Recent and Rapid Speciation with Limited Morphological Disparity in the Genus Rattus

Aitman, 2008, Progress and prospects in rat genetics: a community view, Nat. Genet., 40, 516, 10.1038/ng.147

Aplin, 2006, Ten million years of rodent evolution in Australasia: phylogenetic evidence and a speculative historical biogeography, Evolution and biogeography of Australasian vertebrates, 707

Baldwin, 1998, Age and rate of diversification of the Hawaiian silversword alliance (Compositae), Proc. Natl. Acad. Sci. USA, 95, 9402, 10.1073/pnas.95.16.9402

Baker, 1986, Speciation by monobrachial centric fusions, Proc. Natl. Acad. Sci. USA, 83, 8245, 10.1073/pnas.83.21.8245

Barraclough, 2001, Phylogenetics and speciation, Trends Ecol. Evol., 16, 391, 10.1016/S0169-5347(01)02161-9

Baverstock, 1986, Biochemical differentiation among karyotypic forms of Australian Rattus, Genetica, 71, 11, 10.1007/BF00123228

Baverstock, 1983, Chromosome evolution in Australian Rattus - G-banding and hybrid meiosis, Genetica, 60, 93, 10.1007/BF00127495

Baverstock, 1977, Chromosome evolution in Australian rodents II. The Rattus group, Chromosoma, 61, 227, 10.1007/BF00292807

Breed, 2007, Native mice and rats, 10.1071/9780643095595

Brown, 2010, When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates, Syst. Biol., 59, 145, 10.1093/sysbio/syp081

Burbrink, 2010, How does ecological opportunity influence rates of speciation, extinction, and morphological diversification in New World rat snakes (tribe Lampropeltini)?, Evolution, 64, 934, 10.1111/j.1558-5646.2009.00888.x

Bush, 1977, Rapid speciation and chromosomal evolution in mammals, Proc. Natl. Acad. Sci. USA, 74, 3942, 10.1073/pnas.74.9.3942

Byrne, 2008, Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota, Mol. Ecol., 17, 4398, 10.1111/j.1365-294X.2008.03899.x

Chaimanee, 1998, Plio-Pleistocene rodents of Thailand. Thai Stud, Biodivers, 3, 1

Dennis, 1978, Systematics and chromosomes of New Guinea Rattus, Aust. J. Zool., 26, 197, 10.1071/ZO9780197

Drummond, 2006, Relaxed phylogenetics and dating with confidence, PLoS Biol, 4, e88, 10.1371/journal.pbio.0040088

Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol., 7, 214, 10.1186/1471-2148-7-214

Edwards, 2007, High-resolution species trees without concatenation, Proc. Natl. Acad. Sci. USA, 104, 5936, 10.1073/pnas.0607004104

Edwards, 2009, Is a new and general theory of molecular systematics emerging?, Evolution, 63, 1, 10.1111/j.1558-5646.2008.00549.x

Flannery, 1995, Family Muridae, Mammals of New Guinea, 328

Flannery, 1995, Family Muridae, Mammals of the Southwest Pacific and Moluccan Islands, 151

Freed, 1987, Evolutionary ecology and radiation of Hawaiian passerine birds, Trends Ecol. Evol., 2, 196, 10.1016/0169-5347(87)90020-6

Furano, 1995, DNA “fossils” and phylogenetic analysis, J. Biol. Chem., 270, 25301, 10.1074/jbc.270.43.25301

Gavrilets, 2009, Adaptive radiation: contrasting theory with data, Science, 323, 732, 10.1126/science.1157966

Gittenberger, 1991, What about non-adaptive radiation?, Biol. J. Linn. Soc., 43, 263, 10.1111/j.1095-8312.1991.tb00598.x

Givnish, 1997, Molecular evolution and adaptive radiation

Godthelp, 1990, Pseudomys vandycki, a tertiary murid from Australia, Mem. Queensl. Mus., 28, 171

Godthelp, 1994, Zyzomys rackhami sp. nov. (Rodentia, Muridae) a rockrat from Pliocene Rackham's roost site, Riversleigh, northwestern Queensland, Mem. Queensl. Mus., 41, 329

Graham, 2004, Integrating phylogenetics and environmental niche models to explore speciation mechanisms in Dendrobatid frogs, Evolution, 58, 1781, 10.1111/j.0014-3820.2004.tb00461.x

Grant, 1986, Ecology and evolution of Darwin's finches

Harmon, 2003, Tempo and mode of evolutionary radiation in iguanian lizards, Science, 301, 961, 10.1126/science.1084786

Harmon, 2008, GEIGER: investigating evolutionary radiations, Bioinformatics, 24, 129, 10.1093/bioinformatics/btm538

Hauffe, 1998, Chromosomal heterozygosity and fertility in house mouse ( Mus musculus domesticus ) from northern Italy, Genetics, 150, 1143, 10.1093/genetics/150.3.1143

Hope, 1977, Late Pleistocene faunal remains from Seton rock shelter, Kangaroo Island, South Australia, J. Biogeogr., 4, 363, 10.2307/3038194

Hocknull, 2005, Ecological succession during the Late Cainozoic of central eastern Queensland: extinction of a diverse rainforest community, Mem. Queensl. Mus., 51, 39

Huelsenbeck, 2001, Bayesian inference of phylogeny and its impact on evolutionary biology, Science, 294, 2310, 10.1126/science.1065889

Jacob, 1999, Functional genomics and rat models, Genome Res., 9, 1013, 10.1101/gr.9.11.1013

Jacobs, 1994, The evolution of murine rodents in Asia, Rodent and lagomorph families of Asian origins and diversification, 149

Jansa, 2006, The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences, Syst. Biol., 55, 73, 10.1080/10635150500431254

King, 1993, Species evolution the role of chromosome change

Kirkpatrick, 2005, Chromosome inversions, local adaptation and speciation, Genetics, 173, 419, 10.1534/genetics.105.047985

Kozak, 2005, Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus), Evolution, 59, 2000, 10.1111/j.0014-3820.2005.tb01069.x

Kozak, 2006, Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon), Proc. R. Soc. Lond. B., 273, 539, 10.1098/rspb.2005.3326

Kozak, 2006, Does niche conservatism promote speciation? A case study in North American salamanders, Evolution, 60, 2604, 10.1111/j.0014-3820.2006.tb01893.x

LeCompte, 2008, Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily, BMC Evol. Biol., 8, 199, 10.1186/1471-2148-8-199

Lewis, 2001, A likelihood approach to estimating phylogeny from discrete morphological character data, Syst. Biol., 50, 913, 10.1080/106351501753462876

Liu, 2007, Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions, Syst. Biol., 56, 504, 10.1080/10635150701429982

Losos, 2002, Testing the hypothesis that a clade has adaptively radiated: Iguanid lizard clades as a case study, Am. Nat., 160, 147, 10.1086/341557

Lovette, 1999, Explosive speciation in the New World Dendroica warblers, Proc. R. Soc. Lond. B., 266, 1629, 10.1098/rspb.1999.0825

Lovette, 2001, Clade-specific morphological diversification and adaptive radiation in Hawaiian songbirds, Proc. R. Soc. Lond. B., 269, 37, 10.1098/rspb.2001.1789

Lundrigan, 2002, Phylogenetic relationships in the genus Mus, based on paternally, maternally, and biparentally inherited characters, Syst. Biol., 51, 410, 10.1080/10635150290069878

Maddison, 2003, MacClade 4: analysis of phylogeny and character evolution. Version 4.06

Maddison, 2006, Mesquite: a modular system for evolutionary analysis

Madsen, 2006, Size matters: extraordinary rodent abundance on an Australian tropical flood plain, Aust. Ecol., 31, 361, 10.1111/j.1442-9993.2006.01564.x

Magallon, 2001, Absolute diversification rates in angiosperm clades, Evolution, 55, 1762, 10.1111/j.0014-3820.2001.tb00826.x

Maitz, 2001, Competition and habitat use in native Australian Rattus : is competition intense, or important?, Oecologia, 128, 526, 10.1007/s004420100689

Marshall, 2010, Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees, Syst. Biol., 59, 108, 10.1093/sysbio/syp080

Marshall, 1973, Fossil vertebrate faunas from the Lake Victoria region, Mem. Natl. Mus. Vic., 34, 151, 10.24199/j.mmv.1973.34.03

Martin Suarez, 1998, Revision of the genera Parapodemus, Apodemus, Rhagamys and Rhagapodemus (Rodentia, Mammalia), Geobios, 31, 87, 10.1016/S0016-6995(98)80099-5

McDougall, 1944, An investigation of the rat pest problem in Queensland canefields: 2. species and general habits, Qld. J. Agric. Sci., 1, 48

McPeek, 2008, The ecological dynamics of clade diversification and community assembly, Am. Nat., 172, 270, 10.1086/593137

Meyer, 1993, Phylogenetic relationships and evolutionary processes in East African cichlid fishes, Trends Ecol. Evol., 8, 279, 10.1016/0169-5347(93)90255-N

Moyle, 2009, Explosive Pleistocene diversification and hemispheric expansion of a “greater speciator.”, Proc. Natl. Acad. Sci. USA, 106, 1863, 10.1073/pnas.0809861105

Musser, 2005, Superfamily Muroidea, Mammal species of the world: a taxonomic and geographic reference, 3rd ed, 894

Musser, 1991, Sulawesi rodents (Muridae: Murinae): morphological and geographical boundaries of species in the Rattus hoffmanni group and a new species from Pulau Peleng, Contributions to mammalogy in honor of Karl F. Koopman, 323

Patton, 1983, Chromosome evolution and speciation in rodents. Annu. Rev. Ecol, Syst, 14, 139

Phillimore, 2008, Density-dependent cladogenesis in birds, PLoS Biol., 6, e71, 10.1371/journal.pbio.0060071

Piper, 2007, Early Pleistocene mammals from the Nelson Bay Local Fauna, 492

Pybus, 2000, Testing macro-evolutionary models using incomplete molecular phylogenies, Proc. R. Soc. Lond. B., 267, 2267, 10.1098/rspb.2000.1278

Rabosky, 2006, LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies, Evol. Bioinform. Online, 2, 257, 10.1177/117693430600200024

Rabosky, 2009, Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils, Syst. Biol., 58, 629, 10.1093/sysbio/syp069

Rabosky, 2009, Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions, Ecol. Lett., 12, 735, 10.1111/j.1461-0248.2009.01333.x

Rambaut, 2007

Redhead, 1979, On the demography of Rattus sordidus colletti in monsoonal Australia, Aust. J. Ecol., 4, 115, 10.1111/j.1442-9993.1979.tb01202.x

Rieseberg, 2001, Chromosomal rearrangements and speciation, Trends Ecol. Evol., 16, 351, 10.1016/S0169-5347(01)02187-5

Robins, 2007, Identifying Rattus species using mitochondrial DNA, Mol. Ecol. Notes, 7, 717, 10.1111/j.1471-8286.2007.01752.x

Robins, 2008, Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes, Mol. Phylogenet. Evol., 49, 460, 10.1016/j.ympev.2008.08.001

Ronquist, 2003, MRBAYES 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180

Rowe, 2008, Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): multilocus systematics of the old endemic rodents (Muroidea: Murinae), Mol. Phylogenet. Evol., 47, 84, 10.1016/j.ympev.2008.01.001

Rüber, 2005, Rapid cladogenesis in marine fishes revisited, Evolution, 59, 1119, 10.1111/j.0014-3820.2005.tb01048.x

Rundell, 2009, Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation, Trends. Ecol. Evol., 24, 394, 10.1016/j.tree.2009.02.007

Schluter, 2000, The ecology of adaptive radiation., 10.1093/oso/9780198505235.001.0001

Schluter, 2009, Evidence for ecological speciation and its alternative, Science, 323, 737, 10.1126/science.1160006

Searle, 1993, Chromosomal hybrid zones in eutherian mammals, Hybrid sones and the evolutionary process., 309, 10.1093/oso/9780195069174.003.0012

Simpson, 1953, The major features of evolution., 10.7312/simp93764

Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446

Stanley, 1998, Macroevolution: pattern and process, 106

Steppan, 2004, Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes, Syst. Biol., 53, 533, 10.1080/10635150490468701

Swofford, 2002, PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4

Taylor, 1982, A revision of the genus Rattus (Rodentia, Muridae) in the New Guinean region, Bull. Am. Mus. Nat. Hist., 173, 177

Taylor, 1973, Systematics of native Australian Rattus (Rodentia, Muridae). Results of Archbold Expedition, 98, Bull. Amer. Mus. Nat. Hist., 150, 1

Taylor, 1977, Results of the Archbold expeditions. No. 98. Systematics of native Australian Rattus (Rodentia, Muridae), Bull. Am. Mus. Nat. Hist., 150, 1

Taylor, 1985, Altitudinal distribution and body size among New Guinean Rattus (Rodentia: Muridae), J. Mammal, 66, 353, 10.2307/1381248

Tedford, 1992, Tirari formation and contained faunas, Pliocene of Lake Eyre Basin, South Australia, Beagle (Rec. North. Territory Mus. Arts Sci.), 9, 173

Van Dyck, 2008, The Mammals of Australia, 3rd ed.

Vangegeim, 2006, Age of Vallesian lower boundary (continental Miocene of Europe), Stratigr. Geol. Correl., 14, 655, 10.1134/S0869593806060050

Verneau, 1998, Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons, Proc. Natl. Acad. Sci. USA, 95, 11284, 10.1073/pnas.95.19.11284

Wake, 2006, Problems with species: patterns and processes of species formation in salamanders, Ann. Mo. Bot. Gard., 93, 8, 10.3417/0026-6493(2006)93[8:PWSPAP]2.0.CO;2

Wakefield, 1960, Recent mammal bones in the Buchan district. Part I, Vic. Nat., 77, 164

Watts, 1981, The rodents of Australia

White, 1978, Modes of Speciation

Whitelaw, 1991, Magnetic polarity stratigraphy of Pliocene and Pleistocene fossil vertebrate localities in southeastern Australia, Geol. Soc. Am. Bull., 103, 1493, 10.1130/0016-7606(1991)103<1493:MPSOPA>2.3.CO;2

Wiens, 2004, Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species, Evolution, 58, 193, 10.1111/j.0014-3820.2004.tb01586.x

Wilgenbusch, 2004, AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylo- genetic inference

Wilson, 1974, The importance of gene rearrangements in evolution: Evidence from studies on rates of chromosomal, protein, and anatomical evolution, Proc. Natl. Acad. Sci. USA, 71, 3028, 10.1073/pnas.71.8.3028

Winkler, 2002, Neogene paleobiogeography and East African paleoenvironments: contributions from the Tugen Hills rodents and lagomorphs, J. Hum. Evol., 42, 237, 10.1006/jhev.2001.0501

Winter, 1997, Responses of non-volant mammals to Late Quaternary climatic changes in the Wet Tropics region of north-eastern Australia, Wildl. Res., 24, 493, 10.1071/WR96035

Wood, 1971, The ecology of Rattus fuscipes and Melomys cervinipes (Rodentia: Muridae) in a south-east Queensland rain-forest, Aust. J. Zool., 19, 371, 10.1071/ZO9710371

Yosida, 1980, Cytogenetics of the black rat: Karyotype evolution and species ifferentiation