (Perciformes: Gobioidei) in China
KOREAN JOURNAL OF ICHTHYOLOGY, Vol. 21 Supplement, 63-72, July 2009 Received : April 17, 2009 ISSN: 1225-8598 Revised : June 15, 2009 Accepted : July 13, 2009 Taxonomic Research of the Gobioid Fishes (Perciformes: Gobioidei) in China By Han-Lin Wu, Jun-Sheng Zhong1,* and I-Shiung Chen2 Ichthyological Laboratory, Shanghai Ocean University, 999 Hucheng Ring Rd., 201306 Shanghai, China 1Ichthyological Laboratory, Shanghai Ocean University, 999 Hucheng Ring Rd., 201306 Shanghai, China 2Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan ABSTRACT The taxonomic research based on extensive investigations and specimen collections throughout all varieties of freshwater and marine habitats of Chinese waters, including mainland China, Hong Kong and Taiwan, which involved accounting the vast number of collected specimens, data and literature (both within and outside China) were carried out over the last 40 years. There are totally 361 recorded species of gobioid fishes belonging to 113 genera, 5 subfamilies, and 9 families. This gobioid fauna of China comprises 16.2% of 2211 known living gobioid species of the world. This report repre- sents a summary of previous researches on the suborder Gobioidei. A recently diagnosed subfamily, Polyspondylogobiinae, were assigned from the type genus and type species: Polyspondylogobius sinen- sis Kimura & Wu, 1994 which collected around the Pearl River Delta with high extremity of vertebral count up to 52-54. The undated comprehensive checklist of gobioid fishes in China will be provided in this paper. Key words : Gobioid fish, fish taxonomy, species checklist, China, Hong Kong, Taiwan INTRODUCTION benthic perciforms: gobioid fishes to evolve and active- ly radiate. The fishes of suborder Gobioidei belong to the largest The gobioid fishes in China have long received little group of those in present living Perciformes. -
4. Nuralim ED Author Final Reupload02
Aceh Journal of Animal Science (2020) 5 (2): 87 - 91 Aceh Journal of Animal Science Journal homepage: www.jurnal.unsyiah.ac.id/AJAS Are Awaous ocellaris and Belobranchus belobranchus the two species of Nike fish schools ? Nuralim Pasisingi*, Sitty Ainsyah Habibie, Abdul Hafidz Olii Faculty of Fisheries and Marine Science, Gorontalo State University, Gorontalo, 96128, Indonesia ARTICEL INFO ABSTRACT Keywords: Investigating goby fish is vital to perform an integrated and comprehensive study in order to maintain the roles Awaous of the fish, thus providing balanced ecosystem functions and services, as well as contributing to fish biodiversity. Belobranchus Local societies simply recognize fish species by their local names, which are not common. This condition, in turn, Endemic causes hitches in conducting further studies. Nike, the name of a local fish, refers to the schools of goby fish Goby larvae whose adult phase has not been fully confirmed. This study aimed to reveal the species that categorizes as Gorontalo nike fish through tracing adult goby inhabiting freshwater. Two fish samples, i.e., Unknown 01 and Unknown 02, Nike fish were taken from two sites in Bone River, Gorontalo, Indonesia. These samples were captured purposively using a hand net by considering the morphological similarity between the two target samples and the general Received: 28 April 2020 characteristic of goby. Furthermore, the samples were analyzed genetically through the PCR sequencing method Accepted: 4 June 2020 using the Mitochondrial Cytochrome Oxidase Subunit 1 (CO1) gene. Based on the NCBI database, Unknown 01 Available online: 4 June 2020 had the highest similarity to Belobranchus belobranchus (99.54%), while Unknown 02 was identical with Awaous ocellaris (100%). -
5Th Indo-Pacific Fish Conference
)tn Judo - Pacifi~ Fish Conference oun a - e II denia ( vernb ~ 3 - t 1997 A ST ACTS Organized by Under the aegis of L'Institut français Société de recherche scientifique Française pour le développement d'Ichtyologie en coopération ' FI Fish Conference Nouméa - New Caledonia November 3 - 8 th, 1997 ABSTRACTS LATE ARRIVAL ZOOLOGICAL CATALOG OF AUSTRALIAN FISHES HOESE D.F., PAXTON J. & G. ALLEN Australian Museum, Sydney, Australia Currently over 4000 species of fishes are known from Australia. An analysis ofdistribution patterns of 3800 species is presented. Over 20% of the species are endemic to Australia, with endemic species occuiring primarily in southern Australia. There is also a small component of the fauna which is found only in the southwestern Pacific (New Caledonia, Lord Howe Island, Norfolk Island and New Zealand). The majority of the other species are widely distributed in the western Pacific Ocean. AGE AND GROWTH OF TROPICAL TUNAS FROM THE WESTERN CENTRAL PACIFIC OCEAN, AS INDICATED BY DAILY GROWm INCREMENTS AND TAGGING DATA. LEROY B. South Pacific Commission, Nouméa, New Caledonia The Oceanic Fisheries Programme of the South Pacific Commission is currently pursuing a research project on age and growth of two tropical tuna species, yellowfm tuna (Thunnus albacares) and bigeye tuna (Thunnus obesus). The daily periodicity of microincrements forrned with the sagittal otoliths of these two spceies has been validated by oxytetracycline marking in previous studies. These validation studies have come from fishes within three regions of the Pacific (eastem, central and western tropical Pacific). Otolith microincrements are counted along transverse section with a light microscope. -
Challenges in Biodiversity Conservation in a Highly Modified
water Review Challenges in Biodiversity Conservation in a Highly Modified Tropical River Basin in Sri Lanka Thilina Surasinghe 1,* , Ravindra Kariyawasam 2, Hiranya Sudasinghe 3 and Suranjan Karunarathna 4 1 Department of Biological Sciences, Bridgewater State University, Dana Mohler-Faria Science & Mathematics Center, 24 Park Avenue, Bridgewater, MA 02325, USA 2 Center for Environment & Nature Studies, No.1149, Old Kotte Road, Rajagiriya 10100, Sri Lanka; [email protected] 3 Evolutionary Ecology & Systematics Lab, Department of Molecular Biology & Biotechnology, University of Peradeniya, Kandy 20400, Sri Lanka; [email protected] 4 Nature Explorations & Education Team, No. B-1/G-6, De Soysapura Flats, Moratuwa 10400, Sri Lanka; [email protected] * Correspondence: [email protected]; Tel.: +1-508-531-1908 Received: 11 October 2019; Accepted: 13 December 2019; Published: 19 December 2019 Abstract: Kelani River is the fourth longest river in the South-Asian island, Sri Lanka. It originates from the central hills and flows through a diverse array of landscapes, including some of the most urbanized regions and intensive land uses. Kelani River suffers a multitude of environmental issues: illegal water diversions and extractions, impoundment for hydroelectricity generation, and pollution, mostly from agrochemicals, urban runoff, industrial discharges, and domestic waste. Moreover, loss of riparian forest cover, sand-mining, and unplanned development in floodplains have accentuated the environmental damage. In this study, based on Kelani River basin, we reviewed the status of biodiversity, threats encountered, conservation challenges, and provided guidance for science-based conservation planning. Kelani River basin is high in biodiversity and endemism, which includes 60 freshwater fish species of which 30 are endemic. -
Appendix 8: Freshwater Fishes Sub-Group Report August 2014
Appendix 8: Freshwater Fishes Sub-group Report August 2014 Contributors: Tony Nip (KFBG) Prof. David Dudgeon (HKU) H.T. Cheng C.F. Cheng David Wong Jianhun Liang Philip Yip Tony Chan (AFCD) Samuel Lam (AFCD) Stephen Lai (AFCD) K.W. Cheung (AFCD) 1. Overview of status and trends 1.1. Lowland species are at greatest risk. Many aquatic habitats (lowland streams, lowland marshes) have already been seriously degraded or have disappeared entirely, and at least two lowland fish species (Lin's Minnow 林 氏細鯽, White Cloud Mountain Minnow 白雲山魚) are apparently locally extinct. Some lowland species that were common in the past, like Whitespotted Walking Catfish (塘虱), Paradise Fish (叉尾鬥魚), etc., can now be considered to be Near Threatened or even classified among the threatened categories. This of course is due to a combination of urban expansion, pollution, channelisation, impacts from invasive species and water over-abstraction. 1.2. Many fish species considered to be threatened/ Near Threatened appear in Country Park Enclaves (e.g., HK Paradise Fish 香港鬥魚, Rice Fish 弓背青鱂, Giant Marbled Eel 花錦鱔, Three-lined Catfish 三線擬鱨). The streams, ponds and marshes (and their surrounding riparian zones) in these Enclaves should be protected from development and associated pollution, as well as channelisation, drainage works or construction of dams and weirs. 1.3. Many Ecologically Important Streams (EISs) recognised by the AFCD as well as some recommended to become EISs are habitats for many fish species of conservation concern (e.g., Thick-lipped Barbs 光唇魚, Chinese Rasbora 斯 氏波魚). They should be protected from development and associated pollution, as well as channelisation, drainage works or construction of dams and weirs. -
Occasional Papers of the Museum of Zoology the University of Michigan
OCCASIONAL PAPERS OF THE MUSEUM OF ZOOLOGY THE UNIVERSITY OF MICHIGAN DISCHERODONTUS, A NEW GENUS OF CYPRINID FISHES FROM SOUTHEASTERN ASIA ABSTRACT.-Rainboth, WalterJohn. 1989. Discherodontus, a new genw of cyprinid firhes from southeastern Asia. Occ. Pap. Mzcs. 2001. Univ. Michigan, 718:I-31, figs. 1-6. Three species of southeast Asian barbins were found to have two rows of pharyngeal teeth, a character unique among barbins. These species also share several other characters which indicate their close relationship, and allow the taxonomic recognition of the genus. Members of this new genus, Discherodontzcs, are found in the Mekong, Chao Phrya, and Meklong basins of Thailand and the Pahang basin of the Malay peninsula. The new genus appears to be most closely related to Chagunizcs of Burma and India, and a group of at least six genera of the southeast Asia-Sunda Shelf basins. Key words: Discherodontus, fihes, Cyprinidae, taxonomy, natural history, Southemt Asia. INTRODUCTION Among the diverse array of barbins of southern and southeastern Asia, there are a number of generic-ranked groups which are poorly understood, or which still await taxonomic recognition. One group of three closely related species, included until now in two genera, is the subject of this paper. Prior to this study, two of the three species in this new genus have been relegated to Puntius of Hamilton (1822), but as understood by Weber and de Beaufort (1916), and by Smith (1945). The remaining species has been placed in Acrossocheilus not of *Department of Biology, University of California (UCLA), Los Angeles, CA 90024 2 Walter J. -
Sahami F. M., Kepel R. C., Olii A. H., Pratasik S. B., 2019 Determination
Determination of morphological alteration based on molecular analysis and melanophore pattern of the migrating Nike fish in Gorontalo Bay, Indonesia 1Femy M. Sahami, 2Rene C. Kepel, 1Abdul H. Olii, 2Silvester B. Pratasik 1 Department of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Gorontalo State University, Gorontalo City, Indonesia; 2 Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado City, Indonesia. Corresponding author: F. M. Sahami, [email protected] Abstract. Nike is a term for minuscule fish that frequently appear in Gorontalo waters. This type of fish belongs to the amphidromous goby group. This study aims to describe the morphological alterations of Nike fish from the sea to the estuary area of Gorontalo waters based on molecular analysis and different melanophore pattern. The small size of this fish (larval stage and post-larva) cause difficulties in analysing morphometric and meristic aspects. Therefore, the melanophore pattern approach and molecular analysis using the COI gene were used to identify and study the fish species. Sampling was carried out from 5 to 11 October 2018 in Gorontalo Bay area and the mouth of Bone Bolango river. The study was carried out when this type of fish appeared in the research area. Samples of Nike fish were grouped based on differences in melanophore patterns in the body. It was found there were five different groups. The groups were coded N1, N2, N3, N4 and N5. The molecular analysis using the COI gene was used to identify the fish species. Genetic investigations showed that from five groups, there were two groups (N3 and N5) that had different melanophore patterns, but belong to the same species, Belobranchus segura. -
Fish Assemblage Structure of Two Contrasting Stream Catchments Of
The Open Conservation Biology Journal, 2011, 5, 25-44 25 Open Access Fish Assemblage Structure of Two Contrasting Stream Catchments of the Mahaweli River Basin in Sri Lanka: Hallmarks of Human Exploitation and Implications for Conservation Jayakody A. Sumith*,1,3, Kelly R. Munkittrick1 and N. Athukorale2 1Canadian Rivers Institute and Department of Biology, University of New Brunswick, P.O. Box 5050, Saint John, New Brunswick, E2L 4L5, Canada 2Institute of Fundamental Studies, Hanthana Road, Kandy 20000, Sri Lanka 3Permanent Address: Office of the Registrar of Pesticides, Department of Agriculture, 1056, Getambe, P.O. Box 49, Peradeniya 20400, Sri Lanka Abstract: Patterns of fish community composition in the Mahaweli ichthyological region of Sri Lanka were examined in agricultural tributaries of the Uma-oya catchment of the upper Mahaweli River in comparison to more pristine streams in a nature reserve in the Amban-ganga catchment. The Uma-oya catchment shows characteristics commonly observed in extensive agricultural exploitation such as impaired water quality and altered riparian vegetation. The most abundant fish species in the two regions were Garra ceylonensis, Devario malabaricus, and Rasbora daniconius, although their relative abundance differed between sites. G. ceylonensis and Neomacheilus notostigma were the only endemic fish species in common but the latter has been extremely depauperate. Endemism is higher in the reference sites (62.5%) than agricultural sites (ca. 25%); some of the reference streams showed greater diversity with unique fish species and a few species that have not been recorded previously in the catchment. The ichthyofaunal similarity between two catchments was 39% and fish species diversity was negatively correlated with stream gradients (Pearson correlation (-0.630); r2 = 39.6% p = 0.028). -
Inventory of Fishes in the Upper Pelus River (Perak River Basin, Perak, Malaysia)
13 4 315 Ikhwanuddin et al ANNOTATED LIST OF SPECIES Check List 13 (4): 315–325 https://doi.org/10.15560/13.4.315 Inventory of fishes in the upper Pelus River (Perak river basin, Perak, Malaysia) Mat Esa Mohd Ikhwanuddin,1 Mohammad Noor Azmai Amal,1 Azizul Aziz,1 Johari Sepet,1 Abdullah Talib,1 Muhammad Faiz Ismail,1 Nor Rohaizah Jamil2 1 Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. 2 Department of Environmental Sciences, Faculty of Environmental Studies, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. Corresponding author: Mohammad Noor Azmai Amal, [email protected] Abstract The upper Pelus River is located in the remote area of the Kuala Kangsar district, Perak, Malaysia. Recently, the forest along the upper portion of the Pelus River has come under threat due to extensive lumbering and land clearing for plantations. Sampling at 3 localities in the upper Pelus River at 457, 156 and 89 m above mean sea level yielded 521 specimens representing 4 orders, 11 families, 23 genera and 26 species. The most abundant species was Neolissochilus hexagonolepis, followed by Homalopteroides tweediei and Glyptothorax major. The fish community structure indices was observed to increase from the upper to lower portion of the river, which might reflect differences in water velocity. Key words Faunal inventory; freshwater; species diversity; tropical forest. Academinc editor: Barbára Calegari | Received 28 July 2015 | Accepted 27 June 2017 | Published 18 August 2017 Citation: Ikhwanuddin MEM, Amal MNA, Aziz A, Sepet J, Talib A, Ismail MS, Jamil NR (2017). Inventory of fishes in the upper Pelus River (Perak river basin, Perak, Malaysia). -
Report (Pages 203-318) (5.24
Environmental and Social Impact Assessment June 2017 SOL: Tina River Hydropower Project (Part 5) Prepared by the Government of Solomon Islands for the Asian Development Bank. CURRENCY EQUIVALENTS (as of 9 June 2017) Currency unit – Solomon Islands dollar (SBD) SBD1.00 = $0.1276 $1.00 = SBD7.8308 NOTE (i) In this report, "$" refers to US dollars. This environmental and social impact assessment is a document of the borrower. The views expressed herein do not necessarily represent those of ADB's Board of Directors, Management, or staff, and may be preliminary in nature. Your attention is directed to the “terms of use” section on ADB’s website. In preparing any country program or strategy, financing any project, or by making any designation of or reference to a particular territory or geographic area in this document, the Asian Development Bank does not intend to make any judgments as to the legal or other status of any territory or area. F igure 6c1 Biological sample sites Page 203 of 643 Species of Concern Three categories of habitat disturbance were defined according to their level of disturbance: weakly disturbed habitatsb moderately disturbed habitats and highly disturbed habitats. According to the flora surveyb the highly disturbed areasb such as the areas around the Black Post R oadb have fewer species of concern (see Table 6c1 and Figure 6c2) (see Annex 8 in the Annex R eport for the list of floral speciesb including species of concern). Table 6c1 Number of flora species of concern Number of Percentage S tations species of of species -
An Assessment of the Status of Biodiversity in the Maduganga Mangrove Estuary
Occasional Papers of IUCN Sri Lanka No. 1, November 2002 An Asses sment o f the Status o f Biodiversi ty in the Maduga nga Mangrove Estua r y C. N. B. Bambaradeniya, S. P. Ekanayake, L. D. C. B. Kekulandala, R. H. S. S. Fernando, V. A. P. Samarawickrama and T. G. M. Priyadharshana IUCN - The World Conser vation Union, Sri Lanka Countr y Office This publication ha s been prepared by IUCN - Sri Lanka wit h fina ncial assist ance from the Royal Netherlands Government i Published by : IUCN - Sri Lanka Copyright : 2001, International Union for Conservation of Nature and Natural Resources Reproduction of this publication for educational or other non- commercial purposes is authorised without prior written permission from the copyright holder provided the source is fully acknowledged. Reproduction of this publication for resale or other commercial purposes is prohibited without prior written permission of the copyright holder. Citation : Bambaradeniya, C. N. B., S. P. Ekanayake, L. D. C. B. Kekulandala, R. H. S. S. Fernando, V. A. P. Samarawickrama, & T. G. M. Priyadharshana. 2002. An Assessment of the Status of Biodiversity in the Maduganga Mangrove Estuary. Occ. Pap. IUCN, Sri Lanka., 1:iv + 49 pp. ISBN : 955-8177-15-6 955-8177-12-1 Text : C. N. B. Bambaradeniya and S. P. Ekanayake, IUCN Sri Lanka Cover photograph by : A Kraal - traditional fish trap in Maduganga (Photograph by Channa Bambaradeniya) Produced by : IUCN Sri Lanka. Printed by : Karunaratne & Sons Ltd. 67, UDA Industrial Estate, Katuwana Road, Homagama, Sri Lanka. Available from : IUCN - Sri Lanka No. 53, Horton Place, Colombo 7, Sri Lanka.