A palaeontological case study for species delimitation in diverging fossil lineages

References

• Badgley C, Barry JC, Morgan ME, Nelson SV, Behrensmeyer AK, Cerling TE, Pilbeam D. 2008. Ecological changes in Miocene mammalian record show impact of prolonged climatic forcing. Proc Natl Acad Sci USA. 105(34):12145–12149. doi:10.1073/pnas.0805592105.
   PubMed Web of Science ®Google Scholar
• Banfield JD, Raftery AE. 1993. Model-based Gaussian and non-Gaussian clustering. Biometrics. 49(3):803–821. doi:10.2307/2532201.
   Web of Science ®Google Scholar
• Barry JC, Morgan ME, Flynn LJ, Pilbeam D, Behrensmeyer AK, Raza SM, Khan IA, Badgley C, Hicks J, Kelley J. 2002. Faunal and environmental change in the late Miocene Siwaliks of northern Pakistan. Paleobiol Mem. 28(sp3):1–71. doi:10.1666/0094-8373(2002)28[1:FAECIT]2.0.CO;2.
   Web of Science ®Google Scholar
• Carstens BC, Pelletier TA, Reid NM, Satler JD. 2013. How to fail at species delimitation. Mol Ecol. 22(17):4369–4383. doi:10.1111/mec.12413.
   PubMed Web of Science ®Google Scholar
• Cheema IU, Raza SM, Flynn LJ, Rajpar AR, Tomida Y. 2000. Miocene small mammals from Jalalpur, Pakistan, and their biochronologic implications. Bull Natl Sci Mus Tokyo Ser C. 26:57–77.
   Google Scholar
• Cracraft J. 1983. Species concepts and speciation analysis. Curr Ornithol. 1:159–187.
   Google Scholar
• de Queiroz K. 1998. The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In: Howard DJ, Berlocher SH, editors. Endless forms: species and speciation. Oxford: Oxford University Press; p. 57–75.
   Google Scholar
• de Queiroz K. 2005. Ernst Mayr and the modern concept of species. Proc Natl Acad Sci USA. 102(Suppl. 1):6600–6607. doi:10.1073/pnas.0502030102.
   PubMed Web of Science ®Google Scholar
• de Queiroz K. 2007. Species concepts and species delimitation. Syst Biol. 56(6):879–886. doi:10.1080/10635150701701083.
   PubMed Web of Science ®Google Scholar
• Fraley C, Raftery AE. 2002. Model-based clustering, discriminant analysis, and density estimation. J Am Stat Assoc. 97(458):611–631. doi:10.1198/016214502760047131.
   Web of Science ®Google Scholar
• Fraley C, Raftery AE. 2007. Bayesian regularization for normal mixture estimation and model-based clustering. J Classif. 24(2):155–181. doi:10.1007/s00357-007-0004-5.
   Web of Science ®Google Scholar
• Fraley C, Raftery AE, Murphy TB, Scrucca L. 2012. mclust version 4 for R: normal mixture modeling for model-based clustering, classification, and density estimation. Seattle, WA: Department of Statistics, University of Washington. Technical Report no. 597.
   Google Scholar
• Freudenthal M, Martín-Suárez E. 2013. Estimating body mass of fossil rodents. Scr Geol. 145:1–130.
   Google Scholar
• Jacobs LL. 1977. A new genus of murid rodent from the Miocene of Pakistan and comments on the origin of the Muridae. Paleobios. 25:1–11.
   Google Scholar
• Jacobs LL. 1978. Fossil rodents (Rhizomyidae and Muridae) from Neogene Siwalik deposits, Pakistan. Mus North Arizona Press Bull Ser. 52:1–103.
   Google Scholar
• Jacobs LL, Downs WR. 1994. The evolution of murine rodents in Asia. In: Tomida Y, Li C, Setoguchi T, editors. Rodent and Lagomorph families of Asian origins and diversification. Vol. 8. Tokyo: National Science Museum Monographs; p. 149–156.
   Google Scholar
• Jacobs LL, Flynn LJ. 2005. Of Mice…again: the Siwalik rodent record, murine distribution, and molecular clocks. In: Lieberman DE, Smith RJ, Keller J, editors. Interpreting the past: essays on human, primate, and mammal evolution in honor of David Pilbeam. Leiden: Brill Academic Publishers; p. 63–80.
   Google Scholar
• Jacobs LL, Flynn LJ, Downs WR. 1989. Neogene rodents of southern Asia. In: Black CC, Dawson MR, editors. Papers on fossil rodents in honor of Albert Elmer Wood. Los Angeles, CA: Natural History Museum of Los Angeles County, Science Series, Vol. 33. p. 157–177.
   Google Scholar
• Kimura Y, Jacobs LL, Cerling TE, Uno KT, Ferguson KM, Flynn LJ, Patnaik R, Viriot L. 2013. Fossil mice and rats show isotopic evidence of niche partitioning and change in dental ecomorphology related to dietary shift in Late Miocene of Pakistan. PLoS ONE. 8(8):e69308. doi:10.1371/journal.pone.0069308.
   PubMedGoogle Scholar
• Kimura Y, Jacobs LL, Flynn LJ, Butler RJ. 2013. Lineage-specific responses of tooth shape in murine rodents (Murinae, Rodentia) to late Miocene dietary change in the Siwaliks of Pakistan. PLoS ONE. 8(10):e76070. doi:10.1371/journal.pone.0076070.
   Google Scholar
• Klingenberg CP. 2011. MorphoJ: an integrated software package for geometric morphometrics. Mol Ecol Resour. 11(2):353–357. doi:10.1111/j.1755-0998.2010.02924.x.
   PubMed Web of Science ®Google Scholar
• Mayr E. 1942. Systematics and the origin of species. New York, NY: Columbia University Press.
   Google Scholar
• Mein P, Martín-Suárez E, Agustí J. 1993. Progonomys Schaub, 1938 and Huerzelerimys gen. nov. (Rodentia); their evolution in Western Europe. Scr Geol. 103:41–63.
   Google Scholar
• Quade J, Cerling TE. 1995. Expansion of C4 grasses in the Late Miocene of northern Pakistan: evidence from stable isotopes in paleosols. Palaeogeogr Palaeoclimatol Palaeoecol. 115(1–4):91–116. doi:10.1016/0031-0182(94)00108-K.
   Web of Science ®Google Scholar
• Simpson GG. 1961. Principles of animal taxonomy. New York, NY: Columbia University Press.
   Google Scholar
• Sokal RR, Crovello TJ. 1970. The biological species concept: A critical evaluation. Am Nat. 104(936):127–153. doi:10.1086/282646.
   Web of Science ®Google Scholar
• van Dam JA. 1997. The small mammals from the Upper Miocene of the Teruel-Alfambra region (Spain): paleobiology and paleoclimatic reconstructions. Geol Ultraiectina. 156:1–204.
   Google Scholar
• van de Weerd A. 1976. Rodent faunas of the Mio-Pliocene continental sediments of the Teruel-Alfambra region, Spain. Utrecht Miocropaleontol Bull Spec Publ. 2:1–217.
   Google Scholar
• van Valen L. 1976. Ecological species, multispecies, and oaks. Taxon. 25(2/3):233–239. doi:10.2307/1219444.
   Web of Science ®Google Scholar
• Wessels W. 2009. Miocene rodent evolution and migration: Muroidea from Pakistan. Turkey and North Africa. Geol Ultraiectina. 307:1–290.
   Google Scholar
• Wiens JJ, Servedio MR. 2000. Species delimitation in systematics: inferring diagnostic differences between species. Proc R Soc Ser B. 267(1444):631–636. doi:10.1098/rspb.2000.1049.
   PubMed Web of Science ®Google Scholar
• Wiley EO. 1978. The evolutionary species concept reconsidered. Syst Zool. 27(1):17–26. doi:10.2307/2412809.
   Google Scholar
• Wu C-I. 2001. The genic view of the process of speciation. J Evol Biol. 14(6):851–865. doi:10.1046/j.1420-9101.2001.00335.x.
   Web of Science ®Google Scholar