Biodivers Conserv (2008) 17:893-910 DOI 10.1007/s10531-008-9335-2 SUPPLEMENTARY TABLES AND REFERENCES

Potentials for monitoring gene level biodiversity: using as an example

Linda Laikre · Lena C. Larsson · Anna Palmé · Johan Charlier · Melanie Josefsson · Nils Ryman

Table S1 Molecular genetic studies of natural Swedish populations (as of August 2006) defined taxonomically in alphabetical order

www.zoologi.su.se/research/popgen/monitoring

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Linda Laikre ( ) · Lena C. Larsson · Anna Palmé · Johan Charlier · Nils Ryman Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden e-mail: [email protected]

Melanie Josefsson Department of Environmental Monitoring and Assessment, Swedish Environmental Protection Agency, P.O. Box 7050, 750 07 Uppsala, Sweden

Table S1 Molecular genetic studies of natural Swedish populations (as of August 2006) defined taxonomically in alphabetical order. Note - studies can include several species, the total number of references is 775

No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Animalia Anguilliformes Anguilla anguilla European eel 4 Clupeiformes Alosa fallax twaite shad 1 Clupea harengus Atlantic herring 9 Cypriniformes Abramis blicca white bream 1 Leuciscus cephalus chub 1 Esociformes Esox lucius northern pike 2 Gadiformes Gadus morhua Atlantic cod 8 Gasterosteiformes Syngnathus typhle pipefish 1 Osmeriformes Osmerus eperlanus European smelt 1 Perciformes Gymnocephalus cernua ruffe 2 Perca fluviatilis European perch 5 Pomatoschistus minutus sand goby 1 Pleuronectiformes Platichthys flesus European flounder 1 Platichthys stellatus starry flounder 1 Psetta maxima turbot 3 Salmoniformes Coregonus albula vendace 2 Coregonus spp. whitefish spp. 16 Salmo salar Atlantic salmon 58 Salmo trutta brown trout 68 Salvelinus alpinus char 24 Thymallus thymallus grayling 7 gobio 4 Cottus poecilopus 2 quadricornis fourhorn 3 uncertain uncertain uncertain 1 various various various 2 Amphibia Anura Hyla arborea European tree frog 3 Rana arvalis moor frog 2 Rana esculenta edible frog 1 Rana lessonae pool frog 5 Rana temporaria common frog 9 Annelida Clitellata Aporrectodea rosea earthworm sp. 1 Aulodrilus pluriseta aquatic oligochaete worm sp. 1 Dendrobaena octaedra earthworm sp. 1 Eiseniella tetraedra aquatic oligochaete worm sp. 2 Limnodrilus spp. aquatic oligochaete worm sp. 1

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 1 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Nais elinguis aquatic oligochaete worm sp. 1 Octolasion cyaneum earthworm sp. 1 Peloscolex ferox aquatic oligochaete worm sp. 1 Potamothrix spp. aquatic oligochaete worm spp. 1 Psammoryctides barbatus aquatic oligochaete worm sp. 1 Rhyacodrilus coccineus aquatic oligochaete worm sp. 1 Slavina appendiculata aquatic oligochaete worm sp. 1 Stylaria lacustris aquatic oligochaete worm sp. 1 Stylodrilus heringianus aquatic oligochaete worm sp. 1 Tubifex spp. aquatic oligochaete worm spp. 1 Polychaeta Marenzelleria spp. bristle worms 1 Arthropoda Arachnida Allochemes wideri pseudoscorpion sp. 1 Atypus affinis purse-web spider 1 Larca lata pseudoscorpion sp. 1 Branchiopoda Bosmina coregoni water flea sp. 1 Bosmina longispina water flea sp. 1 Bythotrephes cederstroemi spiny water flea 1 Bythotrephes longimanus spiny water flea 1 Daphnia pulex water flea 2 Daphnia sp. water flea 2 Malacostraca Astacus astacus noble crayfish 2 Gammarus lacustris Gammarus shrimp/scud 1 Gammarus spp. Gammarus shrimp/scud 1 Meganyctiphanes norvegica northern krill 1 Mysis relicta fairy shrimp 1 Neomysis integer mysid shrimp 1 Pacifastacus leniusculus signal crayfish 1 Palaemon adspersus prawn sp. 1 Palaemon squillla prawn sp. 1 Maxillopoda Balanus improvisus bay barnacle 2 Aves Anseriformes Anser erythropus lesser white-fronted goose 1 Branta canadensis Canada goose 1 Somateria mollissima common eider 3 Charadriiformes Calidris alpina dunlin 1 Gallinago media great snipe 1 Larus argentatus herring gull 4 Larus canus common gull 1 Larus fuscus lesser black-backed gull 4 Larus marinus greater black-backed gull 2

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 2 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Limosa limosa black-tailed godwit 1 Scolopax rusticola Eurasian woodcock 1 Tringa totanus common redshank 1 Columbiformes Columba palumbus woodpigeon 1 Falconiformes Falco peregrinus peregrine falcon 1 Haliaeetus albicilla white-tailed eagle 1 Galliformes Lagopus lagopus willow grouse 2 Lagopus mutus ptarmigan 1 Perdix perdix European grey partridge 2 Tetrao tetrix black grouse 2 Passeriformes Acrocephalus arundinaceus great reed warbler 3 Ficedula albicollis collared flycatcher 5 Ficedula hypoleuca pied flycatcher 4 Parus major great tit 1 Parus montanus willow tit 1 Passer montanus tree sparrow 1 Perisoreus infaustus Siberian jay 1 Phylloscopus collybita chiffchaff 3 Phylloscopus trochilus willow warbler 3 Pelecaniformes Phalacrocorax carbo great cormorant 1 Piciformes Dendrocopos leucotos white-backed woodpecker 1 Cnidaria Anthozoa Lophelia pertusa coral sp. 1 Insecta Coleoptera Adoxus obscurus bromius 2 Agabus bipustulatus diving beetle 3 Bolitophagus reticulatus tinder fungus beetle 1 Bromius obscurus western grape rootworm beetle 1 Galerucella sagittariae leaf beetle sp. 1 Haliplus sibiricus crawling water beetle sp. 1 Haliplus wehnckei crawling water beetle sp. 1 Hydroporus glabriusculus diving beetle 1 Ips typographus spruce bark beetle 1 Meligethes aeneus pollen beetle 1 Oplocephala haemorrhoidalis beetle sp. 1 Otiorrhynchus salicis weevil sp. 2 Otiorrhynchus scaber weevil sp. 2 Polydrosus mollis weevil sp. 1 Tomicus piniperda Eurasian pine shoot beetle 1 Collembola Isotoma viridis green springtail 1 Diptera Anopheles spp. Anopheles mosquitoes 1

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 3 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Coelopa frigida seaweed fly 1 Dipsa bifurcata fly sp. 1 Drosophila bifasciata fruit fly sp. 1 Drosophila littoralis fruit fly sp. 1 Drosophila melanogaster fruit fly sp. 3 Drosophila subobscura fruit fly sp. 6 Lucilia sericata blowfly 1 Ephemeroptera Parameletus chelifer minnow mayfly 1 Parameletus minor mayfly sp. 1 Hymenoptera Andrena ferox mining bee 1 Andrena jacobi Andrena bee 2 Aneugmenus padi sawfly sp. 1 Apis mellifera honey bee 3 Biorhiza pallida oak gallwasp 1 Cotesia melitaearum parasitoid wasp 1 Diplolepis rosae rose gall wasp 1 Eurhadinoceraea ventralis sawfly sp. 1 Formica cinerea wood ant 3 Formica exsecta narrow-headed ant 1 Formica pratensis black-backed meadow ant 2 Formica spp. wood ant spp. 2 Lasioglossum boreale arctic/alpine sweat bee 1 Lasius niger black garden ant 1 Leptothorax acervorum ant sp. 2 Nasonia vitripennis jewel wasp 1 Odonata Calopteryx splendens banded demoiselle 1 Lepidoptera Coenonympha sp. heath butterfly 1 Mammalia Artiodactyla Alces alces moose 10 Capreolus capreolus roe deer 5 Cervus elaphus red deer 3 Ovibos moschatus musk ox 1 Rangifer tarandus reindeer 4 Sus scrofa wild boar 1 Carnivora Alopex lagopus arctic fox 3 Canis lupus grey wolf 11 Castor fiber European beaver 1 Gulo gulo wolverine 4 Halichoerus grypus grey seal 1 Lutra lutra European otter 2

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 4 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Lynx lynx Eurasian lynx 4 Phoca hispida ringed seal 1 Phoca vitulina harbor seal 3 Phocoena phocoena harbour porpoise 2 Ursus arctos brown bear 6 Insectivora Neomys fodiens Eurasian water shrew 1 Sorex araneus common shrew 10 Sorex caecutiens Laxmann´s shrew 1 Sorex minutus Eurasian pygmy shrew 1 Lagomorpha Lepus europaeus brown hare 5 Lepus timidus mountain hare 7 Odontoceti Phocoena phocoena harbour porpoise 1 Rodentia Apodemus spp. field mice 1 Apodemus sylvaticus woodmouse 1 Clethrionomys glareolus bank vole 2 Clethrionomys rutilus northern red-backed vole 2 Microtus agrestis field/short-tailed vole 9 Microtus oeconomus tundra or root vole 3 Mus musculus house mouse 2 Myopus schisticolor wood lemming 5 Sciurus vulgaris red squirrel 1 Mollusca Bivalvia Arctica islandica Icelandic cyprine/ocean quahog 1 Macoma balthica Baltic tellin 1 Mytilus edulis blue mussel 3 Mytilus trossulus bay mussel 1 Ostrea edulis European flat oyster 2 Gastropoda Arianta arbostorum copse snail 1 Balea perversa land snail sp. 1 Bithynia tentaculata common bithynia 1 Cepaea hortensis white-lipped snail 1 Cepaea nemoralis grove snail 1 Chondrina clienta land snail sp. 1 Helix pomatia Roman snail 1 Hydrobia spp. hydrobia snail 1 Littorina littorea 2 Littorina mariae flat periwinkle 1 Littorina neglecta rough periwinkle 1 rough periwinkle 9 Littorina tenebrosa lagoon periwinkle 1

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 5 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Lymnaea spp. pond snail spp. 1 Macoma balthica Baltic tellin 1 Melarhaphe neritoides small winkle 1 Myxas glutinosa glutinous snail 1 Theodoxus fluviatilis common river nerite 1 Zonitoides nitidus black gloss 1 Myxini Myxiniformes Myxine circifrons whiteface hagfish 1 Nematoda Chromadorea Heterodera avenae plant-parasitic nematode sp. 1 Dictyocaulidae Dictyocaulus viviparus lungworm 2 Dictyocaulus spp. lungworm spp. 1 Heteroderidae Globodera artemisae potato cyst nematode 1 uncertain Haemonchus contortus Barber's pole worm 1 Nemertea Enopla Oerstedia dorsalis hoplonemertean worm sp. 1 Platyhelminthes Monogenea Gyrodactylus salaris ectoparasitic 1 piriformes fluke sp. 1 Microphallus pygmaeus fluke sp. 1 Priapulida Halicryptomorpha Halicryptus spinulosus priapulid worm 1 Reptilia Squamata Lacerta agilis sand lizard 4 Lacerta vivipara common lizard 1 Vipera berus adder 3 Tardigrada Eutardigrada Richtersius coronifer water bear 1 various various various various 1 Fungi Ascomycota Bacidiaceae Biatora helvola biatora lichen 1 Helotiaceae Gremmeniella abietina Brunchorstia disease 6 Phialocephala spp. dark septate endophytes 1 Hypocreaceae Nectria fuckeliana Nectria sp. 1 Lecideaceae Lecidea ahlesii lecidea lichen sp. 1 Lecidea confluentula lecidea lichen sp. 1 Lecidea promixta lecidea lichen sp. 1 Parmeliaceae Flavocetraria nivalis lichen sp. 1 Pleosporaceae Pyrenophora teres necrotrophic fungal pathogen 1 Tuberaceae Tuber aestivum/Tuber uncinatum truffle 1 uncertain Didymella bryoniae gummy stem blight 1 Letharia vulpina wolf lichen 1 Verticillium dahliae Fungi sp. 1 Verticillium longisporum Fungi sp. 1 Verticillium nigrescens Fungi sp. 1 Venturiaceae Venturia tremulae aspen scab fungus 1 Xyleariacae Daldinia loculata wood decay fungus 4

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 6 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Basidiomycota Atheliceae Tylospora fibrillosa basidiomycete sp. 1 Bondarzewiaceae Heterobasidion annosum root rot 3 Melampsoraceae Melampsora epitea willow rust 4 Melampsora larici-epitea willow leaf rust 4 Meruliaceae Cylindrobasidium evolvens resupinate fungus sp. 1 Polyporaceae Trichaptum abietinum pitted sap rot 1 Poriceae Fomitopsis pinicola red banded polyplore 3 Fomitopsis rosea wood-decay fungus 1 Sclerodermataceae Pisolithus arhizus dyeball/dead man's foot 1 Stereaceae Amylostereum areolatum resupinate fungi sp. 2 Amylostereum chailletii resupinate fungi sp. 2 Amylostereum laevigatum resupinate fungi sp. 1 Stereum sanguinolentum red heart rot 1 Tricholomataceae Tricholoma nauseosum pine mushroom 1 uncertain (Polyporales) Phellinus nigrolimitatus wood decay fungus 1 various various various various 2 Plantae Bryophyta Bryaceae Mielichhoferia elongata elongate copper moss 3 Mielichhoferia mielichhoferiana Mielichofer´s copper moss 2 Hylocomiaceae Hylocomium splendens splendid feather moss 4 Leucodontaceae Leucodon sciuroides leucodon moss 1 Neckeraceae Neckera pennata neckera moss 1 Polytrichaceae Pogonatum dentatum expanding moss 1 Sphagnaceae Sphagnum affine peat moss 1 Sphagnum capillifolium peat moss sp. 4 Sphagnum rubellum peat moss sp. 3 Chlorophyta Ulvophyceae Cladophora rupestris green alga weed 2 Enteromorpha intestinalis gut weed 1 Ulva compressa sea lettuce sp. 1 Ulva intestinalis sea lettuce sp. 1 Hepatophyta Plagiochilaceae Plagiochila porelloides leafy liverwort 1 Magnoliophyta Aceraceae Acer platanoides maple 1 Anthericaceae Anthericum liliago St Bernard's lily 1 Anthericum ramosum spider plant 1 Apiaceae Crithmum maritimum rock samphire 1 Eryngium maritimum sea holly or seaside eryngo 1 Asteraceae Mycelis muralis wall lettuce 1 Taraxacum obtusilobum dandelion sp. 1 Betulaceae Betula nana dwarf birch 1 Betula pendula European white birch/silver birch 4

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 7 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Betula pubescens downy birch 1 Corylus avellana hazel 3 Brassicaceae Arabidopsis arenosa rockcress sp. 2 Arabidopsis lyrata lyre-leaved rock-cress 1 Arabidopsis suecica rockcress sp. 2 Arabidopsis thaliana mouse-ear cress 4 Arabis petraea northern rock-cress 1 Brassica nigra black mustard 1 Cakile maritima European searocket 1 Microthlaspi perfoliatum claspleaf pennycress 1 Thlaspi caerulescens alpine pennycress 1 Caryophyllaceae Cerastium alpinum alpine mouse-ear chickweed 2 Gypsophila fastigiata fastigiate gypsophila 5 Minuartia biflora mountain stitchwort 1 Moehringia trinervia three-veined sandwort 1 Petrorphagia prolifera proliferous pink 1 Silene dioica red campion 12 Silene nutans Eurasian catchfly 1 Silene uniflora sea campion 3 Silene vulgaris bladder campion 4 Silene viscosa white sticky catchfly 1 Viscaria alpina alpine campion 1 Chenopodiaceae Halimione portulacoides sea purslane 1 Salsola kali Russian thistle 1 Clusiaceae Hypericum perforatum St. John's wort 1 Cyperaceae Carex arctogena capitate sedge 1 Carex arenaria sand sedge 1 Carex capitata capitate sedge 2 Carex digitata fingered sedge 2 Carex lepidocarpa little green sedge/yellow sedge 2 Schoenus spp. bog rush spp. 1 Empetraceae/Ericaceae Empetrum hermaphroditum black crowberry 2 Empetrum nigrum black crowberry 1 Ericaceae Vaccinium vitis-idaea lingonberry 5 Fabaceae Hippocrepis emerus scorpion senna 3 Lathyrus vernus spring-vetch 2 Vicia dumetorum vetch sp. 2 Vicia pisiformis pea vetch 4 Fagaceae Castanea sativa European chestnut 1

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 8 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Fagus orientalis Oriental beech 1 Fagus sylvatica European beech 2 Quercus petraea sessile/durmast oak 2 Quercus robur pedunculate oak 2 Lamiaceae Glechoma hederacea ground-ivy 2 Liliaceae Allium vineale wild garlic 1 Oleaceae Fraxinus excelsior common ash 1 Orchidaceae Calypso bulbosa Calypso orchid/fairy slipper 1 Dactylorhiza incarnata spotted orchid/keyflowers 1 Dactylorhiza maculata spotted orchid/keyflowers 1 Dactylorhiza sphagnicola spotted orchid/keyflowers 1 Gymnadenia conopsea fragrant orchid 4 Gymnadenia odoratissima short-spurred fragrant orchid 2 Pseudorchis albida small-white orchid 1 Parnassiaceae Parnassia palustris bog-stars/grass of Parnassus 1 Poaceae Alopecurus pratensis meadow foxtail 1 Briza media common quaking grass 1 Bromus hordeaceus soft brome 1 Calamagrostis sp. small-reed/reedgrass sp. 1 Elymus alaskanus Alaskan wheatgrass 1 Elymus caninus bearded wheatgrass 1 Elymus mutabilis 'Lapland wildrye' 1 Elymus spp. wildrye spp. 1 Festuca ovina sheep's fescue 5 Hordeum secalinum meadow barley 1 Melica ciliata hairy melic grass/silky spike melic 1 Melica nutans mountain melick 2 Melica transsilvanica red spire 1 Polygonaceae Bistorta vivipara alpine bistort 1 Polygonum viviparum alpine bistort 1 Potamogetonaceae Potamogeton pectinatus pondweed 1 Ranunculaceae Ranunculus glacialis glacier buttercup 1 Ranunculus pygmaeus pygmy buttercup 1 Rosaceae Dryas integrifolia entire-leaved avens 1 Dryas octopetala mountain avens 1 Potentilla argentea hoary cinquefoil 3 Rosa caesia dogrose sp. 1 Rosa canina dogrose sp. 1 Rosa dumalis dogrose sp. 2

Laikre et al. 2008 - Potentials for monitoring gene level biodiversity: using Sweden as an example 9 No. of Kingdom Phylum/Division Class/Order/Family Scientific name Common name studies Rosa rubiginosa dogrose sp. 1 Rosa sherardii dogrose sp. 1 Rosa spp. dogrose spp. 1 Rosa villosa dogrose sp. 1 Rubus nessensis blackberry sp. 1 Rubus spp. brambles 2 Sorbus torminalis wild service tree 1 Rubiaceae Galium aparine catchweed bedstraw 1 Salicaceae Populus tremula European aspen 1 Salix viminalis common osier/basket willow 3 Salix caprea sallow 1 Saxifragaceae Saxifraga adscendens wedgeleaf saxifrage 1 Saxifraga cernua drooping saxifrage 2 Saxifraga cespitosa tufted saxifrage 1 Saxifraga osloensis saxifrage sp. 1 Saxifraga tenius saxifrage sp. 1 Saxifraga tridactylites rue-leaved saxifrage 1 Scrophulariaceae Euphrasia stricta drug eyebright 2 Ulmaceae Ulmus spp. elm spp. 2 Zosteraceae Zostera marina eelgrass 2 Zostera noltii dwarf eelgrass 1 Apiacieae Angelica archangelica garden angelica 1 Plantaginaceae Plantago maritima plaintain sp. 1 Pinophyta Cupressaceae Juniperus communis common juniper 1 Pinaceae Picea abies Norway spruce 21 Pinus sylvestris Scots pine 61 Pteridophyta Hyplolepidaceae Pteridium aquilinum common bracken 1 Protista Heterokontophyta Bacillariophyceae Skeletonema marinoi diatom sp. 1 Fucaceae Fucus radicans brown seaweed 1 Fucus serratus toothed wrack 1 Fucus spp. brown algal spp. 1 Fucus vesiculosus bladderwrack 2 Leptolegniaceae Aphanomyces astaci crayfish plaque (water mould) 1 Oomycetes Phytophthora infestans water mould 1 Pythiaceae Pythium group F water mold pathogen 1 Rhodophyta Florideophyceae Scagelia sp. red alga 1 uncertain Ceramium tenuicorne red alga 1 various various various various various 3

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