1. Systematic Relationships among Birds Hypotheses for the evolution of birds Determines how your bird guide is arranged Contentious –Morphology What to measure, convergent evolution –Fossils Missing links / sample bias Lack of soft parts –DNA How to calibrate Which and how many genes to use What species to include in analysis (outgroups especially)

2. Mayr 2014

3. Ericson 2008 Ratites and Tinamous Nightjars, owlet-nightjars, potooes, oilbird, frogmouths, hummingbirds, swifts Shorebirds, gulls, auks Pelicans, cormorants, herons, storks, cranes, rails, loons, penguins, albatrosses, cuckoos, turacos, bustards Parrots and Passerines Accipitrid diurnal raptors, osprey and secretarybird, rollers, woodpeckers, trogons, mousebirds, owls Pheasants, quails, currasows, ducks, geese, swans Heterogeneous assemblage of enigmas

4. Ericson 2008 Ratites and Tinamous Nightjars, owlet-nightjars, potooes, oilbird, frogmouths, hummingbirds, swifts Shorebirds, gulls, auks Pelicans, cormorants, herons, storks, cranes, rails, loons, penguins, albatrosses, cuckoos, turacos, bustards Parrots and Passerines Accipitrid diurnal raptors, osprey and secretarybird, rollers, woodpeckers, trogons, mousebirds, owls Pheasants, quails, currasows, ducks, geese, swans Heterogeneous assemblage of enigmas Suboscine (represented by Tyrannida) Oscine (represented by Passerida) PASSERINES Largest Order of Extant Birds

5. Fundamental Divisions Paleognathae –Primitive palate (left image shows better than Fig 3.6 in text) –Monophyly of many flightless birds Hoatzin primitive but not basal to Neognathae –Opisthocomidae in clade 6 –Galloanserae is basal and monphyletic In Rheas, Tinamous, Ostrich, Cassowaries, Emu, Kiwi, and extinct Moas and Elephant Birds the vomar bone extends back to articulate with palatines and pterygoids to separate both from the parashenoid rostrum

6. Tertiary Big Bang? (Feduccia 2003) K-T boundary (end of Cretaceous; 65 my) Volcanism, mountain building, regression of continental seas meteor in Mexico (Chicxulub crater in Yucatan) Dinosaur extinctions Theory in accordance with Fossil record

7. But Birds were Evolving in Southern Hemisphere Gondwanaland (Cracraft 2001) DNA studies suggest modern birds radiated before KT boundary Vegetation of Antarctic area was not greatly affected by impact

8. Ancestor of Passeriformes was Gondwanan; divergence began before KT Acanthisitta = New Zealand Wrens are most primitive passerine and sister to Suboscines and Oscines (songbirds) They diverged from other passerines about 82my, ancestors moved across connected Antarctic Oscine and Suboscine songbirds began to diverge about 77my (Barker et al. 2004)

9. (Ericson 2008, Ericson et al. 2006) Ratites and Tinamous Nightjars, owlet-nightjars, potooes, oilbird, frogmouths, hummingbirds, swifts Shorebirds, gulls, auks Pelicans, cormorants, herons, storks, cranes, rails, loons, penguins, albatrosses, cuckoos, turacos, bustards Parrots and Passerines Accipitrid diurnal raptors, osprey and secretarybird, rollers, woodpeckers, trogons, mousebirds, owls Pheasants, quails, currasows, ducks, geese, swans Heterogeneous assemblage of enigmas 177 mya 67 mya 68 mya 63 mya 75 mya 95 mya More Substantial Divergence Was Even Earlier

10. (Ericson et al. 2002) (Cracraft 2001)

11. So, the Real Explosion was After the KT event (Barker et al. 2004)

12. Red = Australasia Green = Africa and Eurasia Blue = North and South America Grey = ambiguous ancestral / current area (Barker et al. 2004)

13. Mayr 2014

15. Ravens

16. During the last several million years land connections (via Beringia) between New and Old Worlds waxed and waned with glaciation. Beringia was dry and offered land passage. 50ka

17. Corvids Invade Our World Tied to changes in vegetation and sea level Tertiary forests of Australia were being replaced by deserts perhaps forcing corvid ancestors (related to Birds of Paradise and Orioles) to leave Australia and head north in Oligocene and Miocene to Asia, following northward movement of tropical forests 6-8 mya in Miocene New World Jay ancestor from forests of southeast Asia, radiate in South America (first) and North America 15,000 ya – 2 mya in Pleistocene Old World Jay (Gray Jay) Nutcracker Magpie Crow Raven (from article on evolution of cats; Johnson et al. 2006; Science 311:73-77)

18. Ravens 4 clades diverging in Africa 1.7-3.8my Corvus corax ancestor diverges (closest relative is C. albus) shortly thereafter C. corax invades New World 2my and new and old world ravens begin independent evolution –Old world raven spins off Canary Island Raven 650,000 yr –New world ravens spins off Chihuahuan Raven C. corax reinvades New World 15,000 years ago

19. Complexity Revealed By Genetic Analyses Common Raven –~15,000 years ago old world ravens again invaded the new world via Beringia Holarctic and California clade of ravens now found in North America, but they are becoming more similar, not diverging as they had in past. –Giving us new insights into what constitutes a “species”

20. Fig. 1. FROM DELANEY et al. 2008---Distribution of Island and Western scrub-jays, with associated geographic trends in morphological characteristics. Species distributions are adapted from Curry et al. (2002); orange = Aphelocoma insularis, green = Californica group of Aphelocoma californica, light blue = Woodhouseii group of Aphelocoma californica, and dark blue = sumichrasti group of Aphelocoma californica. Florida Scrub-jay Scrub-jays Currently we recognize 3 species, but there are most likely 5 and maybe 6 isolation has been of paramount importance and novel selective pressures from foods eaten (oaks versus other seeds)

21. A. un. griscomi A. un. unicolor A. un. oaxacae A. un. concolor A. un. guerrerensis CITATION: McCormack, Peterson, Delaney, Knowles, in prep. Unicolor Jay (Aphelocoma unicolor)

22. The 7 Aphelocoma ultramarina traditional subspecies are given in abbreviations (A. ul. Xxx) on the map, the colors refer to the 4 groups I refer to in the text now. These could be labeled as the Central group (orange), the Eastern group (yellow), the Ultramarina group (blue), and the Wollweberi group (green). The four groups are from McCormack et al. 2008. McCormack, J. E., Peterson, A. T., Bonaccorso, E., and T. B. Smith. 2008. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Molecular Ecology 17:2505-2521. A. ul. arizonae A. ul. wollweberi A. ul. gracilis A. ul. colimae A. ul. ultramarina A. ul. potosina A. ul. couchii Mexican Jay

23. Rapid diversification of the 3 major clades Deep divergence in A. unicolor Major phylogenetic structure in Mexican jays Florida scrub-jays basal within scrub- jay complex McCormack, Peterson, Delaney, Knowles, in prep. Also could cite: Delaney et al. 2008, Auk (for scrub jays) McCormack, Peterson, Bonaccorso, and Smith 2008, Mol Ecol (for Mexican jays)

24. Timing of diversification in Aphelocoma Diversification much older than previously thought –Major lineages diverging quickly in the late Miocene –Transvolcanic Mexican jay ancient lineage –Few divergence events in the major glacial period (<0.7 mya) McCormack, Peterson, Delaney, Knowles, in prep.

25. Major division N and S of the Isthmus (6% div) Pliocene Divergences north of Isthmus potentially linked to glacial cycles –Time frame correct for when Mexico was influenced by glacial activity further north 3.5 (6.0,2.5) 2.8 (3.9,1.3) 0.9 (2.0,0.5) 0.5 (1.2,0.3), Guatemala Honduras A. un. griscomi A. un. unicolor A. un. oaxacae A. un. concolor A. un. guerrerensis McCormack, Peterson, Delaney, Knowles, in prep. Unicolor Jay

26. 4.6 (7.4,3.7) 2.8 (3.7,1.5) 1.8 (2.4,0.9) Genetic variation is not continuous & no haplotype sharing among clades Transvolcanic Mexican jays have a long and independent history New major clade in the rugged mountains of the Central Plateau Pleistocene glacial cycles likely not the cause of major diversification events (diversification preceeded the effect of glacial cycles in Mexico which were 650000 yr) West group very structured –North to south (food diffs) –East/West division in sky islands (10,000yr isolation by dispersal barriers) McCormack, Peterson, Bonaccorso, & Smith Mol Ecol 2008 A. ul. arizonae A. ul. wollweberi A. ul. gracilis A. ul. colimae A. ul. ultramarina A. ul. potosina A. ul. couchii

27. Conservation Implications Widespread, common species may actually be comprised of many, relatively rare and specialized species Areas on the fringes of a “species” distribution and therefore perhaps not all that important might be in the core of revised “species” and therefore of high significance to biodiversity –Mexican Highlands are one such area with potentially many endemic species that we currently fail to recognize

28. Bibliography Barker, F. K., Cibois, A., Schikler, P., Feinstein, J., and J. Cracraft. 2004. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Science 101:11040- 11045. Cracraft, J. 2001. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc. Royal Soc. B. 268:459-469. Delaney, K. S., Zafar, S., and R. K. Wayne. 2008. Genetic divergence and differentiation within the western scrub-jay (Aphelocoma californica). The Auk 125:839-849. Ericson, P. G. P. 2008. Current perspectives on the evolution of birds. Contributions to Zoology 77:109-116. Ericson, P.G.P., Anderson, C.L., Britton, T., Elzanowski, A., Johansson, U.S., Kallersjo, M., Ohlson, J.I., Parsons, T. J., Zuccon, D., and Mayr. Gl. 2006. Diversification of Neoaves: integratino of molecular sequence data and fossils. Biology Letters 2:543- 547. Ericson, P. G. P., Christidis, L., Cooper, A., Irestedt, M., Jackson, J., Johansson, U. S., and J. A. Norman. 2002. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc. Royal Soc. B. 269:235-241. Ericson, P. G. P., Jansén, A-L, Johansson, U. S., and J. Ekman. 2005. Inter-generic relationships of the crows, jays, magpies and allied groups (Aves:Corvidae) based on nucleotide sequence data. Journal of Avian Biology 36:222-234. Feduccia, A. 2003. ‘Big bang’ for tertiary birds? Trends in Ecol. And Evol. 18:172-176 Feldman, C. R. and K. E. Omland. 2005. Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and introl 7 of the b-fibrinogen gene in avian molecular systematics. Zoologica Scripta 34:145-156. Mayr, G. 2014. The origins of crown group birds: molecules and fossils. Palaeontology 57:231-242.McCormack, J. 2007. Evolutionary processes generating diversity in a New World jay, Aphelocoma ultramarina. PhD. Dissertation. University of California, Los Angeles. McCormack, J. E., Bowen, B. S., Smith, T. B. 2008. Integrating paleoecology and genetics of bird populations in two sky island archipelagos. BMC Biology 6:28. McCormack, J. E., Peterson, A. T., Bonaccorso, E., and T. B. Smith. 2008. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay. Molecular Ecology 17:2505-2521. Omland, K. E., C. L.Tarr, W. I Boarman, J. M. Marzluff, and R. C. Fleischer. 2000. Cryptic genetic variation and paraphyly in ravens. Proceedings of the Royal Society of London B. 267:2475-2482. Omland, K. E., J. M. Baker, and J. L. Peters. 2006. Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax). Molecular Ecology 15:795-808. Peterson, A. T. 1993. Adaptive geographic variation in bill shape of Scrub Jays (Aphelocoma coerulescens). American Naturalist 142:508-527