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Phylogeography and
Population Genetics in Crustacea
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CRUSTACEAN ISSUES
General editor
Prof. Dr. Stefan Koenemann
Department of Biology and Didactics
Science and Technology
University of Siegen
Germany
1 Crustacean Phylogeny
Schram, F.R. (ed.)
1983 ISBN 90 6191 231 8 Sold out
2 Crustacean Growth: Larval Growth
Wenner, A. (ed.)
1985 ISBN 90 6191 294 6
3 Crustacean Growth: Factors in Adult Growth
Wenner, A. (ed.)
1985 ISBN 90 6191 535 X
4 Crustacean Biogeography
Gore, R.H. & Heck, K.L. (eds.)
1986 ISBN 90 6191 593 7
5 Barnacle Biology
Southward, A.J. (ed.)
1987 ISBN 90 6191 628 3
6 Functional Morphology of Feeding and Grooming in Crustacea
Felgenhauer, B.E., Thistle, A.B. & Watling, L. (eds.)
1989 ISBN 90 6191 777 8
7 Crustacean Egg Production
Wenner, A. & Kuris, A. (eds.)
1991 ISBN 90 6191 098 6
8 History of Carcinology
Truesdale, F.M. (ed.)
1993 ISBN 90 5410 137 7
9 Terrestrial Isopod Biology
Alikhan, A.M.
1995 ISBN 90 5410 193 8
10 New Frontiers in Barnacle Evolution
Schram, F.R. & Hoeg, J.T. (eds.)
1995 ISBN 90 5410 626 3
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11 Crayfish in Europe as Alien Species - How to Make the Best of a Bad Situation?
Gherardi, F. & Holdich, D.M. (eds.)
1999 ISBN 90 5410 469 4
12 The Biodiversity Crisis and Crustacea - Proceedings of the Fourth International
Crustacean Congress, Amsterdam, Netherlands
Vaupel Klein, J.C. von & Schram, F.R. (eds.)
2000 ISBN 90 5410 478 3
13 Isopod Systematics and Evolution
Kensley, B. & Brusca, R.C. (eds.)
2001 ISBN 90 5809 327 1
14 The Biology of Decapod Crustacean Larvae
Anger, K.
2001 ISBN 90 2651 828 5
15 Evolutionary Developmental Biology of Crustacea
Scholtz, G. (ed.)
2004 ISBN 90 5809 637 8
16 Crustacea and Arthropod Relationships
Koenemann, S. & Jenner, R.A. (eds.)
2005 ISBN 0 8493 3498 5
17 The Biology and Fisheries of the Slipper Lobster
Lavalli, K.L. & Spanier, E. (eds.)
2007 ISBN 0 8493 3398 9
18 Decapod Crustacean Phylogenetics
Martin, J.W., Crandall, K.A. & Felder, D.L. (eds.)
2009 ISBN 1 4200 9258 8
19 Phylogeography and Population Genetics in Crustacea
Held, C., Koenemann, S. & Schubart, C.D. (eds.)
2011 ISBN 978 1 4398 4074 3
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Phylogeography and
Population Genetics in Crustacea
Edited by
Christoph Held
Alfred Wegener Institute for Polar and Marine Research
Bremerhaven, Germany
Stefan Koenemann
University of Siegen
Siegen, Germany
Christoph D. Schubart
University of Regensburg
Regensburg, Germany
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CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742
© 2011 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business
No claim to original U.S. Government works
Version Date: 20111111
International Standard Book Number-13: 978-1-4398-4074-0 (eBook - PDF)
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Contents
Preface ix
CHRISTOPHHELD,STEFANKOENEMANN,&CHRISTOPHD.SCHUBART
I ANALYSES OF POPULATION GENETICS: GUIDELINES AND 1
DEVELOPMENTS
Analyzingintraspecificgeneticvariation:apracticalguideusingmitochondrial 3
DNAandmicrosatellites
FLORIANLEESE&CHRISTOPHHELD
Detectingandmeasuringgeneticdifferentiation 31
CHRISTOPHERE.BIRD,STEPHENA.KARL,PETERE.SMOUSE&ROBERTJ.
TOONEN
Rethinkingthemechanismsthatshapemarinedecapodpopulationstructure 57
BREEK.YEDNOCK&JOSEPHE.NEIGEL
Causesofchaos: spatialandtemporalgeneticheterogeneityintheintertidal 75
anomurancrabPetrolisthescinctipes
ROBERTJ.TOONEN&RICHARDK.GROSBERG
II POPULATION GENETICS AND PHYLOGEOGRAPHY OF 109
MARINE CRUSTACEANS
ComparativephylogeographyofIndo-WestPacificintertidalbarnacles 111
LINGMINGTSANG,TSZHUENWU,WAICHUENNG,GRAYA.WILLIAMS,
BENNYK.K.CHAN&KAHOUCHU
EvolutionandconservationofmarinebiodiversityintheCoralTriangle: 129
insightsfromstomatopodCrustacea
PAULH.BARBER,SAMANTHAH.CHENG,MARKV.ERDMANN,KIMBERLY
TENGGARDJAJA&AMBARIYANTO
Comparativephylogeographyofthreeachelatelobsterspeciesfrom 157
Macaronesia(northeastAtlantic)
ELSAFROUFE,PATRICIACABEZAS,PAULOALEXANDRINO&MARCOS
PE´REZ-LOSADA
GeneticvariationanddifferentiationofFenneropenaeusmerguiensisinthe 175
ThaiPeninsula
WARAPONDWANNA&AMORNRATPHONGDARA
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viii Contents
PopulationgeneticsintherockyshorecrabPachygrapsusmarmoratusfrom 191
thewesternMediterraneanandeasternAtlantic: complementaryresultsfrom
mtDNAandmicrosatellitesatdifferentgeographicscales
SARAFRATINI,CRISTOPHD.SCHUBART&LAPORAGIONIERI
III POPULATION GENETICS AND PHYLOGEOGRAPHY OF 215
LIMNIC CRUSTACEANS
ThehistoryoftheDaphniapulexcomplex: asexuality,hybridization,and 217
polyploidy
FRANCEDUFRESNE
PhylogeographicpatternsinArtemia: amodelorganismforhypersaline 233
crustaceans
ILIASKAPPAS,ATHANASIOSD.BAXEVANIS&THEODOREJ.ABATZOPOULOS
Intraspecificgeographicdifferentiationandpatternsofendemisminfreshwater 257
shrimpspeciesflocksinancientlakesofSulawesi
KRISTINAVONRINTELEN
Molecularandconservationbiogeographyoffreshwatercarideanshrimpsin 273
north-westernAustralia
BENJAMIND.COOK,TIMOTHYJ.PAGE&JANEM.HUGHES
ComparingphylogeographicpatternsacrossthePatagonianAndesintwo 291
freshwatercrabsofthegenusAegla(Decapoda: Aeglidae)
MARCOSPE´REZ-LOSADA,JIAWUXU,CARLOSG.JARA&KEITHA.CRANDALL
Moleculardiversityofriverversuslakefreshwateranomuransinsouthern 305
Chile(Decapoda:Aeglidae)andmorphometricdifferentiationbetweenspecies
andsexes
HEATHERD.BRACKEN-GRISSOM,TIFFANYENDERS,CARLOSG.JARA&
KEITHA.CRANDALL
Populationstructureoftwocrayfishwithdiversephysiologicalrequirements 323
JESSEW.BREINHOLT,PAULE.MOLER&KEITHA.CRANDALL
ShallowphylogeographicstructureofPuertoRicofreshwatercrabs: an 345
evolutionaryexplanationforlowspeciesdiversitycomparedtoJamaica
CHRISTOPHD.SCHUBART,NICOLET.RIVERA,KEITHA.CRANDALL&TOBIAS
SANTL
Contributors 367
Index 371
Colorinsert
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Preface
CHRISTOPHHELD1,STEFANKOENEMANN2,&CHRISTOPHD.SCHUBART3
1DivisionofBiosciences,AlfredWegenerInstituteforPolarandMarineResearch,Bremerhaven,Germany
2DepartmentofBiologyandDidactics,UniversityofSiegen,Siegen,Germany
3Biology1,UniversityofRegensburg,Regensburg,Germany
CrustaceanIssues19,“PhylogeographyandPopulationGeneticsinCrustacea,”dealswithasubject,
theanalysisandinterpretationofintraspecificgeneticvariation,thathasbecomeagainthefocusof
attentionafteralongperiodofneglectbythescientificcommunity. Thetheoreticalfoundationfor
thisfieldwaslaidinthefirsthalfofthelastcentury; theHardy-Weinbergprinciplewaspublished
morethan100yearsago,andinthedecadesthatfolloweditwasmainlytheworksofR.A.Fisher,
S.Wright, and J.B.S.Haldane that formed the basis of population genetics as we know it today.
At that time its practical use was severely limited by the fact that the underlying variants in the
genotypehadtobevisibleinthephenotypeinordertobeamenabletoanalysis. Now,however,the
use of molecular tools has become more widespread in application and effectiveness, so much so
that putting the predictions of population genetic theory to the test became feasible in real-world
scenarios.
The advance of phylogenetic analysis during the 1990s has permanently added sophisticated
molecular techniques to the zoologist’s toolbox. However, it was almost exclusively the genetic
variationtobefoundamongspeciesthatwasunderinvestigationwhereastheintraspecificvariance
was routinely down-weighted or entirely excluded in earlier phylogenetic studies. Therefore new
modes of analyzing have had to be adopted to adequately handle and appreciate the part of the
genetic variation to be found within species. In addition to population genetics, which describes
patterns of differentiation at any given moment, phylogeography emphasizes the element of time
andquicklygainedafootholdasanalternativemethodofanalysis. Phylogeographymakesuseof
spatialinformationmappedontohaplotypenetworksorgenetreesandisperhapsmoreintuitively
understoodthanpopulationgeneticsstatistics,especiallyforanaudiencetrainedinphylogeny.Nev-
ertheless, more recently both methods have evolved in ways that have bridged the gap between
phylogenetic(macroevolutionary)studiesandpopulationgenetic(microevolutionary)studies.
Weallhaveseenhowtheincreasedeffortsfocusedonphylogeneticresearchandinternational
barcoding campaigns of the past ten years have increased the availability of data useful for phy-
logeography on a massive scale. Phylogeography, population genetics, and the ever-accelerating
progress in technology collectively have put larger and larger molecular datasets into play, rekin-
dlingtheinterestinthestudyofintraspecificvariation.
Ascrustaceanzoologistswithverydiversebackgroundsandresearchinterestssetouttoinves-
tigatepatternsonthescaleofpopulationsusingmoleculartools,theyareexposedtoabewildering
varietyofgeneticmarkers,analyticalmethods,andcomputerprogramsfromwhichtochoose. The
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