A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes:Marsupialia) based on nuclear DNA sequences

Robert W. Meredith; Michael Westerman; Mark S. Springer

doi:10.1071/zo08044

A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes:Marsupialia) based on nuclear DNA sequences

Australian Journal of Zoology ◽

10.1071/zo08044 ◽

2008 ◽

Vol 56 (6) ◽

pp. 395 ◽

Cited By ~ 76

Author(s):

Robert W. Meredith ◽

Michael Westerman ◽

Mark S. Springer

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Late Eocene ◽

Ancestral State ◽

Crown Group ◽

Protein Coding ◽

Early Oligocene ◽

Ecological Changes ◽

Living Species ◽

Divergence Estimates

Kangaroos and kin (Macropodiformes) are the most conspicuous elements of the Australasian marsupial fauna. The approximately 70 living species can be divided into three families: (1) Hypsiprymnodontidae (the musky rat kangaroo); (2) Potoroidae (potoroos and bettongs); and (3) Macropodidae (larger kangaroos, wallabies, banded hare wallaby and pademelons). Here we examine macropodiform relationships using protein-coding portions of the ApoB, BRCA1, IRBP, Rag1 and vWF genes via maximum parsimony, maximum likelihood and Bayesian methods. We estimate times of divergence using two different relaxed molecular clock methods to present a timescale for macropodiform evolution and reconstruct ancestral states for grades of dental organisation. We find robust support for a basal split between Hypsiprymnodontidae and the other macropodiforms, potoroid monophyly and macropodid monophyly, with Lagostrophus as the sister-taxon to all other macropodids. Our divergence estimates suggest that kangaroos diverged from Phalangeroidea in the early Eocene, that crown-group Macropodiformes originated in the late Eocene or early Oligocene and that the potoroid–macropodid split occurred in the late Oligocene or early Miocene followed by rapid cladogenesis within these families 5 to 15 million years ago. These divergence estimates coincide with major geological and ecological changes in Australia. Ancestral state reconstructions for grades of dental organisation suggest that the grazer grade evolved independently on two different occasions within Macropodidae.

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Revision of Oligocene ‘Paraphiomys’ and an origin for crown Thryonomyoidea (Rodentia: Hystricognathi: Phiomorpha) near the Oligocene–Miocene boundary in Africa

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz148 ◽

2019 ◽

Vol 190 (1) ◽

pp. 352-371 ◽

Cited By ~ 1

Author(s):

Hesham M Sallam ◽

Erik R Seiffert

Keyword(s):

Type Species ◽

Close Agreement ◽

New Genus ◽

Late Eocene ◽

Long Period ◽

Early Oligocene ◽

South West ◽

South West Africa ◽

Divergence Estimates ◽

First Time

Abstract ‘Paraphiomys’ simonsi is a phiomorph rodent from the early Oligocene of Egypt (~29–30 Mya) that has historically been aligned with much younger (< ~20 Mya) Miocene species of the genera Paraphiomys and Neosciuromys. Here, we use Bayesian tip-dating analysis of a 109-character morphological matrix containing 57 living and extinct ctenohystricans to test these proposed placements for ‘Paraphiomys’ simonsi. Our analyses provide support for the exclusion of ‘Paraphiomys’ simonsi from both Paraphiomys and Neosciuromys and justify the establishment of a new genus (Monamys gen. nov.) for this stem thryonomyoid. These analyses also indicate that the divergence of the extant dassie rat Petromus from the extant cane rat Thryonomys (i.e. origin of crown Thryonomyoidea) occurred ~23.7 Mya, close to the Oligocene–Miocene boundary and in close agreement with recent molecular estimates for this split. Miocene Neosciuromys, Paraulacodus, Protohummus and the type species of Paraphiomys are identified as stem thryonomyids, whereas the Namibian species Apodecter stromeri, Tufamys woodi, ‘Paraphiomys’ australis and ‘Paraphiomys’ roessneri are identified for the first time as stem petromurids, raising the possibility of a long period of endemic petromurid evolution in south-west Africa. Comparison of molecular divergence estimates with our optimal tip-dated topology suggests that stem bathyergoids are most likely to have arisen from late Eocene and early Oligocene ‘phiomyids’.

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A dated molecular perspective of eucalypt taxonomy, evolution and diversification

Australian Systematic Botany ◽

10.1071/sb18015 ◽

2019 ◽

Cited By ~ 5

Author(s):

Andrew H. Thornhill ◽

Michael D. Crisp ◽

Carsten Külheim ◽

Kristy E. Lam ◽

Leigh A. Nelson ◽

...

Keyword(s):

Dna Sequences ◽

Molecular Study ◽

Late Eocene ◽

Early Oligocene ◽

Eastern Australia ◽

Statistical Support ◽

Rapid Diversification ◽

Penalised Likelihood ◽

Inland Water Bodies ◽

First Time

The eucalypts, which include Eucalyptus, Angophora and Corymbia, are native to Australia and Malesia and include over 800 named species in a mixture of diverse and depauperate lineages. We assessed the fit of the eucalypt taxonomic classification to a phylogeny of 711 species scored for DNA sequences of plastid matK and psbA–trnH, as well as nuclear internal transcribed spacer and external transcribed spacer. Two broadly similar topologies emerge from both maximum likelihood and Bayesian analyses, showing Angophora nested within Corymbia, or Angophora sister to Corymbia. The position of certain species-poor groups on long branches fluctuated relative to the three major Eucalyptus subgenera, and positions of several closely related species within those subgenera were unstable and lacked statistical support. Most sections and series of Eucalyptus were not recovered as monophyletic. We calibrated these phylogenies against time, using penalised likelihood and constraints obtained from fossil ages. On the basis of these trees, most major eucalypt subgenera arose in the Late Eocene and Early Oligocene. All Eucalyptus clades with taxa occurring in south-eastern Australia have crown ages <20million years. Several eucalypt clades display a strong present-day geographic disjunction, although these clades did not have strong phylogenetic statistical support. In particular, the estimated age of the separation between the eudesmids (Eucalyptus subgenus Eudesmia) and monocalypts (Eucalyptus subgenus Eucalyptus) was consistent with extensive inland water bodies in the Eocene. Bayesian analysis of macroevolutionary mixture rates of net species diversification accelerated in five sections of Eucalyptus subgenus Symphyomyrtus, all beginning 2–3million years ago and associated with semi-arid habitats dominated by mallee and mallet growth forms, and with open woodlands and forests in eastern Australia. This is the first time that a calibrated molecular study has shown support for the rapid diversification of eucalypts in the recent past, most likely driven by changing climate and diverse soil geochemical conditions.

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Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding

Journal of Molecular Evolution ◽

10.1007/bf02102360 ◽

1985 ◽

Vol 21 (3) ◽

pp. 278-288 ◽

Cited By ~ 39

Author(s):

B. Edwin Blaisdell

Keyword(s):

Markov Chain ◽

Significant Influence ◽

Dna Sequences ◽

Nuclear Dna ◽

Markov Chain Analysis ◽

Protein Coding ◽

Chain Analysis

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Exceptionally preserved North American Paleogene metatherians: adaptations and discovery of a major gap in the opossum fossil record

Biology Letters ◽

10.1098/rsbl.2007.0090 ◽

2007 ◽

Vol 3 (3) ◽

pp. 318-322 ◽

Cited By ~ 43

Author(s):

Marcelo Sánchez-Villagra ◽

Sandrine Ladevèze ◽

Inés Horovitz ◽

Christine Argot ◽

Jeremy J Hooker ◽

...

Keyword(s):

Fossil Record ◽

Critical Time ◽

Sister Group ◽

Early History ◽

Crown Group ◽

White River ◽

Early Oligocene ◽

History Of ◽

New Material ◽

Divergence Estimates

A major gap in our knowledge of the evolution of marsupial mammals concerns the Paleogene of the northern continents, a critical time and place to link the early history of metatherians in Asia and North America with the more recent diversification in South America and Australia. We studied new exceptionally well-preserved partial skeletons of the Early Oligocene fossil Herpetotherium from the White River Formation in Wyoming, which allowed us to test the relationships of this taxon and examine its adaptations. Herpetotheriidae, with a fossil record extending from the Cretaceous to the Miocene, has traditionally been allied with opossums (Didelphidae) based on fragmentary material, mainly dentitions. Analysis of the new material reveals that several aspects of the cranial and postcranial anatomy, some of which suggests a terrestrial lifestyle, distinguish Herpetotherium from opossums. We found that Herpetotherium is the sister group to the crown group Marsupialia and is not a stem didelphid. Combination of the new palaeontological data with molecular divergence estimates, suggests the presence of a long undocumented gap in the fossil record of opossums extending some 45 Myr from the Early Miocene to the Cretaceous.

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Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

Annals of the Missouri Botanical Garden ◽

10.3417/2018269 ◽

2019 ◽

Vol 104 (1) ◽

pp. 33-48 ◽

Cited By ~ 4

Author(s):

Alejandro Zuluaga ◽

Martin Llano ◽

Ken Cameron

Keyword(s):

Dna Sequences ◽

Pacific Islands ◽

R Package ◽

Morphological Characters ◽

Ancestral State ◽

Seed Shape ◽

Long Distance ◽

The Pacific ◽

And Migration ◽

The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

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