Rangewide microsatellite phylogeography of the endangered tidewater goby, Eucyclogobius newberryi (Teleostei: Gobiidae), a genetically subdivided coastal fish with limited marine dispersal

Conservation Genetics

Volumn 11, Issue 1, 2010, Pages 103-114

  Earl, Dent A ^a   Louie, Kristina D ^a   Bardeleben, Carolyne ^a   Swift, Camm C ^b   Jacobs, David K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ENTRIX INC   (United States)

Author keywords

Endangered; Estuary; Metapopulation; Phylogeography; Tidewater goby

Indexed keywords

ANTHROPOGENIC EFFECT; CONSERVATION GENETICS; DISPERSAL; ENDANGERED SPECIES; ESTUARINE ECOSYSTEM; EXTINCTION; FOUNDER EFFECT; GENETIC VARIATION; METAPOPULATION; PERCIFORM; PHYLOGEOGRAPHY; POPULATION BOTTLENECK; SEA LEVEL CHANGE; SPATIAL DISTRIBUTION;

EUCYCLOGOBIUS NEWBERRYI; GOBIIDAE; TELEOSTEI; VERTEBRATA;

EID: 74749087068     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-009-0008-9     Document Type: Article

References (44)

1. Ahnelt H, Göschl J, Dawson MN, Jacobs DK (2004) Geographical variation in the cephalic lateral line canals of Eucyclogobius newberryi (Teleostei: Gobiidae) and its comparison with molecular phylogeography. Folia Zoologica 53: 385-398.
2. Barlow M (2002) Phylogeographic structure of the tidewater goby, Eucyclogobius newberryi (Teleostei: Gobiidae), in the San Francisco Bay area and Ventura County: implications for Conservation Management. A thesis submitted in partial satisfaction of the requirements for the degree Master of Arts in Biology, University of California at Los Angeles.
3. Bernatchez L (1995) A role for molecular systematics in defining evolutionary significant units (ESU) in fishes. In: Nielsen JL (ed) Evolution and the aquatic ecosystem: defining unique units in population conservation. Am Fish Soc Symp 17, Bethesda, MD, pp 114-132.
4. Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF (2001) M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques 31: 25-28.
5. Burton RS (1998) Intraspecific phylogeography across the Point Conception biogeographic boundary. Evolution 52: 734-745.
6. Clemento A, Anderson EC, Boughton D, Girman D, Garza JC (2008) Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California. Conserv Genet. Online First, doi: 10. 1007/s10592-008-9712-0.
7. Coats R, Swanson M, Williams DP (1989) Hydrologic analysis for coastal wetland restoration. Environ Manage doi: 13: 715-727. 10. 1007/BF01868311.
8. Coyne JA, Orr HA (2004) Speciaton. Sinauer Associates, Sunderland, MA.
9. Dawson MN, Staton JL, Jacobs DK (2001) Phylogeography of the tidewater goby, Eucyclogobius newberryi (Teleostei, Gobiidae), in coastal California. Evolution 55: 1167-1179. doi: 10. 1111/j. 0014-3820. 2001. tb00636. x.
10. Dawson MN, Louie KD, Barlow M, Jacobs DK, Swift CC (2002) Comparative phylogeography of sympatric sister species Clevelandia ios & Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition Zone. Mol Ecol 11: 1065-1075. doi: 10. 1046/j. 1365-294X. 2002. 01503. x.
11. Dawson M, Waples R, Bernardi G (2006) Phylogeography. In: Allen LG, Pondella DJ, II, Horn MH (eds) The ecology of marine fishes: California and adjacent waters. UC Press, Berkeley.
12. Duvernell DD, Turner BT (1998) Evolutionary genetics of Death Valley pupfish populations: mitochondrial DNA sequence variation and population structure. Mol Ecol 7: 279-288. doi: 10. 1046/j. 1365-294X. 1998. 00347. x.
13. Echelle AA, Carson EW, Echele AF et al (2005) Historical biogeography of the new-world pupfish genus Cyprinodon (Teleostei: Cyprinodontidae). Copeia 2005: 320-339. doi: 10. 1643/CG-03-093R3.
14. Edmands S (2001) Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes. Mol Ecol 10: 1743-1750. doi: 10. 1046/j. 0962-1083. 2001. 01306. x.
15. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620. doi: 10. 1111/j. 1365-294X. 2005. 02553. x.
16. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3. 0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
17. Hall CA (2002) Nearshore marine paleoclimatic regions, increasing zoogeographic provinciality, molluscan extinctions, and paleoshorelines, California: Late Oligocene (27 Ma) to Late Pliocene (2. 5 Ma). Geol Soc Am Spec Pap 357: 1-489.
18. Hayes SA, Bond MH, Hanson CV, Freund EV, Smith JJ, Anderson EC, Amman AJ, MacFarlane RB (2008) Steelhead growth in a small California watershed: upstream and estuarine rearing patterns. Trans Am Fish Soc 137: 114-128.
19. Jacobs DK, Haney TA, Louie KD (2004) Genes, diversity, and geologic process on the Pacific coast. Annu Rev Earth Planet Sci 32: 601-652. doi: 10. 1146/annurev. earth. 32. 092203. 122436.
20. Jacobs DK, Louie KD, Earl DA et al (2005) Genetics of Eucyclogobius newberryi in Mission Creek Santa Barbara: a regional metapopulation analysis using mitochondrial control region sequence and microsatellites. Final Report Prepared for US Army Corps of Engineers. 19 August 2005.
21. Jakobsson M, Rosenberg N (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14): 1801-1806. doi: 10. 1093/bioinformatics/btm233.
22. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genetics 6: 13. v. 3. 15 http://ibdws.sdsu.edu/. Accessed 15 July 2009.
23. Jones KC, Levine KF, Banks JD (2002) Characterization of 11 polymorphic tetranucleotide microsatellites for forensic applications in California elk (Cervus elaphus canadensis). Mol Ecol Notes 2: 425-427. doi: 10. 1046/j. 1471-8286. 2002. 00264. x.
24. Lafferty KD, Page CJ (1997) Predation on the endangered tidewater goby, Eucyclogobius newberryi, by the introduced African clawed frog, Xenopus laevis, with notes on the frog's parasites. Copeia 1997: 589-592.
25. Lafferty KD, Swift CC, Ambrose RF (1999a) Postflood persistence and recolonization of endangered tidewater goby populations. North Am J Fish Manag 19: 618-622.
26. Lafferty KD, Swift CC, Ambrose RF (1999b) Extirpation and recolonization in a metapopulation of an endangered fish, the tidewater goby. Conserv Biol 13: 1447-1453. doi: 10. 1046/j. 1523-1739. 1999. 98016. x.
27. Langella O (1999) POPULATIONS 1. 2. 30 Population genetic software. http://bioinformatics.org/~tryphon/populations/. Accesed 15 July 2009.
28. MATLAB (2008) The MathWorks. Natick, MA.
29. Mayr E (1995) Species, classification, and evolution. In: Arai R, Kato M, Doi Y (eds) Biodiversity and evolution. National Science Museum Foundation, pp 3-12.
30. Mendonca H, Smith J, Brinegar C (2001) Isolation and characterization of four microsatellite loci in the tidewater goby (Eucyclogobius newberryi). Mar Biotechnol 3: 91-95.
31. National Marine Fisheries Service (2007) Federal recovery outline for the distinct population segment of southern California coast steelhead. National Marine Fisheries Service, Southwest Regional Office, Santa Barbara, CA, 56 pp.
32. Nei M, Tajima F, Tateno Y (2003) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19: 153-170.
33. Nielsen JL, Gan C, Wright J, Thomas WK (1994) Phylogeographic patterns in California steelhead as determined by mtDNA and microsatellite analyses. California Cooperative Oceanic Fisheries Investigations Reports 35, pp 90-92.
34. Pritchard JK, Wen W (2004) Documentation for structure software. The University of Chicago Press, Chicago.
35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
36. Rathbun G (1991) Status of declining aquatic reptiles, amphibians, and fishes in the lower Santa Rosa Creek, Cambria, California. Report to Greenspace; A land trust, Cambria, California.
37. Raymond M, Rousset F (1995) GENEPOP (Version 1. 2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
38. Ryder OA (1986) Species conservation and systematics: the dilemma of subspecies. Trends Ecol Evol 1: 9-10.
39. Swenson RO (1999) The ecology, behavior, and conservation of the tidewater goby, Eucyclogobius newberryi. Environ Biol Fish 55: 99-114.
40. Swift CC, Nelson JL, Maslow C, Stein T (1989) Biology and distribution of the tidewater goby, Eucyclogobius newberryi (Pisces: Gobiidae) of California. Natural History Museum of Los Angeles: Contributions in Science 404, pp 1-19.
41. Swift CC, Haglund TR, Ruiz M, Fisher RN (1993) The status and distribution of the freshwater fishes of southern California. Bull South Calif Acad Sci 92: 101-167.
42. US Fish and Wildlife Service (2005) Recovery plan for the tidewater goby (Eucyclogobius newberry). U. S. Fish and Wildlife Service, Portland, OR. vi + 199 pp.
43. Waples RS (1991) Pacific Salmon. Oncorhynchus spp., and the definition of species under the Endangered Species Act. Mar Fish Rev 53: 11-22.
44. Zedler JB (1996) Coastal mitigation in southern California: the need for a regional restoration strategy. Ecol Appl 6: 84-93.