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The taxonomic status of populations of southern brown bandicoots, Isoodon obesulus, from eastern and southern Australia based on mitochondrial and nuclear gene analyses.

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Abstract and Figures

The sub-specific status of different populations of Isoodon obesulus has been questioned in several genetic studies utilising mitochondrial DNA (mtDNA) and nuclear gene sequence data, leading to a proposal to revise the current distribution of the eastern Australian sub-species I. o. obesulus to include additional localities in South Australia (SA) and Tasmania. However, these genetic studies were based on limited samples, and were not able to fully resolve the status of Tasmanian populations, previously classified as the subspecies I. obesulus affinis. In the current study we have extended the genetic analysis of I. obesulus (and a related taxon I. auratus) by including samples from across the range of the species in Australia, and assess the taxonomic status of the Tasmanian population and populations of I. obesulus from South Australia using mitochondrial (mtDNA) and nuclear gene sequence data. Our genetic analyses reveal that there is a major phylogenetic split within I. obesulus, supported by both mtDNA and nuclear gene analyses, with the SA Mt. Lofty Ranges, Kangaroo Island and Franklin Island populations grouping with populations of I. obesulus and I. auratus from Western Australia and a second group comprising I. obesulus from southeast SA, Victoria, NSW and Tasmania. MtDNA analyses further showed that all Tasmanian samples formed a distinct evolutionary lineage (monophyletic group of haplotypes) to the exclusion of all other mainland samples of I. obesulus. The level of sequence divergence among these lineages suggests that the Tasmanian population has been genetically isolated from the mainland population, potentially over hundreds of thousands of years, including multiple ice age cycles. Support from nuclear gene analyses for the distinction of the Tasmanian population was absent, possibly due to the low intra-specific variation in the nuclear genes used in the current study. Taken overall, there is no clear genetic basis for the removal of the separate sub-specific status of the Tasmanian population and the genetic analyses suggest that I. o. obesulus is limited in its distribution to NSW, Victoria and southeast SA. The latter represents a significant reduction in the known range of this subspecies.
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1
The taxonomic status of populations of southern brown bandicoots, Isoodon obesulus, from eastern and southern
Australia based on mitochondrial and nuclear gene analyses.
A report for Natural Resources Adelaide and Mount Lofty Ranges South Australia and the federal Department of
Environment
By Prof. Steven Cooper (South Australian Museum)
Dr Kym Ottewell (Department of Parks and Wildlife, WA)
Dr Anna J MacDonald (University of Canberra, ACT)
Summary
The sub-specific status of different populations of Isoodon obesulus has been questioned in several genetic studies
utilising mitochondrial DNA (mtDNA) and nuclear gene sequence data, leading to a proposal to revise the current
distribution of the eastern Australian sub-species I. o. obesulus to include additional localities in South Australia (SA)
and Tasmania. However, these genetic studies were based on limited samples, and were not able to fully resolve the
status of Tasmanian populations, previously classified as the subspecies I. obesulus affinis. In the current study we
have extended the genetic analysis of I. obesulus (and a related taxon I. auratus) by including samples from across
the range of the species in Australia, and assess the taxonomic status of the Tasmanian population and populations
of I. obesulus from South Australia using mitochondrial (mtDNA) and nuclear gene sequence data. Our genetic
analyses reveal that there is a major phylogenetic split within I. obesulus, supported by both mtDNA and nuclear
gene analyses, with the SA Mt. Lofty Ranges, Kangaroo Island and Franklin Island populations grouping with
populations of I. obesulus and I. auratus from Western Australia and a second group comprising I. obesulus from
south-east SA, Victoria, NSW and Tasmania. MtDNA analyses further showed that all Tasmanian samples formed a
distinct evolutionary lineage (monophyletic group of haplotypes) to the exclusion of all other mainland samples of I.
obesulus. The level of sequence divergence among these lineages suggests that the Tasmanian population has been
genetically isolated from the mainland population, potentially over hundreds of thousands of years, including
multiple ice age cycles. Support from nuclear gene analyses for the distinction of the Tasmanian population was
absent, possibly due to the low intra-specific variation in the nuclear genes used in the current study. Taken overall,
there is no clear genetic basis for the removal of the separate sub-specific status of the Tasmanian population and
the genetic analyses suggest that I. o. obesulus is limited in its distribution to NSW, Victoria and south-east SA. The
latter represents a significant reduction in the known range of this subspecies.
Introduction
The southern brown bandicoot (Isoodon obesulus) has declined in number dramatically over the last 220 years,
leading to a much contracted distribution and local population extinctions (Coates et al. 2008; Department of
Environment and Conservation 2006; Paull 1993, 1995). The south-east mainland population (I. o. obesulus), which is
the focus of this study, is one of only two surviving members of the family Peramelidae in South Australia, and is
currently listed as nationally endangered (the Australian Environment Protection and Biodiversity Conservation Act
1999). However, there has been a recent proposal for this conservation status to be revoked based on the
suggestion that the subspecies I. o. obesulus is much more widespread than previously thought, occurring across
eastern mainland Australia, Tasmania and South Australia.
Based on their geographical distribution and morphological variations, five subspecies of I. obesulus have historically
been distinguished: I. o. obesulus, from south-east mainland (the coastal fringe of New South Wales, southern
Victoria and South Australia), I. o. nauticus (from Nuyts Archipelago, SA, including the St Francis and Franklin Islands),
I. o. peninsulae (from north Queensland), I. o. fusciventer (from south-western Western Australia), and I. o. affinis
(from Tasmania) (Fig. 1, Paull 2008; Paull et al. 2013). Recent studies based on mtDNA markers suggest that there is
little genetic differentiation between I. obesulus and the golden bandicoot I. auratus, distributed in the Northern
Territory and Western Australia, and that they should be treated as a single species (Pope et al. 2001; Zenger et al.
2
2005). Furthermore, Zenger et al. (2005) suggested that there was little support for the genetic distinctiveness of I. o.
nauticus (suggesting its inclusion within I. o. obesulus) and also stated that “based on the allozyme data of Close et
al. (1990) I. o. affinis would most likely be placed within I. o. obesulus”
.
To date, there have been limited mtDNA data
on the Tasmanian I. o. affinis, with the exception of a relatively recent analysis by Westerman et al. (2012) which
included one sample that grouped closely with an I. o. obesulus individual from eastern Australia. The latter study
also supported the distinctiveness of I. auratus, although the unusual position of the root in this Isoodon
monophyletic group, which rendered I. obesulus polyphyletic, suggests further analyses are required.
Fig. 1. Distribution of subspecies of I. obesulus. The map was adapted from Paull et al. (2013).
A problem with the above conclusions on subspecies/species status is that they were based on very few samples and
generally very little sequence data (mtDNA Control Region data only in the studies by Zenger et al. (2005) and Pope
et al. (2001)). Ideally, one should sample broadly from across the distribution of each species/ subspecies and use
multiple genetic loci (mtDNA and nuclear) to assess whether there is population differentiation associated with each
discrete taxonomic unit. Long term isolation of populations, either through allopatry (geographic) or reproductive
isolation, leaves distinct patterns in gene trees over time, with a progression from polyphyly, to paraphyly and then
reciprocal monophyly (see Fig. 2) of the discrete allopatric populations or reproductive units (Avise 1994). However,
coalescent theory also predicts that this progression from polyphyly to paraphyly is strongly influenced by
population size, with large populations taking much longer to achieve reciprocal monophyly than small populations.
Therefore, given the possibility of historically high population sizes of I. obesulus (Short and Smith 1994), it is
possible that individual subspecies may not be reciprocally monophyletic with respect to other subspecies.
Fig. 2. Gene trees for haplotypes (e.g. mtDNA sequences) from two populations ‘a’ and ‘b’. A. Paraphyly of population ‘a’ relative
to population ‘b’: haplotypes a
*
are more closely related to haplotypes from population ‘b’ than other haplotypes in ‘a’. B.
Reciprocal monophyly of population ‘a’ and ‘b’: haplotypes within each population are more closely related to each other (i.e. in
monophyly). The expectation for taxonomic units (e.g. species) showing long term genetic isolation is reciprocal monophyly of
mtDNA haplotypes. Figure adapted from Kizirian and Donnelly (2004).
A
a
a
a
a
a
*
a
*
b
b
b
a
a
a
a
a
a
b
b
b
B
3
We recently carried out a genetic study of SA populations of the endangered southern brown bandicoot, I. o.
obesulus, including populations from the Mt Lofty Ranges (MLR), Kangaroo Island (KI) and south-east of SA. In the
course of this study we found that the MLR/KI populations were genetically highly distinct from a population in the
south-east of SA and western Victoria, each population showing reciprocal monophyly and representing distinct
Evolutionarily Significant Units (ESUs) (Li et al. 2014) based on the criteria of Moritz (1994). In collaboration with Dr
Kym Ottewell from the Department of Parks and Wildlife in Western Australia, Mark Adams from the South
Australian Museum, Dr Mark Eldridge (Australian Museum), Dr Anna MacDonald (University of Canberra) and Prof.
Mike Westerman (La Trobe University), and with funding support from Natural Resources Adelaide and Mount Lofty
Ranges South Australia we broadened our study to genetically compare the South Australian populations with
samples of I. obesulus from across Australia and a related taxon I. auratus from Western Australia, using a
combination of mitochondrial and nuclear gene sequence data.
The current report focuses on the taxonomic status and distribution of the subspecies I. o. obesulus, and, specifically,
whether populations of I. obesulus from the MLR, KI, Franklin and St. Francis Islands and Tasmania represent
additional localities where I. o. obesulus is distributed (as proposed by Zenger et al. 2005) or whether they represent
genetically distinct populations, which should be considered as separate subspecies from I. o. obesulus. It should be
noted that this research has not yet been submitted for journal publication and subjected to peer review.
Methods
Samples
The analyses presented in this report are based on a total of 128 samples from populations of I. obesulus and I.
auratus from across Australia, including 21 samples from Tasmania (including Flinders Island), 24 samples from
south-eastern mainland Australia (NSW, Victoria and south-east SA), 12 samples from the Franklin and St. Francis
Islands (SA), 11 samples from the Mt Lofty Ranges (SA), 3 samples from Kangaroo Island (SA), 5 samples from north
Queensland, 17 samples of I. auratus from WA and the NT, and 35 samples of I. o. fusciventer from WA (Fig. 3;
Appendix 1). A further 18 samples from the related species Isoodon macrourus were also included in the genetic
analyses. Additional samples from the south-east of SA, Mt Lofty Ranges SA, Kangaroo Island and western Victoria
were sequenced in a previous study by Li et al. (2014), and the above samples from these regions represent
exemplars of the Li et al. (2014) study. DNA was extracted from skin or liver tissue using the Gentra Puregene
extraction kit and methods specified by the manufacturer (Gentra Systems Inc.).
Fig. 3. Location of samples collected across Australia (A) and from Tasmania and Victoria (B). Further locality details are given in
Appendix 1. Symbols for subspecies/ population groups are as follows: I.o.a (I. obesulus affinis), I.o.n (I. obesulus nauticus), I.mac
(I. macrourus), I.o.p (I. obesulus peninsulae), I.a.a (I. auratus auratus), I.a.b (I. auratus barrowensis), I.o.f (I. obesulus fusciventer),
I.o (MLR) (I. obesulus Mt. Lofty Ranges SA), I.o. (KI) (I. obesulus Kangaroo Island SA), I.o.o (I. obesulus obesulus).
A
B
4
Molecular Methods
Two mitochondrial gene segments and three nuclear fragments were amplified (Table 1): the noncoding control
region (CR, also called “D-loop region” in vertebrates), the NADH dehydrogenase subunit 2 (ND2); protein coding
portions of the breast and ovarian cancer susceptibility gene (BRCA1, exon 11), recombination activating gene-1
(RAG1, intronless) and vonWillebrand factor gene (vWF, exon 28). The primers we used to amplify these genes and
their annealing temperatures are listed in Table 1. PCR amplifications were carried out in 25μL volumes containing
0.1U AmpliTaq Gold® polymerase (Applied Biosystems), 10 × Gold Buffer (Applied Biosystems), 0.20 mM dNTPs, 2.5
mM MgCl2, 0.5 μM of each primer and approximately 100 ng genomic DNA. Thermocycling conditions were: initial
activation at 94 for 3 minutes; 35 cycles of denaturation at 94 for 30 seconds, annealing at 48 – 55 for 45
seconds, and extension at 72 for 60 seconds; and a final extension at 72 for 3 minutes. PCR products were
purified using Millipore MultiScreen PCR
384
Filter Plates (Millipore) and were sent to the Australian Genome Research
Facility (AGRF) for sequencing.
DNA sequences were edited and aligned using the Geneious alignment option within Geneious 6.1.4
(www.geneious.com). Pairwise distances (p-distances) among mitochondrial haplotypes was determined using
Geneious. Geneious was also used to construct Neighbour Joining (NJ) trees, using the HKY-85 (Hasegawa et al.
1985) model of sequence evolution. Before concatenating the two mitochondrial genes (CR + ND2), we constructed
separate phylogenetic trees to check their concordance. The robustness of nodes in the NJ trees was assessed by
1000 bootstrap replicates. A maximum likelihood (ML) analysis was also conducted using the program RAxML and
the WEB-based RAxML ‘black box’ version 7.7.1 (http://phylobench.vital-it.ch/raxml-bb/; Stamatakis et al. 2008)
provided by the Vital-IT Unit of the Swiss Institute of Bioinformatics using a single model of evolution, General Time
Reversible (GTR) model (Rodríguez et al. 1990) with unequal variation at sites modelled using a Gamma (G)
distribution (Yang 1996) applied to the concatenated sequence data. Robustness of branches on the tree was
assessed using 100 bootstrap pseudoreplicates. Trees were visualised and rooted using a midpoint rooting approach
using FigTree (version 1.4.2; http://tree.bio.ed.ac.uk/).
Table 1. Primers and annealing temperatures (Tm) used to amplify segments of CR, ND2, BRCA1, RAG1, and vWF
from I. obesulus, I. auratus and I. macrourus.
Gene Primer name Source Sequence (5' - 3') Tm
CR
m989 (L15999M) Fumagalli et al. 1997 ACCATCAACACCCAAAGCTGA 55
m990 (H16498M) Fumagalli et al. 1997 CCTGAAGTAGCAACCAGTAG 55
ND2
m635 (mmND2.1) Bulazel et al. 2007 AGGGTGTTATACCTTCATTTTTGG 48
m636 (mrND2c) Osborne & Christidis
2001 GCACCATTCCACTTYTGAGT 48
BRCA1
G1800 (F9) Meredith et al. 2008 AGTTCTGAAAGTGGATTCTTT 50
G1801 (R-1MAC9-20) Meredith et al. 2008 CTGACCTRCAGCCTGAGGATTTCAT 50
RAG1
G2311 (F2204) Amrine-Madsen et al.
2003 GCTTCTGGCTCWGTCTACATYTGTAC 50
G2312 (R2794) Amrine-Madsen et al.
2003 AAACGCTGTGARTTGAAACT 50
vWF
G2313 (MF119) Amrine-Madsen et al.
2003 GACTTGGCYTTYCTSYTGGATGG 55
G2314 (MR1140) Amrine-Madsen et al.
2003 TTGATCTCATCSGTRGCRGGATTGC 55
Divergence levels among haplotypes within and between currently recognised subspecies and populations in SA
were determined using MEGA (version 6.0; Tamura et al. 2013).
5
Due to the low sequence variation for nuclear genes, we constructed haplotype networks to visualise the
relationships between haplotypes derived from different populations of I. obesulus, I. auratus and I. macrourus. The
distance based (NJ) method and p-distances between sequences was used to derive a gene tree in Newick format,
using Geneious, which was then used as input into the program Haploviewer (developed by G.Ewing,
http://www.cibiv.at/~greg/haploviewer) to generate a haplotype network.
Results
MtDNA sequence analyses
MtDNA sequence data were obtained from CR (~550 bp) and ND2 (629-698 bp) from 111 I. obesulus samples, 17 I.
auratus samples and 18 I. macrourus samples. Separate NJ analyses of CR and ND2 revealed concordant
phylogenetic trees and, therefore, the data were concatenated for further phylogenetic analyses using maximum
likelihood methods. There were no indels and premature stop codons evident in the ND2 data, suggesting it was
most likely mitochondrial DNA in origin rather than a nuclear copy of mtDNA. NJ and ML analyses of the
concatenated data revealed similar phylogenetic trees, so we describe and present the ML tree only (Fig. 4A and 4B).
Overall, there was evidence for considerable phylogenetic structure, with at least three major evolutionary lineages
evident, one comprising samples of I. o. peninsulae from north Queensland, a second “western and southern group”
comprising I. o. fusciventer, I. auratus and I. obesulus (Mt. Lofty Ranges, Kangaroo Island and Franklin Islands) and a
third comprising “east coast” I. o. obesulus and Tasmanian I. o. affinis. The latter subspecies formed a distinct
monophyletic group supported with an 87% bootstrap value and was in paraphyly with I. o. obesulus from the east
coast of Australia (Fig 4A). Additional divergent mtDNA lineages, one occurring at Mt. Burr in south-east SA, one
from St. Francis Island in SA, and one from Cranbourne in Victoria, were also evident within the “east coast” group.
Within the “western and southern” group, supported with an 85% bootstrap value, considerable mtDNA diversity
was evident, with groups of divergent mtDNA haplotypes associated with each of the species, populations or
subspecies, and no sharing of mtDNA haplotypes. However, only I. auratus barrowensis formed a discrete
monophyletic group, albeit with only three specimens sequenced, and I. auratus auratus was in polyphyly with I.
obesulus fusciventer and I. obesulus from the Mt. Lofty Ranges (Fig. 4B).
6
Fig. 4A. Maximum Likelihood phenogram derived using RAxML based on concatenated mtDNA sequence data from
the NADH dehydrogenase subunit 2 gene (ND2) and Control Region (CR) of I. obesulus from east coast and southern
Australia, including Tasmania and the south-east of SA. The clade representing the west coast of Australia and Mt.
Lofty Ranges/KI/Franklin/St Francis Island populations in SA has been collapsed, with details shown in Fig. 4B.
Diversity within I. macrourus has also been collapsed. Numbers above branches represent bootstrap values from 100
pseudoreplicates. The tree was rooted using a mid-point root, but an identical tree was obtained using I. macrourus
as an outgroup.
95
87
62
61
62
70
100
100
100
Isoodon obesulus obesulus (east coast)
Isoodon obesulus affinis (Tasmania)
Isoodon macrourus
Isoodon obesulus nauticus (Franklin/ St Francis Islands SA)
Isoodon obesulus (southern and western group)
7
Fig. 4B. Maximum Likelihood phenogram derived using RAxML based on concatenated mtDNA sequence data from
the NADH dehydrogenase subunit 2 gene (ND2) and Control Region (CR) of I. obesulus and I. auratus from western
and southern Australia. The clade representing the east coast of Australia, Tasmania and south-east SA populations
has been collapsed, with details shown in Fig. 4A. Diversity within I. macrourus has also been collapsed. Numbers
above branches represent bootstrap values from 100 pseudoreplicates. The tree was rooted using a mid-point root,
but an identical tree was obtained using I. macrourus as an outgroup.
99
56
85
96
99
100
53
97
99
85
61
93
91
100
93 100
74
100
67
80 91
62
65
82
100
Isoodon obesulus fusciventer
Isoodon auratus auratus
Isoodon obesulus fusciventer
Isoodon obesulus fusciventer
Isoodon obesulus(Kangaroo Island, SA)
Isoodon obesulus(Mt. Lofty Ranges, SA)
Isoodon obesulus nauticus(Franklin/ S t Francis islands, SA)
Isoodon auratus auratus
Isoodon auratus barrowensis
Isoodon obesulus peninsulae
Isoodon obesulus fusciventer
Isoodon auratus auratus
Isoodon macrourus
Isoodon obesulus(eastern group)
8
Estimates of average p-distances among populations and subspecies (i.e., total number of nucleotide differences
divided by the sequence length and averaged among individuals from the two populations) ranged from 0.013
between the Kangaroo Island population and I. o. fusciventer to 0.038 between the Kangaroo Island population of I.
obesulus and I. o. affinis from Tasmania (Table 2). The latter showed a divergence level of 0.023 from I. o. obesulus
from the east coast of Australia. The Mt. Lofty Ranges population and KI population showed lowest divergences with
I. o. fusciventer and I. auratus from Western Australia and diverged from east coast I. o. obesulus by p-distances of
0.035 – 0.036 (CR: 0.046 - 0.05; ND2: 0.025).
Table 2.
Estimates of average sequenc
e divergence (p
-
distances) over sequence pairs (
ND2
and
CR
data combined) within (boxed on diagonal) and between (below diagonal) subspecies and populations
of I. obesulus and I. auratus.
Ioa Ioo Ion Iaa Iof Iab Iok Iomlr Iop
Ioa 0.008
Ioo 0.023 0.009
Ion
0.033 0.031 0.017
Iaa 0.036 0.035 0.021 0.013
Iof 0.036 0.035 0.023 0.016 0.009
Iab
0.036 0.033 0.022 0.015 0.018 0.008
Iok 0.038 0.036 0.024 0.016 0.013 0.020 0.000
Iomlr 0.037 0.035 0.020 0.014 0.015 0.015 0.016 0.009
Iop 0.037 0.035 0.030 0.027 0.025 0.026 0.028 0.026 0.003
Symbols for subspecies/ population groups are as follows: Ioa (I. obesulus affinis), Ioo (I. obesulus obesulus), Ion (I. obesulus
nauticus), Iaa (I. auratus auratus), Iof (I. obesulus fusciventer), Iab (I. auratus barrowensis), Iok (I. obesulus Kangaroo Island SA),
Iomlr (I. obesulus Mt. Lofty Ranges SA), Iop (I. obesulus peninsulae)
Table 3.
Estimates of average sequence divergence (p
-
distances) over sequence pairs for individual
mtDNA genes (ND2 above diagonal and CR below diagonal) within and between subspecies and
populations of I. obesulus and I. auratus.
Ioa Ioo Ion Iaa Iof Iab Iok Iomlr
Iop
Ioa
-
0.018
0.025
0.030
0.028
0.031
0.028
0.029
0.031
Ioo
0.029
-
0.021
0.028
0.026
0.028
0.025
0.025
0.027
Ion
0.042
0.043
-
0.015
0.012
0.017
0.012
0.011
0.020
Iaa
0.043
0.044
0.030
-
0.006
0.011
0.006
0.007
0.019
Iof
0.046
0.048
0.038
0.027
-
0.008
0.005
0.005
0.016
Iab
0.041
0.041
0.030
0.021
0.030
-
0.009
0.009
0.020
Iok
0.050
0.050
0.041
0.030
0.023
0.034
-
0.004
0.016
Iomlr
0.046
0.046
0.031
0.022
0.027
0.023
0.033
-
0.017
Iop
0.044
0.047
0.042
0.037
0.038
0.033
0.043
0.038
-
Symbols for subspecies/ population groups are as follows: Ioa (I. obesulus affinis), Ioo (I. obesulus obesulus), Ion (I. obesulus
nauticus), Iaa (I. auratus auratus), Iof (I. obesulus fusciventer), Iab (I. auratus barrowensis), Iok (I. obesulus Kangaroo Island SA),
Iomlr (I. obesulus Mt. Lofty Ranges SA), Iop (I. obesulus peninsulae)
Nuclear sequence analyses
Nuclear sequence data were derived from three genes, vWF, BRCA1 and RAG1, from 113, 81, and 116 Isoodon
samples covering the range of each species (including I. macrourus) and subspecies in Australia. Low levels of
divergence among sequences was observed for each gene, with only four haplotypes identified for RAG1, 10 in
BRCA1 and 19 haplotypes identified for vWF. Coupled with low levels of nucleotide variation, generation of
bifurcating trees using standard phylogenetic analyses was problematic and hence a “haplotype network” approach
was used to infer relationships among haplotypes (Fig. 5). Of the markers sequenced, vWF was most informative,
showing several private haplotypes that were fixed in different populations. For example, I. obesulus from the Mt.
Lofty Ranges, Kangaroo Island (KI) and the Franklin/St Francis Islands showed a fixed haplotype difference from all
other populations/subspecies; I. o. affinis (Tas) shared a haplotype with I. o. obesulus (east coast) and I. o.
9
peninsulae. Isoodon auratus had five private vWF haplotypes, and shared one haplotype with I. o. peninsulae.
Isoodon macrourus had eight private haplotypes and shared no haplotypes with I. obesulus or I. auratus. For BRCA1,
although one haplotype was shared among I. obesulus subspecies and I. macrourus, other haplotypes were private in
different geographic regions. One BRCA1 haplotype was found at high frequency in both I. o. obesulus (east coast)
and I. o. affinis (Tasmania) and a second haplotype was private to I. obesulus from the Mt. Lofty Ranges, KI and the
Franklin/ St Francis Islands. In contrast, there was considerable haplotype sharing among subspecies and
populations for RAG1 haplotypes, with only two private haplotypes detected in I. macrourus. However, one RAG1
haplotype was exclusively found in the Mt. Lofty Ranges, KI, Franklin/ St Francis Islands and I. o. fusciventer (WA).
Fig 5. Haplotype networks for three nuclear genes, vWF, BRCA1 and RAG1, based on Neighbour Joining trees and
derived using the program Haploviewer (G.Ewing, http://www.cibiv.at/~greg/haploviewer). Colour codes for each of
the populations are given in the key and the frequency of the different haplotypes is shown within the circle.
Symbols for subspecies/ population groups are as follows: I.o.a (I. obesulus affinis), I.o.o (I. obesulus obesulus), I.o.n
(I. obesulus nauticus), I.a.a (I. auratus auratus), I.o.f (I. obesulus fusciventer), I.a.b (I. auratus barrowensis), I.o. (KI) (I.
obesulus Kangaroo Island SA), I.o (MLR) (I. obesulus Mt. Lofty Ranges SA), I.o.p (I. obesulus peninsulae), I.mac (I.
macrourus).
Discussion
The analyses presented here considerably extend previous mtDNA sequence analyses of the southern brown
bandicoot, I. obesulus, and its related species I. auratus, particularly incorporating many additional samples from
Tasmania and South Australia, which were poorly represented in the past genetic studies by Zenger et al. (2005),
Pope et al. (2001) and Westerman et al. (2012). Additional analyses of three nuclear genes are also presented here,
and, although these genes are relatively conservative (i.e. they show low levels of nucleotide variation), they do
provide useful information on the population genetic structure of I. obesulus and I. auratus. However, it should be
noted that we have not yet provided a comprehensive population genetic analysis of these data, which is planned
for a future manuscript, as the main focus of this report is to consider the taxonomic status and distribution of the
RAG1
vW
F
BRCA
1
1
I.o.a
I.o.n
I.mac
I.o.p
I.a.a
I.a.b
I.o.f
I.o (MLR)
I.o (KI)
I.o.o
10
subspecies I. o. obesulus and whether populations of I. obesulus from the MLR, KI, Franklin/St Francis Islands and
Tasmania represent additional localities where I. o. obesulus is distributed.
The status of South Australian (MLR, KI and Franklin/St Francis Island) populations of I. obesulus
In our previous study (Li et al. 2014) we proposed that the MLR and KI populations of I. obesulus represented a
distinct ESU based on the criteria of Moritz (1994), compared to I. obesulus from south-eastern SA and western
Victoria. Given the expectation that subspecies should represent discrete evolutionary lineages, or, at least,
genetically differentiated populations, our study suggested that the MLR and KI populations should not be regarded
as I. o. obesulus. The current study has further verified this conclusion and shown that I. obesulus in the MLR and KI
is more closely related to I. o. fusciventer and I. auratus from WA than to the east coast subspecies I. o. obesulus and
Tasmanian I. o. affinis. Based on mtDNA sequence data both MLR and KI comprised distinct groups of haplotypes
that are embedded within a lineage (referred to here as the “western lineage”) that includes I. o. fusciventer and I.
auratus. The high level of divergence in mtDNA (>3.5% combined data; >4.6% for CR and 2.5% for ND2) from
populations of I. o. obesulus from south-eastern SA and east coast Australia, suggests there has been long term
isolation of these populations. We have not yet carried out comprehensive analyses of the date of divergence of
populations, as ideally, additional nuclear gene sequence data are required. However, previous dating analyses by
Westerman et al. (2012) estimated divergence times of I. auratus from I. o. obesulus of the order of ~2.4 million
years (MY) based on molecular clock analyses of multiple mtDNA genes and five nuclear genes, and, given the above
phylogenetic results, a similar divergence estimate would be predicted for the divergence of the MLR/KI population
from I. o. obesulus.
The distinction of the MLR and KI populations from I. o. obesulus was also supported by the nuclear gene analyses,
where they showed fixed haplotype differences, when compared to I. o. obesulus and I. o. affinis, for vWF, BRCA and
RAG1. Indeed, the nuclear data revealed a close association of the MLR/KI population with I. o. nauticus from the
Franklin/St Francis Islands, with each of these populations sharing a distinct vWF and BRCA1 haplotype that was not
found in any other population of I. obesulus in Australia. They also shared a RAG1 haplotype that was also detected
at high frequency in I. o. fusciventer. These data confirm the close association of the MLR, KI and Franklin/ St Francis
Island populations and suggest that, together, they may also represent a distinct evolutionary lineage that could
warrant separate subspecies status. For mtDNA, multiple divergent haplotype lineages were evident, some shared
between the MLR and Franklin Islands, but others representing distinct lineages more closely related to haplotypes
found in I. o. fusciventer, I. auratus and I. o. obesulus (south-east SA). These relationships most likely represent
ancient connections of these populations and chance fixation of haplotypes by genetic drift in island populations. For
example, St Francis Island has a fixed mtDNA haplotype that is most closely related to a haplotype from Mt Burr in
the south-east of SA, but these haplotypes diverge by ~1.7% (combined mtDNA data), suggesting that it represents
an ancient connection between these populations following retention of an ancestral mtDNA lineage and not recent
gene flow across southern Australia. That St Francis Island shared identical nuclear gene haplotypes with the Franklin
Island, KI and MLR populations, distinct from those found in the south-east of SA, supports its close genetic
association with these former populations, rather than an association with the latter population. The fixation of
different and divergent mtDNA lineages within St Francis Island and the Franklin Islands despite the close proximity
of these islands off the Eyre Peninsula in SA is interesting, as it reflects their potential long term isolation, or a lack of
maternal gene flow among them, despite being connected during previous glacial maxima until ~9,800 years ago.
Further investigation of nuclear gene data and morphology of these island populations is warranted to determine
whether the mtDNA differences are associated with any additional genetic differences.
Taken overall, the current genetic data do not support a conclusion that I. o. obesulus is distributed in the MLR, KI or
Franklin/ St Francis Islands of South Australia. The genetic data support the existence of a distinct population from
MLR, KI and the Franklin/St Francis Islands that may warrant separate subspecies (or conservation) status.
The status of the Tasmanian population of I. obesulus
The current study included 21 samples of I. obesulus from across the range of the species in Tasmania (including
Flinders Island) and phylogenetic analyses revealed that the population was in monophyly for mtDNA haplotypes
relative to I. o. obesulus from east coast mainland Australia. The latter, however, did not show reciprocal monophyly
of mtDNA haplotypes; a single haplotype from Mt. Burr in south-east SA was more closely related to a haplotype
from St Francis Island in SA, and a haplotype from Cranbourne, Victoria, also grouped outside the main I. o. obesulus
east coast mtDNA clade. These findings indicate that I. o. obesulus (east coast) is a paraphyletic taxon based on
analyses of mtDNA. The monophyly of the Tasmanian population and moderate level of sequence divergence
11
(~2.3%) from I. o. obesulus provides evidence of long term isolation of this population from the nearest mainland
population. Given an observation that 3.6% mtDNA divergence level here equates to an approximately 2.4 MY
divergence time estimate based on the study of Westerman et al. (2012), a 2.3% level of divergence would equate to
a coalescent time of ~1.5 MY years, representing a Pleistocene time period. It should be noted that population
divergence time is often substantially less than the coalescent time of individual genes and there can be
considerable stochastic variation in coalescent time estimates at recent time scales (Ho et al. 2011). Hence, there is a
need for additional nuclear gene analyses and alternative approaches to time estimation that model the isolation of
populations (e.g. Isolation-Migration model; Hey 2010). However, given the above coalescent time estimates, taken
overall it would seem unlikely that there has been any recent (e.g. last Ice Age) mtDNA gene flow between the
Tasmanian population of I. obesulus and mainland population of I. o. obesulus, despite the likelihood that these two
populations came into contact across the land bridge between Tasmania and the mainland.
For the nuclear DNA markers, vWF, RAG1 and BRCA1, there was no evidence for differentiation of east coast I. o.
obesulus and the Tasmanian population of I. obesulus, with each population sharing identical haplotypes. However,
the three genes are relatively slow evolving and, for vWF and RAG1 loci, the haplotypes observed in the Tasmanian
population were also shared with I. o. peninsulae and I. macrourus respectively, suggesting they represent ancestral
haplotypes that became fixed in the Tasmanian population. Therefore, these two loci are essentially uninformative
about whether there has been long term genetic isolation of the Tasmanian population from I. o. obesulus (east
coast). Similarly, the finding that these two populations shared an alternative BRCA1 haplotype may reflect a
historical connection between them, but should not be considered as evidence for recent population connectivity.
In conclusion, the monophyletic status and significant divergence of the Tasmanian population of I. obesulus from
east coast I. o. obesulus, based on analyses of mtDNA, strongly supports their genetic distinction and long-term
isolation. Together with a lack of information about population differentiation from the nuclear markers, there is no
basis for removing the separate subspecies status of the Tasmanian population, which was previously suggested by
Zenger et al. (2005).
The distribution of I. obesulus subspecies
Our interpretation of the above phylogeographic analyses suggest that the distribution of the subspecies I. o.
obesulus is most likely restricted to localities in NSW, Victoria and the south-east of SA. This proposal has important
implications for estimations of the population size of I. o. obesulus and, hence, its conservation status in Australia. A
separate subspecies is likely to be distributed in the MLR, KI and Franklin Island localities of SA, but whether this
subspecies is distinct from or represents an extension of the range of I. o. fusciventer is currently uncertain and
requires additional genetic (and morphological) analyses. However, until these data are available it would seem
sensible to manage these populations separately.
Summary of recommendations for consideration of I. o. obesulus:
Recommendation 1: Based on mtDNA and nuclear gene data, South Australian populations (MLR, KI, Franklin/ St
Francis Island populations) of I. obesulus represent a sub-species distinct from east coast mainland I. o. obesulus.
Recommendation 2: Based on mtDNA data, the Tasmanian population of I. obesulus is genetically-distinct from east
coast mainland I. obesulus supporting its current sub-species status as I. o. affinis.
Recommendation 3: Further genetic and morphological analyses should be conducted to compare the Franklin
Islands vs St Francis Island populations, but in the interim, each population should be treated as separate units for
conservation management.
Recommendation 4: Given the above genetic groupings, I. o. obesulus is restricted in its distribution to localities in
NSW, Victoria and south-east SA, reducing its formerly recognised distribution. Given this, we recommend the
current EPBC Act threat status of I. o. obesulus be maintained at least until a re-assessment against the threat
criteria has been undertaken.
Recommendation 5: Given their genetic distinctiveness, each of the South Australian (MLR, KI, Franklin/ St Francis
Islands), Tasmanian and east coast mainland populations of I. obesulus should be managed separately pending
further confirmation of sub-specific relationships.
12
Acknowledgments
We are grateful for the numerous people that have contributed samples and data for this analysis, but particularly
You Li, A. McLean, K. Saint, J. Packer, M. Eldridge, L. Pope, M. Adams, M. Westerman, L. Price, K. Long, J. Bentley, N.
Snelling, M. Bachmann, S. Jones, N. Haby, T. Horn, B. Haywood, R. Mengler, F. Christian, H. Nistelberger, A. Hillman,
B. Chambers, D. Wrigley, P. Spencer, Parks and Wildlife (WA) regional staff, S. Troman, E. Dewar (Dept of Primary
Industry, Parks, Water and Environment, Tasmania). Additional samples were also sourced from the Australian
National Wildlife Collection and Tasmanian Museum and Art Gallery. We thank S. Carthew and M. Byrne for advice
and support for the research. Funding for these sequence analyses was provided by Natural Resources Adelaide and
Mount Lofty Ranges (AMLR) South Australia via the AMLR Threatened Fauna Ecologist, Department of Parks and
Wildlife in WA, the Australian Research Council Linkage grant (LP0668987), Native Vegetation Council, Wildlife
Conservation Fund, DEWNR, the Department of Environment and Primary Industries (Victoria), The Roy and Marjory
Edwards Scholarship provided by the Nature Foundation (SA) and through project 1.L.21, of the Invasive Animals
Cooperative Research Centre (PI Stephen Sarre). Sample collections in this study were performed under the
University of Adelaide Animal Ethics Committee (project no. S-2011-041), Department of the Environment and
Heritage (DEH) permit to undertake scientific research (permit no.G23771-13) and under DPIPWE permit TFA 12289.
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14
Appendix 1. List of samples used for molecular analyses (all sequenced for ND2 and CR)
code Sp/Sub-sp location State latitude longitude Nuclear Genes
ABTC66742 Iaa Jensen Bay, Marchinbar Is. NT NA NA R
ABTC66754 Iaa Jensen Bay, Marchinbar Is. NT NA NA
D2096 (ABTC66736) Iaa Jensen Bay, Marchinbar Is. NT NA NA V R B
D2111 (ABTC66751) Iaa Jensen Bay, Marchinbar Is. NT NA NA R B
1352 Iaa Augustus Is. WA -15.35 124.56 R B
1354 Iaa Mt Trafalgar WA -15.28 125.07
1B (ABTC66056) Iaa George Water WA -15.81 124.73 R
26_2B (ABTC66052) Iaa George Water WA -15.81 124.73 V R B
DEC00245 Iaa Augustus Is. WA -15.39 124.59 V R B
DEC00247 Iaa Lachlan Is. WA -16.62 123.47 V R
DEC00248 Iaa Storr Is. WA -15.95 124.56 V R
DEC00249 Iaa Augustus Is. WA -15.39 124.59 V
DEC00252 Iaa Uwins Is. WA -15.26 124.80 V R
DEC00257 Iaa Storr Is. WA -15.95 124.56 V R
IA1 (ABTC10413) Iab Barrow Is. WA -20.80 115.45 V R B
1 (ABTC07769) Iab Barrow Is. WA -20.80 115.45 V R B
DEC00043 Iab Barrow Is. WA -20.80 115.45 V R
1650 Ioa Peter Murrell Reserve TAS -43.00 147.30 V B
305 Ioa Peter Murrell Reserve TAS -43.00 147.30 V B
3278 Ioa Launceston TAS NA NA
3279 Ioa Launceston TAS NA NA
7842 Ioa Peter Murrell Reserve TAS -43.00 147.30 V B
A3411 Ioa Mongtagu Is. TAS -40.75 144.92
AA15116 Ioa Port Arthur TAS -43.14 147.85 V R
AA15117 Ioa Longley TAS -42.98 147.16 V R
AA15118 Ioa Geeveston TAS -43.16 146.93 V R
AA63247 Ioa Fortescue Bay TAS -43.14 147.96 V R
IoA1f Ioa Inner Sister Is., Flinders Is. TAS -39.69 147.92 V B
Ioa8f Ioa Inner Sister Is., Flinders Is. TAS -39.69 147.92 V B
M29477 Ioa Burnie TAS -41.08 145.92 R
MW1 Ioa near Launceston TAS NA NA
Tas2 Ioa near Elliot TAS -41.10 145.77 R B
UC0623 Ioa Midlands Hwy TAS -41.72 147.33 V R
UC1247 Ioa Devonport TAS -41.16 146.34 R
UC1553 Ioa Cambridge TAS -42.82 147.46 V R
UC1562 Ioa Orielton TAS -42.74 147.53 R
UC1580 Ioa NinepinPt TAS -43.28 147.17 V R
UC1591 Ioa Pyengana TAS -41.29 148.01 V R
1331 Iof Albany WA -35.02 117.88 R B
1334 Iof Balingup WA -33.77 115.99 R B
1337 Iof Albany WA -35.01 117.87 R B
1338 Iof Perup WA -34.22 116.35 R B
3 (ABTC07847) Iof Daw Is. WA -33.85 124.14 V R B
DEC0004 Iof Kelmscott WA -32.08 116.05 V R
DEC00352 Iof Kewdale WA -31.99 115.93 V R
DEC00385 Iof Perth Airport WA -31.92 115.98 V R
DEC00415 Iof Beeliar Lake WA -32.13 115.82 V R
DEC00479 Iof Busselton WA -33.66 115.25 V R
15
DEC00480 Iof Waroona WA -32.85 115.93 V R
DEC00485 Iof Ellenbrook WA -31.75 116.04 R
DEC00487 Iof Twin Swamps WA -31.72 116.01 R
DEC00509 Iof Buller NR WA -32.88 115.83 V R
DEC00551 Iof Kooljerrenup WA -32.79 115.73 V R
DEC00584 Iof Forrestfield WA -31.97 116.01 V R
DEC00587 Iof Parmelia WA -32.24 115.85 V R
DEC00599 Iof Roe Hwy Inter WA -32.07 115.85 V R
DEC00676 Iof Mandurah WA -32.47 115.77 V R
DEC00766 Iof Safety Bay WA -32.31 115.79 V R
DEC00846 Iof Whiteman Park WA -33.38 115.62 V R
DEC00847 Iof Mundaring WA -32.07 115.84 V R
DEC00856 Iof Roleystone WA -32.11 116.08 V R
DEC00869 Iof Roleystone WA -32.10 116.05 V
DEC00983 Iof Murdoch University WA -32.07 115.84 V
DEC01044 Iof Gnangara Forest WA -31.79 115.87 V
DEC01067 Iof Cardup WA -32.25 116.00 V
DEC01166 Iof Banjup WA -32.15 115.88 V
DEC01190 Iof Twin Swamps WA -31.72 116.01 V
DEC01203 Iof Ellenbrook WA -31.75 116.04 V
DEC01236 Iof The Vale WA -31.79 115.99 V
ebu68968 Iof Kwinana WA -32.22 115.76 V B
ebu68969 Iof Ravensthorpe WA -33.58 120.05 V B
IoA1 Iof Albany WA -35.03 117.88
M29952 Iof Albany WA -35.00 117.87 R
94_116 (ABTC27196) Iok Stokes Bay SA -35.70 137.03 V R B
N908 Iok Kangaroo Is. SA -35.81 137.13 V R B
N909 Iok Kangaroo Is. SA -35.81 137.13 V R B
94_197 (ABTC27226) Iomlr East of Mt Compass SA -35.35 138.73 V R B
N411 Iomlr Cleland CP, Mt Lofty Ra SA -34.97 138.70 V R B
N524 Iomlr Mt Lofty Ra. SA -35.40 138.53 V R B
N534 Iomlr Mt Lofty Ra. SA -35.42 138.52 R B
N539 Iomlr Mt Lofty Ra. SA -35.05 138.65 V R B
N690 Iomlr Belair NP, Mt Lofty Ra. SA -35.02 138.67 V R B
N746 Iomlr Mt Lofty Ra. SA -35.08 138.70 R B
N782 Iomlr Mt Lofty Ra. SA -35.09 138.73 R B
N861 Iomlr Deep Ck. CP, Fleurieu Pen. SA -35.64 138.22 V R B
N874 Iomlr Mt Lofty Ra. SA -35.45 138.60 V R B
N895 Iomlr Mt Lofty Ra. SA -35.04 138.74 R B
9852 Ion East Franklin Is. SA -32.45 133.67 V R B
9853 Ion East Franklin Is. SA -32.45 133.67 V R B
9855 Ion East Franklin Is. SA -32.45 133.67 V R B
9802 Ion St Francis Is. SA -32.51 133.29 V R B
9803 Ion St Francis Is. SA -32.51 133.29 V R B
9804 Ion St Francis Is. SA -32.51 133.29 V R B
9805 Ion St Francis Is. SA -32.51 133.29 V R B
9806 Ion St Francis Is. SA -32.51 133.29 V R B
53 (ABTC26723) Ion West Franklin Is. SA -32.46 133.64 V R B
9832 Ion West Franklin Is. SA -32.46 133.64 V R B
9849 Ion West Franklin Is. SA -32.46 133.64 V R B
16
ABTC09876 Ion West Franklin Is. SA -32.46 133.64 V R
ebu53747 Ioo Duffys Forest NSW -33.67 151.20 V B
ebu68962 Ioo Eden (Kiah State Forest) NSW -37.19 149.87
ebu68963 Ioo Eden (Kiah State Forest) NSW -37.17 149.70
ebu68970 Ioo West Head NSW -33.57 151.30 V B
G1 Ioo Garigal NP, Sydney NSW NA NA V R B
G2 Ioo Garigal NP, Sydney NSW -33.68 151.16 V R B
K1 Ioo Garigal NP, Sydney NSW -33.66 151.23 V R B
K2 Ioo Garigal NP, Sydney NSW -33.66 151.23 R B
29020 (ABTC37433) Ioo Donovans SA -37.97 140.94 V R B
N15 Ioo Mt Burr SA -37.63 140.60 V R B
N57 Ioo Mt Burr SA -37.68 140.66 V R B
N65 Ioo Mt Burr SA -37.71 140.75
N66 Ioo Mt Burr SA -37.71 140.75 V R B
C5819 Ioo Wandin VIC -37.78 145.43
ebu53723 Ioo East Gippsland VIC -37.78 148.84
N961 Ioo Grampians VIC -37.44 142.48
N962 Ioo Grampians VIC -37.44 142.48
N977 Ioo Grampians VIC -37.15 142.56
N985 Ioo Lower Glenelg River VIC -38.00 140.97 R B
N986 Ioo Lower Glenelg River VIC -38.00 140.97
Vict Ioo NA VIC NA NA V R B
Z15979 Ioo Cranbourne VIC -38.10 145.28
Z22738 Ioo Grampians NP VIC -37.45 142.28
Z25136 Ioo Tooradin VIC -38.19 145.39
ebu68965 Iop Mt White QLD -13.93 143.20
ebu68966 Iop Davies Creek QLD -17.03 145.58 V
ebu68971 Iop Bridle Creek QLD -16.97 145.59 V B
ebu68972 Iop Emu Creek QLD -17.10 145.52 V B
ebu68973 Iop Bridle Creek QLD -16.97 145.58 V B
I36 Im Sydney region NSW NA NA V R B
M16317 Im North Coffs Harbour NSW -13.82 143.44 V R
Darwin1 Im Darwin NT -12.92 130.88 V B
NBB1 Im Mudgniberri NT -12.59 132.86 V B
NBB2 Im Jabiru NT -12.66 132.84 V B
NBB3 Im NA NT NA NA
Tiwi1 Im Bathurst Is. NT -11.77 130.55 V B
Tiwi5 Im Bathurst Is. NT -11.77 130.55 V B
U5881 Im Arnhem Hway NT NA NA V R
U5917 Im Humpty Doo NT NA NA R
ebu68964 Im Davies Creek QLD -17.03 145.58
M16380 Im North Rockhampton QLD -22.77 150.56 R
1341 Im Lone Dingo WA -14.78 125.79 B
1344 Im Lone Dingo WA -14.78 125.79 B
1360 Im Mt Trafalga WA -15.28 125.07 B
22 (ABTC07795) Im Mitchell Plateau WA NA NA
ABTC66055 Im Bachsten Ck WA NA NA
Species/ sub-species codes are as follows: Ioa (I. obesulus affinis), Ioo (I. obesulus obesulus), Ion (I. obesulus nauticus), Iaa (I.
auratus auratus), Iof (I. obesulus fusciventer), Iab (I. auratus barrowensis), Iok (I. obesulus Kangaroo Island SA), Iomlr) (I. obesulus
Mt. Lofty Ranges and Fleurieu Peninsula SA), Iop (I. obesulus peninsulae), Im (I. macrourus). Full locality information is available
upon request to the authors. Nuclear genes sequenced for each specimen are coded as follows: V- vWF, R- RAG1, B- BRCA1.
... Alternatively, the relatively abundant food resources in urbanised environments may be allowing quenda to grow larger in accordance with inherent genetic potential. Previous research supports such "phenotypic plasticity" in quenda (Hale, 2000) and in Isoodon auratus (Dunlop, 2015), a species that is genetically so closely related to quenda that conspecific status is justified (Pope et al., 2001;Zenger et al., 2005;Cooper et al., 2015). ...
... Quenda have an oestrous in late lactation, and therefore if optimally fertile are capable of having an active pouch continuously, or continuously throughout the breeding season in populations where breeding occurs seasonally (Heinsohn, 1966;Stoddart and Braithwaite, 1979). These results, indicating that quenda in the greater Perth region breed in autumn (as well as spring and winter), correspond to those for southern brown bandicoots in South Australia (Copley et al., 1990;Sanderson and Kraehenbuehl, 2006), which form an I. obesulus phylogenetic group with Western Australian quenda (Cooper et al., 2015). Research suggests that southern brown bandicoot populations from eastern Australian locations, which form a separate phylogenetic group of I. obesulus (Cooper et al., 2015), breed seasonally, with autumn not part of the breeding season (Heinsohn, 1966;Stoddart and Braithwaite, 1979;Lobert and Lee, 1990;Dowle, 2012). ...
... These results, indicating that quenda in the greater Perth region breed in autumn (as well as spring and winter), correspond to those for southern brown bandicoots in South Australia (Copley et al., 1990;Sanderson and Kraehenbuehl, 2006), which form an I. obesulus phylogenetic group with Western Australian quenda (Cooper et al., 2015). Research suggests that southern brown bandicoot populations from eastern Australian locations, which form a separate phylogenetic group of I. obesulus (Cooper et al., 2015), breed seasonally, with autumn not part of the breeding season (Heinsohn, 1966;Stoddart and Braithwaite, 1979;Lobert and Lee, 1990;Dowle, 2012). ...
Article
Some wildlife species are capable of surviving in urbanised environments. However, the implications of urbanisation on wildlife health, and public health regarding zoonoses, are often unknown. Quenda (syn. southern brown bandicoots, Isoodon obesulus) survive in many areas of Perth, Australia, despite urbanisation. This study investigated differences in gastrointestinal and macroscopic ecto-parasitic infections, morphometrics and reproductive status between bushland and urban dwelling quenda. 287 quenda in the greater Perth region were captured and sampled for faeces (to detect gastrointestinal parasites), blood (to detect Toxoplasma gondii antibodies), ectoparasites, and morphometrics. Data were analysed using multivariable logistic and linear regression. Most parasitic infections identified in quenda were of native parasite taxa that are either not known to, or considered highly unlikely to, infect humans or domestic animals. However, stickfast fleas (Echidnophaga spp.) were present at low prevalences and intensities, and Giardia spp., Cryptosporidium spp. and Amblyomma spp. infections require further investigation to clarify their anthropozoonotic significance. Quenda captured in urbanised environments had differing odds of or intensity of certain parasitic infections, compared to those in bushland – likely attributable to quenda population density, and in some cases the availability of other host species or anthropogenic sources of infection. Urbanised environments were associated with an increase in net weight of adult male quenda by 189.0 g (95% CI 68.6–309.5 g; p = 0.002; adjusted R2 = 0.06) and adult female quenda by 140.1 g (95% CI 3.9–276.3 g; p = 0.044; adjusted R2 = 0.07), with study findings suggesting a tendency towards obesity in urbanised environments. Adult female quenda in bushland had increased odds of an active pouch (adjusted OR = 4.89, 95% CI 1.7–14.5), suggesting decreased reproductive activity in quenda from urbanised environments. These results highlight the subtle, yet extensive impacts that urbanised environments may have on wildlife ecology, even for those species which apparently adjust well to urbanisation. Link: authors.elsevier.com/a/1VS2RB8cccm4G
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