The New Zealand Thrush: an extinct oriole.

The New Zealand Thrush: An Extinct Oriole
Ulf S. Johansson1*, Eric Pasquet2, Martin Irestedt3
1Department of Vertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden, 2Departement Syste´matique et Evolution, Muse´um National d’Histoire
Naturelle, UMR7205-CNRS, F-75231, Paris, France, 3Molecular Systematics Laboratory, Swedish Museum of Natural History, Stockholm, Sweden
Abstract
The New Zealand Thrush, or Piopio, is an extinct passerine that was endemic to New Zealand. It has often been placed in its
own family (Turnagridae), unresolved relative to other passerines, but affinities with thrushes, Australaian magpies,
manucodes, whistlers, birds-of-paradise and bowerbirds has been suggested based on morphological data. An affinity with
the bowerbirds was also indicated in an early molecular study, but low statistical support make this association uncertain. In
this study we use sequence data from three nuclear introns to examine the phylogenetic relationships of the piopios. All
three genes independently indicate an oriole (Oriolidae) affinity of the piopios, and the monophyly of the typical orioles
(Oriolus), figbirds (Sphecotheres), and the piopios is strongly supported in the Bayesian analysis of the concatenated data set
(posterior probability = 1.0). The exact placement of the piopios within Oriolidae is, however, more uncertain but in the
combined analysis and in two of the gene trees the piopios are placed basal to the typical orioles while the third gene
suggest a sister relationship with the figbirds. This is the first time an oriole affinity has been proposed for the piopios.
Divergence time estimates for the orioles suggest that the clade originated ca 20 million years ago, and based on these
estimates it is evident that the piopios must have arrived on New Zealand by dispersal across the Tasman Sea and not as a
result of vicariance when New Zealand separated from Gondwana in the late Cretaceous.
Citation: Johansson US, Pasquet E, Irestedt M (2011) The New Zealand Thrush: An Extinct Oriole. PLoS ONE 6(9): e24317. doi:10.1371/journal.pone.0024317
Editor: Samuel T. Turvey, Zoological Society of London, United Kingdom
Received May 23, 2011; Accepted August 7, 2011; Published September 9, 2011
Copyright: � 2011 Johansson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This research was supported by the Swedish Research Council (Grant No. 621-2010-5321; www.vr.se) to Per Ericson. The funders had no role in study
design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: ulf.johansson@nrm.se
Introduction
The New Zealand thrush, or Piopio, was an endemic, but now
extinct, passerine on New Zealand. It was widely distributed on
both the North and the South Island, from north of Auckland to
Steven Island [1]. The birds on the two main islands were
morphologically quite similar and have historically often been
considered conspecific. They did, however, show some differences
in plumage patterns as well as in size and other morphological
characters [2] and are today often treated as two different species;
the South Island Piopio (Turnagra capensis) and the North Island
Piopio (T. tanagra) [3,4]. The piopios apparently favoured forest
undergrowth and fed on a wide range of food items, including
berries, seeds, various invertebrates, eggs and other birds [1]. Of
the two species the South Island Piopio was the first to be
described in 1787 by Anders Sparrman but in the hundred years
that followed it declined from being ‘‘common’’ to virtually extinct
by the late 1800s. The North Island Piopio went through a similar
decline, and for both species the last confirmed sightings were
made at the turn of the century. The primary cause for the decline
and final extirpation was apparently caused by predation from
introduced predators such as cats, dogs, ferrets, stoats and rats [3].
Historically, the Piopio has often been referred to as the ‘‘New
Zealand thrush’’ and was in some 19th century classifications
placed in Turdidae [5,6] (see [2] for a detailed review). However,
Buller [7] questioned this association and placed the piopios in
their own family, Turnagridae. Later studies have also shown that
the thrush-like appearance does not reflect its phylogenetic affinity,
but so far no consensus about its actual position within the
passerine tree has been reached [4]. For instance, Oliver [1,8]
noted that the palate of the piopios indicated affinity with the
Australian magpies (Gymnorhina tibicen) or manucodes (Manucodia).
Mayr and Amandon [9], on the other hand, placed the piopios in
their Pachycephalini together with e.g., Pachycephala, Colluricincla,
and Falcunculus. However, Mayr and Amandon [9] also placed
Pitohui, Oreoica, Hylocitrea, and Pachycare in this group, all of which
are now considered part of other passerine radiations [10,11,12].
Olson et al. [2] examined the osteology, myology and pterolysis of
the piopios and concluded that, albeit with considerable conflict
among the characters, the piopios were related to the ‘‘birds-of-
paradise and bowerbird assemblage’’. Recent molecular studies,
however, have shown that this assemblage is not monophyletic,
but rather consists of three separate, unrelated lineages; bower-
birds (Ptilonorhynchidae), birds-of-paradise (Paradisaeidae) and
satinbirds (Cnemophilidae) [13].
Nevertheless, a possible relationship with the bowerbirds was
also indicated in a molecular study based on 900 base pair (bp) of
cytochrome b by Chrisitidis et al. [14]. Unfortunately, low
bootstrap support for the indicated relationships as well as a
limited taxon sampling makes it difficult to draw any firm
conclusions from these results. Furthermore, Gibb [15] has
recently questioned the accuracy of the sequence used by
Chrisitidis et al. [14] and noted that this sequence differs in 45
out of 307 positions (14.7%) compared to a new cytochrome b
sequence from another individual. In a re-analysis based on
1783 bp of mitochondrial DNA, Gibb [15] instead concluded that
the piopios likely belong in the ‘‘core Corvoidea’’ radiation, but
were unable to confidently place it in any particular clade within
that group.
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The majority of the land bird species native to New Zealand,
excluding those intentionally or unintentionally introduced by
humans, appear to be the result of oversea colonization from the
Australian continent [16,17]. These colonization events range from
a few decades (e.g. the Pacific Swallow Hirundo tahitica and White-
faced Heron Egretta novaehollandiae) to many million years ago. But it
has also been suggested that some groups, e.g. moas (Dinornithi-
formes) and New Zealand Parrots (Strigopidae), became isolated
when New Zealand broke off from the Gondwanan continent, 80-
60 million years ago (mya) [18,19]. Among passerines, the New
Zealand wrens (Acanthisittidae), which represent the first split in the
passerine tree, may be another of these groups [13,20,21,22], and it
has also been suggested that the New Zealand Wattlebirds
(Callaeatidae) became isolated at this event [23] (but see [24]).
The fact that it has been difficult to place the Piopios relative to
other groups of passerines could possibly indicate that they are
another of these ‘‘ancient lineages’’ that became isolated when
New Zealand separated from Gondwana. [23]. The purpose of
this study is to resolve the phylogenetic position of the piopios and
discern whether this lineage represents one of these potential early
divergences or a more recent dispersal.
Methods
Taxon sampling, amplification and sequencing
We examined the phylogenetic affinity of the South Island
Piopio, Turnagra capensis, by analyzing DNA sequences from three
nuclear introns; myoglobin intron 2, ornithine decarboxylase
introns 6 to 7 (ODC), and glyceraldehyde-3-phosphodehydrogenase
intron 11 (GAPDH). DNA was extracted from a foot pad sample
obtained from one specimen of Turnagra capensis (MNHN 1999-
1258), housed in the collections of Muse´um National d’Histoire
Naturelle, Paris. We used the Qiagen DNeasy Tissue Micro Kit for
the extraction following the manufacturer’s recommendation,
except for that 20 ml of 1 molar DTT (dithiothreitol) was added
during the lysis stage and the sample was heated to 72uC for
10 minutes after the buffer AL had been added. To minimize the
risk of contamination, extraction where done in a special facility
dedicated to the preparation of DNA samples from museum
specimen and prior to extraction all equipment and buffers were
sterilized with UV light.
Amplification and sequencing of fragmented DNA from old
study skins require careful primer design, as target regions usually
need to be divided into short, overlapping fragments. We
amplified fragments of ca 200–250 bp, generally by using primer
combinations that have previously successfully amplified a broad
selection of passerine birds, e.g. [25,26], but for some fragments
new primers were also designed. The glyceraldehyde-3-phospho-
dehydrogenase intron 11 GAPDH was amplified in two fragments
using the primer combinations G3Pcora1R [26]/G3PintL1 [27]
and G3Pcora1F [26]/G3P14b [27], myoglobin intron 2 was
amplified in four fragments using the primer combinations Myo2
[28]/Myo-cora182H [26], Myo-cora159L [26]/Myo344H [22],
Myo-TurnF343 (AGT GAC TGG ACA CAA GGG ACA)/Myo-
TurnR515 (GCA GAA GCA CTG GGC TCT AT), and Myo-
cora491L [26]/Myo3F [29], and ornithine decarboxylase introns
6 to 7 (ODC) was amplified in three fragments using the primer
combinations ODintF2 [25]/OD-TurnR1 (CAT GGA AAC
TAC AAA AAG ATA CAA AC), OD-TurnF3 (TGT GTG
TTT GAT ATG GGA GTA AGT)/OD-TurnR3 (GTA ATA
GTC ATT TGA GTT TGA GCT G), and OD-TurnF4 (CTC
ATC TAC AGA TGC ACT AAA ATT G)/ODintR4 [25]. We
used hot-start touchdown PCR, with annealing temperatures for
the first cycles generally just 1–2uC below the melting temperature
of the primer with the lowest melting temperature. A represen-
tative thermocycling program for a given primer combination
started with an initial denaturation at 95uC for 5 min, followed by
two cycles of 95uC for 30 s, 59uC for 30 s, 72uC for 60 s, and two
sets of cycles, each repeated two times, were the annealing
temperature was lowered to 57uC and 55uC, respectively (all other
temperatures and intervals identical). The thermocycling program
was completed with 34 cycles with the annealing temperature set
to 53uC and a final 72uC for 5 min. The extractions, ampli-
fications, and sequencing procedures otherwise followed the
procedures described in Irestedt et al. [25].
Our taxon sampling includes a broad selection of oscine birds,
including representatives of the bowerbirds, satinbirds, birds-of-
paradise, thrushes and whistlers. As preliminary assessments of our
first sequences from Turnagra capensis indicted an oriole (Oriolidae)
affinity, Oriolidae have been particularly densely sampled in the
final data set. Menura novaehollandiae was used as outgroup as Menura
novaehollandiae has been found to form the sister clade to all other
oscine birds [13]. Voucher and GenBank accession numbers are
given in Table 1.
Phylogenetic analyses
We used Bayesian inference to estimate phylogenetic relation-
ships. The models for nucleotide substitutions used in the analyses
were selected for each gene individually by the Akaike Information
Criterion using the program MRMODELTEST 2.2 [30] in
conjunction with PAUP* [31]. The number of indels was low and
the sequences could easily be aligned by eye. The final alignment
of the three gene segments included 1744 bp and all gaps were
treated as missing data in the analyses.
Posterior probabilities of trees and parameters in the substitu-
tion models were approximated with MCMC and Metropolis
coupling using the program MRBAYES 3.1.1 [32]. Analyses were
performed for each of the individual genes (10 million generations)
as well as on the concatenated data set (50 million generations),
with trees sampled every 1000 generations. The program AWTY
[33] was used to estimate when the chains had reached their
apparent target distributions, and trees sampled during the burn-in
phase were discarded.
Results
In total we obtained 1504 bp of nuclear DNA sequences from the
Turnagra capensis sample (707 bp from myoglobin intron 2, 501 bp
from ornithine decarboxylase introns 6 to 7 (ODC), excluding a
region of about 100 bp that we were unable to sequence, and
296 bp from glyceraldehyde-3-phosphodehydrogenase intron 11
GAPDH). No mismatches between overlapping fragments were
found in any of the target sequences, no heterozygotic sites were
found, and none of the sequence fragments turned out to be identical
to any other corresponding fragment in any other species checked.
The analysis of the concatenated, three-gene data set strongly
supports an oriole affinity of the piopios (Fig. 1). The Turnagra
forms a strongly supported clade (posterior probability [PP] = 1.0)
together with the two oriole clades Oriolus and Sphecotheres. Within
this clade the Turnagra is placed with weak support (PP = 0.69) as
the sister of Oriolus. Pitohui dichrous, another species with a proposed
oriole affinity [34,35] is placed as the sister group of these three
lineages. In this tree, the whistlers (Pachycephalidae), a group to
which the piopios sometimes have been assigned, are placed as the
sister group of the orioles.
All of the individual gene trees (not shown) indicate an oriole
affinity of the piopios, although each gene indicates a slightly
different topology. Both myoglobin and G3P place Turnagra as the
The New Zealand Thrush: An Extinct Oriole
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sister of the three included Oriolus species, but the two gene trees
differ in the placement of Sphecotheres and Pitohui relative to this
group. In the myoglobin gene tree Sphecotheres and Pitohui are
placed as sister taxa, and this clade is in turn placed as the sister
group of the Oriolus/Turnagra clade, but in this gene tree there is
also weak support for placing the Yellow-green Vireo Vireo
flavoviridis with the former two taxa (PP = 0.60). In G3P, neither
Sphecotheres nor Pitohui are placed with the Oriolus/Turnagra clade,
but are placed with different taxa in different parts of the tree. The
support values in the G3P gene tree are generally low (PP,0.95),
and this tree is, in those parts of importance for this study, basically
unresolved due to low posterior probabilities for the indicated
relationships. The ODC gene tree is similar to the combined tree
in that Pitohui is placed basal relative to an Oriolus/Turnagra/
Sphecotheres clade, but in this tree Turnagra is placed as the sister
group of Sphecotheres rather than Oriolus.
Discussion
Our data strongly point at an oriole affinity for the piopios and
that they are nested within the Oriolidae. This clade consists of the
typical orioles Oriolus (27 species) and figbirds Sphecotheres (3 species)
[36], and in our study the piopios are placed with weak support as
the sister group of the Oriolus, basal relative to other species of that
clade (cf. [35]). Our study also confirms that the Hooded Pithoui
Pitoui dichrous is part of this clade, but rather placed basal relative to
the other taxa in this group instead of sisters to the figbirds as
indicated by Jønsson et al. [35].
Table 1. List of samples, with specimen numbers and GenBank accession numbers.
Species Clade MYO Ref. ODC Ref. G3PDH Ref.
Campephaga flava Campephagidae EF052822 [44] EU380410 [26] DQ406639 [45]
Cnemophilus loriae Cnemophilidae EU272107 [46] EU272126 [46] EU272096 [46]
Colluricincla harmonica Pachycephalidae EU273396 [34] EU273356 [34] EU273376 [34]
Coracina cinerea Campephagidae EF052827 [44] EU380417 [26] EF052800 [44]
Dicrurus bracteatus Dicruridae EF052839 [44] EU272113 [46] EF052813 [44]
Eopsaltria australis Petroicidae AY064732 [47] EF441238 [48] EF441216 [48]
Epimachus albertisii Paradisaeidae AY064735 [47] EU380436 [26] EU380475 [26]
Gymnorhina tibicen Cractidae AY064741 [47] EU272119 [46] DQ406669 [45]
Hirundo rustica Hirundidae AY064258 [47] EF441240 [48] EF441218 [48]
Lalage leucomela Campephagidae EF052840 [44] EU380438 [26] EF052814 [44]
Malurus amabilis Maluridae AY064729 [47] EF441241 [48] EF441219 [48]
Manucodia ater Paradisaeidae EU726218 [49] EU726228 [49] EU726210 [49]
Monarcha melanopsis Monarchidae DQ084110 [50] EU272114 [46] EU272089 [46]
Oriolus chinensis Oriolidae EU273404 [34] EU273362 [34] EU273382 [34]
Oriolus flavocinctus Oriolidae EF441258 [48] EF441243 [48] EF441221 [48]
Oriolus oriolus Oriolidae EF052766 [44] EU273363 [34] EF052755 [44]
Oriolus xanthornus Oriolidae AY529929 [51] EU272111 [46] DQ406645 [45]
Pachycephala rufiventris Pachycephalidae EU380510 [26] EU380445 [26] EU380481 [26]
Pericrocotus erythropygius Campephagidae EF052765 [44] EU380451 [26] EF052754 [44]
Picathartes gymnocephalus Picathartidae AY228314 [52] EF441247 [48] EF441225 [48]
Pitohui dichrous EU273412 [34] EU273371 [34] EU273390 [34]
Pomatostomus temporalis Pomatostomatidae AY064730 [47] EF441248 [48] EF441226 [48]
Prunella modularis Prunellidae AY228318 [52] EF441249 [48] EF441227 [48]
Ptilonorhynchus violaceus Ptilonorhynchidae AY064742 [47] EF441250 [48] EF441228 [48]
Ptiloprora plumbea Meliphagidae AY064736 [47] EF441251 [48] EF441229 [48]
Saltator atricollis Cardinalidae AY228320 [52] EF441252 [48] EF441230 [48]
Sturnus vulgaris Sturnidae AY228322 [52] EF441253 [48] EF441231 [48]
Sylvia atricapilla Sylviidae AY228323 [52] EF441254 [48] EF441232 [48]
Sphecotheres vieilloti Oriolidae FJ821107 [12] GQ901707 [35] GQ901790 [35]
Terpsiphone viridis Monarchidae AY529939 [51] EU380458 [26] DQ406641 [45]
Turdus philomelos Turdidae DQ466848 [53] GU358902 [54] GU359037 [54]
Turnagra capensis JN571533 JN571534 JN571532
Vireo flavoviridis Vireonidae EU273417 [34] EU273374 [34] EU273394 [34]
OUTGROUP
Menura novaehollandiae Menuridae AY064744 [47] EF441242 [48] EF441220 [48]
doi:10.1371/journal.pone.0024317.t001
The New Zealand Thrush: An Extinct Oriole
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Orioles are distributed in the Eurasian, Afrotropical, Indoma-
layan and Australasian zoogeographical regions [36]. Most species
of orioles in the former regions are bright yellow or red, whereas
the figbirds and the other orioles of the Australasian region are
mostly drab brown or olive green. The piopios, being olive-grey to
olive-brown, were in this respect most similar to the Australasian
orioles, and the South Island Piopio had brown streaking on the
breast similar to e.g. the Australian Olive-backed Oriole (Oriolus
sagittatus) as well as females and juveniles of many other oriole
species. Very little is known about the biology of the piopios but
they appear to have been omnivorous and fed on a wide range of
food items, including insects, worms, fruits and berries, much like
Figure 1. Bayesian consensus tree of the concatenated, mixed model analysis of three nuclear introns (myoglobin, ODC and
GAPDH). Posterior probabilities are indicated at nodes. An asterisk * indicates a posterior probability of 1.0. The South Island Piopio (Turnagra
capensis) is indicated in bold.
doi:10.1371/journal.pone.0024317.g001
The New Zealand Thrush: An Extinct Oriole
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the orioles. In contrast to the orioles, which rarely descend to the
ground for feeding [36], piopios appear to a large extent have
foraged on the ground ‘‘grubbing with its bill among the dry leaves
and other forest debris’’ [7]. This change in behavior to a more
ground-living lifestyle has been rather common among New
Zealand birds, and several species of e.g. rails, ducks, parrots and
passerines have evolved flightlessness on New Zealand. However,
this behavior made them more vulnerable to the introduced
predators that arrived in the 19th century and ultimately caused
the extinction of many species, including the piopios.
Biogeographical analyses [35] have shown that the Oriolidae
likely originated in Australasia, and from there dispersed to other
regions. Within the Oriolidae, figbirds, pithouis and the basalmost
lineage of Oriolus are confined to the Australia, New Guinea and
Wallacea; and the placement of the piopios among these groups
indicate that the ancestor of the piopios also lived in this region
and at some point dispersed to New Zealand. The dating analysis
by Jønsson et al [35] indicate that the split between Sphecotheres/
Pithoui and Oriolus took place around 20 Mya, and the earliest split
within Oriolus, i.e. between the Australasian clade and all other
Oriolus species, took place around 13 Mya. These estimates
provide a rough time frame for the dispersal of the ancestor of
the piopios and suggest that the dispersal to New Zealand took
place no earlier than approximately 20 Mya.
New Zealand is part of the largely submerged continent
Zealandia. This continent, which extends from Caledonia to the
subantarctic islands off the cost of New Zealand, was in the
Cretaceous above sea level and attached to the large southern
hemisphere continent Gondwana. By the end of the Cretaceous
(ca 82 Mya) the two continents had begun to separate but may
have remained connected in what is now northern Australia until
the Early Paleocene (65–61 Mya) or the Early Eocene (ca 52 Mya)
[37,38,39,40,41]. Shortly after Zealandia had separated from
Gondwana crustal thinning and stretching resulted in marine
transgressions in the Eocene and Oligocene, and by the Late
Oligocene most of this region was deep under water [39,42]. The
extent of the Oligocene transgression is unknown but it is clear
that much of this region was under water and it has even been
suggested that New Zealand was completely submerged around
25 Mya [42,43].
The phylogenetic position of the piopios within the Oriolidae
makes it unlikely that they became isolated on New Zealand when
this continent broke off from Gondwana in the Cretaceous.
Instead, the divergence time estimate for the Oriolidae [35]
suggests that the dispersal took place long after the isolation of
New Zealand. Based on these estimates it is likely that the piopios
arrived after the Oligocene transgressions, which occurred around
25 Mya, but even though this is a reasonable assumption, these
estimates are too crude to establish this with certainty. It is,
nevertheless, evident that the piopios add to the list of species that
colonized New Zealand once the Tasman Sea had opened rather
than being Gondwana relicts.
Acknowledgments
We thank Per Ericson for invaluable input and support for the study. We
also thank Pia Eldena¨s and three anonymous for valuable comments on the
manuscript.
Author Contributions
Conceived and designed the experiments: UJ EP MI. Performed the
experiments: MI. Analyzed the data: UJ MI. Contributed reagents/
materials/analysis tools: EP. Wrote the paper: UJ MI.
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The New Zealand Thrush: An Extinct Oriole
PLoS ONE | www.plosone.org 5 September 2011 | Volume 6 | Issue 9 | e24317