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  • 1
    Electronic Resource
    Electronic Resource
    Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 307-322 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Mammalian phylogeny — Mitochondrial proteins — Trees of individual proteins — Maximum-likelihood method — ND1 — Convergent evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006389
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  • 2
    Electronic Resource
    Electronic Resource
    The evolution of protamine P1 genes in dasyurid marsupials (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 549-555 
    Details
    ISSN: 1432-1432
    Keywords: Dasyurid marsupials ; Protamine ; Molecular phylogeny ; Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report the complete DNA sequences of the protamine P1 gene and flanking regions for 13 species of the marsupial family Dasyuridae. The structure of the protamine locus is conserved in dasyurids and consists of two exons (of lengths 142–151 and 47 bp) separated by an intron (208–240 bp). A key feature of the dasyund intron is a 38–40 by duplication found in all species examined to date. This duplication apparently predates the radiation of modern dasyurid lineages and may be homologous to a similar feature in the marsupial mole (Notoryctes). Sequences from a species of Planigale demonstrate that this genus is unique among marsupials in possessing cysteine residues in its protamine P1 molecules. Cysteines may provide enhanced chemical stability for condensed sperm nuclei, a physiological feature that would converge on the common eutherian pattern. Phylogenetic analysis of the protamine genes yields a tree that is largely congruent with previous molecular systematic studies in two areas: (1) There are three main dasyurid lineages corresponding to the Sminthopsinae, Dasyurinae, and Phascogalinae; (2) Dasyurinae and Phascogalinae are sister groups. This study is the first estimate of dasyurid relationships based on a nuclear DNA sequence.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00175812
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  • 3
    Electronic Resource
    Electronic Resource
    Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation (1994)
    Springer
    Journal of mammalian evolution 2 (1994), S. 85-115 
    Details
    ISSN: 1573-7055
    Keywords: molecular systematics ; marsupials ; phylogeny ; 12S ribosomal RNA ; mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Part of the mitochondrial 12S ribosomal RNA gene was amplified and sequenced for 26 marsupials. Multiple alignments for these sequences as well as seven additional sequences taken from GenBank were obtained using CLUSTAL. PAUP was used for phylogenetic analysis and to obtain random tree-length distributions. Analyses were performed with and without phylogenetic constraints. Our results clearly show that 12S rDNA contains phylogenetic signal at and above the ordinal level and is thus appropriate for addressing phylogenetic questions deep in the mammalian tree. Standard parsimony analyses provide some support for a clade containing diprotodontians, dasyurids,Dromiciops, andNotoryctes; transversion parsimony analysis suggests the possible inclusion of peramelids as well. Within the Diprotodontia, vombatids and phascolarctids cluster together on transversion parsimony and phalangerids may be associated with this clade. The enigmatic tarsipedids are apparently part of a clade that also contains pseudocheirids, petaurids, and acrobatids. The 12S sequences suggest that the origination of extant marsupial orders peaked 15 million years later than the equivalent taxonomic diversification of extant placental orders and may be entirely post-Cretaceous. Families of diprotodontian marsupials originated during the Eocene and early Oligocene, which is consistent with previous single-copy DNA hybridization results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01464363
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  • 4
    Electronic Resource
    Electronic Resource
    Phylogenetic Relationships Within the Genus Potorous (Marsupialia: Potoroidae) Based on Allozyme Electrophoresis and Sequence Analysis of the Cytochrome b Gene (1997)
    Springer
    Journal of mammalian evolution 4 (1997), S. 147-161 
    Details
    ISSN: 1573-7055
    Keywords: Gilbert's potoroo ; Potorous ; allozyme electrophoresis ; cytochrome b ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Controversy over the taxonomic designations within the genus Potorous has highlighted problems associated with using only morphological data. The recent rediscovery of Gilbert's Potoroo has allowed us to reexamine the relationship of this species to other extant potoroos. Phylogenetic relationships and estimated divergence times are presented, based on electrophoretic and cytochrome b sequence data. There was considerable concordance between the data sets. We conclude that Gilbert's Potoroo is a separate species and should be referred to by its original name, Potorous gilbertii (Gould 1841). Estimates for potoroid divergences are in line with those of Flannery (1989).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1027335907895
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  • 5
    Electronic Resource
    Electronic Resource
    Molecular Relationships of the Extinct Pig-Footed Bandicoot Chaeropus ecaudatus (Marsupialia: Perameloidea) Using 12S rRNA Sequences (1999)
    Springer
    Journal of mammalian evolution 6 (1999), S. 271-288 
    Details
    ISSN: 1573-7055
    Keywords: 12S rRNA ; pig-footed bandicoot ; Chaeropus ecaudatus ; Perameloidea ; marsupial phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The pig-footed bandicoot, Chaeropus ecaudatus, is presumed to be extinct as no specimens have been collected or seen since early this century. Usually classified as a specialized member of the family Peramelidae, there is nevertheless still some doubt as to its taxonomic affinities, because this animal is highly specialized and shows several uniquely derived characters. We report here the first attempt to determine the molecular relationships of this animal using mitochondrial 12S rRNA sequences derived from spirit-preserved museum specimens. Phylogenetic analysis shows that the sequence derived from the Chaeropus sample is clearly that of a bandicoot. Within the bandicoot clade, the pig-footed bandicoot is quite distinct from all other taxa. Divergence-time estimates from the 12S rRNA sequences suggest that Chaeropus diverged from the other bandicoot genera in the late Oligocene or early Miocene and that bandicoots diverged from other Australian families in the late Paleocene–early Eocene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1020565724799
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  • 6
    Electronic Resource
    Electronic Resource
    DNA Sequence Analysis of Familial Relationships Among Dasyuromorphian Marsupials (2000)
    Springer
    Journal of mammalian evolution 7 (2000), S. 95-108 
    Details
    ISSN: 1573-7055
    Keywords: phylogeny ; cytochrome b ; 12S rRNA ; protamine P1 ; partitioning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Although modern morphological and molecular analyses support the monophyly of the Australasian marsupial order Dasyuromorphia, there is much less certainty about relationships among its constituent families (Dasyuridae, Myrmecobiidae, and Thylacinidae). While most authors regard Dasyuridae as monophyletic, a few have suggested that thylacines, numbats, or both have their closest relatives among dasyurids. Recent morphocladistic studies have identified several basicranial characters as putative synapomorphies of dasyurids, but no features that clearly implicate thylacinids, myrmecobiids, or both, as the sister group of Dasyuridae. Only two previous DNA studies have included both thylacine and numbat sequences along with dasyurids, and neither provided strong resolution of interfamilial relationships. In this study, we report a more thorough analytical treatment of complete cytochrome b, 12S rRNA, and protamine P1 gene sequences from dasyuromorphians than has heretofore been attempted. Our results concur with previous morphological studies in showing that Dasyuridae is monophyletic and with immunological findings that thylacinids and dasyurids are sister groups, apart from myrmecobiids. However, the level of support for nodes is highly dependent on the method of phylogenetic analysis employed. Our results also suggest that partitioning of sequence data sets to account for substitutional heterogeneity within and among genes does not necessarily lead to a major reduction in the precision of estimated phylogenies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009454515671
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  • 7
    Electronic Resource
    Electronic Resource
    Phylogenetic relationships within the class mammalia: A study using mitochondrial 12S RNA sequences (1994)
    Springer
    Journal of mammalian evolution 2 (1994), S. 3-23 
    Details
    ISSN: 1573-7055
    Keywords: 12S rRNA ; marsupials ; molecular evolution ; monotremes ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The interrelationships of the three mammalian groups, Monotremata, Marsupialia, and Eutheria, have been studied using DNA sequences from the mitochondrial 12S ribosomal RNA gene. The results suggest that the monotremes diverged from the living therians only shortly before eutherians and marsupials separated from each other, although there is some evidence for a slowdown in rate of base change in the monotreme lineage. Whtin the Monotremata, the two extant species of tachyglossids show a very close genetic relationship and the data suggest a very recent divergence. We have also confirmed that the Patagonian Monito del Monte,Dromiciops australis, is more closely related to the australidephian marsupials than it is to other South American species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01464347
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  • 8
    Electronic Resource
    Electronic Resource
    Phylogenetic structure of the marsupial family dasyuridae based on cytochromeb DNA sequences (1994)
    Springer
    Journal of mammalian evolution 2 (1994), S. 25-35 
    Details
    ISSN: 1573-7055
    Keywords: Dasyuridae ; cytochromeb ; marsupial phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Archer provided the most recent and comprehensive suprageneric classification of dasyurid marsupials. Five extant subfamilies, two with constituent tribes, were recognized on the basis of morphological, serological, and allozyme data. Phylogenetic relationships among these groups, however, were totally unresolved. Subsequent molecular studies suggested that the endemic New Guinean subfamilies Muricinae and Phascolosoricinae are parts of larger Australian clades. Our objective in this study was to test the monophyly of Archer's seven groups and estimate relationships among them using DNA sequences from the mitochondrial cytochromeb (cyt-b) gene. We report 657 bp ofcyt-b from 32 dasyuroid species. Phylogenetic analysis of these data leads to the following conclusions: (1) muricines form a clade within Phascogalinae that includes endemic New GuineanAntechinus species; (2) the two genera of Phascolosoricinae are part of a more inclusive Dasyurinae; (3) Sminthopsinae is monophyletic, but the tribes Sminthopsini and Planigalini are not; and (4) the dasyurine tribes Dasyurini and Parantechini are probably not monophyletic. Relationships among Sminthopsinae, Dasyurinae (including phascolosoricines), and Phascogalinae (including muricines) remain unresolved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01464348
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  • 9
    Electronic Resource
    Electronic Resource
    Phylogenetic analysis of cytochromeb sequences in the dasyurid marsupial subfamily phascogalinae: Systematics and the evolution of reproductive strategies (1996)
    Springer
    Journal of mammalian evolution 3 (1996), S. 81-91 
    Details
    ISSN: 1573-7055
    Keywords: dasyurids ; Phascogalinae ; Muricinae ; cytochromeb ; molecular phylogeny ; reproductive strategies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report DNA sequence variation in 861 bp of the mitochondrial cytochromeb gene from 10 species of the dasyurid marsupial subfamily Phascogalinae (including the New Guinean genusMurexia) and an outgroup planigale (Planigale ingrami). Phylogenetic analyses of these sequences indicate that (1) the subfamily consists of three major clades corresponding to (a)Phascogale, (b) AustralianAntechinus, and (c) New Guinean “Antechinus” andMurexia; (2) “Antechinus” habbema constitutes the earliest branch of the New Guinean clade; and (3); “Antechinus” melanurus and “A.” naso are sister species within the New Guinean clade. Among Australian antechnuses,A. stuartii andA. swainsonii are more closely related to each other than either is toA. flavipes, a result that is seemingly at odds with all previous systematic studies. Although resolution is limited, it appears thatAntechnius andMurexia species form a clade to the exclusion ofPhascogale. This relationship suggests that male semelparity is not a strong synapomorphy for Australian antechinuses and phascogales, despite its apparent physiological similarity in the two groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01454254
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  • 10
    Electronic Resource
    Electronic Resource
    Reconstructing the Evolutionary Radiation of Dasyurine Marsupials with Cytochrome b, 12S rRNA, and Protamine P1 Gene Trees (1997)
    Springer
    Journal of mammalian evolution 4 (1997), S. 217-236 
    Details
    ISSN: 1573-7055
    Keywords: Dasyuridae ; cytochrome b ; 12S rRNA ; protamine P1 ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report complete sequences of the cytochrome b, 12S rRNA, and protamine P1 genes from 18 of the 21 extant species of dasyurine marsupials (family Dasyuridae). Partial sequences are included for Pseudantechinus ningbing, but no data are available for Ps. mimulus or Phascolosorex doriae. Phylogenetic analyses of these sequences yield compatible gene trees with limited resolution. Simultaneous parsimony analysis of all three genes suggests the following: (a) a basal polytomy of eight lineages; (b) a sister-group relationship between “phascolosoricine” genera (Neophascogale and Phascolosorex, which are monophyletic) and Dasyums + Sarcophilus; (c) monophyly of Dasyurus viverrinus, D. albopunctatus, D. geoffroii, and D. spartacus apart from other quolls and Sarcophilus; and (d) sister-pairing of D. geoffroii and D. spartacus Previous attempts at unraveling the phylogenetic history of dasyurines have produced strikingly inconsistent results, due in part to differences in character systems examined, interpretations of character homology and independence, and analytical methods employed. We provide some evidence that the basal polytomy is the result of rapid cladogenesis and suggest that this episode of dasyurine evolution is temporally correlated with the onset of aridification following the New Guinean uplift of 15 million years ago.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1027349725642
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