Casowary defense
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My Master Thesis Defense: a Phylogeographic, Molecular Clasification of the Cassowaries (Casuariiformes: Casuaridae)
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Casowary defense
- 1. San Francisco State University In partial fulfillment of The Requirements for The Degree Master of Science In Biology: Ecology and Systematic Biology PHYLOGENETIC ANALYSIS AND PHYLOGEOGRAPHY OF THE FAMILY CASUARIIDAE (AVES: CASUARIIFORMES) Jean C. Mattos – Reaño July 2011 1
- 2. Overview of the Study • Taxonomy And Distribution • Cassowaries in the Fossil Record • Why this work is important • Questions • Materials and Methods • Phylogenetic Analysis • Results • Discussion • Acknowledgments 2
- 3. Taxonomy and Distribution The avian family Casuariidae (Aves: Casuariiformes) comprises three currently recognized species in a single genus, Casuarius and 21 subspecies (Howard and Moore 2003). Cassowaries - from the Malayan word kasuari –are distributed within the lowlands of mainland New Guinea, Queensland, Australia, and the islands of New Britain (Papua New Guinea), Aru (Papua, Indonesia), and Seram, in the Moluccas (Indonesia). 3
- 4. Northern Cassowary Casuarius unappendiculatus Blyth 1860 Distributed in the coastal lowland of Northern Papua New Guinea and the islands of Japen (Jobi) and Salawati Listed as VULNERABLE by IUCN 6 recognized subspecies 4
- 5. Southern Cassowary Casuarius casuarius Brisson 1760 Distributed in Southern New Guinea, Northeastern Australia and the Aru Islands, in lowland range. Listed as VULNERABLE by IUCN Expected to disappear from its Australian range in the next 70 years. 8 recognized subspecies 5
- 6. Mountain Cassowary Casuarius bennetti Gould 1857 Distributed in the Mountain Range of Papua New Guinea, New Britain and Jobi Island Occurrence range of 258,000 Km2 Listed as Near threatened by IUCN Seven recognized subspecies 6
- 7. Walter Rothschild described 22 Cassowary taxa between 1900 and 1937, based on only 3 characters Helmet Shape ( DIMORPHIC and high variability within populations) Color of Bare Skin (used to describe subspecies) Wattle arrangement Aberrant forms documented 7
- 8. “A majority of the forms –14 out of 22 described by Rothschild– were described using zoological garden specimens of unknown origin” Ernst Mayr, 1940 Curator of the Rothschild Ornithology Collection- AMNH 8
- 9. = Am I a Splitter? 9
- 10. Original Distributions affected by Anthropogenic Influence 10
- 11. MAIN SUBSPECIES DISTRIBUTION BREAKS FOR NORTHERN AND SOUTHERN CASSOWARIES 11
- 12. 3-5 Mya 1.5-2.5 Mya 1.5-2.5 Mya 5 Mya 5 Mya 5 Mya AGE OF PAPUA NEW GUINEA BASINS AND DISPERSAL BARRIERS 1.5 Mya 3-4 Mya 1.5 Mya 12
- 13. Presence of Cassowaries and relatives in the Fossil Record New Guinea 1) Casuarius aff. bennetti – Pleistocene in [ Plane 1967 ] 2) Casuarius aff. bennetti- 80, 000 years old [ Boles 2001, Rich et al 1988) Australia 1) Casuarius lydekkeri – Plio-Pleistocene 2) Emuarius- Oligo-Miocene 13
- 14. Why this work is important • 1) There has been no revision since Mayr’s work in 1940 • 2) There is significant phenotypic variation in the species distributed in northern and southern coasts of Papua New Guinea • 3) Traits used to describe many taxa in this group were shown to be subject of great variation within populations. • 4) There is a potential artifactual distribution due to trade of Cassowaries between native inhabitants of Papua New Guinea (Mayr 1940) 14
- 15. Questions • 1) Are the three currently recognized species well differentiated? What is the amount of genetic difference within species and between subspecies? • 2) There’s correlation between genetic difference and geographic distribution for the three recognized species? • 3) What is the approximate divergence time of the Casuarius clade? • 4) Is it possible to trace the origin of the Casuarius group to Australia or New Guinea? 15
- 16. Materials and Methods • 18 Historic DNA samples from Cassowary specimens -AMNH (NY, U.S.) • 12 Historic DNA samples from Cassowary specimens- BMNH Tring (UK) • 3 modern samples of Mountain Cassowary (C. bennetti) –University of Kansas and Andrew Mack (Carnegie Museum, Pittsburg) • Genbank sequences of Emu (Dromaius novaehollandiae), Kiwi (Apteryx haasti) and Ostrich (Struthio camelus) 16
- 17. GEOGRAPHIC DISTRIBUTION OF HISTORIC SPECIMENS Casuarius bennetti Casuarius unappendiculatus Casuarius casuarius 17
- 18. Materials and Methods • Three mitochondrial regions • 1) Cytochrome B (cyt b; 307 bp) • 2) NADH dehydrogenase subunit 2 (ND2; 251 bp) • 3) Control Region (D-loop ; 440 bp) 18
- 19. Materials and Methods Phylogenetic analysis • California Academy of Sciences Phylocluster • PAUP* and the program MODELTEST 3.7– to get the best fit model • I Used Emu (Dromaius novaehollandiae) as outgroup. • Used best fit model to perform ML tree search to obtain best fit trees and parameter estimates to assess support for particular nodes 1) parsimony bootstrap (1000 replicates) and 2) Bayesian analyses for posterior probabilities 19
- 20. CHARACTER BREAKDOWN Gene Taxa Constant Variable parsimony uninformative Variable parsimony Informative Total Characters Total 27 814 101 50 965 Cyt b 27 271 20 16 307 ND2 27 199 29 23 251 Dloop 27 344 52 11 407 20
- 21. RESULTS 21
- 22. Parsimony Analysis Strict Consensus Tree 10 most parsimonious trees Length = 183 Consistency Index= 0.869 Retention Index= 0.914 PTP Test P=0.01 22
- 23. Evolution model chosen General Time Reversible Model with Site Specific Rate by codon within gene (GTR + SSR7) Maximum Likelihood Tree Top Values: Posterior probability (>0.9) Below Values: ML Bootstrap (> 0.7) 23
- 24. CLUSTER HKY85 Minimum HKY85 Maximum C. bennetti -C. casuarius 0.0174009 0.02076008 C.bennetti -C. unappendiculatus 0.03203658 0.04329242 C. unappendiculatus-C. casuarius 0.04102542 0.04444984 C. casuarius 1 - C. casuarius 2 0.00975641 0.01083401 ESTIMATED DIVERGENCE TIMES 1.08 mya 0.5 mya Using average pairwise distances between main clades and dividing the score by the Molecular clock rate for RATITES proposed by Cooper et al 2001. 24
- 25. NORTHERN CASSOWARY CLADE AND GEOGRAPHIC DISTRIBUTION 25
- 26. SOUTHERN CASSOWARY CLADE AND GEOGRAPHICAL DISTRIBUTION 26
- 27. BACK TO THE QUESTIONS 27
- 28. Are the three currently recognized Cassowary species well differentiated? • My results agree with Mayr’s recommendation: the three main clades have high parsimony bootstrap support (>90%) and high posterior probability support (>0.9) • Average HKY85 pairwise distances are in the range of 1.8%- 2% between the subclades Southern-Mountain Cassowary • Average HKY85 pairwise distances are in the range of 3.2%- 4.4% between the clade Northern Cassowary and the clade formed by Southern-Mountain Cassowaries. • Intraspecific average HKY85 pairwise distances for the Southern Cassowary subclade are in the range of 0.9%- 1% 28
- 29. There is correlation between genetic difference and geographic distribution for the three recognized species? • Distribution of the Southern Cassowary subclade is discontinuous and doesn’t reflect the topology of the phylogenetic analysis. • Data used for the Northern Cassowary clade is insufficient to answer this question. 29
- 30. What is the approximate divergence time of the Casuarius clade? • Since the molecular clock was rejected in my analysis, I could only make a rough estimate of the divergence for the main two clades in approximately 1 million years, using a theoretical rate for ratites and the average HKY85 distances between clades (Cooper et al 2001). • However, the estimated divergence time set the arrival of Cassowary ancestors in New Guinea very posterior to the the formation of the Papua New Guinea Basins. Northern lowland basins formation is 3.5 My old in average while Southern lowland basins are 5 Million years old. 30
- 31. Is it possible to trace the origin of the Casuarius group to Australia or New Guinea? It is unknown whether the original Cassowary group similarly originated in Australia and migrated northward and eastward as a consequence of the aridification of the Australian plate, or if, alternatively, the group originated in New Guinea and migrated southwards to the forest habitat in Australia (Queensland). Since most of New Guinea was underwater at the end of the Pliocene, the New Guinean origin of the Cassowaries seems unlikely. My analysis sets the presence of the Cassowaries in Papua New Guinea as a recent event, supporting indirectly the hypothesis of the Australian origin of this group. 31
- 32. Summary and Conclusions • Phylogenetic analysis supports the separation of three main clades in the Casuarius group. • Southern and Dwarf Cassowaries evolved from a common ancestor approximately half a million years ago. • Cassowaries arrived in Papua New Guinea after the formation of the main basins. Evidence supports a potential ancestor from Australia, and a speciation event in Papua New Guinea. • Northern Cassowaries form their own clade which separated from the Southern-Mountain Cassowary Clade approximately 1 million years ago. • Further genetic work is needed to solve the geographical distribution of Southern Cassowaries on both Coasts of Papua New Guinea. 32
- 33. Acknowledgements • I would like to thank John Dumbacher, Greg Spicer, Eric Routman, Maureen Flannery, Brian Simison and Anna Sellas for their support and guidance. I also thank Frank Almeda and Lakeside Foundation, David P. Mindell and California Academy of Sciences for funding. I thank the following people: Bob Patterson for school admission, Robert Prys-Jones, Paul Sweet, David Haddrath, Andy Mack and Marcelo Stucchi for access to specimens and for information and help with graphics and maps. Also, I would like to thank Ore Carmi, Hazel Twin, Jerome Fuchs, and Zach Hannah, all my friends and teachers, and especially my wife Mapi Tudela and family, for their constant support during bad and good times. 33
Editor's Notes
- In the 19 hundreds Sir Walter Rothschild published a key for twenty taxa – eight of them newly described by him – and also provided the first distribution map for sixteen of the taxa. In 1932 he was forced to sell his avian collection to the American Museum of Natural History, which became the famous Rothschild Bird Collection.
- Ernst Mayr was appointed curator of the Rothschild Collection and Mayr noted that many specimens were captured, transported and raised in different places from their original range by local people, creating potential artifacts when interpreting geographic distribution of particular taxa. Exchange of cassowaries as ceremony gifts between tribes in New Guinea highlands is very well documented This human movement of specimens (and possibly genetic material among populations) may have profound effects on our present-day ability to study natural gene flow and taxonomic distinctions.
- In 1940 Mayr revised and updated cassowary taxonomy (focusing mainly on the works of Salvadori and Rothschild), and synonomized several taxa into earlier described species. In Mayr’s List of New Guinea Birds (1941) Forty eight previously-described taxa were coalesced into 3 species, with 13 total subspecies (4 subspecies for Casuarius casuarius, 4 subspecies for Casuarius unappendiculatus and 5 subspecies for Casuarius bennetti.)
- Mayr pointed out all the artifactual distributions of cassowaries, at least in three of the Islands that are currently included in the distribution range. Cassowaries have long been used and traded by native cultures and may have potentially been moved long distances by their carriers. Human trade in cassowaries may be a confounding factor, and ancient DNA may help. Humans first arrived in PNG around 45,000 years ago, and they do use cassowaries in trade. That said, human movements, especially within NG were probably very limited until recently. Human rests associated with cassowaries have been found in New Guinea as far as 8500 years.
- This is a schematic map of the distribution of the main subspecies for the Northern and Southern Cassowary groups. C.c. bicarunculatus (Aru Islands, NW New Guinea), C.c. tricarunculatus (Geelvink Bay, New Guinea). Also, we can notice the overlapping range of both species in Vogelkop.
- The configuration of the basins in the geological history of New Guinea is fundamental because it has influenced greatly general distribution patterns of birds (Dumbacher & Mack 2007). Here we can appreciate the average age of the formation of the Papua New Guinea basins. Northern basins were formed between 1.5 and 5 million years ago, while southern basins were formed 5 million years ago. The brackets represent dispersal barriers and number of species that are changin across the barriers in terms of subspecies distribution.
- As Ernst Mayr (1979b) points out, the current taxonomy is not definitive in any sense for the group Casuarius, but basically a working skeleton that is quite tentative due to our lack of information on geographic distribution. The extreme variation in characters used for taxonomy and poor sampling, both at single localities as well as across the range, suggest that morphology will likely not be useful. This is the main reason why a phylogenetic analysis is priority
- Subspecies chosen for this study represent the geographical range of the genus, and attempt to sample individuals from different localities throughout the major lowland basins. The objective of this work is to study the divergence of these individuals in the framework of a major phylogeographic history of lowland New Guinea during the Tertiary-Quaternary ages tracking dispersal routes and barriers for the ancestors of these species.
- I performed a Permutation Tail Probability (PTP) test on the data with 1000 replicates obtaining a p value=0.01 to confirm the phylogenetic signal in the data (Faith & Cranston 1991, Slowinski 1998). The unordered parsimony analysis produced 10 most parsimonious trees with tree length (L) = 183, a consistency index (CI) =0.869 and a Retention Index (RI) = 0.914. The strict-consensus unordered parsimony tree is shown with bootstrap values bigger than 70% at the branch nodes.
- Bayesian posterior probabilities are presented for each node over 0.9, and support is given in percentages, while numbers below the branches are bootstrap values from 100 fast-addition ML bootstrap replicates with values bigger than 70%.
- I used HKY85-corrected (Hasegawa 1985) average pairwise distance between the main clades in the ML tree – 0.03485798167– and then subtracted the average within-clade pairwise distances – 0.00553333– (Nei 1987) and finally dividing the score by the molecular clock rate of 0.0027 per million years for ratites –proposed by Cooper et al 2001–, I calculated an estimated age of 1.08 mya for the split between the Clade Casuarius unappendiculatus and the Clade formed by C. casuarius - C. bennetti
- As we can see in the diagram, there’s a partial geographical correlation in the Northern Cassowary clade, with the a subclade with distribution east of the border mountains. It’s important to mention this barrier because is the vicariant barrier for 5 species of passerine birds. However, calculated divergence times for the northern cassowaries are more recent than the formation of this barrier.
- I found this mosaic pattern in the Southern Cassowary clade. I re-sequenced and confirmed the sequences of AMNH291990 to rule out the possibility of contamination or tube mixing. I examined photos of both specimens and found no morphological characters useful for assessing the taxonomic validity of their identification – absence of wattles and color in specimen – I didn’t find any bibliographic evidence in support of natural presence of Casuarius casuarius in the northern coast o New Guinea.