References
Amery-Gale, J., Vaz, P. K., Whiteley, P., Tatarczuch, L., Taggart, D.
A., Charles, J. A., . . . Wilks, C. R. (2014). Detection and
identification of a gammaherpesvirus in Antechinus spp . in
Australia. J Wildl Dis, 50 (2), 334-339. doi:10.7589/2013-07-165
Amoasii, L., Sanchez-Ortiz, E., Fujikawa, T., Elmquist, J. K.,
Bassel-Duby, R., & Olson, E. N. (2019). NURR1 activation in skeletal
muscle controls systemic energy homeostasis. Proc Natl Acad Sci U
S A, 116 (23), 11299-11308. doi:10.1073/pnas.1902490116
Argiles, J. M., Campos, N., Lopez-Pedrosa, J. M., Rueda, R., &
Rodriguez-Manas, L. (2016). Skeletal Muscle Regulates Metabolism via
Interorgan Crosstalk: Roles in Health and Disease. Journal of the
American Medical Directors Association, 17 (9), 789-796.
doi:10.1016/j.jamda.2016.04.019
Austad, S. N., & Fischer, K. E. (2016). Sex Differences in Lifespan.Cell Metab, 23 (6), 1022-1033. doi:10.1016/j.cmet.2016.05.019
Baker, A., & Dickman, C. (2018). Secret lives of carnivorous
marsupials : CSIRO PUBLISHING.
Baker, A. M., & Van Dyck, S. (2013). Taxonomy and redescription of the
Yellow-footed Antechinus, Antechinus flavipes (Waterhouse)
(Marsupialia: Dasyuridae). Zootaxa, 3649 , 1-62.
doi:10.11646/zootaxa.3649.1.
Balasubramanian, M. N., Butterworth, E. A., & Kilberg, M. S. (2013).
Asparagine synthetase: regulation by cell stress and involvement in
tumor biology. Am J Physiol Endocrinol Metab, 304 (8), E789-799.
doi:10.1152/ajpendo.00015.2013
Bao, W., Kojima, K. K., & Kohany, O. (2015). Repbase Update, a database
of repetitive elements in eukaryotic genomes. Mob DNA, 6 , 11.
doi:10.1186/s13100-015-0041-9
Barker, I., Beveridge, I., Bradley, A., & Lee, A. (1978). Observations
on spontaneous stress-related mortality among males of the dasyurid
marsupial Antechinus stuartii Macleay. Australian Journal
of Zoology, 26 (3), 435-447.
Barrows, T. T., Stone, J. O., Fifield, L. K., & Cresswell, R. G.
(2002). The timing of the last glacial maximum in Australia.Quaternary Science Reviews, 21 (1-3), 159-173.
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA
sequences. Nucleic Acids Res, 27 (2), 573-580.
doi:10.1093/nar/27.2.573
Birney, E., Clamp, M., & Durbin, R. (2004). GeneWise and Genomewise.Genome Res, 14 (5), 988-995. doi:10.1101/gr.1865504
Boonstra, R. (2005). Equipped for life: the adaptive role of the stress
axis in male mammals. Journal of Mammalogy, 86 (2), 236-247.
Bradley, A., McDonald, I., & Lee, A. (1980). Stress and Mortality in a
Small Marsupial (Antechinus stuartii , Macleay). Gen Comp
Endocrinol, 40 (2), 188-200. doi:10.1016/0016-6480(80)90122-7
Bradley, A. J. (2003). Stress, hormones and mortality in small
carnivorous marsupials. In Predators with Pouches–The Biology of
Carnivorous Marsupials (pp. 255-267). Collingwood, VIC, Australia:
CSIRO Publishing.
Braithwaite, R. W., & Lee, A. K. (1979). A mammalian example of
semelparity. American Naturalist , 151-155.
Brandies, P. A., Tang, S., Johnson, R. S. P., Hogg, C. J., & Belov, K.
(2020a). The first Antechinus reference genome provides a
resource for investigating the genetic basis of semelparity and
age-related neuropathologies. Gigabyte, 1 , 7.
doi:10.46471/gigabyte.7
Brandies, P. A., Tang, S., Johnson, R. S. P., Hogg, C. J., & Belov, K.
(2020b). Supporting data for ”The first Antechinus reference genome
provides a resource for investigating the genetic basis of semelparity
and age-related neuropathologies”. GigaScience Database .
doi:10.5524/100807
Bujak, A. L., Crane, J. D., Lally, J. S., Ford, R. J., Kang, S. J.,
Rebalka, I. A., . . . Steinberg, G. R. (2015). AMPK activation of muscle
autophagy prevents fasting-induced hypoglycemia and myopathy during
aging. Cell Metab, 21 (6), 883-890. doi:10.1016/j.cmet.2015.05.016
Burge, C., & Karlin, S. (1997). Prediction of complete gene structures
in human genomic DNA. J Mol Biol, 268 (1), 78-94.
doi:10.1006/jmbi.1997.0951
Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., &
Shendure, J. (2013). Chromosome-scale scaffolding of de novo genome
assemblies based on chromatin interactions. Nat Biotechnol,
31 (12), 1119-1125. doi:10.1038/nbt.2727
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J.,
Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and
applications. BMC Bioinformatics, 10 , 421.
doi:10.1186/1471-2105-10-421
Childs, B. G., Gluscevic, M., Baker, D. J., Laberge, R. M., Marquess,
D., Dananberg, J., & van Deursen, J. M. (2017). Senescent cells: an
emerging target for diseases of ageing. Nat Rev Drug Discov,
16 (10), 718-735. doi:10.1038/nrd.2017.116
Clarkson, C., Jacobs, Z., Marwick, B., Fullagar, R., Wallis, L., Smith,
M., . . . Pardoe, C. (2017). Human occupation of northern Australia by
65,000 years ago. Nature, 547 (7663), 306-310.
doi:10.1038/nature22968
Collett, R. A., Baker, A. M., & Fisher, D. O. (2018). Prey productivity
and predictability drive different axes of life-history variation in
carnivorous marsupials. Proceedings of the Royal Society B,
285 (1890), 20181291.
Cosentino, S., & Iwasaki, W. (2019). SonicParanoid: fast, accurate and
easy orthology inference. Bioinformatics, 35 (1), 149-151.
doi:10.1093/bioinformatics/bty631
Croft, D. B. (2003). Behaviour of carnivorous marsupials. InPredators with pouches: the biology of carnivorous marsupials(pp. 332-346). Collingwood, VIC, Australia: CSIRO Publishing.
Deakin, J. E., & O’Neill, R. J. (2020). Evolution of Marsupial Genomes.Annu Rev Anim Biosci, 8 , 25-45.
doi:10.1146/annurev-animal-021419-083555
Diamond, J. M. (1982). Big-bang reproduction and ageing in male
marsupial mice. Nature, 298 (5870), 115-116.
Diez-Del-Molino, D., Sanchez-Barreiro, F., Barnes, I., Gilbert, M. T.
P., & Dalen, L. (2018). Quantifying Temporal Genomic Erosion in
Endangered Species. Trends in Ecology & Evolution, 33 (3),
176-185. doi:10.1016/j.tree.2017.12.002
Dodt, M., Roehr, J. T., Ahmed, R., & Dieterich, C. (2012).
FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation
Sequencing Platforms. Biology (Basel), 1 (3), 895-905.
doi:10.3390/biology1030895
Dudchenko, O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M.,
Durand, N. C., . . . Aiden, E. L. (2017). De novo assembly of theAedes aegypti genome using Hi-C yields chromosome-length
scaffolds. Science, 356 (6333), 92-95. doi:10.1126/science.aal3327
Dudchenko, O., Shamim, M. S., Batra, S. S., Durand, N. C., Musial, N.
T., Mostofa, R., . . . Aiden, E. L. (2018). The Juicebox Assembly Tools
module facilitates de novo assembly of mammalian genomes with
chromosome-length scaffolds for under $1000. Preprint at
http://biorxiv.org/content/10.1101/254797v1 . doi:10.1101/254797
Durand, N. C., Robinson, J. T., Shamim, M. S., Machol, I., Mesirov, J.
P., Lander, E. S., & Aiden, E. L. (2016). Juicebox Provides a
Visualization System for Hi-C Contact Maps with Unlimited Zoom.Cell Syst, 3 (1), 99-101. doi:10.1016/j.cels.2015.07.012
Elderfield, H., Ferretti, P., Greaves, M., Crowhurst, S., McCave, I. N.,
Hodell, D., & Piotrowski, A. M. (2012). Evolution of ocean temperature
and ice volume through the mid-Pleistocene climate transition.Science, 337 (6095), 704-709. doi:10.1126/science.1221294
Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008). LTRharvest, an
efficient and flexible software for de novo detection of LTR
retrotransposons. BMC Bioinformatics, 9 , 18.
doi:10.1186/1471-2105-9-18
Faurby, S., Davis, M., Pedersen, R. O., Schowanek, S. D., Antonelli, A.,
& Svenning, J. C. (2018). PHYLACINE 1.2: The Phylogenetic Atlas of
Mammal Macroecology. Ecology, 99 (11), 2626. doi:10.1002/ecy.2443
Feigin, C. Y., Newton, A. H., Doronina, L., Schmitz, J., Hipsley, C. A.,
Mitchell, K. J., . . . Pask, A. J. (2018). Genome of the Tasmanian tiger
provides insights into the evolution and demography of an extinct
marsupial carnivore. Nat Ecol Evol, 2 (1), 182-192.
doi:10.1038/s41559-017-0417-y
Fisher, D. O., Dickman, C. R., Jones, M. E., & Blomberg, S. P. (2013).
Sperm competition drives the evolution of suicidal reproduction in
mammals. Proc Natl Acad Sci U S A, 110 (44), 17910-17914.
doi:10.1073/pnas.1310691110
Froy, H., Sparks, A. M., Watt, K., Sinclair, R., Bach, F., Pilkington,
J. G., . . . Nussey, D. H. (2019). Senescence in immunity against
helminth parasites predicts adult mortality in a wild mammal.Science, 365 (6459), 1296-1298. doi:10.1126/science.aaw5822
García‐Navas, V., Kear, B. P., & Westerman, M. (2020). The geography of
speciation in dasyurid marsupials. Journal of Biogeography .
doi:10.1111/jbi.13852
Gems, D. (2014). Evolution of sexually dimorphic longevity in humans.Aging (Albany NY), 6 (2), 84-91. doi:10.18632/aging.100640
Geyle, H. M., Woinarski, J. C., Baker, G. B., Dickman, C. R., Dutson,
G., Fisher, D. O., . . . Kutt, A. (2018). Quantifying extinction risk
and forecasting the number of impending Australian bird and mammal
extinctions. Pacific Conservation Biology, 24 (2), 157-167.
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D.
A., Amit, I., . . . Regev, A. (2011). Full-length transcriptome assembly
from RNA-Seq data without a reference genome. Nat Biotechnol,
29 (7), 644-652. doi:10.1038/nbt.1883
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D.,
Bowden, J., . . . Regev, A. (2013). De novo transcript sequence
reconstruction from RNA-seq using the Trinity platform for reference
generation and analysis. Nat Protoc, 8 (8), 1494-1512.
doi:10.1038/nprot.2013.084
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis,
J., . . . Wortman, J. R. (2008). Automated eukaryotic gene structure
annotation using EVidenceModeler and the Program to Assemble Spliced
Alignments. Genome Biol, 9 (1), R7. doi:10.1186/gb-2008-9-1-r7
Hayes, G., Simmons, L., Dugand, R., Mills, H. R., Roberts, J., Tomkins,
J., & Fisher, D. (2019). Male semelparity and multiple paternity
confirmed in an arid‐zone dasyurid. Journal of Zoology, 308 (4),
266-273.
Henschel, R., Lieber, M., Wu, L.-S., Nista, P. M., Haas, B. J., &
LeDuc, R. D. (2012). Trinity RNA-Seq assembler performance
optimization. Paper presented at the Proceedings of the 1st Conference
of the Extreme Science and Engineering Discovery Environment: Bridging
from the eXtreme to the campus and beyond, Chicag, IL, USA.
Hughes, P. W. (2017). Between semelparity and iteroparity: Empirical
evidence for a continuum of modes of parity. Ecol Evol, 7 (20),
8232-8261. doi:10.1002/ece3.3341
Johansen, T., & Lamark, T. (2020). Selective Autophagy: ATG8 Family
Proteins, LIR Motifs and Cargo Receptors. J Mol Biol, 432 (1),
80-103. doi:10.1016/j.jmb.2019.07.016
Johnson, R. N., O’Meally, D., Chen, Z., Etherington, G. J., Ho, S. Y.
W., Nash, W. J., . . . Belov, K. (2018). Adaptation and conservation
insights from the koala genome. Nat Genet, 50 (8), 1102-1111.
doi:10.1038/s41588-018-0153-5
Jucker, M. (2010). The benefits and limitations of animal models for
translational research in neurodegenerative diseases. Nat Med,
16 (11), 1210-1214. doi:10.1038/nm.2224
Jukes, T. H., & Cantor, C. R. (1969). Evolution of protein molecules.
In H. N. Munro (Ed.), Mammalian Protein Metabolism (III ed., Vol.
3, pp. 132).
Kahle, D., & Wickham, H. (2013). ggmap: Spatial Visualization with
ggplot2. The R Journal, 5 (1), 144-161.
Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto Encyclopedia of Genes and
Genomes. Nucleic Acids Res, 28 (1), 27-30.
Kent, W. J. (2002). BLAT–the BLAST-like alignment tool. Genome
Res, 12 (4), 656-664. doi:10.1101/gr.229202
Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019).
Graph-based genome alignment and genotyping with HISAT2 and
HISAT-genotype. Nat Biotechnol, 37 (8), 907-915.
doi:10.1038/s41587-019-0201-4
Koh, H. J., Arnolds, D. E., Fujii, N., Tran, T. T., Rogers, M. J.,
Jessen, N., . . . Goodyear, L. J. (2006). Skeletal muscle-selective
knockout of LKB1 increases insulin sensitivity, improves glucose
homeostasis, and decreases TRB3. Mol Cell Biol, 26 (22),
8217-8227. doi:10.1128/MCB.00979-06
Kopylova, E., Noe, L., & Touzet, H. (2012). SortMeRNA: fast and
accurate filtering of ribosomal RNAs in metatranscriptomic data.Bioinformatics, 28 (24), 3211-3217.
doi:10.1093/bioinformatics/bts611
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., &
Phillippy, A. M. (2017). Canu: scalable and accurate long-read assembly
via adaptive k -mer weighting and repeat separation. Genome
Res, 27 (5), 722-736. doi:10.1101/gr.215087.116
Krajewski, C., Woolley, P. A., & Westerman, M. (2000). The evolution of
reproductive strategies in dasyurid marsupials: implications of
molecular phylogeny. Biological Journal of the Linnean Society,
71 (3), 417-435.
Kumar, S., Stecher, G., Suleski, M., & Hedges, S. B. (2017). TimeTree:
A Resource for Timelines, Timetrees, and Divergence Times. Mol
Biol Evol, 34 (7), 1812-1819. doi:10.1093/molbev/msx116
Lada, H., Thomson, J. R., Mac Nally, R., & Taylor, A. C. (2008).
Impacts of massive landscape change on a carnivorous marsupial in
south‐eastern Australia: inferences from landscape genetics analysis.Journal of Applied Ecology, 45 (6), 1732-1741.
Leiner, N. O., Setz, E. Z., & Silva, W. R. (2008). Semelparity and
factors affecting the reproductive activity of the Brazilian slender
opossum (Marmosops paulensis ) in southeastern Brazil.Journal of Mammalogy, 89 (1), 153-158.
Lemaitre, J. F., Ronget, V., Tidiere, M., Allaine, D., Berger, V.,
Cohas, A., . . . Gaillard, J. M. (2020). Sex differences in adult
lifespan and aging rates of mortality across wild mammals. Proc
Natl Acad Sci U S A, 117 (15), 8546-8553. doi:10.1073/pnas.1911999117
Lesuis, S. L., Weggen, S., Baches, S., Lucassen, P. J., & Krugers, H.
J. (2018). Targeting glucocorticoid receptors prevents the effects of
early life stress on amyloid pathology and cognitive performance in
APP/PS1 mice. Transl Psychiatry, 8 (1), 53.
doi:10.1038/s41398-018-0101-2
Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.Bioinformatics, 34 (18), 3094-3100.
doi:10.1093/bioinformatics/bty191
Li, H., & Durbin, R. (2011). Inference of human population history from
individual whole-genome sequences. Nature, 475 (7357), 493-496.
doi:10.1038/nature10231
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., .
. . Genome Project Data Processing, S. (2009). The Sequence
Alignment/Map format and SAMtools. Bioinformatics, 25 (16),
2078-2079. doi:10.1093/bioinformatics/btp352
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M.,
Ragoczy, T., Telling, A., . . . Dekker, J. (2009). Comprehensive mapping
of long-range interactions reveals folding principles of the human
genome. Science, 326 (5950), 289-293. doi:10.1126/science.1181369
Lisiecki, L. E., & Raymo, M. E. (2005). A Pliocene‐Pleistocene stack of
57 globally distributed benthic δ18O records. Paleoceanography,
20 (1).
Liu, B., Shi, Y., Yuan, J., Hu, X., Zhang, H., Li, N., . . . Fan, W.
(2013). Estimation of genomic characteristics by analyzing k -mer
frequency in de novo genome projects. arXiv preprint
arXiv:1308.2012 .
Loytynoja, A., & Goldman, N. (2005). An algorithm for progressive
multiple alignment of sequences with insertions. Proc Natl Acad
Sci U S A, 102 (30), 10557-10562. doi:10.1073/pnas.0409137102
Luo, Z. X., Yuan, C. X., Meng, Q. J., & Ji, Q. (2011). A Jurassic
eutherian mammal and divergence of marsupials and placentals.Nature, 476 (7361), 442-445. doi:10.1038/nature10291
Majoros, W. H., Pertea, M., & Salzberg, S. L. (2004). TigrScan and
GlimmerHMM: two open source ab initio eukaryotic gene-finders.Bioinformatics, 20 (16), 2878-2879.
doi:10.1093/bioinformatics/bth315
Mak, S. S. T., Gopalakrishnan, S., Caroe, C., Geng, C., Liu, S.,
Sinding, M. S., . . . Gilbert, M. T. P. (2017). Comparative performance
of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for
palaeogenomic sequencing. Gigascience, 6 (8), 1-13.
doi:10.1093/gigascience/gix049
Manoli, I., Alesci, S., Blackman, M. R., Su, Y. A., Rennert, O. M., &
Chrousos, G. P. (2007). Mitochondria as key components of the stress
response. Trends in Endocrinology & Metabolism, 18 (5), 190-198.
doi:10.1016/j.tem.2007.04.004
Marcais, G., & Kingsford, C. (2011). A fast, lock-free approach for
efficient parallel counting of occurrences of k -mers.Bioinformatics, 27 (6), 764-770. doi:10.1093/bioinformatics/btr011
Martocchia, A., Stefanelli, M., Falaschi, G. M., Toussan, L., Ferri, C.,
& Falaschi, P. (2016). Recent advances in the role of cortisol and
metabolic syndrome in age-related degenerative diseases. Aging
Clin Exp Res, 28 (1), 17-23. doi:10.1007/s40520-015-0353-0
McAllan, B. (2006). Dasyurid marsupials as models for the physiology of
ageing in humans. Australian Journal of Zoology, 54 (3), 159-172.
McDowell, I. C., Barrera, A., D’Ippolito, A. M., Vockley, C. M., Hong,
L. K., Leichter, S. M., . . . Reddy, T. E. (2018). Glucocorticoid
receptor recruits to enhancers and drives activation by motif-directed
binding. Genome Res, 28 (9), 1272-1284. doi:10.1101/gr.233346.117
Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E.,
Miller, J., . . . Schuster, S. C. (2011). Genetic diversity and
population structure of the endangered marsupial Sarcophilus
harrisii (Tasmanian devil). Proc Natl Acad Sci U S A, 108 (30),
12348-12353. doi:10.1073/pnas.1102838108
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P.,
Bridge, A., . . . Finn, R. D. (2019). InterPro in 2019: improving
coverage, classification and access to protein sequence annotations.Nucleic Acids Res, 47 (D1), D351-D360. doi:10.1093/nar/gky1100
Mitchell, K. J., Pratt, R. C., Watson, L. N., Gibb, G. C., Llamas, B.,
Kasper, M., . . . Cooper, A. (2014). Molecular phylogeny, biogeography,
and habitat preference evolution of marsupials. Mol Biol Evol,
31 (9), 2322-2330. doi:10.1093/molbev/msu176
Mutton, T. Y., Phillips, M. J., Fuller, S. J., Bryant, L. M., & Baker,
A. M. (2019). Systematics, biogeography and ancestral state of the
Australian marsupial genus Antechinus (Dasyuromorphia:
Dasyuridae). Zoological Journal of the Linnean Society, 186 (2),
553-568.
Naylor, R., Richardson, S. J., & McAllan, B. M. (2008). Boom and bust:
a review of the physiology of the marsupial genus Antechinus .J Comp Physiol B, 178 (5), 545-562. doi:10.1007/s00360-007-0250-8
Nilsson, M. A., Churakov, G., Sommer, M., Tran, N. V., Zemann, A.,
Brosius, J., & Schmitz, J. (2010). Tracking marsupial evolution using
archaic genomic retroposon insertions. PLoS Biol, 8 (7), e1000436.
doi:10.1371/journal.pbio.1000436
O’Donovan, C., Martin, M. J., Gattiker, A., Gasteiger, E., Bairoch, A.,
& Apweiler, R. (2002). High-quality protein knowledge resource:
SWISS-PROT and TrEMBL. Brief Bioinform, 3 (3), 275-284.
doi:10.1093/bib/3.3.275
O’Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D.,
McVeigh, R., . . . Pruitt, K. D. (2016). Reference sequence (RefSeq)
database at NCBI: current status, taxonomic expansion, and functional
annotation. Nucleic Acids Res, 44 (D1), D733-745.
doi:10.1093/nar/gkv1189
Perogamvros, I., Ray, D. W., & Trainer, P. J. (2012). Regulation of
cortisol bioavailability–effects on hormone measurement and action.Nat Rev Endocrinol, 8 (12), 717-727. doi:10.1038/nrendo.2012.134
Phillips, M. J., Bennett, T. H., & Lee, M. S. (2009). Molecules,
morphology, and ecology indicate a recent, amphibious ancestry for
echidnas. Proc Natl Acad Sci U S A, 106 (40), 17089-17094.
doi:10.1073/pnas.0904649106
Phuc Le, P., Friedman, J. R., Schug, J., Brestelli, J. E., Parker, J.
B., Bochkis, I. M., & Kaestner, K. H. (2005). Glucocorticoid
receptor-dependent gene regulatory networks. PLoS Genet, 1 (2),
e16. doi:10.1371/journal.pgen.0010016
Poskitt, D., Barnett, J., Duffey, K., Lee, A., Kimpton, W., & Muller,
H. (1984). Stress related involution of lymphoid tissues in Australian
marsupial mice. Immunobiology, 166 (3), 286-295.
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree
2–approximately maximum-likelihood trees for large alignments.PLoS One, 5 (3), e9490. doi:10.1371/journal.pone.0009490
Pruitt, K. D., Tatusova, T., & Maglott, D. R. (2007). NCBI reference
sequences (RefSeq): a curated non-redundant sequence database of
genomes, transcripts and proteins. Nucleic Acids Res, 35 (Database
issue), D61-65. doi:10.1093/nar/gkl842
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,
. . . Glockner, F. O. (2013). The SILVA ribosomal RNA gene database
project: improved data processing and web-based tools. Nucleic
Acids Res, 41 (Database issue), D590-596. doi:10.1093/nar/gks1219
Riordan, C. E., Pearce, C., McDonald, B. J. F., Gynther, I., & Baker,
A. M. (2020). Vegetation structure and ground cover attributes describe
the occurrence of a newly discovered carnivorous marsupial on the Tweed
Shield Volcano caldera, the endangered black-tailed dusky antechinus
(Antechinus arktos ). Ecol Evol, 10 (4), 2104-2121.
doi:10.1002/ece3.6045
Roehr, J. T., Dieterich, C., & Reinert, K. (2017). Flexbar 3.0 - SIMD
and multicore parallelization. Bioinformatics, 33 (18), 2941-2942.
doi:10.1093/bioinformatics/btx330
Romero, L. M. (2004). Physiological stress in ecology: lessons from
biomedical research. Trends in Ecology & Evolution, 19 (5),
249-255. doi:10.1016/j.tree.2004.03.008
Ruan, J., & Li, H. (2020). Fast and accurate long-read assembly with
wtdbg2. Nat Methods, 17 (2), 155-158.
doi:10.1038/s41592-019-0669-3
Sakamoto, K., McCarthy, A., Smith, D., Green, K. A., Grahame Hardie, D.,
Ashworth, A., & Alessi, D. R. (2005). Deficiency of LKB1 in skeletal
muscle prevents AMPK activation and glucose uptake during contraction.EMBO J, 24 (10), 1810-1820. doi:10.1038/sj.emboj.7600667
Saltre, F., Rodriguez-Rey, M., Brook, B. W., Johnson, C. N., Turney, C.
S., Alroy, J., . . . Bradshaw, C. J. (2016). Climate change not to blame
for late Quaternary megafauna extinctions in Australia. Nat
Commun, 7 , 10511. doi:10.1038/ncomms10511
Schloissnig, S., Kawaguchi, A., Nowoshilow, S., Falcon, F., Otsuki, L.,
Tardivo, P., . . . Tanaka, E. M. (2021). The giant axolotl genome
uncovers the evolution, scaling, and transcriptional control of complex
gene loci. Proc Natl Acad Sci U S A, 118 (15).
doi:10.1073/pnas.2017176118
Seim, I. (2020a). de novo genome assemblies of black-tailed dusky
antechinus (Antechinus arktos ), silver-headed antechinus
(Antechinus argentus ), and black-tailed dasyure (Murexia
melanurus ). doi:10.5281/zenodo.3735672
Seim, I. (2020b). Gapfilled nuclear genome assemblies of black-tailed
dusky antechinus (Antechinus arktos ), silver-headed antechinus
(Antechinus argentus ), and black-tailed dasyure (Murexia
melanurus ). doi:10.5281/zenodo.3735686
Seim, I. (2020c). ROPUS - Reference-guided Ortholog Pipeline for
Unannotated species. doi:10.5281/zenodo.3722900
Selwood, L. (1980). A timetable of embryonic development of the dasyurid
marsupial Antechinus stuartii (Macleay). Australian Journal
of Zoology, 28 (4), 645-669.
Seppey, M., Manni, M., & Zdobnov, E. M. (2019). BUSCO: Assessing Genome
Assembly and Annotation Completeness. Methods Mol Biol, 1962 ,
227-245. doi:10.1007/978-1-4939-9173-0_14
Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C. J., Vert,
J. P., . . . Barillot, E. (2015). HiC-Pro: an optimized and flexible
pipeline for Hi-C data processing. Genome Biol, 16 , 259.
doi:10.1186/s13059-015-0831-x
Smit, A. F., & Hubley, R. (2010). RepeatModeler Open-1.0. 2008-2015.
Available at http://www.repeatmasker.org.
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based
phylogenetic analyses with thousands of taxa and mixed models.Bioinformatics, 22 (21), 2688-2690.
doi:10.1093/bioinformatics/btl446
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., &
Morgenstern, B. (2006). AUGUSTUS: ab initio prediction of alternative
transcripts. Nucleic Acids Res, 34 (Web Server issue), W435-439.
doi:10.1093/nar/gkl200
Stanke, M., & Waack, S. (2003). Gene prediction with a hidden Markov
model and a new intron submodel. Bioinformatics, 19 Suppl 2 ,
ii215-225. doi:10.1093/bioinformatics/btg1080
Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after
removing divergent and ambiguously aligned blocks from protein sequence
alignments. Syst Biol, 56 (4), 564-577.
doi:10.1080/10635150701472164
Tarailo-Graovac, M., & Chen, N. (2009). Using RepeatMasker to identify
repetitive elements in genomic sequences. Curr Protoc
Bioinformatics, Chapter 4 , Unit 4 10. doi:10.1002/0471250953.bi0410s25
Tatusov, R. L., Galperin, M. Y., Natale, D. A., & Koonin, E. V. (2000).
The COG database: a tool for genome-scale analysis of protein functions
and evolution. Nucleic Acids Res, 28 (1), 33-36.
doi:10.1093/nar/28.1.33
Thomson, D. M., Porter, B. B., Tall, J. H., Kim, H. J., Barrow, J. R.,
& Winder, W. W. (2007). Skeletal muscle and heart LKB1 deficiency
causes decreased voluntary running and reduced muscle mitochondrial
marker enzyme expression in mice. Am J Physiol Endocrinol Metab,
292 (1), E196-202. doi:10.1152/ajpendo.00366.2006
UniProt, C. (2012). Reorganizing the protein space at the Universal
Protein Resource (UniProt). Nucleic Acids Res, 40 (Database
issue), D71-75. doi:10.1093/nar/gkr981
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A.,
Sakthikumar, S., . . . Earl, A. M. (2014). Pilon: an integrated tool for
comprehensive microbial variant detection and genome assembly
improvement. PLoS One, 9 (11), e112963.
doi:10.1371/journal.pone.0112963
Woollard, P. (1971). Differential mortality of Antechinus
stuartii (Macleay): nitrogen balance and somatic changes.Australian Journal of Zoology, 19 (4), 347-353.
Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood.Mol Biol Evol, 24 (8), 1586-1591. doi:10.1093/molbev/msm088