Cpdna rbcL sequences for Biodiverse analyses Final Report



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Utility of Biodiverse spatial and phylogenetic analyses


This study is one of the first to utilise PD, PWE and CANAPE in analyses of the entire vascular flora of an archipelago at two taxonomic ranks, with previous studies having focused on species within genera or genera within families in continental Australia.

The results of this study are generally consistent with current understanding of New Zealand areas of vascular plant endemism and regional biogeographic patterns. However, the analyses presented here importantly provide new insights into the positions of some of the major biogeographic boundaries and to the types of endemism observed. New centres of endemism can be revealed using the sophisticated analyses in Biodiverse, and patterns of endemism can be identified at a finer scale of resolution and more accurately than in earlier studies. The types of analyses presented here have wide application, including: 1) new hypotheses of areas, boundaries and types of endemism; 2) enabling significant areas to be identified to plan and prioritise conservation efforts; and 3) the phylogenetic metrics can be utilised for environmental reporting to provide insights to and measures of biodiversity at genetic scales not previously possible.

In conclusion, Biodiverse provides a valuable framework for objectively analysing and visualising biodiversity data for the entire vascular flora of the widely dispersed New Zealand archipelago. Further research is needed to better understand the behaviour of endemism metrics with regard to the effects of data biases, taxonomic rank and geographic scale.

Additional rbcL sequencing requirements


  1. Complete the sequencing for the 10 samples with a sequence gap between internal 3′ and 5′ primers and obtain the complete sequence for the 14 samples missing either the 5′ or 3′ half of rbcL.

18For the 31 genera for which we have not obtained DNA sequences from New Zealand indigenous species, this missing data should be obtained to complete the dataset of rbcL sequences representative of all New Zealand genera. This is achievable and loans from other herbaria with recent collections of these genera and some field work is required to obtain suitable plant material for sequencing. It should be noted that the orchids Gastrodia and Molloybas and the parasitic Dactylanthus do not have chlorophyll and therefore are not able to be sequenced for rbcL.

19Having almost completed the construction of an rbcL phylogeny for New Zealand indigenous vascular plant genera, consideration should be given to expanding this to include indigenous non-vascular moss, liverwort and hornwort genera (bryophytes).

20Discussions have been held with Dr Robbie Holdaway (Landcare Research) about utilising the New Zealand indigenous genus rbcL phylogeny as part of the environmental DNA project (A national framework for biological heritage assessment across natural and productive landscapes) in The National Science Challenge, New Zealand’s Biological Heritage. Completing the rbcL sequencing for the missing genera is a priority as the resulting dataset would have multiple uses.

21References


Laffan, S.W., Lubarsky, E. and Rosauer, D.F., 2010. Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography, 33, 643–647. doi:10.1111/j.1600-0587.2010.06237.x

Mishler, B.D., Knerr, N.J., Gonzalez-Orozco, C.E., Thornhill, A.H., Laffan, S. and Miller, J.T., 2014. Phylogenetic measures of biodiversity and neo- and palaeo-endemism in Australian Acacia. Nature Communications, 4, 4473.



Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739.

Appendix 1. Sample information for the new rbcL sequences generated for this contract

Sorted alphabetically by genus


Family

Genus

Species

GenBank number

Accession number

Sequence length (5' + 3', 1324 max)

Asteraceae

Abrotanella

A. caespitosa

KT626656

CHR 607884

1115

Rosaceae

Acaena

A. rorida

KT626657

CHR 688794

1324

Gramineae

Achnatherum

A. petriei

KT626658

CHR 586059

691; 5' only

Orchidaceae

Acianthus

A. sinclairii

KT626659

CHR 603051

1200

Cunoniaceae

Ackama

A. rosifolia

KT626660

CHR 688775

1110

Apiaceae

Actinotus

A. novae-zelandiae

KT626661

CHR 688799

1162

Orchidaceae

Adenochilus

A. gracilis

KT626662

CHR 530208

1324

Sapindaceae

Alectryon

A. excelsus subsp. grandis

KT626663

CHR 688787

1044

Loranthaceae

Alepis

A. flavida

KT626664

CHR 535350

1121

Amaranthaceae

Alternanthera

A. nahui

KT626665

CHR 688757

1180

Asteraceae

Anaphalioides

A. trinervis

KT626807

CHR 569864

1221; 42 bp gap

Ranunculaceae

Anemone

A. tenuicaulis

KT626808

CHR 591709

1303

Apiaceae

Apium

A. prostratum

KT626666

CHR 688801

1301

Ericaceae

Archeria

A. traversii

KT626667

CHR 596813

1233

Asteraceae

Argyrotegium

A. mackayi

KT626804

CANU 37228

553; 5' only

Tectariaceae

Arthropteris

A. tenella

KT626668

CHR 552984

970

Urticaceae

Australina

A. pusilla

KT626669

CHR 617174

1070

Gramineae

Austrostipa

A. stipoides

KT626838

CHR 688815

1324

Lauraceae

Beilschmiedia

B. tawa

KT626839

CHR 688816

1324

Asteraceae

Brachyscome

B. montana

KT626670

CHR 688802

1181

Asphodelaceae

Bulbinella

B. angustifolia

KT626671

CHR 605120A

1197; 105 bp gap

Plantaginaceae

Callitriche

C. petriei

KT626809

CHR 688803

1324

Ranunculaceae

Caltha

C. novae-zelandiae

KT626672

CHR 506838

1314

Convolvulaceae

Calystegia

C. soldanella

KT626673

CHR 480414

1304

Brassicaceae

Cardamine

C. aff. corymbosa

KT626674

CHR 688807

1115

Cyperaceae

Carex

C. impexa

KT626675

CHR 688774

1290

Leguminosae

Carmichaelia

C. muritai

KT626676

CHR 688789

1116

Gramineae

Cenchrus

C. caliculatus

KT626677

CHR 580706

1088

Apiaceae

Centella

C. uniflora

KT626678

CHR 625866

1046

Asteraceae

Centipeda

C. aotearoana

KT626810

CHR 688830

1324

Apiaceae

Chaerophyllum

C. novae-zelandiae

KT626679

CHR 688806

1070

Amaranthaceae

Chenopodium

C. detestens

KT626680

CHR 688808

1181

Ranunculaceae

Clematis

C. paniculata

KT626681

CHR 688785

1113

Caryophyllaceae

Colobanthus

C. sp. Manahune

KT626682

CHR 688765

1318

Gramineae

Connorochloa

C. tenuis

KT626811

CHR 635134

1324

Convolvulaceae

Convolvulus

C. fractosaxosa

KT626683

CHR 564693

1184

Orchidaceae

Corunastylis

C. pumila

KT626812

CHR 324126

700; 3' only

Asteraceae

Cotula

C. australis

KT626684

CHR 688768

1310

Asteraceae

Craspedia

C. sp.

KT626806

RDSmissen 143S; no voucher

1215; 130 bp gap

Crassulaceae

Crassula

C. helmsii

KT626832

CHR610093

1324

Dryopteridaceae

Cystopteris

C. tasmanica

KT626685

CHR 606990

1101

Podocarpaceae

Dacrydium

D. cuppresinum

KT626686

CHR 688752

1324

Asteraceae

Damnamenia

D. vernicosa

KT626687

CHR 303822

1159

Apiaceae

Daucus

D. glochidiatus

KT626688

CHR 620205

1324

Gramineae

Deyeuxia

D. aucklandica

KT626689

CHR 604569

1324

Hemerocallidaceae

Dianella

D. latissima

KT626690

CHR 688770

1064

Gramineae

Dichelachne

D. micrantha

KT626691

CHR 564101

725; 3' only

Convolvulaceae

Dichondra

D. repens

KT626692

CHR 688766

1308

Dryopteridaceae

Diplazium

D. australe

KT626693

CHR 510484

647; 5' only

Aizoaceae

Disphyma

D. australe subsp. australe

KT626694

CHR 604292

1300

Asteraceae

Dolichoglottis

D. lyallii

KT626695

CHR 515343

1324; 223 bp gap

Orchidaceae

Drymoanthus

D. adversus

KT626813

CHR 592300

825; 3' only

Meliaceae

Dysoxylum

D. spectabile

KT626696

CHR 471369

690; 5' only

Amaranthaceae

Dysphania

D. pusilla

KT626697

CHR 688809

1180

Orchidaceae

Earina

E. mucronata ?

KT626698

CHR 615991

1303

Elaeocarpaceae

Elaeocarpus

E. hookerianus

KT626814

CHR 523579

1295

Elatinaceae

Elatine

E. gratioloides

KT626699

CHR 592133

1208

Urticaceae

Elatostema

E. rugosum

KT626700

CHR 472985

1263

Ericaceae

Epacris

E. pauciflora var. sinclairii

KT626815

CHR 503909

1315

Onagraceae

Epilobium

E. nummularifolium

KT626701

CHR 688776

1071

Apiaceae

Eryngium

E. vesiculosum

KT626702

CHR 610065

1136

Euphorbiaceae

Euphorbia

E. glauca

KT626703

CHR 688761

1103

Orobanchaceae

Euphrasia

E. wettsteiniana

KT626704

CHR 619184

1149

Gramineae

Festuca

F. actae

KT626816

CHR 620407

1035

Cyperaceae

Ficinia

F. spiralis

KT626817

CHR 550373

1235

Cyperaceae

Fimbristylis

F. squarrosa

KT626818

CHR 466163

688; 5' only

Pandanaceae

Freycinetia

F. banksii

KT626705

CHR 605445 A

1185

Onagraceae

Fuchsia

F. perscandens

KT626706

CHR 688810

1129

Cyperaceae

Gahnia

G. lacera

KT626707

CHR 614507

1121; 41 bp gap

Rubiaceae

Galium

G. "Limestone"

KT626708

CHR 688811

697; 5' only

Ericaceae

Gaultheria

G. antipoda

KT626709

CHR 596532

1283

Loganiaceae

Geniostoma

G. ligustrifolium var majus

KT626710

CHR 688786

1071

Gentianaceae

Gentianella

G. bellidifolia

KT626711

CHR 688812

1195

Rosaceae

Geum

G. cockaynei

KT626819

CHR 688763

1324

Apiaceae

Gingidia

G. haematitica

KT626712

CHR 514866

1116

Haloragaceae

Gonocarpus

G. aggregatus

KT626713

CHR 614461

973

Plantaginaceae

Gratiola

G. concinna

KT626714

CHR 618106

1202

Haloragaceae

Haloragis

H. erecta

KT626715

CHR 688753

1184

Asteraceae

Helichrysum

H. filicaule

KT626716

CHR 607937

1324

Malvaceae

Hibiscus

H. richardsonii

KT626717

CHR 688777

1314

Araliaceae

Hydrocotyle

H. robusta

KT626718

CHR 688795

1042

Hypericaceae

Hypericum

H. rubicundulum

KT626719

CHR 688792

1068

Orchidaceae

Ichthyostomum

I. pygmaeum

KT626820

CHR 316371

667; 3' only

Loranthaceae

Ileostylus

I. micranthus

KT626720

CHR 567741

1265

Colchicaceae

Iphigenia

I. novae-zelandiae

KT626721

CHR 554363

1324

Convolvulaceae

Ipomoea

I. cairica

KT626722

CHR 518158

1218

Gramineae

Isachne

I. globosa

KT626723

CHR 619240

1324

Calceolariaceae

Jovellana

J. sinclairii

KT626821

CHR 688782

1295

Thymelaeaceae

Kelleria

K. dieffenbachii

KT626834

CHR 688817

1318

Santalaceae

Korthalsella

K. clavata

KT626724

CHR 688813

1187

Myrtaceae

Kunzea

K. robusta

KT626835

CHR 688818

1324

Gramineae

Lachnagrostis

L. tenuis

KT626725

CHR 619124

1318

Asteraceae

Lagenophora

L. barkeri

KT626803

CHR 507891

1184; 47 bp gap

Rutaceae

Leionema

l. nudum

KT626726

CHR 688773

1324

Brassicaceae

Lepidium

L. banksii

KT626727

CHR 553591 A

1324

Cyperaceae

Lepidosperma

L. australe

KT626728

CHR 602893

1181

Ericaceae

Leptecophylla

L. robusta

KT626729

CHR 688796

1111

Rubiaceae

Leptostigma

L. setulosum

KT626730

CHR 688800

1300

Apiaceae

Lignocarpa

L. diversifolia

KT626731

CHR 471842

1324

Scrophulariaceae

Limosella

L. lineata

KT626732

CHR 688771

1286

Lauraceae

Litsea

L. calcicaris

KT626733

CHR 550254

1314

Campanulaceae

Lobelia

L. physaloides

KT626734

CHR 688756

1214

Polypodiaceae

Loxogramme

L. dictyopteris

KT626735

CHR 539841

1324

Luzuriagaceae

Luzuriaga

L. parviflora

KT626736

CHR 630362

1324

Cyperaceae

Machaerina

M. sinclairii

KT626822

CHR 591924

1324

Juncaceae

Marsippospermum

M. gracile

KT626737

CHR 503298

1115

Phrymaceae

Mazus

M. radicans

KT626738

CHR 618785

1324

Rutaceae

Melicope

M. ternata

KT626739

CHR 688781

1313

Labiatae

Mentha

M. cunninghamii

KT626740

CHR 508454

1157

Asteraceae

Microseris

M. scapigera

KT626823

CHR 420451

1324

Loganiaceae

Mitrasacme

M. helmsii

KT626741

CHR 624366

1071

Cyperaceae

Morelotia

M. affinis

KT626742

CHR 554079

1070

Scrophulariaceae

Myoporum

M. laetum

KT626743

CHR 688760

1070

Boraginaceae

Myosotidium

M. hortensia

KT626744

CHR 594776

1129

Boraginaceae

Myosotis

M. drucei

KT626745

CHR 620110

553; 5' only

Haloragaceae

Myriophyllum

M. propinquum

KT626746

CHR 688762

1318

Primulaceae

Myrsine

M. aquilonia

KT626747

CHR 688784

1284

Orchidaceae

Nematoceras

N. orbicularis

KT626824

CHR 688820

1324

Rubiaceae

Nertera

N. balfouriana

KT626748

CHR 688754

1235

Oleaceae

Nestegis

N. apetala

KT626749

CHR 688780

1231

Brassicaceae

Notothlaspi

N. australis

KT626750

CHR 688814

1318

Gramineae

Oplismenus

O. hirtellus

KT626751

CHR 565709

1116

Cyperaceae

Oreobolus

O. impar

KT626752

CHR 619190

1071

Orchidaceae

Orthoceras

O. novae-zeelandiae

KT626753

CHR 525816

1168

Plantaginaceae

Ourisia

O. sessilifolia

KT626825

CHR 595645

1324

Asteraceae

Ozothamnus

O. leptophylla

KT626754

CHR 688772

1324

Gramineae

Paspalum

P. orbiculare

KT626840

CHR 688821

1324

Passifloraceae

Passiflora

P. tetrandra

KT626755

CHR 688797

1168

Geraniaceae

Pelargonium

P. inodorum

KT626826

CHR 505483

1324

Piperaceae

Peperomia

P. urvilleana

KT626756

CHR 603162

1161

Orchidaceae

Petalochilus

P. varigatus

KT626757

CHR 609677

1146

Lycopodiaceae

Phlegmariurus

P. varius

KT626758

CHR 602463 A

1187

Asteraceae

Picris

P. burbidgei

KT626841

CHR 688822

1324

Pittosporaceae

Pittosporum

P. cornifolium

KT626759

CHR 688778

1318

Sapotaceae

Planchonella

P. costata

KT626760

CHR 585498

1097

Plantaginaceae

Plantago

P. “Sewell Peak”

KT626761

CHR 688758

1114

Labiatae

Plectranthus

P. parviflorus

KT626762

CHR 466161

1260; 73 bp gap

Aspleniaceae

Pleurosorus

P. rutifolius

KT626833

CHR 474971

1324

Thelypteridaceae

Pneumatopteris

P. pennigera

KT626763

CHR 620410

1198; 32 bp gap

Gramineae

Poa

P. sudicola

KT626764

CHR 546759 B

1184

Phyllanthaceae

Poranthera

P. alpina

KT626765

CHR 605954

1110

Potamogetonaceae

Potamogeton

P. suboblongus

KT626827

CHR 607282

660; 5' only

Rosaceae

Potentilla

P. anserinoides

KT626766

CHR 688798

1324

Urticaceae

Pouzolzia

P. australis

KT626767

CHR 500267

1090

Orchidaceae

Prasophyllum

P. colensoi

KT626768

CHR 620570

1115

Asteraceae

Pseudognaphalium

P. luteoalbum

KT626769

CHR 688759

1324

Paracryphiaceae

Quintinia

Q. acutifolia

KT626828

CHR 630350

652; 5' only

Asteraceae

Rachelia

R. glaria

KT626805

CANU 35555

1157; 48 bp gap

Ranunculaceae

Ranunculus

R. ranceorum

KT626770

CHR 688764

1318

Ripogonaceae

Ripogonum

R. scandens

KT626771

CHR 630348

1126

Brassicaceae

Rorippa

R. divaricata

KT626842

CHR 688823

1324

Rosaceae

Rubus

R. parvus

KT626843

CHR 688824

1324

Polygonaceae

Rumex

R. flexuosus

KT626844

CHR 688825

1324

Amaranthaceae

Sarcocornia

S. quinqueflora

KT626772

CHR 509368 A

1259

Goodeniaceae

Scaevola

S. gracilis

KT626773

CHR 473386

1324

Apiaceae

Scandia

S. rosaefolia

KT626774

CHR 550309

1150

Cyperaceae

Schoenoplectus

S. tabernaemontani

KT626775

CHR 503128 B

1324

Cyperaceae

Schoenus

S. apogon

KT626776

CHR 552946

1185

Caryophyllaceae

Scleranthus

S. uniflorus

KT626777

CHR 688793

1045

Labiatae

Scutellaria

S. novae-zelandiae

KT626778

CHR 553817

1183

Gentianaceae

Sebaea

S. ovata

KT626779

CHR 536601

1324

Asteraceae

Senecio

S. carnosula

KT626836

CHR 688826

1324

Cucurbitaceae

Sicyos

S. mawhai

KT626780

CHR 518213

1175

Solanaceae

Solanum

S. latifolium

KT626781

CHR 688791

1072

Asteraceae

Sonchus

S. kirkii

KT626829

CHR 610068

1202

Leguminosae

Sophora

S. longicarinata

KT626782

CHR 688779

1305

Sparganiaceae

Sparganium

S. subglobosum

KT626783

CHR 636696

1047

Caryophyllaceae

Spergularia

S. tasmanica

KT626845

CHR 688827

1324

Gramineae

Spinifex

S. sericeus

KT626784

CHR 553001

1125

Orchidaceae

Spiranthes

S. novae-zelandiae

KT626785

CHR 607274

1100

Orchidaceae

Stegostyla

S. lyallii

KT626786

CHR596931

1110

Caryophyllaceae

Stellaria

S. gracilenta

KT626837

CHR 688828

1324

Moraceae

Streblus

S. smithii

KT626787

CHR 688755

1150

Amaranthaceae

Suaeda

S. novae-zelandiae

KT626788

CHR 506556

1295

Myrtaceae

Syzygium

S. maire

KT626830

CHR 592285

1296

Asteraceae

Taraxacum

T. magellanicum

KT626802

CHR 514144

1324; 42 bp gap

Bignoniaceae

Tecomanthe

T. speciosa

KT626789

CHR 688788

1195

Orchidaceae

Thelymitra

T. carnea

KT626790

CHR 550399

1078

Thelypteridaceae

Thelypteris

T. confluens

KT626846

CHR 688829

1308

Phrymaceae

Thyridia

T. repens

KT626791

CHR 605428

1159

Asteraceae

Traversia

T. baccharoides

KT626792

CHR 595605

1115

Gramineae

Trisetum

T. youngii

KT626793

CHR 635187

1324

Typhaceae

Typha

T. orientalis

KT626831

CHR 495389

1116

Urticaceae

Urtica

U. linearifolia

KT626794

CHR 606040

1071

Violaceae

Viola

V. cunninghamii

KT626795

CHR 688804

1005

Labiatae

Vitex

V. lucens

KT626796

CHR 688783

1284

Asteraceae

Vittadinia

V. australis

KT626797

CHR 552797

1070

Campanulaceae

Wahlenbergia

W. albomarginata

KT626798

CHR 617821

697; 5' only

Cunoniaceae

Weinmannia

W. racemosa

KT626799

CHR 688790

1136

Orchidaceae

Winika

W. cunninghamii

KT626800

CHR 530204

1111

Gramineae

Zoysia

Z. minima

KT626801

CHR 632533

1128


Appendix 2. Genus rbcL phylogeny



Appendix 3. Generic phylogenetic endemism


A. Richness, main New Zealand islands. B. Corrected Weighted Endemism, main New Zealand islands. C. Corrected Weighted Endemism, New Zealand archipelago. Dark blue: primary endemism (top 1%) CWE values; light blue: secondary endemism (top 5%) CWE values; +: greater CWE than expected from random; •: less CWE than expected from random; white: empty cell.


Appendix 4. Genus-level patterns of PD, PWE and neo- and palaeo-endemism


Genus-level patterns and types of neo- and palaeo-endemism. A. Relative phylogenetic diversity significance levels resulting from a randomization test. B. Relative phylogenetic endemism significance levels resulting from a randomization test. C. CANAPE areas of neo-, mixed- and palaeo-endemism. D. Barplot of CANAPE analysis for New Zealand archipelago. E. Barplot of CANAPE analysis for North Island. F. Barplot of CANAPE analysis for South Island. G. Barplot of CANAPE analysis for offshore islands. A, B: red values indicate cells that contain significantly less RPD and RPE than expected; blue values indicate cells that contain significantly more RPD and RPE than expected.


Appendix 5. Species-level patterns of PD, PWE and neo- and palaeo-endemism


A. Relative phylogenetic diversity significance levels resulting from a randomization test. B. Relative phylogenetic endemism significance levels resulting from a randomization test. C. CANAPE areas of neo-, mixed- and palaeo-endemism. D. Barplot of CANAPE analysis for New Zealand archipelago. E. Barplot of CANAPE analysis for North Island. F. Barplot of CANAPE analysis for South Island. G. Barplot of CANAPE analysis for offshore islands. A, B: red values indicate cells that contain significantly less RPD and RPE than expected; blue values indicate cells that contain significantly more RPD and RPE than expected.



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