Sciurid phylogeny and the evolution of African ground squirrels

1. Sciurid phylogenyand the evolution ofAfrican ground squirrels Matthew D. HerronUniversity of Central Florida Department of Biology

2. Seminar outline • Part 1: Sciurid phylogeny • Higher level evolutionary relationships • Relationships within the tribe Marmotini • Taxonomy vs. phylogeny • Part 2: Evolution of African ground squirrels • Evolutionary relationships within the tribe Xerini • Phylogeography of Xerus inauris

3. Sciurus carolinensis Sciurus niger Rocky Glaucomys volans

4. Family Sciuridae(Mammalia: Rodentia) • Tree squirrels – Sciurus, Microsciurus, Tamiasciurus • Flying squirrels – Glaucomys, Pteromys • Chipmunks – Tamias • Groundsquirrels – Spermophilus, Ammospermophilus • Prairie dogs – Cynomys • Marmots - Marmota • African ground squirrels – Xerus

5. Family Sciuridae • Widespread – all continents except Australia & Antarctica • Conspicuous – large, mostly diurnal • Phylogeny poorly known

6. Family Sciuridae • Wide range of ecological, behavioral and life history traits • Terrestrial, fossorial, arboreal • Habitats from tundra to desert • Solitary to highly social • Ideal subjects for studies of character evolution • Several comparative studies of behavioral and life history traits limited by • Phylogenies based on limited taxonomic sampling • Taxonomy, rather than phylogeny, used as a basis for comparison

7. Objectives • To develop hypotheses of the evolutionary history of the family Sciuridae • Reconstruct the evolutionary history (phylogeny) of the group • Compare current taxonomy with proposed phylogeny • A robust phylogeny with extensive taxon sampling will facilitate analyses of character evolution

8. Strategy • Sequenced the mitochondrial cytochrome b gene • 1140 base pairs • Widely used for phylogenetic analyses • Large number of sequences available

9. Methods • Extract DNA from hair and tissue samples using phenol/chloroform • PCR and sequence mt cyt-b gene(1140 bp)

10. Taxon sampling • Available sequences were downloaded from GenBank • Two novel sequences (Xerus inauris, X. rutilus) were generated for this study • Taxon sampling: • 114 species in 21 genera • Multiple individuals included when available • Multiple named subspecies included when available • Total of 169 OTUs

11. Analyses • Sequences were aligned in GeneDoc • Maximum parsimony analyses in PAUP* • Smallest number of mutational steps • Nodal support assessed with 300 bootstrap pseudoreplicates (BS) • Bayesian analyses in MrBayes • Model-based approach • Nodal support assessed with Bayesian posterior probabilities (BPP)

12. Results ofphylogenetic analyses

13. BPP BS (* = <50%) Outgroups 99 Sciurillus Xerini * 93 Callosciurus * Tamiasciurus 98 Sciurus 60 * * Flying squirrels Results: Bayesian phylogram for the Sciuridae 70 99 * * Tamiini 99 76 100 100 Marmotini 10 Changes

14. Differences among studies Sciurillus Sciurillus Sciurillus Sciurini/ Pteromyinae Sciurini/ Pteromyinae Xerini Xerini Callosciurini Xerini Sciurini/ Pteromyinae Callosciurini Callosciurini Mercer & Roth 2003 2659 nuclear & mt bp 54 species in 50 genera Steppan, et al. in press 4500 nuclear bp 34 species in 24 genera Herron, et al. in press 1140 mt bp 114 species in 21 genera

15. BPP BS (* = <50%) Outgroups 99 Sciurillus Xerini * 93 Callosciurus * Tamiasciurus 98 Sciurus 60 * * Flying squirrels Results: Bayesian phylogram for the Sciuridae 70 99 * * Tamiini 99 76 100 100 Marmotini 10 Changes

16. BPP BS (* = <50%) 100 Tamiasciurus 100 100 78 Sciurus 100 92 Microsciurus Pteromys 99 Petaurista * Belomys Hylopetes Petinomys Glaucomys 10 Changes Tree squirrels & flying squirrels

17. BPP BS (* = <50%) Eutamias 72 Tamias * 100 100 Neotamias Chipmunks 10 Changes

18. Summary • Flying squirrels are monophyletic, sister to tree squirrels • Sciurillus phylogenetic position does not agree with taxonomy • Sciurus is paraphyletic with respect to Microsciurus

19. BPP BS (* = <50%) Outgroups 99 Sciurillus Xerini * 93 Callosciurus * Tamiasciurus 98 Sciurus 60 * * Flying squirrels Results: Bayesian phylogram for the Sciuridae 70 99 * * Tamiini 99 76 100 100 Marmotini 10 Changes

20. Tribe Marmotini Spermophilus Marmota Ammospermophilus Cynomys

21. Tribe Marmotini • >60 species in 4 genera • Holarctic distribution: • Europe east of the Alps • Asia • North America

22. BPP BS 90 Ammospermophilus 85 100 Cynomys 100 100 100 Marmota 10 Changes

23. BPP BS Ground Squirrels 100 Poliocitellus 100 100 Xerospermophilus 87 100 Callospermophilus 88 10 Changes

24. 100 BPP BS 60 Otospermophilus Ground Squirrels 99 Ammospermophilus 52 100 Otospermophilus 100 92 88 Callospermophilus 10 Changes

25. BPP BS Ground Squirrels New World 99 90 Spermophilus + S. undulatus 100 92 Old World Spermophilus 10 Changes

26. BPP BS (* = <50%) Ground Squirrels 100 Ictidomys 98 100 54 94 57 100 Ictidomys 100 10 Changes

27. Summary - Marmotini • Cynomys, Marmota, Ammospermophilus monophyletic • Spermophilus paraphyletic w/ respect to • Ammospermophilus • Cynomys • Marmota • Diphyletic Spermophilus subgenera: • Spermophilus • Ictidomys • Otospermophilus

28. Conclusions – Part 1 • Sciurid taxonomy has problems at all levels: • Subfamily designations are not phylogenetically informative • Sciurillus does not belong in tribe Sciurini • Sciurus is paraphyletic with respect to Microsciurus • Spermophilus is polyphyletic • Genus, subgenera and even some species have multiple origins • Elevating subgenera will not resolve

29. Xerini - differences among studies Sciurillus Sciurillus Sciurillus Sciurini/ Pteromyinae Sciurini/ Pteromyinae Xerini Xerini Callosciurini Xerini Sciurini/ Pteromyinae Callosciurini Callosciurini Mercer & Roth 2003 Herron, et al. in press Steppan, et al. in press

30. Atlantoxerus Spermophilopsis X. erythropus X. rutilus X. princeps X. inauris

31. Xerine phylogeny – background Spermophilopsis • Intergeneric relationships based on DNA sequence data Atlantoxerus Xerus

32. Xerine phylogeny – background X. rutilus • Xerus relationships based on skull and dental morphology X. erythropus X. inauris X. princeps

33. Are X. inauris & X. princeps specifically distinct? Xerus inauris Xerus princeps

34. Are X. inauris & X. princeps distinct species? • Behavioral differences • X. inauris is highly social • Both male and female social groups • X. princeps is essentially asocial

35. Objectives • Infer phylogenetic hypotheses for the four recognized species of Xerus • Estimate historical biogeographic patterns leading to current distributions of Xerus species • Establish roles of gene flow and climate change in the phylogeographic history of X. inauris • Assess the validity of the specific distinction between X. inauris and X. princeps

36. Methods • Extract DNA from hair and tissue samples using phenol/chloroform • PCR and sequence mt cyt-b gene(1140 bp)

37. Taxon sampling • cyt b sequences obtained for • 3 X. erythropus • 66 X. inauris • 9 X. princeps • 2 X. rutilus • Spermophilopsis leptodactylus used as outgroup in all phylogenetic analyses

38. Analyses • Sequences were aligned in GeneDoc • Bayesian analysis in MrBayes • Nodal support assessed with Bayesian posterior probabilities • Maximum parsimony analysis in PAUP* • Nodal support assessed with 500 bootstrap pseudoreplicates

39. BPP BS Spermophilopsis leptodactylus 100 Xerus erythropus 100 90 X. rutilus 100 100 75 X. princeps 100 59 100 100 99 100 Results: Bayesian phylogram of Xerus X. inauris 5 changes

40. Biogeography of Africa • Well-known pattern of plant disjunctions between the Horn of Africa and the Cape of Good Hope • Hypothesized “arid corridor” from eastern to southern Africa • Southern Africa – climate change in the Pliocene and Pleistocene • Several wet-dry cycles • Temperature change due to glaciation

41. X. rutilus X. erythropus X. princeps X. inauris

42. Spermophilopsis leptodactylus Xerus erythropus Xerus rutilus X. princeps I Genetic structure of X. inauris & X. princeps II X. inauris I III III II

43. Methods – nested clade analysis • Haplotype network reconstructed with parsimony criterion in TCS • Similar haplotypes hierarchically nested into progressively older and larger clades • Clades tested for associations with geographic distance in GeoDis • Used to infer historical processes leading to present distributions

44. Xerus inauris nested cladogram

45. Results of NCA • Restricted gene flow with isolation by distance (IBD) inferred for older clades • IBD for a maternally inherited marker is congruent with X. inauris social system (female philopatry) • Suggests xeric conditions were widespread early in the species’ history

46. Results of NCA • Habitat fragmentation inferred for one more recent clade • Suggests interruption of continuous arid conditions • Congruent with wet-dry cycles in the Late Pliocene and Pleistocene • Southern Africa is low in elevation, so small changes in precipitation would cause large changes in vegetation

47. Biogeographic summary • Xeric conditions widespread in southern Africa early in X. inauris evolution • Xeric conditions interrupted by Plio-Pleistocene wet-dry cycles • “Arid corridor” from Horn of Africa to Cape of Good Hope lasted at least until the Early Pleistocene

48. Species status • X. inauris, X. princeps are well supported, reciprocally monophyletic clades • Highest sequence divergence within taxa (4%) is less than lowest divergence between taxa (6%) • Sympatric ranges, overlapping habitats • Suggests that reproductive isolation results from factors other than geography

49. Other differences betweenX. inauris and X. princeps • Single heterochromatic difference in one autosomal chromosome pair • Differences in thermoregulation and urine and fecal content • Minor differences in skull morphology

50. Summary • Higher-level taxonomy of squirrels needs revision • Spermophilus is polyphyletic • Sciurus paraphyletic with respect to Microsciurus • Sciurillus basal to remaining sciurids • Flying squirrels monophyletic, sister to tree squirrels