Date of Award


Degree Type


Degree Name

Master of Science (MS)




Using phylogenetic and phylogeographic tools to uncover hidden diversity within the genus Newtonia in Madagascar

Madagascar is known for its rich biodiversity and high level of endemic species that are found nowhere else. Cryptic diversification, defined as genetically and evolutionarily distinct species that are hard to detect because they are morphologically indistinguishable from their closest relatives, has been hypothesized to occur in many groups on Madagascar. Currently it is unclear to what extent this phenomenon occurs in birds because only a few studies have been conducted. My study examined the phylogenetic and phylogeographic patterns within a songbird genus, Newtonia, that is endemic to Madagascar. This genus includes four species: N. amphichroa, N. brunneicauda, N. archboldi, and N. fanovanae. The objective of my study was to determine the following: 1. What are the phylogenetic relationships among the species of Newtonia? 2. Is there phylogeographic structure to indicate cryptic differentiation or recent speciation within Newtonia species? 3. If there is evidence of differentiation, are lineages diverging due to habitat type or geography? 4. Are there misidentified specimens or hybrids in certain geographic areas or elevations? I used DNA sequences to examine the evolutionary relationships and diversification patterns among and within the Newtonia species. I conducted a phylogenetic analysis using two-mitochondrial loci, ND3 and CYTB, and three nuclear loci, GAPDH, FIB5, MUSK. The phylogenetic

analysis showed strong support for monophyly among the three Newtonia species. I examined geographic structure within two widespread species to determine the potential for cryptic species. My study found that N. amphichroa is divided into two deeply divergent clades associated with distinct regions in the eastern humid forest. The two major clades of N. amphichroa split 1.25 MYA, indicating a deep split within this population showing that they have been separated for quite some time and on the order of other sister species pairs. Within Newtonia, N. archboldi separated from N. amphichroa and N. brunneicauda roughly 7.36 MYA and N. amphichroa separated from N. brunneicauda 4.38 MYA. Both the species delimitation analysis and the molecular clock analyses showed that the two divergent clades of N. amphichroa are distinct species that have been separated long enough to be considered different species. However, N. brunneicauda did not show any geographic structure and no genetically distinct lineages to indicate segregation within distinct areas. I further examined the issue of misidentifications - some sequences from individuals identified in the field as N. brunneicauda consistently grouped within the N. amphichroa clade and vice versa in the phylogenetic analysis. I was able to rule out lab error by repeating extractions and sequencing. I then examined museum specimens of these species in a comparative series, and found that although the individuals of the two species are similar to one another, there are some features that clearly separate these species. Therefore, careful examination of plumage indicated that these individuals were misidentified in the field. My study is an important step in better understanding the phylogenetic relationships and the phylogeographic patterns of endemic birds of Madagascar in order to uncover hidden diversity.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.

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