cpDNA rbcL sequences for
Biodiverse analyses
Final Report
Prepared for the Ministry for the Environment by Dr Peter Heenan
Allan Herbarium (Landcare Research)
Disclaimer
This report has been prepared by Landcare Research for Ministry for the Environment.
If used by other parties, no warranty or representation is given as to its accuracy and
no liability is accepted for loss or damage arising directly or indirectly from reliance on
the information in it.
This report may be cited as:
Ministry of the Environment. 2015. cpDNA rbcL sequences for Biodiverse analyses:
Final Report. Wellington: Ministry for the Environment.
Published in October 2015 by the
Ministry for the Environment
Manatū Mō Te Taiao
PO Box 10362, Wellington 6143, New Zealand
ISBN: 978-0-908339-13-6 (electronic)
Publication number: ME 1218
© Crown copyright New Zealand [Year]
This document is available on the Ministry for the Environment’s website:
www.mfe.govt.nz
Contents
1
Aim
1
2
Background
1
3
Work completed
1
Obtain plant material
DNA extraction and PCR
DNA sequencing
Data analyses
1
1
2
2
Spatial and phylogenetic analyses results and discussion
3
Generic phylogenetic corrected weighted endemism
Phylogenetic diversity and endemism at genus level
Phylogenetic diversity and endemism at species level
Genus-level categorical analyses of neo- and palaeo-endemism
Species-level categorical analyses of neo- and palaeo-endemism
Utility of Biodiverse spatial and phylogenetic analyses
Additional rbcL sequencing requirements
3
3
3
4
4
4
5
References
5
4
5
Appendix 1. Sample information for the new rbcL sequences
generated for this contract
Sorted alphabetically by genus
6
6
Appendix 2. Genus rbcL phylogeny
12
Appendix 3. Generic phylogenetic endemism
13
Appendix 4. Genus-level patterns of PD, PWE and neo- and
palaeo-endemism
14
Appendix 5. Species-level patterns of PD, PWE and neo- and
palaeo-endemism
15
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
iii
1 Aim
To obtain DNA sequence data for the chloroplast large subunit of ribulose 1, 5 bisphosphate
carboxylase/oxygenase (rbcL) from New Zealand samples representing c. 200 genera for
analyses in Biodiverse, and to use these data to undertake spatial analyses in Biodiverse.
2 Background
There are 436 genera accepted in the New Zealand indigenous flora. Recent spatial and genetic
analyses of the New Zealand flora used a generic level phylogeny to obtain genetic metrics for
Biodiverse analyses (Heenan unpubl. data). Of the 436 genera included in the Biodiverse study,
214 genera were represented by sequences of species indigenous to New Zealand. However,
222 sequences were ‘surrogates’, being based on non-New Zealand species of the same genus
or, in a small number of cases, a close generic relative.
This project was to obtain rbcL sequences from indigenous New Zealand species to replace
sequences obtained from non-New Zealand samples and used as surrogates in the Biodiverse
analyses. Spatial analyses utilising the new rbcL sequence data in the phylogenetic dataset will
be undertaken.
3 Work completed
Obtain plant material
1.
We obtained samples representing 211 indigenous New Zealand genera from dried
collections in the Allan Herbarium or fresh collections from cultivated material. These 211
genera represented 95% of the 222 genera that were represented by surrogates in the
Biodiverse study.
2.
Herbarium vouchers information is presented in Appendix 1.
DNA extraction and PCR
1.
We extracted DNA from 309 samples and obtained suitable PCR product and clean
sequences from 191 samples.
2.
For 118 samples we did not obtain sequences as we obtained no PCR product, weak PCR
product, or the sequencing was messy.
3.
For some species we included more than one sample as we attempted multiple DNA
extractions.
4.
Using a robot for DNA extractions has meant we were able to increase the sample number
analysed, so we have been able to send three plates (each with c. 95 samples) for
sequencing, rather than the two plates we initially envisaged. This has meant that for some
samples that were unsuccessful in plate 1 (or plate 2) we were able to attempt another DNA
extraction, PCR and sequence with a different sample in plates 2 and/or 3. For some genera
we have attempted sequencing up to three different samples, and this has meant we have
been able to obtain sequences representing more genera.
5.
For some samples identified as being particularly difficult, we attempted DNA extractions
using a mortar & pestle and altered PCR protocols to obtain suitable DNA product for
sequencing.
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
1
DNA sequencing
1.
We obtained sequences for 191indigenous species that are representative of New Zealand
indigenous genera; this is 86% of the target number of 222. For 167 samples we obtained
read lengths of between 970 and the maximum of 1324 bases; for 10 samples there was a
gap (32–223 bases) in the sequence between the internal primers; and for 14 samples we
obtained only the 5′ or 3′ half of rbcL.
2.
Appendix 1 provides a summary of the successful sequence results, including GenBank
numbers.
Data analyses
1.
A data matrix was constructed comprising rbcL sequences representing 405 genera from
this study and GenBank sequences that are based on indigenous New Zealand species.
Sequences representing 31 genera that are based on non-New Zealand species acted as
surrogates where there was not a sequence available based on a New Zealand indigenous
species. One sequence was selected to represent each genus.
2.
The total dataset comprised 436 genera and was aligned in MEGA 5.0 (Tamura et al. 2011).
A model of sequence evolution for rbcL was selected using ModelTest.
3.
An optimised Maximum Likelihood tree was used as the base tree for model likelihood
calculations and the best model of sequence substitution was selected using the Bayesian
information criterion. Bayesian inference of phylogeny was performed using MrBayes
version 3.2.3 through the CIPRES Science Gateway version 3.3. Two runs with eight
chains and a sample frequency of 5000 were run for 36,000,000 generations resulting in a
total of 7200 trees for each run. The first 6000 trees of each run were discarded as burn-in
and the remaining 2400 trees of both runs were combined in a 95% majority rule consensus
tree using SumTrees version 3.3.1. The consensus tree is presented in Appendix 2.
4.
The Biodiverse software package version 1.0 was used for all analyses (Laffan et al., 2010).
Spatial data used for this study comprised 213,141 georeferenced specimens from the New
Zealand Virtual Herbarium (NZVH). All analyses were performed using a cell size of
0.12°, resulting in 2393 cells.
5.
The genus-level spatial data and phylogenetic tree were used to calculate phylogenetic
diversity (PD) and phylogenetic corrected weighted endemism (PE_CWE) for the entire
New Zealand archipelago and the main New Zealand islands. Statistical significance of the
resulting patterns of endemism for each of the phylogenetic and non-phylogenetic analyses
was assessed with a two-tailed test involving 999 random realisations of the observed
datasets using the preserved model implemented in Biodiverse.
6.
Categorical Analyses of Neo- and Palaeo- Endemism (CANAPE) analyses. Phylogenetic
diversity (PD) and phylogenetic weighted endemism (PWE) were calculated following
Mishler et al. (2014) at genus and species rank. Statistical significance of the resulting
biodiversity patterns for PD and PWE was assessed with 999 random realisations of the
observed datasets using the preserved model implemented in Biodiverse. This model
randomises the spatial locations of each taxon while preserving the taxon range and
maintaining the taxon richness within each cell.
7.
A CANAPE analysis was performed on the genus and species spatial and phylogenetic data
following Mishler et al. (2014). Differences in neo- and palaeo-endemism among islands
were visualised as barplots by plotting the distribution of p(RPE) values for the entire New
Zealand archipelago, North Island, South Island and offshore islands.
2Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
4 Spatial and phylogenetic analyses
results and discussion
Generic phylogenetic corrected weighted
endemism
For the New Zealand archipelago generic phylogenetic CWE has most primary and secondary
endemism concentrated in the northern offshore islands (Kermadec and Three Kings islands)
and the upper North Island areas of Surville Cliffs, Karikari Peninsula, Great Barrier Island, and
greater Auckland area (Appendix 3C). Randomisations showed that primary and secondary
areas of generic phylogenetic CWE for the northern offshore Kermadec and Three Kings
islands, along with northern North Island areas of Surville Cliffs and Karikari Peninsula, are
significantly greater than expected from random. The majority of primary and secondary areas
of CWE on the main New Zealand islands were not significantly different from random. In the
South Island, the majority of cells with significantly higher values of phylogenetic CWE than
expected from random occurred in inner montane basins and eastern areas, and cells with
significantly less CWE than expected from random were scattered throughout the island. In the
North Island, the majority of cells with significantly less generic phylogenetic CWE than
expected from random occurred in the lower half of the island.
For the main New Zealand islands, generic phylogenetic diversity (Appendix 3A) shows high
richness in the North Island and parts of the upper South Island. The general pattern is
decreasing richness with increasing latitude. Generic phylogenetic CWE for the main New
Zealand islands is very similar to generic phylogenetic CWE for the New Zealand archipelago
(Appendix 3B, 3C). The main differences are additional primary cells on the main New Zealand
islands being associated with Surville Cliffs, Kaitaia, Great Barrier Island and greater Auckland
area, and new single primary cells on the Volcanic Plateau and near Wellington City. No South
Island cells were part of the top 1% for generic phylogenetic endemism.
Phylogenetic diversity and endemism at genus
level
In the genus-level analyses of phylogenetic diversity (PD) few cells with significantly high PD
were indicated by randomisation analysis (Appendix 4). Those few that were indicated were
mostly in the northern and central North Island or in the southern South Island (blue cells in
Appendix 4A). However, cells with significantly low values of PD were distributed more or less
throughout the archipelago (red cells in Appendix 4A). Many more cells had significantly high
values of PWE (blue cells in Appendix 4B) than had significantly high PD. The most prevalent
concentrations of PWE cells were in the northern North Island, Three Kings Islands and
Kermadec Islands but a number of areas also appeared in the South Island. Areas with
significantly low values of PWE were less frequent than were significantly low values of PD,
and were entirely absent from the northern North Island but still frequent in the central and
southern North Island and the South Island.
Phylogenetic diversity and endemism at species
level
Few cells with significantly high PD were observed in the species level analysis and all of these
occurred in the central or northern North Island (blue cells in Appendix 5A). Cells with
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
3
significantly low PD were scattered throughout the northern North Island but much more
frequent and contiguous in the southern North Island and South Island, Stewart Island and
Chatham and subantarctic islands (red cells in Appendix 5A). Cells with significantly high PWE
were most frequent in the northern North Island, Kermadec Islands and Three Kings Islands and
found in scattered patches throughout the southern North Island and South Island (blue cells in
Appendix 5B). Cells with significantly low CWE were common in the lower North Island and
throughout the South Island (red cells in Appendix 5B). A cluster of cells on Stewart Island and
one cell from the Chatham Islands had high PWE, and Auckland and Antipodes islands each
had a single low PWE cell.
Genus-level categorical analyses of neo- and
palaeo-endemism
The New Zealand archipelago has a relatively even distribution of genus-level endemism types
with similar numbers of neo- and palaeo-endemics (Appendix 4C, D). Detailed analyses
revealed there are some distinct patterns and a two-sample Bootstrap Kolmogorov-Smirnov test
confirmed differences among the distribution of endemism types between the North and South
islands (D = 0.4251, p-value < 0.001). The North Island is biased toward palaeo-endemics,
including mixed-endemics being strongly skewed toward palaeo-endemics, and neo-endemics
are poorly represented (Appendix 4C, E). The South Island has similar numbers of neo- and
palaeo-endemics and a more even distribution of mixed-endemics (Appendix 4C, F). The
offshore islands, with the exception of the Antipodes Islands, all show cells with high levels of
endemism with a latitudinal trend of increasing neo-endemics with increasing latitude
(Appendix 4C, G). The northern Kermadec and Three Kings islands have only mixed-endemic
cells, the mid-latitude Chatham Islands have neo- and mixed-endemic cells, the Snares have
mixed-endemic cells, and the southernmost subantarctic islands, Auckland and Campbell
islands, have only neo-endemic cells.
Species-level categorical analyses of neo- and
palaeo-endemism
The analyses of species-level endemism for the New Zealand archipelago revealed a
predominance of neo- and palaeo-endemics (Appendix 5C, D). There are some well-defined
geographic patterns and a two-sample Bootstrap Kolmogorov-Smirnov test confirmed
differences in endemism types between the North and South islands (D = 0.8665, p-value <
0.001). In the northern North Island there are extensive areas of palaeo-endemism, accompanied
by only a few neo- and mixed-endemism cells (Appendix 5C, E). The South Island is dominated
by extensive and contiguous areas of neo-endemism in the northern South Island and southern
South Island (Appendix 5C, F). Stewart Island is a hotspot of neo-endemism. The offshore
islands are all hotspots of endemism, with the northernmost Kermadec and Three Kings islands
comprising mixed- and palaeo-endemics, whereas the Chatham and subantarctic islands are
dominated by neo-endemics (Appendix 5C, G).
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.
4Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
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.
2.
For 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.
3.
Having 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).
4.
Discussions 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.
5 References
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.
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
5
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. novaezelandiae
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. novaezelandiae
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-
KT626679
CHR 688806
1070
6Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
Family
Genus
Species
GenBank
number
Accession
number
Sequence length
(5' + 3', 1324
max)
zelandiae
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
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
7
Family
Genus
Species
GenBank
number
Accession
number
Sequence length
(5' + 3', 1324
max)
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
8Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
Family
Genus
Species
GenBank
number
Accession
number
Sequence length
(5' + 3', 1324
max)
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. novaezeelandiae
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
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
9
Family
Genus
Species
GenBank
number
Accession
number
Sequence length
(5' + 3', 1324
max)
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. novaezelandiae
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. novaezelandiae
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. novaezelandiae
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
10Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
Family
Genus
Species
GenBank
number
Accession
number
Sequence length
(5' + 3', 1324
max)
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
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
11
Appendix 2. Genus rbcL phylogeny
12Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
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.
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
13
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.
14Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь отображаться.
Appendix 5. Species-level patterns of
PD, PWE and neo- and palaeoendemism
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.
Ошибка! Используйте вкладку "Главная" для применения Title к тексту, который должен здесь
отображаться.
15