Phylogenetics

A higher-level MRP supertree of placental mammals

by Andy Purvis

Getting to the roots of matrix representation

by Andy Purvis

Supertrees are a necessary not-so-evil: a comment on Gatesy et al

by Andy Purvis

A phylogenetic supertree of the bats (Mammalia: Chiroptera)

by Andy Purvis

A Composite Estimate of Primate Phylogeny

by Andy Purvis

Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia)

by Andy Purvis

Phylogenetic supertrees: Assembling the trees of life

by Andy Purvis

Cretaceous ichthyosaurs: dwindling diversity or the empire strikes back?

by Maria Zammit

published in 'Geosciences' 2012

Recent descriptions of new taxa and recognition of survivorship of Jurassic genera across the Jurassic–Cretaceous... more Recent descriptions of new taxa and recognition of survivorship of Jurassic genera across the Jurassic–Cretaceous boundary bring the total number of Cretaceous ichthyosaur genera to eight. Taxa currently known from the Cretaceous include Ophthalmosaurus, Caypullisaurus, Aegirosaurus, Platypterygius, Maiaspondylus, Athabascasaurus, Sveltonectes, and Acamptonectes. This review summarizes the occurrence of all Cretaceous genera. A discussion of morphological diversity demonstrates the different, though overlapping, ecological niches occupied by the different taxa, while the comparison of phylogenetic hypotheses shows the problems inherent in understanding the evolutionary relationships between Cretaceous genera. The Late Jurassic radiation indicated in the competing phylogenetic hypotheses may correlate with the opening of the Atlantic Ocean or additional dispersal routes established by the breakup of Gondwana. Inclusion of the stratigraphically oldest Platypterygius species may aid in resolving these evolutionary relationships.

What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades

by M. Caitlin Fisher-Reid

in press at BMC Evolutionary Biology

Sequential cladogenesis of the reef fish Pomacentrus moluccensis (Pomacentridae) supports the peripheral origin of marine biodiversity in the Indo-Australian archipelago

by Joshua Drew

Systematics of Malaysian woolly bats (Vespertilionidae: Kerivoula ) inferred from mitochondrial, nuclear, karyotypic. 2010. F AISAL A LI A NWARALI .J.Mammology

by M.T. Abdullah, PhD

Read the paper by Hassan & Abdullah 2011 on morphometrics of Kerivoula. Mammalian Studies

Phylogenetic Analysis of the Malaysian Rhinolopus and Hipposideros using mtDNA cytochrome b gene. PJTAS 34(2):281-294.

by M.T. Abdullah, PhD

Read Abdullah (2003)

The phylogenetic relationships among 10 species of Rhinolophus and 10 species of Hipposideros from Borneo and... more The phylogenetic relationships among 10 species of Rhinolophus and 10 species of Hipposideros from Borneo and Peninsular Malaysia were successfully inferred from the partial mitochondrial DNA (mtDNA) cytochrome (cyt) b sequences. Of the 413 nucleotide positions examined, there were 171 positions (41.4%), of which 164 positions (95.9%) were parsimoniously informative. The phylogenetic trees reconstruction using neighbour-joining (NJ), unweighted maximum parsimony (MP) and maximum likelihood (ML) methods suggest the monophyletic clustering of these families. The interspecific relationships within Rhinolophidae were completely resolved, while those within Hipposideridae were not fully resolved, as supported by the low bootstrap values. Overall, the phylogenetic analysis using partial mtDNA cyt b gene was useful to discriminate these complicated taxa and successfully revealed the misidentification of several specimens before due to their similar morphologies.

Keywords: Cytochrome b, Hipposideros, mitochondrial DNA, phylogenetics, Rhinolophus

A Predictive Model to Differentiate the Fruit Bats Cynopterus brachyotis and C. cf. brachyotis Forest (Chiroptera: Pteropodidae) from Malaysia Using Multivariate Analysis. 2012

by M.T. Abdullah, PhD

Read also Abdullah (2003)

Field discrimination of Cynopterus brachyotis and C. cf. brachyotis Forest (as designated by Francis 2008) in southern... more Field discrimination of Cynopterus brachyotis and C. cf. brachyotis Forest (as designated by Francis 2008) in southern Thailand, Peninsular Malaysia, and Borneo is problematic. These 2 forms are sympatric in this region but are confined to different habitat types: C. brachyotis inhabits open habitats, orchards, and agricultural areas, while C. cf. brachyotis Forest is confined to primary and old secondary forests. In this study, we attempted to develop prediction models to identify both C. brachyotis and C. cf. brachyotis Forest in this region based on multivariate statistics. Two predictive models were generated using a canonical discriminant function, and it was found that 5 characters can be used to accurately identify museum vouchers of C. brachyotis and C. cf. brachyotis Forest. Four characters are needed for field identification of these 2 forms of Cynopterus in southern Thailand, Peninsular Malaysia, and Borneo. A review of the current taxonomy and classification indicated that there is a need to describe the 6 existing forms of the C. brachyotis complex in the Indo-Malayan region. This will aid conservationists, field ecologists, and taxonomists in taxonomic- and conservation-related decisions about this species complex.

Malaysian fruit bats phylogeny inferred using ribosomal RNA. Ryan, J.R., K.H.G. Andy, V.K. Jayaraj, Y. Esa, A.A. Sallehin and Abdullah, M.T. 2008. Pertanika Journal of Tropical Agricultural Science 31(1):107-117. (SCOPUS-Cited Publication).

by M.T. Abdullah, PhD

Fourteen species of the Malaysian fruit bats (Pteropodidae) were used in this DNA taxonomy using 1,334bp of the 12S... more Fourteen species of the Malaysian fruit bats (Pteropodidae) were used in this DNA taxonomy using 1,334bp of the 12S ribosomal RNA (rRNA), transfer RNA (tRNA) valine and 16S rRNA gene segments. Previous studies using DNA found contradictions between morphology and molecular data in inferring the phylogeny of the fruit bats proposed by Andersen (1912). Our phylogenetic analysis using the neighbor-joining and the maximum parsimony methods did not support the monophyly of the subfamily Macroglossinae and the cynopterine group of the subfamily Pteropodinae as proposed by classical taxonomists. This is congruent with previous molecular studies. Here, we provide the first registered 12S rRNA, tRNA valine and 16S rRNA sequence records for Dyacopterus spadiceus in the GenBank database. This study represents the first attempt to infer the phylogenetic relationship of fruit bats from Malaysia using molecular methods.

A morphological analysis of Malaysian Kerivoula (Chiroptera, Vespertilionidae).

by M.T. Abdullah, PhD

Related study by Faisal Anwali Khan et al. 2010

Recent identification of new species within the genus Kerivoula from the Southeast Asian region has indicated that... more Recent identification of new species within the genus Kerivoula from the Southeast Asian region has indicated that this genus was understudied and currently underestimated in terms of its species diversity. Thus, this morphological study was carried out to record and analyse the morphological characters of available specimens of Malaysian Kerivoula from the Museum of Zoology, Universiti Malaysia Sarawak. Thirty-one external, skull and dental characters were taken and analysed using the multivariate analysis, dicriminant function analysis. As the result, six groupings of Kerivoula was identified, namely K. intermedia, K. hardwickii, K. pellucida, K. lenis and K. papillosa which were divided into two distinctive groupings of K. papillosa type large (K.
papillosa type L, hereafter) and K. papillosa type small (K. papillosa type S, hereafter). Variable dentary length was identified as the best predictor to characterize each group of Kerivoula. The
separation of the K. papillosa specimens into two separate morphotypes were characterised by their different sizes whereby the former group was larger in size compared to the latter. It is suggested that each represents an independent species even though both morphotypes occur sympatrically. The homogenising effect of the previous environmental events might have been the primary factor of the sympatric occurrence of both morphotypes. Nevertheless, further study regarding ecology, morphology and genetics should be carried out to provide a better insight regarding the cryptic population of K. papillosa in Borneo and Malaysia.

Hasan, N.H., Abdullah, M.T. 2011. Mammal Study 36: 87-97.

Biogeography and variation of the Malaysian fruit bat, Cynopterus brachyotis, in Sunda Shelf 2003

by M.T. Abdullah, PhD

Five more studies by BU, UKM & UNIMAS had tested and confirmed similar findings in this 2003 PhD study.

There are more then one species in the Malayan fruit bat, Cynopterus brachyotis, species complex based on the... more There are more then one species in the Malayan fruit bat, Cynopterus brachyotis, species complex based on the mophological and MtDNA cytochorome b analyses. The small form is found in the closed canopy forest while the larger form utilised the open habitat. There is a new species within the C. brachyotis populations yet to be described.

Complete, accurate, mammalian phylogenies aid conservation planning, but not much

by Thomas Brooks

Rodrigues, A.S.L., Grenyer, R., Baillie, J.E.M., Bininda-Emonds, O.R.P., Gittleman, J.L., Hoffmann, M., Safi, K., Schipper, J., Stuart, S.N. & Brooks, T.M. (2011) Complete, accurate, mammalian phylogenies aid conservation planning, but not much. Philosophical Transactions of the Royal Society of London B 366: 2652–2660.
DOI: 10.1098/rstb.2011.0104.

In the face of unprecedented global biodiversity loss, conservation planning must balance between refining and... more In the face of unprecedented global biodiversity loss, conservation planning must balance between refining and deepening knowledge versus acting on current information to preserve species and communities. Phylogenetic diversity (PD), a biodiversity measure that takes into account the evolutionary relationships between species, is arguably a more meaningful measure of biodiversity than species diversity, but cannot yet be applied to conservation planning for the majority of taxa for which phylogenetic trees have not yet been developed. Here, we investigate how the quality of data on the taxonomy and/or phylogeny of species affects the results of spatial conservation planning in terms of the representation of overall mammalian PD. The results show that the better the quality of the biodiversity data the better they can serve as a basis for conservation planning. However, decisions based on incomplete data are remarkably robust across different levels of degrading quality concerning the description of new species and the availability of phylogenetic information. Thus, given the level of urgency and the need for action, conservation planning can safely make use of the best available systematic data, limited as these data may be.

Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates

by Jeffrey Townsend

Monitors cross the Red Sea: The biogeographic history of Varanus yemenensis

by Daniel Portik

Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa

by Daniel Portik