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Record of an alleged extinct rodent: molecular analyses of the
endemic Octodon pacificus from Chile
Juliana a. Vianna, Daly noll, lucila Moreno, carolina SilVa, SebaStián Muñoz-leal, María naJle, anD
Daniel González-acuña*
Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica
de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile (JAV, DN)
Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Barrio Universitario
S/N, Concepción 4030000, Chile (LM)
Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez #595,
Chillán, Chile (CS, MN, DG-A)
Programa de Doctorado en Ciencias Veterinarias, Facultad de Ciencias Veterinarias, Chillán 3820000, Chile (CS)
Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia,
Universidade de São Paulo, Av. Prof. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP 05508-270, Brasil
(SM-L)
* Correspondent: danigonz@udec.cl
Octodon (Octodontidae) is an endemic genus of rodents that is typical of southwestern South America and
represented by 4 species. Octodon pacificus, commonly referred to as the Mocha Island degu, was initially
described from specimens collected in 1959 at Mocha Island, a small coastal island located along the central
coast of Chile. Fifty-seven years after its original collection, we report the discovery of a female O. pacificus
carcass, identified by its morphological characteristics and its specific locality. In addition, based on the
cytochrome b (Cytb) gene of the mitochondrial DNA obtained from O. pacificus and other congeneric species, we
assessed phylogenetic relationships within the Octodontidae. Bayesian phylogenetic reconstruction indicated that
O. degus represented the basal Octodon sp., followed by O. lunatus; O. bridgesii and O. pacificus were identified
as sister taxa. Remarkably, the genetic divergence between O. bridgesii and O. pacificus is low, which suggests
that 1 of 2 scenarios may be at play: the occurrence of a recent peripatric speciation process in O. pacificus, or
the presence of O. bridgesii on Mocha Island. Documented collections of archeozoological material obtained
from Mocha Island only include specimens of O. pacificus, a finding that supports our 1st proposed scenario.
While the core of Mocha Island is a national reserve, strong anthropogenic landscape modifications have affected
the coastal plains—the only known habitat of O. pacificus. Rodent control using killing traps and poison is a
common practice on the island; therefore, population surveys and conservation initiatives are needed to conserve
this endangered species.
El género Octodon (Octodontidae) se compone por cuatro especies de roedores endémicos del suroeste de América
del Sur. Ocotodon pacificus fue descrito a partir de especímenes colectados en 1959 en Isla Mocha, una pequeña
isla ubicada en la costa de Chile Central. Cincuenta y siete años después de su único registro, mediante un estudio
morfológico, reportamos la identificación de una carcasa de una hembra de O. pacificus colectada en la localidad
tipo para la especie. Adicionalmente, utilizando secuencias parciales del gen mitocondrial Cytb de esta y las otras
tres especies del género, mediante un análisis Bayesiano se reconstruyeron las relaciones filogenéticas dentro de
la familia Octodontidae. Con un elevado soporte de valores de probabilidad posterior, Octodon degu figura en un
clado basal separado de un grupo hermano compuesto por Octodon lunatus, Octodon bridgesii y O. pacificus.
La alta similitud genética observada entre O. bridgesii y O. pacificus es sugestivo de dos posibles escenarios:
la ocurrencia de un evento de especiación peripátrica, o que O. brigdesii posee una población en la Isla Mocha.
Análisis de osamentas de roedores en restos arqueológicos colectados en la isla, solo incluyen el diagnóstico de
Journal of Mammalogy, xx(x):1–8, 2017
DOI:10.1093/jmammal/gyw193
© 2017 American Society of Mammalogists, www.mammalogy.org
Journal of Mammalogy Advance Access published January 2, 2017
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2 JOURNAL OF MAMMALOGY
O. pacificus, lo que soporta nuestra primera hipótesis. Aun cuando el centro de Isla Mocha corresponde a una
Reserva Nacional, la intensa actividad humana en las estrechas planicies costeras, ha modificado drásticamente
el hábitat de O. pacificus. Los métodos comunes para el control de roedores, utilizando veneno y trampas son
actividades comunes en la isla; por este motivo, se necesitan estudios poblacionales e iniciativas de conservación
para proteger a esta especie amenazada.
Key words: Chile, endangered species, Octodon pacificus, Octodontidae, phylogeny, rodent
Environmental changes in southern South America dur-
ing the Miocene have shaped the evolutionary history of the
Octodontidae, resulting in extinction of some species and adap-
tive changes in other species (Verzi et al. 2016). Therefore, a
radiation process molded by an organism’s adaptation to differ-
ent habitats has led to the speciation of this group of rodents in
western regions of southern South America (Muñoz-Pedreros
2000). Octodontid species diverged during the Miocene, about
9.0 million years ago (mya) (6.7–11.6 mya), with a 2nd burst
occurring in the early Pliocene (Upham and Patterson 2012).
Today, there are 14 extant species in the family Octodontidae:
Aconaemys fuscus, A. porteri, A. sagei, Octodon degus, O. luna-
tus, O. bridgesii, O. pacificus, Octodontomys gliroides, Octomys
mimax, Spalacopus cyanus, Tympanoctomys barrerae, T. kirch-
nerorum, T. aureus, and T. loschalchalerosorum (Patton et al.
2015). The genus Octodon is comprised of 4 species of aboveg-
round generalists (Gallardo and Kirsch 2001), which are pri-
marily distributed in Chile; their distribution extends to the
Neuquén Province in Argentina (Patton et al. 2015). Octodon
degus has the northernmost distribution in Chile, occupying the
western slopes of the Andes between Vallenar and Curicó, up to
a maximum of 1,200 m of elevation (−28.5666S, −70.7500W to
−34.9833S, −71.2333W—Woods and Kilpatrick 2005); O. luna-
tus ranges from Limarí to Quilpué in central Chile (−30.6167S,
−71.2667W to −32.7333S, −70.7W—Osgood 1943); O. bridg-
esii is distributed in Chile (−34.25S, −70.5667W to −38.5667S,
−71.5667W) and Argentina (−40.1602S, −71.3575W—Redford
and Eisenberg 1992; Patton et al. 2015); and O. pacificus occurs
exclusively on Mocha Island (−38.3667S and −73.9333W), a
small coastal island located off the coast of central Chile, within
the Valdivian Rainforest region (Hutterer 1994). Currently,
O. bridgesii is allopatrically distributed with respect to O. luna-
tus and O. degus, whereas in the past, these 3 species occurred
in sympatry (Saavedra and Simonetti 2003). Human activities
were responsible for the disappearance of O. bridgesii from the
coastal and Andean regions of central Chile (Simonetti 1989;
Saavedra and Simonetti 2003).
Octodon pacificus, commonly referred to as the Mocha
Island degu, was described in 1994 from 3 females and 2 juve-
nile specimens collected in 1959 during a German zoological
expedition to Mocha Island (Hutterer 1994). The species was
identified as larger and heavier than the other Octodon spp.,
and it featured soft, long hair, which was brown and orange
in color; the species also had a long tail, equaling 77% of its
body and head length. Current information on these rodents
has been restricted to the material collected in 1959, which has
been maintained in the Alexander Koenig Research Museum in
Bonn, Germany. While the finding of archeozoological material
(bones and postcranial elements) on Mocha Island supports
the long-term existence of O. pacificus (1,200–450 years ago
[ya]—Saavedra et al. 2003), no living specimens have been
observed or collected in the field since its original description
in 1959.
The taxonomic relationship of O. pacificus is based entirely
on morphology. Given the morphological characteristics of the
species’ skull and dentition, Hutterer (1994) grouped O. paci-
ficus with O. bridgesii as its sister taxa, leaving O. degus and
O. lunatus in a separate group. Subsequent molecular analyses
of the genus Octodon revealed an alternate relationship, where
O. degu was the basal species, and O. bridgesii and O. lunatus
were sister taxa; the researchers did not include O. pacificus in
this relationship (Gallardo and Kirsch 2001; Honeycutt et al.
2003; Upham and Patterson 2012). To clarify the evolutionary
history of the genus Octodon, it is imperative that the genetic
relationships among the 4 species are further assessed.
In this study, we report the rediscovery of the allegedly extinct
O. pacificus at Mocha Island. Using partial mtDNA Cytb gene
sequences, we reconstructed the phylogenetic relationships of
the genus Octodon, and subsequently incorporated new data
obtained from O. pacificus. We also discuss the conservation
status and concerns associated with this rediscovered species.
Materials and Methods
Study site and sample collection.—In December 2015, we
conducted a small mammal survey at Mocha Island, a popu-
lated insular Chilean territory of about 48 km2, located 34 km
offshore from the Bío Bío region. Decades of anthropogenic
landscape modifications led to the disappearance of the native
Valdivian rainforest vegetation along the entire coast of the
island. The native forest currently persists only within elevated
areas of the central part of the island, which are now protected
as a national reserve.
We spent a total of 800 traps nights in an area of approxi-
mately 3 ha during 3 field surveys in the southern part of Mocha
Island (Fig. 1). On 29 December 2015, in the same area, a
carcass of a female Octodon sp. was recovered from a lethal
trap (−38.3955S, −73.9163W; 30 m above sea level) that was
installed by local inhabitants to control the rodent population.
Immediately after the carcass was discovered, a sample of
muscle was obtained from the dead specimen and preserved in
95% ethanol. We also obtained tissues from other congeneric
representatives: 10 muscle samples of O. degus from Bosque
de Fray Jorge National Park (FJ, −30.6333S; −71.6666W), Las
Chinchillas National Reserve (CHIN, −31.5005S; −71.1000W),
Peñuelas National Reserve (PEN, −33.1666S; −71.4500W),
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VIANNA ET AL.—OCTODON PACIFICUS (OCTODONTIDAE) FROM CHILE 3
and Til Til (TIL, −34.0666S; −70.95000W), and 2 muscle sam-
ples of O. lunatus from FJ (Fig. 1). The tissue collection of all 3
species was conducted under a Servicio Agricola Ganadero per-
mit (number: 3348/2013), as well as with permission from the
ethics committee of the Universidad de Concepción (18-2012;
granted by Universidad de Concepción). The research on live
animals followed the guidelines established by the American
Society of Mammalogists (Sikes et al. 2011).
Morphological data.—To perform a morphological analy-
sis, we used the terminology of Wood and Wilson (1936) and
Woods and Howland (1979), including the following corporal
dimensions: 1) body: total, tail, hindfoot and ear lengths; and
2) skull: greatest length, zygomatic width, interorbital width,
nasalia length, nasalia width, diastema length, upper toothrow
crown lengths, P4–P4 width, and widths of both upper I1.
All measurements were obtained using a Mitutoyo caliper
(0.01 mm; Mitutoyo Corporation, Japan) and are given in milli-
meters. These measurements were compared to the dimensions
of the paratype and holotype of O. pacificus, as well as with
those of the O. bridgesii and O. lunatus specimens. Necropsy
Fig. 1.—Geographic distribution of Octodon species in Chile (based on Patton et al. 2015). White circles: collection sites of O. degus (this study),
and white square: collection site of O. lunatus (this study).
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4 JOURNAL OF MAMMALOGY
was performed and full-body radiography was analyzed with
the aim of determining whether fetuses were present. The skull
and body were placed in ethanol and deposited in the zoologi-
cal collection of the Universidad de Concepción under acces-
sion number MZUC-UCCC: 44277 (skull), 44278 (body), and
44279–44281 (3 young).
Molecular methods.—DNA was extracted using a simple
salt method described in Aljanabi and Martínez (1997). The
mtDNA Cytb gene was selected for genetic analyses due to the
availability of Cytb sequences in GenBank for several octodon-
tine rodents. An approximately 1,000-base pair (bp) fragment
of the Cytb gene was amplified using the primers MVZ05,
MVZ16, MVZ108, and MVZ127 (Leite and Patton 2002).
Specifically, the reactions contained 1 µl of DNA at 20 ng/µl,
1× reaction buffer, 1.5 mM of MgCl2, 200 µM of each dNTP,
0.4 µM of each primer, and 0.8 units of Taq DNA polymerase
Platinum (Invitrogen, Thermo Fisher Scientific, Waltham,
Massachusetts), with a final reaction volume of 40 µl. The poly-
merase chain reaction (PCR) protocol has 2 phases as described
by Korbie and Mattick (2008): 1) 10 min at 95°C, and 11 cycles
of 95°C for 15 s; a touchdown of annealing temperature at
60°C–50°C for 30 s, with 1 cycle at each annealing temper-
ature of 1°C interval, and 72°C for 45 s; 2) 35 amplification
cycles at 95°C for 15 s, 50°C for 30 s, and 72°C for 45 s; and
a final extension period of 30 min at 72°C. PCR products were
visualized on 1% agarose gel with sodium borate (SB) buffer
and RedGel; they were run for 20 min at 200 V, and ampli-
cons of expected size were purified and sequenced bi-direc-
tionally at Macrogen, Inc. (Seoul, South Korea). The sequences
were assembled and the polymorphic sites were confirmed by
eye from the chromatograms using Sequencher v. 5.1 (Gene
Codes, Ann Arbor, Michigan). Sequences were deposited in
GenBank under the accession numbers KX298475–KX298482
(Supplementary Data SD1).
Phylogenetic reconstruction.—Sequences of all Octodon
spp., including O. bridgesii (n = 1) obtained from GenBank
(KJ742651), as well as Ctenomys (Ctenomyidae) and
Trichomys (Echimyidae; Supplementary Data SD1), were
aligned using the Clustal X software (Thompson et al. 1997).
The sequence of Thrichomys laurentius (Echimyidae, Thomas
1904) was used as the outgroup. A Bayesian-inferred phyloge-
netic tree was constructed using MrBayes 3.1.2 (Huelsenbeck
and Ronquist 2001; Ronquist and Huelsenbeck 2003). The evo-
lutionary model was selected using jModelTest 0.1.1 (Guindon
and Gascuel 2003; Posada 2008) and the Akaike Information
Criterion (AIC). The best-fit model of nucleotide substitution
was GTR+I+G. Two Bayesian analyses were run for 2,000,000
generations, with sampling performed every 1,000 generations.
The SD of split frequencies was < 0.01, indicating that both
runs had converged. Additionally, the potential scale reduction
factor (PSRF—Gelman and Rubin 1992) was very close to 1
for all parameters, indicating that we had adequately sampled
their posterior distributions. A consensus tree was visualized in
FigTree 1.2.2 (Rambaut 2009). Genetic distances at intra- and
interspecific levels for Octodontinae and Ctenomys spp. were
calculated with MEGA 6 (Tamura et al. 2013).
results
We captured 281 rodents (a success rate of 31.6%) using
Sherman traps; the rodent species were Abrothrix longipilis
(n = 221), A. olivaceus (n = 32), and Rattus rattus (n = 18). No
Octodon was captured with the Sherman traps.
Morphological characteristics.—The fur color of the col-
lected specimen matched the pattern found for O. pacificus, as
described by Hutterer (1994). The color of the pelage of O. paci-
ficus is brown–orange, with brighter orange tips observed on
the hairs of the underside. Octodon degus have agouti-colored
fur, a lighter venter, and white ear tufts. Octodon lunatus have
an agouti color that is very similar to that of O. degus, but with
softer and longer pelage. The color of the pelage of O. bridgessi
is a mixture of brown and yellow, not orange (Hutterer, 1994).
Likewise, the morphological measurements of the skull and
body of the specimen were concordant with the dimensions of
O. pacificus, as detailed in the original description. The total
length and tail length are generally longer in O. pacificus when
Table 1.—External and cranial measurements of Octodon pacificus from this study compared to the holotype and paratype measurements
described by Hutterer (1994). Measurements (averages and ranges) of other Octodon species were obtained from Redford and Eisenberg (1992).
This study O. pacificus O. bridgesii O. lunatus O. degus
Holotype Paratype
Total length 375 380 390 323 (250–370) 360 (328–382) 266.5 (200–307)
Tail length 180 170 165 138.3 (102–167) 157 (152–161) 111.4 (81–138)
Hindfoot 38 40 42 38.5 (34–40) 40.7 (40–42) 35.5 (31–40)
Ear 18.7 20 20 22 (20–23) 28 24.7 (19–31)
Greatest length 48.5 46.3 41.8–44.8 46.5 43.3
Zygomatic width 25.2 25.9 25.3 23.7–23.9 23.8 23.9
Interorbital width 9.1 10 8.6 8.1–9.0 9.1 10.3
Nasalia length 19.5 19.6 19.5 17.6 18.0 15.6
Nasalia width 5.9 5.9 5.6 5.1–5.8 5.8 5.3
Diastma length 10.7 10.8 10.6 8.1–9.9 8.7 8.8
Upper toothrow, crowns 10.6 10.3 10.9 9.5–10.0 9.3 9.5
Upper toothrow, alv. 11.2 11.1 11.3 9.6–10.6 10.7 10.1
Width P4–P4 8.2 7.8 8.2 6.5–7.7 8.6 6.2
Width of both upper I1 4.3 4 4.2 3.1–3.7 4.2 3.6
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VIANNA ET AL.—OCTODON PACIFICUS (OCTODONTIDAE) FROM CHILE 5
compared to the measurements of O. bridgesii; likewise, the
ear is smaller in O. pacificus than in the other Octodon spp.
(Table 1). Pictures of the analyzed skull are presented in Fig. 2.
The necropsy procedure and radiographic study of the adult
female identified at least 6 unborn pups (Fig. 3).
Phylogenetic analysis.—We analyzed a 1,093-bp fragment of
the Cytb gene for all 4 Octodon spp. We identified 1 haplotype
from O. lunatus (n = 2) and 6 haplotypes for O. degus (n = 10).
The Bayesian phylogenetic reconstruction illustrates the genus
Octodon as a monophyletic clade within the Octodontidae fam-
ily, exhibiting a high posterior support value (0.99–1; Fig. 4).
Octodon degus is basal to the remaining Octodon with a poly-
tomy of O. degus haplotypes from FJ and CHIN, and another
clade with haplotypes from PEN and TIL. Octodon lunatus
branches off second, while O. bridgesii and O. pacificus rep-
resent sister taxa. The genetic distance between O. bridgesii
and O. pacificus is very low (0.3%). This value is similar to
the variation at the intraspecific level observed within O. degus
(0.2–0.9%; Table 2), and it is lower than the genetic distance
between several Ctenomys spp. (0.5–0.8%; Supplementary
Data SD2). Only 4 polymorphic sites were identified between
O. bridgesii and O. pacificus, whereas 57 polymorphic sites
were found between O. lunatus, O. bridgesii, and O. pacifi-
cus (there were 139 polymorphic sites for the entire Octodon
data set).
discussion
We report a new record of an insular endemic species that
was alleged to be extinct. No further reports of this spe-
cies were documented after its original description from the
material collected in 1959 (Hutterer 1994), with the excep-
tion of a few archaeozoological skeletal remains (1,200–450
ya—Saavedra et al. 2003). Our morphological analyses
revealed that the body, skull, and dentition morphometry
were concordant with the dimensions of the type specimens
Fig. 2.—Lateral (a) and ventral (b) view of the skull, and the occlusal view of upper molars (c) of the collected Octodon pacificus.
Fig. 3.—Full-body radiograph of the studied specimen of Octodon pacificus with osteological evidence of 6 fetuses observed.
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6 JOURNAL OF MAMMALOGY
(holotype and paratype) of O. pacificus, which strongly sug-
gest that the collected specimen indeed corresponds to the
endangered species. However, our genetic analysis of Cytb
sequences revealed a low genetic distance (0.3%) between
this species and its sister, O. bridgesii, suggesting that the
taxonomic status of O. pacificus should be carefully assessed.
While the genetic divergence within O. bridgesii has yet to be
evaluated, the low genetic divergence observed for the Cytb
gene between these 2 Octodon spp. could be interpreted as
intraspecific genetic variation, which would challenge the
status of O. pacificus as a full species. One might argue that
the discovered specimen is of O. bridgesii and not O. pacifi-
cus. However, O. bridgesii has not been reported on Mocha
Island, and the closest mainland distribution to the island is
Nahuelbuta (−33.6166S; −79.0333W). On the other hand, the
minor genetic divergence of O. pacificus could be the result of
a recent peripatric speciation process, implying that an origi-
nal founder effect occurred on the island. The larger body size
of O. pacificus with respect to O. brigdesii and the other con-
tinental Octodon spp. could be the result of insular evolution
(Lomolino 2005; Lomolino et al. 2012). Further molecular
assessments including nuclear markers are needed to ascer-
tain the evolutionary history of O. pacificus.
Biodiversity conservation on islands is a major global con-
cern due to the high endemism and extinction rates of insu-
lar biota (Alcover et al. 1998). Octodon pacificus from Mocha
Island is not an exception. Since its original description in 1959,
no live specimens have been reported, rendering the status of
this rodent as a critically endangered species (IUCN 2015).
While the central region of Mocha Island has been declared a
national reserve (Verdugo 1989), human settlements and agri-
cultural activities along the shoreline have degraded most of the
potential habitat of O. pacificus. In addition, the local people
often use lethal traps to control rodent populations. These fac-
tors likely serve as primary threats to the remaining O. pacifi-
cus populations. We were unable to capture O. pacificus, and
this species was not caught during previous small mammal
surveys. The Sherman traps that were used in our survey are
generally capable of capturing semifossorial and social rodents,
such as Octodon. However, Tomahawk traps were shown to be
most effective in capturing O. degus (Burger et al. 2009). This
highlights the importance of trap type in specimen capture,
Fig. 4.—Bayesian phylogenetic reconstruction among the Octodon species, with several other members of the family Octodontidae included.
Posterior support values are indicated on each node.
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VIANNA ET AL.—OCTODON PACIFICUS (OCTODONTIDAE) FROM CHILE 7
and future surveys should consider using Tomahawk-style traps
to increase the trapping success rate. It is critical to note that
the female analyzed in this report was pregnant with at least
6 young, indicating that the population of this threatened spe-
cies is still reproductively active. More individuals of O. paci-
ficus from Mocha Island and a larger sample of O. bridgesii
are required to better understand the evolutionary history of
O. pacificus.
acknowledgMents
We thank the government agencies SAG (Servicio Agrícola
y Ganadero) and CONAF (Corporación Nacional Forestal)
for rodent capture permits. We thank F. Astete and G. Reyes
(Mocha Island National Reserve, CONAF) for their valuable
help in field-work. Financial support for this study was pro-
vided by FONDECYT 1130948.
suppleMentary data
Supplementary data are available at Journal of Mammalogy
online.
Supplementary Data SD1.—Table of all Octodon sequences
and representatives of the Octodontinae subfamily obtained
from GenBank with respective accession numbers and
references.
Supplementary Data SD2.—Table of genetic distances
between species of Ctenomys. In bold the lowest genetic dis-
tance calculated between several pairwise Ctenomys species.
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Table 2.—Pairwise genetic distances between species of Octodon (different populations of Octodon degus are treated separately). In bold is the
genetic distance between the studied O. pacificus and O. bridgesii.
O. degus (FJ1) O. degus (CHIN1) O. degus (PEN1) O. degus (PEN2) O. degus (TIL1) O. degus (TIL2) O. lunatus O. bridgesii
O. degus (FJ1)
O. degus (CHIN1) 0.005
O. degus (PEN1) 0.009 0.009
O. degus (PEN2) 0.009 0.009 0.002
O. degus (TIL1) 0.007 0.007 0.002 0.002
O. degus (TIL2) 0.009 0.006 0.003 0.003 0.002
O. lunatus 0.099 0.099 0.101 0.103 0.101 0.101
O. bridgesii 0.099 0.098 0.099 0.101 0.099 0.097 0.051
O. pacificus 0.099 0.098 0.099 0.101 0.099 0.097 0.049 0.003
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Submitted 7 June 2016. Accepted 21 December 2016.
Associate Editor was Tereza Jezkova.
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