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Resolving Cypriniformes Relationships Using an Anchored Enrichment Approach Carla C
Stout et al. BMC Evolutionary Biology (2016) 16:244 DOI 10.1186/s12862-016-0819-5 RESEARCH ARTICLE Open Access Resolving Cypriniformes relationships using an anchored enrichment approach Carla C. Stout1*†, Milton Tan1†, Alan R. Lemmon2, Emily Moriarty Lemmon3 and Jonathan W. Armbruster1 Abstract Background: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). Results: Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. Conclusions: Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited. Keywords: Fish, High-throughput -
Effect of Diverse Abiotic Conditions on the Structure and Biodiversity Of
water Article Effect of Diverse Abiotic Conditions on the Structure and Biodiversity of Ichthyofauna in Small, Natural Water Bodies Located on Agricultural Lands Adam Brysiewicz 1,* , Przemysław Czerniejewski 2 and Małgorzata Bonisławska 2 1 Institute of Technology and Life Sciences, al. Hrabska 3, 05-090 Falenty, Poland 2 Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology in Szczecin, K. Królewicza 4 Street, 71-550 Szczecin, Poland; [email protected] (P.C.); [email protected] (M.B.) * Correspondence: [email protected] Received: 28 August 2020; Accepted: 22 September 2020; Published: 24 September 2020 Abstract: Mid-field natural ponds promote regional biodiversity, providing alternative habitats for many valuable animal species. The study’s objective was to determine the most important abiotic factors, including hydrochemical and morphometric parameters, affecting fish occurrence in natural, small water bodies on agricultural lands. The studies were conducted in nine randomly selected water bodies located in Poland (the North European Plain). Eleven species of fish were recorded in the waterbodies, with the most abundant being cyprinids (mainly crucian carp). Canonical correspondence analysis (CCA) showed that an increase in oxygenation, temperature, amount of macrophytes, and K concentration and a decrease in the concentration of phosphates, electrical conductivity (EC), Mg, and Cl is associated with the most beneficial living conditions for the most frequently occurring species in the studied water bodies—crucian carp and tench. Aside from the hydrochemical parameters of water in the natural ponds, the number of fish correlates with the basin area and the pond area, maximum depth, area of the buffer zone surrounding the water bodies, and the number of macrophytes. -
Parasites of Lake Minnow, Eupallasella Percnurus (Pall.): the State of Knowledge and Threats
Arch. Pol. Fish. (2011) 19: 167-173 DOI 10.2478/v10086-011-0021-8 MINI REVIEW Parasites of lake minnow, Eupallasella percnurus (Pall.): The state of knowledge and threats Received – 29 July 2011/Accepted – 28 August 2011. Published online: 30 September 2011; ©Inland Fisheries Institute in Olsztyn, Poland Marcin Popio³ek, Joanna Kubizna, Jacek Wolnicki, Jan Kusznierz Abstract. The lake minnow, Eupallasella percnurus (Pall.), Knowledge of parasites of fish species which are of no has not been subject to any comprehensive economic importance is usually scanty and fragmen- ichthyoparasitological study; most information on its parasites tary. The lake minnow, Eupallasella percnurus (Pall.), comes from studies focused on other fish species. The is one of such species. Its vast distribution range ex- knowledge of the geographical distribution of its parasites is especially incomplete. This paper presents the most up-to-date tends from the Oder River system to the Chukchi Pen- list of E. percnurus parasites throughout its distribution range. insula and the Japanese island of Hokkaido. In the Most of the trematodes, tapeworms, and nematodes found in western part of its range, it is a relict species inhabiting this host are larval forms. This means that the parasites use the small, shallow water bodies which are prone to disap- E. percnurus mainly as an intermediate or paratenic host, and pearance as a result of shallowing and vegetation over- not the definitive host, which is important in light of potential growth (Kottelat and Freyhof 2007). The number of parasite pathogenicity. E. percnurus habitats which are subject to Keywords: Eupallasella percnurus, parasites, species anthropogenic stress is increasing; nearly all known composition, geographical distribution. -
CURRICULUM VITAE Ming Chen
CURRICULUM VITAE Ming Chen School of Genome Sci & Tech University of Tennessee Knoxville, TN37996 Email: [email protected] Education 2015 ~ present Graduate student at GST program, University of Tennessee, Knoxville, TN 2012 ~ 2015.05 M.S. Biology Department of Biology at Baylor University Waco, TX, USA 2009 ~ 2012 M.S. Zoology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan City, Hubei Province, China Thesis Title: "Characteristic Analysis of Behaviors Related to Reproduction of the Rose Bitterling (Rhodeus Ocellatus)" 2005 ~ 2009 B.S. Aquaculture Department of Animal Sciences at Yangtze University Jingzhou City, Hubei Province, China Teaching Experience Teaching Assistants in the following courses: independently teaching laboratories, grading homework and exams, holding office hours for answering students’ questions Bio2106 Genetics Laboratory 2014 Spring, Summer and Fall at Baylor University Bio2106 Genetics Laboratory 2013 Spring, Summer, and Fall at Baylor University Bio1402 Introductory Microbiology 2013 Spring at Baylor University Bio2106 Genetics Laboratory 2012 Fall at Baylor University Research Experience 2015.07 ~ present School of Genome Sci & Tech, University of Tennessee, Knoxville, TN37996 Development of a search module which integrates the Hardwood Genomics Databases (HGD) with elastic search 2013 ~ 2015.05 Department of Biology, Baylor University A test of postzygotic isolation and Haldane’s rule in Lake Malawi cichlids By comparing fitnessrelated traits and sex ratio between hybrids -
Amur Fish: Wealth and Crisis
Amur Fish: Wealth and Crisis ББК 28.693.32 Н 74 Amur Fish: Wealth and Crisis ISBN 5-98137-006-8 Authors: German Novomodny, Petr Sharov, Sergei Zolotukhin Translators: Sibyl Diver, Petr Sharov Editors: Xanthippe Augerot, Dave Martin, Petr Sharov Maps: Petr Sharov Photographs: German Novomodny, Sergei Zolotukhin Cover photographs: Petr Sharov, Igor Uchuev Design: Aleksey Ognev, Vladislav Sereda Reviewed by: Nikolai Romanov, Anatoly Semenchenko Published in 2004 by WWF RFE, Vladivostok, Russia Printed by: Publishing house Apelsin Co. Ltd. Any full or partial reproduction of this publication must include the title and give credit to the above-mentioned publisher as the copyright holder. No photographs from this publication may be reproduced without prior authorization from WWF Russia or authors of the photographs. © WWF, 2004 All rights reserved Distributed for free, no selling allowed Contents Introduction....................................................................................................................................... 5 Amur Fish Diversity and Research History ............................................................................. 6 Species Listed In Red Data Book of Russia ......................................................................... 13 Yellowcheek ................................................................................................................................... 13 Black Carp (Amur) ...................................................................................................................... -
Evidence of an Ancient Connectivity and Biogeodispersal of a Bitterling
www.nature.com/scientificreports OPEN Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula Hari Won1, Hyung-Bae Jeon 1,2 & Ho Young Suk1* The modern-day distribution of freshwater fshes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven diferent rivers to obtain better understand historical gene fow of freshwater fsh on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and frst colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers fowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the frst genetic attempt to confrm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning. Primary freshwater fsh species living in separate river systems are not able to come into contact naturally. Even within a single river system, populations can be isolated by landscape structures1–3. Te high degree of interpop- ulation genetic diferentiation normally found in freshwater fsh species has ofen been attributed to the frag- mented nature of freshwater environments4–7. -
Parasites of Lake Minnow, Eupallasella Percnurus (Pall.): the State of Knowledge and Threats
Arch. Pol. Fish. (2011) 19: 167-173 DOI 10.2478/v10086-011-0021-8 MINI REVIEW Parasites of lake minnow, Eupallasella percnurus (Pall.): The state of knowledge and threats Received – 29 July 2011/Accepted – 28 August 2011. Published online: 30 September 2011; ©Inland Fisheries Institute in Olsztyn, Poland Marcin Popio³ek, Joanna Kubizna, Jacek Wolnicki, Jan Kusznierz Abstract. The lake minnow, Eupallasella percnurus (Pall.), Knowledge of parasites of fish species which are of no has not been subject to any comprehensive economic importance is usually scanty and fragmen- ichthyoparasitological study; most information on its parasites tary. The lake minnow, Eupallasella percnurus (Pall.), comes from studies focused on other fish species. The is one of such species. Its vast distribution range ex- knowledge of the geographical distribution of its parasites is especially incomplete. This paper presents the most up-to-date tends from the Oder River system to the Chukchi Pen- list of E. percnurus parasites throughout its distribution range. insula and the Japanese island of Hokkaido. In the Most of the trematodes, tapeworms, and nematodes found in western part of its range, it is a relict species inhabiting this host are larval forms. This means that the parasites use the small, shallow water bodies which are prone to disap- E. percnurus mainly as an intermediate or paratenic host, and pearance as a result of shallowing and vegetation over- not the definitive host, which is important in light of potential growth (Kottelat and Freyhof 2007). The number of parasite pathogenicity. E. percnurus habitats which are subject to Keywords: Eupallasella percnurus, parasites, species anthropogenic stress is increasing; nearly all known composition, geographical distribution. -
Life History Traits of the Chinese Minnow Rhynchocypris
Liang et al. Zoological Studies 2014, 53:36 http://www.zoologicalstudies.com/content/53/1/36 RESEARCH Open Access Life history traits of the Chinese minnow Rhynchocypris oxycephalus in the upper branch of Yangtze River, China Yangyang Liang1,2, Xiaoyun Sui1,3*, Yifeng Chen1, Yintao Jia1 and Dekui He1 Abstract Background: Study of the life history traits of any species plays an essential role for understanding their relationship with the surrounding environment and scientific management. The Chinese minnow Rhynchocypris oxycephalus,an ecologically and economically important species which was widely distributed in East Asia, is currently diminishing. In the present study, we depicted the main life history traits of R. oxycephalus for the first time. Results: A total of 442 individuals were collected from April 2012 to March 2013, with total length (TL) ranging from 32.2 to 158.0 mm. The otolith (lapillus) was proved suitable for age determination. Moreover, the results from marginal increment ratio (MIR) analyses demonstrated its unusual growth pattern: two pairs of opaque and transparent bands were formed each year, which might provide some implications for the age determination of other species. The maximum age for females (4 years) was higher than for males (3 years), while 1- and 2-year-old individuals dominated the population. Both females and males reached maturity at 1 year, and the TL at first maturity was 78.8 mm for females and 60.3 mm for males. Obvious sexual dimorphism was observed as females growing faster and larger than males after maturity. As a multiple spawner, R. oxycephalus releases batches of eggs from April to August. -
A Cyprinid Fish
DFO - Library / MPO - Bibliotheque 01005886 c.i FISHERIES RESEARCH BOARD OF CANADA Biological Station, Nanaimo, B.C. Circular No. 65 RUSSIAN-ENGLISH GLOSSARY OF NAMES OF AQUATIC ORGANISMS AND OTHER BIOLOGICAL AND RELATED TERMS Compiled by W. E. Ricker Fisheries Research Board of Canada Nanaimo, B.C. August, 1962 FISHERIES RESEARCH BOARD OF CANADA Biological Station, Nanaimo, B0C. Circular No. 65 9^ RUSSIAN-ENGLISH GLOSSARY OF NAMES OF AQUATIC ORGANISMS AND OTHER BIOLOGICAL AND RELATED TERMS ^5, Compiled by W. E. Ricker Fisheries Research Board of Canada Nanaimo, B.C. August, 1962 FOREWORD This short Russian-English glossary is meant to be of assistance in translating scientific articles in the fields of aquatic biology and the study of fishes and fisheries. j^ Definitions have been obtained from a variety of sources. For the names of fishes, the text volume of "Commercial Fishes of the USSR" provided English equivalents of many Russian names. Others were found in Berg's "Freshwater Fishes", and in works by Nikolsky (1954), Galkin (1958), Borisov and Ovsiannikov (1958), Martinsen (1959), and others. The kinds of fishes most emphasized are the larger species, especially those which are of importance as food fishes in the USSR, hence likely to be encountered in routine translating. However, names of a number of important commercial species in other parts of the world have been taken from Martinsen's list. For species for which no recognized English name was discovered, I have usually given either a transliteration or a translation of the Russian name; these are put in quotation marks to distinguish them from recognized English names. -
Rhynchocypris Oxycephalus) and Amur Minnow (Rhynchocypris Lagowskii): a Review
Mini Review ISSN: 2574 -1241 DOI: 10.26717/BJSTR.2021.34.005600 The Studies of Chinese Minnow (Rhynchocypris oxycephalus) and Amur Minnow (Rhynchocypris lagowskii): A Review In-Seok Park* Division of Convergence on Marine Science, College of Ocean Science and Engineering, Korea Maritime & Ocean University, Republic of Korea *Corresponding author: In-Seok Park, Division of Convergence on Marine Science, College of Ocean Science and Engineering, Korea Maritime & Ocean University, Republic of Korea ARTICLE INFO ABSTRACT Received: March 18, 2021 The Rhynchocypris minnows (Teleostei: Cyprinidae) are typically small cold water Published: March 24, 2021 (Rhynchocypris oxycephalus) and Amur minnow (Rhynchocypris lagowskii) based on thefish, studies mainly collecteddistributed so in far Asia. and This could paper form briefly the basis reviews for thea wide studies category of Chinese of researches minnow including zootaxy, reproduction & development, ecology, starvation, environmental Citation: In-Seok Park. The Studies of Chinese Minnow (Rhynchocypris oxyceph- alus) and Amur Minnow (Rhynchocypris biology, and techniques in order to highlight the recent progress in different fields of Review; lagowskii): A Review. Biomed J Sci & Tech studyKeywords: using these species,Rhynchocypris which were oxycephalus; done over Rhynchocypris a period of 21 lagowskiiyears from 1998 to 2019. Res 34(5)-2021. BJSTR. MS.ID.005600. Introduction and R. lagowskii, which were done over a period of 21 years from The Chinese minniw, Rhynchocypris oxycephalus (Sauvage & Dabry de Thiersant, 1874; synonyms: Lagowskiella czekanowskii suifunensis; Leuciscus costatus; Moroco oxycephalus; Phoxinus Zootaxy1998 to 2019. (Refer to Appendix) czekanowskii suifunensis; Phoxinus lagowskii oxycephalus; Phoxinus Rhynchocypris oxycephalus: oxycephalus; Phoxinus percnurus suifunensis; Pseudophoxinus oxycephalus) is an Asian species of small freshwater cyprinid Two species of Moroco oxycephalus and M. -
Minnows and Molecules: Resolving the Broad and Fine-Scale Evolutionary Patterns of Cypriniformes
Minnows and molecules: resolving the broad and fine-scale evolutionary patterns of Cypriniformes by Carla Cristina Stout A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 7, 2017 Keywords: fish, phylogenomics, population genetics, Leuciscidae, sequence capture Approved by Jonathan W. Armbruster, Chair, Professor of Biological Sciences and Curator of Fishes Jason E. Bond, Professor and Department Chair of Biological Sciences Scott R. Santos, Professor of Biological Sciences Eric Peatman, Associate Professor of Fisheries, Aquaculture, and Aquatic Sciences Abstract Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world. Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. The goal of this dissertation is to provide robust support for relationships at various taxonomic levels within Cypriniformes. For the entire order, an anchored hybrid enrichment approach was used to resolve relationships. This resulted in a phylogeny that is largely congruent with previous multilocus phylogenies, but has much stronger support. For members of Leuciscidae, the relationships established using anchored hybrid enrichment were used to estimate divergence times in an attempt to make inferences about their biogeographic history. The predominant lineage of the leuciscids in North America were determined to have entered North America through Beringia ~37 million years ago while the ancestor of the Golden Shiner (Notemigonus crysoleucas) entered ~20–6 million years ago, likely from Europe. Within Leuciscidae, the shiner clade represents genera with much historical taxonomic turbidity. Targeted sequence capture was used to establish relationships in order to inform taxonomic revisions for the clade. -
Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society
animals Review Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society Yuri Phedorovich Kartavtsev A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; [email protected] Simple Summary: The main issues of the report are focused on four items. (1) A combination of nDNA and mtDNA markers best suits the hybrid identification and estimates of genetic introgression between different biological species. (2) The available facts on nDNA and mtDNA diversity seemingly make obvious the introgression presence among many taxa, although, it is evident that introgression may be quite restricted or asymmetric, thus holding at least the “source” taxon (taxa) intact. (3) If we accept that sexually reproducing species in marine and terrestrial realms are introgressed, as it is still evident for many cases, then we should recognize that the biological species concept, in terms of complete lack of gene flow among species, is inadequate due to the fact, that many zoological species are not biological species yet. However, vast modern molecular data proved that with time they definitely become biological species. (4) The recent investigation of fish taxa divergence using central DNA barcoding database shows that most gene trees are, basically, appeared monophyletic and interspecies reticulations are rare. Abstract: Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of world- Citation: Kartavtsev, Y.P. Some wide biodiversity. Both are provided in the present meta-analysis and a review as the main signal.