Our Disappearing Desert Fishes by David L, Soltz
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Deterministic Shifts in Molecular Evolution Correlate with Convergence to Annualism in Killifishes
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.09.455723; this version posted August 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deterministic shifts in molecular evolution correlate with convergence to annualism in killifishes Andrew W. Thompson1,2, Amanda C. Black3, Yu Huang4,5,6 Qiong Shi4,5 Andrew I. Furness7, Ingo, Braasch1,2, Federico G. Hoffmann3, and Guillermo Ortí6 1Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48823, USA. 2Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA. 3Department of Biochemistry, Molecular Biology, Entomology, & Plant Pathology, Mississippi State University, Starkville, MS 39759, USA. 4Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Marine, Shenzhen 518083, China. 5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. 6Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA. 7Department of Biological and Marine Sciences, University of Hull, UK. Corresponding author: Andrew W. Thompson, [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.08.09.455723; this version posted August 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract: The repeated evolution of novel life histories correlating with ecological variables offer opportunities to test scenarios of convergence and determinism in genetic, developmental, and metabolic features. Here we leverage the diversity of aplocheiloid killifishes, a clade of teleost fishes that contains over 750 species on three continents. -
The Mystery of the Banded Killifish Fundulus Diaphanus Population Explosion: Where Did They All Come From?
The Mystery of the Banded KillifishFundulus ( diaphanus) Population Explosion: Where Did They All Come from? Philip W. Willink, Jeremy S. Tiemann, Joshua L. Sherwood, Eric R. Larson, Abe Otten, Brian Zimmerman 3 American Currents Vol. 44, No. 4 THE MYSTERY OF THE BANDED KILLIFISH FUNDULUS DIAPHANUS POPULATION EXPLOSION: WHERE DID THEY ALL COME FROM? Philip W. Willink, Jeremy S. Tiemann, Joshua L. Sherwood, La Grange Park, IL Illinois Natural History Survey Illinois Natural History Survey Eric R. Larson, Abe Otten, Brian Zimmerman University of Illinois at Scott Community The Ohio State University Urbana-Champaign College Stream and River Ecology Lab Banded Killifish Fundulus diaphanus are no strangers to NAN- and have not been seen since, they were only known from a hand- FAers. Over the past several years, there have been multiple arti- ful of inland lakes in the far northeastern corner the state (Fig. 1). cles in American Currents covering their distribution (Hatch 2015; Even there, population numbers were low. Schmidt 2016a, 2018; Olson and Schmidt 2018; Li 2019), stocking So it was with great excitement that in the early 2000s Illinois to restore populations (Bland 2013; Schmidt 2014), and appear- ichthyologists started to find more and more presumed Western ance in a hatchery (Schmidt 2016b). Their range extends from the Banded Killifish in Lake Michigan (Willink et al. 2018). They Canadian Maritime provinces south along the Atlantic coast to were even showing up in downtown Chicago (Willink 2011). It the Carolinas, as well as westward through the Great Lakes region was hoped that this range expansion was evidence of an uncom- to the upper Mississippi watershed. -
Relation of Desert Pupfish Abundance to Selected Environmental Variables
Environmental Biology of Fishes (2005) 73: 97–107 Ó Springer 2005 Relation of desert pupfish abundance to selected environmental variables in natural and manmade habitats in the Salton Sea basin Barbara A. Martin & Michael K. Saiki U.S. Geological Survey, Biological Resources Division, Western Fisheries Research Center-Dixon Duty Station, 6924 Tremont Road, Dixon, CA 95620, U.S.A. (e-mail: [email protected]) Received 6 April 2004 Accepted 12 October 2004 Key words: species assemblages, predation, water quality, habitat requirements, ecological interactions, endangered species Synopsis We assessed the relation between abundance of desert pupfish, Cyprinodon macularius, and selected biological and physicochemical variables in natural and manmade habitats within the Salton Sea Basin. Field sampling in a natural tributary, Salt Creek, and three agricultural drains captured eight species including pupfish (1.1% of the total catch), the only native species encountered. According to Bray– Curtis resemblance functions, fish species assemblages differed mostly between Salt Creek and the drains (i.e., the three drains had relatively similar species assemblages). Pupfish numbers and environmental variables varied among sites and sample periods. Canonical correlation showed that pupfish abundance was positively correlated with abundance of western mosquitofish, Gambusia affinis, and negatively correlated with abundance of porthole livebearers, Poeciliopsis gracilis, tilapias (Sarotherodon mossambica and Tilapia zillii), longjaw mudsuckers, Gillichthys mirabilis, and mollies (Poecilia latipinna and Poecilia mexicana). In addition, pupfish abundance was positively correlated with cover, pH, and salinity, and negatively correlated with sediment factor (a measure of sediment grain size) and dissolved oxygen. Pupfish abundance was generally highest in habitats where water quality extremes (especially high pH and salinity, and low dissolved oxygen) seemingly limited the occurrence of nonnative fishes. -
Gene Expression After Freshwater Transfer in Gills and Opercular Epithelia of Killifish: Insight Into Divergent Mechanisms of Ion Transport Graham R
The Journal of Experimental Biology 208, 2719-2729 2719 Published by The Company of Biologists 2005 doi:10.1242/jeb.01688 Gene expression after freshwater transfer in gills and opercular epithelia of killifish: insight into divergent mechanisms of ion transport Graham R. Scott1,*, James B. Claiborne2, Susan L. Edwards2,3, Patricia M. Schulte1 and Chris M. Wood4 1Department of Zoology, University of British Columbia, Vancouver BC, Canada V6T 1Z4, 2Department of Biology, Georgia Southern University, Statesboro, GA 30460-8042, USA, 3Department of Physiology and Pharmacology, James Cook University, Cairns, QLD 4879, Australia and 4Department of Biology, McMaster University, Hamilton ON, Canada L8S 4K1 *Author for correspondence (e-mail: [email protected]) Accepted 17 May 2005 Summary We have explored the molecular basis for differences in epithelium, NHE2 was not expressed; furthermore, physiological function between the gills and opercular Na+,K+-ATPase activity was unchanged after transfer to epithelium of the euryhaline killifish Fundulus freshwater, CA2 mRNA levels decreased, and NHE3 levels heteroclitus. These tissues are functionally similar in increased. Consistent with their functional similarities in seawater, but in freshwater the gills actively absorb Na+ seawater, killifish gills and opercular epithelium expressed – + + + + – but not Cl , whereas the opercular epithelium actively Na ,K -ATPase α1a, Na ,K ,2Cl cotransporter 1 absorbs Cl– but not Na+. These differences in freshwater (NKCC1), cystic fibrosis transmembrane conductance physiology are likely due to differences in absolute levels regulator (CFTR) Cl– channel and the signalling protein of gene expression (measured using real-time PCR), as 14-3-3a at similar absolute levels. Furthermore, NKCC1 several proteins important for Na+ transport, namely and CFTR were suppressed equally in each tissue after Na+,H+-exchanger 2 (NHE2), carbonic anhydrase 2 (CA2), freshwater transfer, and 14-3-3a mRNA increased in both. -
Table 7: Species Changing IUCN Red List Status (2018-2019)
IUCN Red List version 2019-3: Table 7 Last Updated: 10 December 2019 Table 7: Species changing IUCN Red List Status (2018-2019) Published listings of a species' status may change for a variety of reasons (genuine improvement or deterioration in status; new information being available that was not known at the time of the previous assessment; taxonomic changes; corrections to mistakes made in previous assessments, etc. To help Red List users interpret the changes between the Red List updates, a summary of species that have changed category between 2018 (IUCN Red List version 2018-2) and 2019 (IUCN Red List version 2019-3) and the reasons for these changes is provided in the table below. IUCN Red List Categories: EX - Extinct, EW - Extinct in the Wild, CR - Critically Endangered [CR(PE) - Critically Endangered (Possibly Extinct), CR(PEW) - Critically Endangered (Possibly Extinct in the Wild)], EN - Endangered, VU - Vulnerable, LR/cd - Lower Risk/conservation dependent, NT - Near Threatened (includes LR/nt - Lower Risk/near threatened), DD - Data Deficient, LC - Least Concern (includes LR/lc - Lower Risk, least concern). Reasons for change: G - Genuine status change (genuine improvement or deterioration in the species' status); N - Non-genuine status change (i.e., status changes due to new information, improved knowledge of the criteria, incorrect data used previously, taxonomic revision, etc.); E - Previous listing was an Error. IUCN Red List IUCN Red Reason for Red List Scientific name Common name (2018) List (2019) change version Category -
The African Turquoise Killifish: a Model for Exploring Vertebrate Aging and Diseases in the Fast Lane
Downloaded from symposium.cshlp.org on June 11, 2016 - Published by Cold Spring Harbor Laboratory Press The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane 1 1,2 ITAMAR HAREL AND ANNE BRUNET 1Department of Genetics, Stanford University, Stanford, California 94305 2Glenn Laboratories for the Biology of Aging at Stanford, Stanford, California 94305 Correspondence: [email protected] Why and how organisms age remains a mystery, and it defines one of the biggest challenges in biology. Aging is also the primary risk factor for many human pathologies, such as cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. Thus, manipulating the aging rate and potentially postponing the onset of these devastating diseases could have a tremendous impact on human health. Recent studies, relying primarily on nonvertebrate short-lived model systems, have shown the importance of both genetic and environmental factors in modulating the aging rate. However, relatively little is known about aging in vertebrates or what processes may be unique and specific to these complex organisms. Here we discuss how advances in genomics and genome editing have significantly expanded our ability to probe the aging process in a vertebrate system. We highlight recent findings from a naturally short-lived vertebrate, the African turquoise killifish, which provides an attractive platform for exploring mechanisms underlying vertebrate aging and age-related diseases. MODELING AGING IN THE ing vertebrate aging and age-related diseases (Harel et al. LABORATORY 2015). Aging research has greatly benefited from investigating short-lived nonvertebrate models (Fig. 1A), specifically THE AFRICAN TURQUOISE KILLIFISH yeast (Saccharomyces cerevisiae), worm (Caenorhabdi- tis elegans), and fly (Drosophila melanogaster). -
Draft Risk Assessment Report Nothobranchius Furzeri (Turquoise
APPLICATION TO AMEND THE LIST OF SPECIMENS SUITABLE FOR LIVE IMPORT Draft Risk Assessment Report 1. Taxonomy of the species a. Family name: Aplocheilidae b. Genus name: Nothobranchius c. Species: N. furzeri d. Subspecies: No e. Taxonomic Reference: http://www.uniprot.org/taxonomy/105023 f. Common Names: Turquoise killifish g. Is the species a genetically-modified organism (GMO)? No 2. Status of the species under CITES Species is not listed in the CITES Appendices. 3. Ecology of the species a. Longevity: what is the average lifespan of the species in the wild and in captivity? The average lifespan of the species in captivity is 13 weeks (1). Wild derived N. furzeri from three different habitats showed a maximum lifespan of 25-32 weeks (1). b. What is the maximum length and weight that the species attains? Provide information on the size and weight range for males and females of the species. As per the original formal description of the species, the standard length of N. furzeri from a wild population ranged from 2.5cm to 4.4cm (2). The maximum length the species can attain is 7cm (3). The mean maximal body weight reported for males is 3.8 ± 1.1 g (range: 0.5 – 6.7 g) and 2.2 ± 0.6 g (range: 0.2 - 3.6 g) for females (4). Growth rates of Nothobranchius in the wild have been reported to be similar to those in captivity (5). c. Discuss the identification of the individuals in this species, including if the sexes of the species are readily distinguishable, and if the species is difficult to distinguish from other species. -
The Effects of Introduced Tilapias on Native Biodiversity
AQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS Aquatic Conserv: Mar. Freshw. Ecosyst. 15: 463–483 (2005) Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/aqc.699 The effects of introduced tilapias on native biodiversity GABRIELLE C. CANONICOa,*, ANGELA ARTHINGTONb, JEFFREY K. MCCRARYc,d and MICHELE L. THIEMEe a Sustainable Development and Conservation Biology Program, University of Maryland, College Park, Maryland, USA b Centre for Riverine Landscapes, Faculty of Environmental Sciences, Griffith University, Australia c University of Central America, Managua, Nicaragua d Conservation Management Institute, College of Natural Resources, Virginia Tech, Blacksburg, Virginia, USA e Conservation Science Program, World Wildlife Fund, Washington, DC, USA ABSTRACT 1. The common name ‘tilapia’ refers to a group of tropical freshwater fish in the family Cichlidae (Oreochromis, Tilapia, and Sarotherodon spp.) that are indigenous to Africa and the southwestern Middle East. Since the 1930s, tilapias have been intentionally dispersed worldwide for the biological control of aquatic weeds and insects, as baitfish for certain capture fisheries, for aquaria, and as a food fish. They have most recently been promoted as an important source of protein that could provide food security for developing countries without the environmental problems associated with terrestrial agriculture. In addition, market demand for tilapia in developed countries such as the United States is growing rapidly. 2. Tilapias are well-suited to aquaculture because they are highly prolific and tolerant to a range of environmental conditions. They have come to be known as the ‘aquatic chicken’ because of their potential as an affordable, high-yield source of protein that can be easily raised in a range of environments } from subsistence or ‘backyard’ units to intensive fish hatcheries. -
Gill Trematodes (Flukes) in Wild-Caught Killifish (<I>Fundulus
NOTES Gill Trematodes (Flukes) in Wild-Caught Killifish (Fundulus heteroclitus) DAVID R. GOULDING, BS, RLAT,1* TERRY L. BLANKENSHIP-PARIS, DVM, MS, DIPLOMATE, ACLAM,1 GREGORY A. LEWBART, MS, VMD, DIPLOMATE, ACZM,2 PAGE H. MYERS, BS, LATG,1 TRACY K. DEMIANENKO, BS, RLAT,1 JAMES A. CLARK, LATG,1 AND DIANE B. FORSYTHE, DVM, DIPLOMATE, ACLAM1 Three wild caught killifish (Fundulus heteroclitus) on an Institutional Animal Care and Use Committee-approved protocol were found dead within 2 days after being received. The fish were housed in two separate aquaria. Aquarium water was evaluated, and pH, salinity, ammonia, nitrate, and nitrite levels were within acceptable parameters. Several remaining fish appeared to be slow-moving and were presented for necropsy. Multiple, scattered, ulcerated skin lesions (diameter, 1 to 5 mm) were noted at necropsy and were cultured. No pathogenic bacteria were isolated. Wet-mount samples of the gills revealed multiple cysts at the gill margins, each containing a motile organism. No other gill parasites were detected. A diagnosis of trematodiasis was made. The cysts were identified as encysted metacercariae of a digenetic trematode. We surmise that the large numbers of gill flukes combined with the stress of recent shipment likely caused the observed morbidity and mortality. Sixty-two wild-caught killifish (Fundulus heteroclitus) obtained from Duke Marine Center (Beaufort, N.C.) were group-housed upon receipt in two 38-gallon aquaria containing conditioned brack- ish water. Thirty-six fish were placed in tank A, and 26 fish were placed in tank B. One day after arrival, two fish were found dead in tank B, and 2 days after arrival, one fish was found dead in tank A. -
Southern Exposures
Searching for the Pliocene: Southern Exposures Robert E. Reynolds, editor California State University Desert Studies Center The 2012 Desert Research Symposium April 2012 Table of contents Searching for the Pliocene: Field trip guide to the southern exposures Field trip day 1 ���������������������������������������������������������������������������������������������������������������������������������������������� 5 Robert E. Reynolds, editor Field trip day 2 �������������������������������������������������������������������������������������������������������������������������������������������� 19 George T. Jefferson, David Lynch, L. K. Murray, and R. E. Reynolds Basin thickness variations at the junction of the Eastern California Shear Zone and the San Bernardino Mountains, California: how thick could the Pliocene section be? ��������������������������������������������������������������� 31 Victoria Langenheim, Tammy L. Surko, Phillip A. Armstrong, Jonathan C. Matti The morphology and anatomy of a Miocene long-runout landslide, Old Dad Mountain, California: implications for rock avalanche mechanics �������������������������������������������������������������������������������������������������� 38 Kim M. Bishop The discovery of the California Blue Mine ��������������������������������������������������������������������������������������������������� 44 Rick Kennedy Geomorphic evolution of the Morongo Valley, California ���������������������������������������������������������������������������� 45 Frank Jordan, Jr. New records -
Compare and Contrast the Water Environment Between Death Valley Pupfish Specie and Devil’S Hole Pupfish Specie
Compare and Contrast the Water environment between Death Valley Pupfish Specie and Devil’s Hole Pupfish Specie By Roy Tianran Gao 1 Table of Contents Title page 1 Abstract 3 Introduction and Background 3 Water Temperature 4 Salinity 6 Water Level 7 Conservation 10 Conclusion 11 References 12 2 ABSTRACT The two types of pupfish (Cyprinodon) in Death Valley National Park are Death Valley pupfish and Devil’s Hole pupfish. Death Valley pupfish has been existed over 10,000 years and Devil’s Hole pupfish has been existed for over 20,000 years. Both of the pupfishes are endangered species. The average number of Death Valley pupfish has decreased by about 100 since 1990s, and the number of Devil’s Hole pupfish has decreased by 400 since 1995. Comparing the water level, water temperature and the water salinity between the two species of pupfish would help to define the living requirements and reason of decreasing population. The research toward the result is based on 7 journal articles, 4 websites, and 1 book. As the result shows, Death Valley Pupfish and Devil’s Hole Pupfish live in different water environments and functioned differently. Understanding the water environment of the two types of pupfishes will help people building new habitats for pupfishes and increase their population so that would be possible to avoid the extinction of pupfishes from the earth. INTRODUCTION AND BACKGROUND Pupfish is a small killifish in the Southwest of America. There are five pupfish species in Death Valley which are Armargosa pupfish, Saratoga Pupfish, Devil’s Hole pupfish, Death Valley pupfish, and Cotton ball Marsh pupfish (National Park Service, 2008). -
The Endangered White Sands Pupfish (Cyprinodon Tularosa)
The Endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation Andrew Black1, Janna Willoughby2, Anna Br¨uniche-Olsen3, Brian Pierce4, and Andrew DeWoody1 1Purdue University 2Auburn University 3University of Copenhagen 4Texas A and M University College Station November 24, 2020 Abstract The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in Southwestern North America, is of conservation concern due in part to invasive species, chemical pollution, and groundwater withdrawal. Herein, we developed a high quality draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. Specifically, we localized microsatellite markers previously used to demarcate Evolutionary Significant Units, evaluated the possibility of introgression into the C. tularosa genome, and compared genomic diversity among related species. The de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08Gb draft genome with a contig N50 of 1.4Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterigii conserved orthologs. Many of the previously described C. tularosa microsatellite markers fell within or near genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Genetic distances between C. tularosa and the widespread invasive species C. variegatus, which diverged ~1.6-4.7 MYA, were 0.027 (nuclear) and 0.022 (mitochondrial). Nuclear alignments revealed putative tracts of introgression that merit further investigation. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from related species, likely because of smaller long-term effective population sizes constrained by their isolated and limited habitat.