Phylogeography of the Komodo monitor Varanus komodoensis (Reptilia: Varanidae) inferred from mitochondrial DNA Control Region I and the implications for in situ management plans [Elektronische Ressource] / Evy Ayu Arida

Evy Ayu Arida

Informations

• Publié par: rheinische_friedrich-wilhelms-universitat_bonn
• Publié le: 01 janvier 2011
• Nombre de lectures: 41
• Langue: English
• Poids de l'ouvrage: 2 Mo

Extrait

Phylogeography of the Komodo monitor
Varanus komodoensis (Reptilia: Varanidae)
inferred from mitochondrial DNA Control Region I
and the implications for in situ management plans






Doctoral thesis

Dissertation



zur Erlangung der Doktorwürde (Dr. rer. nat.)

der

Mathematisch-Naturwissenchaftlichen Fakultät

der

Rheinischen Friedrich-Wilhelms-Universität Bonn






vorgelegt von

Evy Ayu Arida

aus

Jogjakarta in Indonesien




Bonn, im Januar 2011















































Gedruckt mit Unterstützung des Deutschen Akademischen Austauschdienstes
Angefertig mit der Genehmigung von
Mathematisch-Wissenschaftlichen Fakultät der
Rheinischen Friedrich-Wilhelms-Universität Bonn


Die Arbeit wurde am
Zoologisches Forschunginstitut und Museum Alexander Koenig
(ZFMK), Bonn durchgeführt







































Referent: Prof. Dr. Wolfgang Böhme
Koreferent: Prof. Dr. Steven F. Perry
Tag der Mündlichen Prüfung: 10. 03. 2011
Erscheinungsjahr: 2011

i
für meine Familie:
Mum, Dad, und Daz












































ii Summary
The Komodo monitor (Varanus komodoensis) is the largest living lizard in the
world. However, it was discovered by scientists only about one hundred years ago, and
is now vulnerable to extinction in the wild. The total population size is currently
estimated to be about 2,300 individuals, while habitat degradation associated with
human activities seems to have accelerated the decrease in population size over time.
Worldwide, the wild populations of the Komodo monitor occur only in the Lesser Sunda
Islands, in southern Wallacea. Located between the Asian and Australian biogeographic
realms, the degree of endemism in Wallacea is relatively high. Given the relatively small
population size, limited distribution, and habitat degradation, a sound conservation
programme needs to be designed to protect the existing wild populations of the Komodo
monitor. To help design the programmes for conservation, I investigated the population
genetic structure across the distribution range by applying a molecular phylogeographic
approach. Eleven (11) mitochondrial DNA (mtDNA) lineages were determined in this
study, and the phylogenetic relationships among these lineages formed two major
clades. This genealogy was rooted with the Lace monitor (Varanus varius), the
Australian sister species of the Komodo monitor. Further, I assessed the extent of the
population genetic structure across the entire population using AMOVA, which is a
method in population genetics to evaluate the diversity of haplotypes in hierarchical
subdivisions. To illustrate the relationships among populations distributed across the
current range of the Komodo monitor, I used Statistical Parsimony method. Finally, I
discussed the resulting population genetic structure with regard to palaeogeographical
and palaeontological data, i.e. Pleistocene sea level fluctuations and the fossil Komodo
monitors recovered in Australasia to infer the historical processes involved in shaping
the current state of maternal population structure. The results from my study can serve
as basic data that complement the existing information on ecology, behaviour, and
population genetics, which are among the important components to devise management
programmes for conservation.
The Komodo National Park in the province of Nusa Tenggara Timur, Indonesia,
is established to protect the extant populations of the Komodo monitor. Within the
National Park, populations occur on four islands, i.e. Komodo, Rinca, Gili Motang, and
Nusa Kode. Beyond the National Park, two Nature Reserves are established on the
western and northern coasts of Flores. In particular, the population on Flores is facing
iii extinction threats from habitat degradation and loss aggravated by the poaching of the
adult’s main prey, i.e. the Timor deer (Cervus timorensis), resulting in a significantly
reduced distribution range. A population used to occur on Padar, a small island that lies
between Komodo and Rinca. Padar was completely burnt by a wild fire about thirty (30)
years ago. This population is now considered extinct. Two other small populations occur
on the small islands of Gili Motang and Nusa Kode. Because small island populations
often exhibit a lower genetic diversity, which is associated with reduced population
viability, these areas may call for prioritisation in the conservation management plan.
Therefore, an identification of areas with lower genetic diversity is one of the main foci
in this study.
To help identify priority areas for conservation, I characterised the level of
genetic diversity across the extant populations using three hundred and sixty six (366)
mtDNA Control Region I (CRI) sequences of the Komodo monitor. Based on nucleotide
substitution, sequence length, and the position of single indels, I determined eleven (11)
haplotypes. The geographic distribution of these haplotypes representing maternal
lineages is non-random. More specifically, three regions with unique maternal lineage
compositions were identified. These regions will be referred to as the Western, Central,
and Eastern regions. The Western region includes Komodo, whereas the Central region
is composed of populations distributed on the islands of Rinca, Gili Motang, and Nusa
Kode, as well as a population on the western coast of Flores. The Eastern region consists
a single population on the northern coast of Flores. An assessment of the genetic
diversity across island populations revealed a higher level of genetic diversity in larger
island populations and low level of genetic diversity in small island populations. The
number of haplotypes found on the larger islands is greater than that on the small
islands. Komodo, Rinca, and Flores harbour four (4), six (6), and four (4) haplotypes,
respectively. By contrast, only one haplotype was found on both Gili Motang and Nusa
Kode. Haplotype diversity (h) and nucleotide diversity ( π ) are also greater in larger n
island populations than those on small island populations.
For a more detailed assessment on the populations of the Komodo monitor aimed
at helping the conservation management, I investigated the phylogenetic relationships
among the eleven haplotypes as well as the geographic distribution of these maternal
lineages. Three phylogenetic methods were applied to infer the relationships among
haplotypes and the results revealed two clades, an Eastern clade and a Central-Western
iv clade. The Central-Western haplotype group clusters nine (9) lineages representing all
individuals distributed in the Central and Western regions, the otherwise Eastern. On the
other hand, the Eastern haplotype group consists two (2) lineages distributed mainly on
the northern coast of Flores. It is interesting to note, that one individual sampled from a
population on the western coast of Flores (the Central region) expressed haplotype H10,
which was otherwise found only in the Eastern region. Haplotype divergence across the
whole population seems to be relatively small, with a range of 0-2%. Pairwise p
distances among all haplotypes indicate that the Eastern haplotypes are the most
divergent. The non-random geographic distribution of these haplotypes was tested using
AMOVA. I explored two alternative hypotheses of population genetic structure.
Grouping haplotypes according to each of the five islands they were from, explained
only about 54% of the total molecular variance. Alternatively, grouping the data
according to the three regions, i.e. Western, Central, and Eastern accounted for about
90% of the total molecular variance. I generated a haplotype network using the
Statistical Parsimony method to illustrate the relationships among populations
distributed across regions. In the network, the populations in the Western and Central
regions are largely characterised by the distribution of the Western and Central
haplotypes. These two populations are connected by a hypothetical intermediate
haplotype, which is not found in this study. On the other hand, the population in the
Eastern region is characterised exclusively by the Eastern haplotypes and is separated
entirely from both the Western and Central regions. In brief, these results suggest a
strong ge