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    Recent Publications in Evolutionary Biology at SDSU

2010 / 2011 / 2012 / 2013 / 2014 / 2015
[Bold=EB faculty and students; *=graduate students; **=undergraduate students]

Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2015. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk: Ornithological Advances 132: 333-348. 
Hedin M, D Carlson, and F Coyle. 2015. Sky island diversification meets the multispecies coalescent – divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia. Molecular Ecology, In Press
Hedin, M. 2015. High stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas. Molecular Ecology 24, 346-361.
Leavitt DH, Starrett J, Westphal M and M Hedin. 2015. Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae). Molecular Phylogenetics & Evolution 91, 56-67.
Mason, N.A.* and K. J. Burns. 2015. The effect of habitat and body size on the evolution of vocal displays in Thraupidae (tanagers), the largest family of songbirds. Biological Journal of the Linnean Society 114: 538–551.
Schönhofer AL, C Vernesi, J Martens & M Hedin. 2015. Molecular phylogeny, biogeographic history, and evolution of cave-dwelling taxa in the European harvestmen genus Ischyropsalis (Opiliones: Dyspnoi). Journal of Arachnology 43:40-53.
Title, P. O.* and K. J. Burns. 2015. Rates of climatic niche evolution are correlated with species richness in a large and ecologically diverse radiation of songbirds. Ecology Letters 18:433-440. 

Benet-Pierce, N. and M. G. Simpson. 2014. The taxonomy of Chenopodium desiccatum and C. nitens, sp. nov. Journal of the Torrey Botanical Society 141:161-172.
Bond JE, NL Garrison, CA Hamilton, RL Godwin, M Hedin & I Agnarsson. 2014. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution. Current Biology 24, 1765-1771.
Burns, K. J., A. J. Shultz*, P. O. Title*, N. A. Mason*, F. K. Barker, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution 75: 41-77. 
Derkarabetian S, M Hedin. 2014. Integrative taxonomy and species delimitation in harvestmen: A revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea). PLoS ONE 9(8): e104982.
Fritz, J. A., J. Brancale, M. Tokita, K. J. Burns, M. B. Hawkins, A. Abzhanov, and M. P. Brenner. 2014. Shared developmental program strongly constrains beak shape diversity in songbirds. Nature Communications, 5, 3700. 
Klicka, J., F. K. Barker, K. J. Burns, S. M. Lanyon, I. J. Lovette, J. A. Chaves, R. W. Bryson. 2014. A comprehensive multilocus assessment of sparrow (Aves: Passerellidae) relationships. Molecular Phylogenetics and Evolution 77: 177-182.
Mason, N. A.*, P. O. Title*, C. Cicero, K. J. Burns, and R. C. K. Bowie. 2014. Genetic variation among western populations of the Horned Lark (Eremophila alpestris) indicates recent colonization of the Channel Islands off southern California, mainland-bound dispersal, and postglacial range shifts. The Auk: Ornithological Advances 131: 162-174. 
Mason, N. A.*, Shultz, A. J.*, and K. J. Burns. 2014. Elaborate visual and acoustic signals evolve independently in a large, phenotypically diverse radiation of songbirds. Proceedings of the Royal Society B, Biological Sciences 281 1788 20140967.
Powell, A. F. L. A., F. K. Barker, S. M. Lanyon, K. J. Burns, J. Klicka, and I. J. Lovette. 2014. A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae) 71: 94-112. 
Ripma, L.*, M. G. Simpson, and K. Hasenstab-Lehman*. 2014. Geneious! Simplified genome skimming methods for phylogenetic systematic studies: A case study in Oreocarya (Boraginaceae). Applications in Plant Sciences doi: 10.3732/apps.1400062. 
Simpson, M. G., K. Hasenstab-Lehman, and R. B. Kelley. 2014. Lectotypification of Johnstonella (Boraginaceae). Taxon 63: 930-931.
Simpson, M. G., R. Dowdy*, J. P. Rebman, R. B. Kelley, and L. M. Simpson. 2014. The recognition of two species in Eremocarya (Boraginaceae): Evidence from fornix bodies, nutlets, corolla size, and biogeography. Madroño 61: 259-275.


Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2013. Going to extremes: Contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62: 298-320. 
Carney, L. T.*, A. J. Bohonak, M. S. Edwards, and F. Alberto. in press. Genetic and experimental evidence for a mixed age, mixed origin bank of kelp microscopic stages in southern California. Ecology.
Friedman, J.*, A. J. Bohonak, and R. A. Levine. in press. When are two pieces better than one: Fitting and testing OLS and RMA regressions. Environmetrics.
Guilliams, C. M.*, B. A. Veno, M. G. Simpson, and R. B. Kelley. 2013. Pectocarya anisocarpa, a new species of Boraginaceae, and a revised key for the genus in western North America. Aliso 31: 1-13.

Hedin M, J Starrett and C Hayashi. 2013. Crossing the uncrossable: Novel trans-valley biogeographic patterns revealed in the genetic history of low dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California. Molecular Ecology, 22, 508-526.

Král J, nine others, M Hedin. 2013. Evolution of the karyotype, sex chromosomes, and meiosis in mygalomorph spiders (Araneae: Mygalomorphae). Biological Journal of the Linnean Society, In Press.

Mason, N. A.* and K. J. Burns. 2013. Molecular phylogenetics of the Neotropical Seedeaters and Seed-finches (Sporophila, Oryzoborus, Dolospingus). Ornitología Neotropical 24: 139-155.
Racicot, R.* and A. Berta. 2013. Comparative morphology of true porpoise (Cetacea: Phocoenidae) pterygoid sinuses: phylogenetic and functional implications. Journal of Morphology 274 (1): 49-62.
Ryan, P. G., L. B. Klicka*, F. K. Barker, and K. J. Burns. 2013. The origin of finches on Tristan da Cunha and Gough Island, central South Atlantic ocean. Molecular Phylogenetics and Evolution 69: 299-305.

Schönhofer AL, M McCormack, N Tsurusaki, J Martens & M Hedin. 2013. Molecular phylogeny of the harvestmen genus Sabacon (Arachnida: Opiliones: Dyspnoi) reveals multiple Eocene-Oligocene intercontinental dispersal events in the Holarctic. Molecular Phylogenetics and Evolution, 66, 303-315.

Shultz, A. J.* and K. J. Burns. 2013. Plumage evolution in relation to light environment in a novel clade of Neotropical tanagers. Molecular Phylogenetics and Evolution 66: 112-125.
Shultz, A. J.* and K. J. Burns. 2013. Plumage evolution in relation to light environment in a novel clade of Neotropical tanagers. Molecular Phylogenetics and Evolution 66: 112-125.
Silveira, M.* and M. G. Simpson. 2013. Phylogenetic systematics of the mesa mints: Pogogyne (Lamiaceae). Systematic Botany 38: 782-794.
Simovich, M. A. , Davis, K. A. and A. J. Bohonak. in press. Landscape homogenization threatens the genetic integrity of the endangered San Diego fairy shrimp Branchinecta sandiegonensis (Branchiopoda: Anostraca). Journal of Crustacean Biology.

Simpson, M. G., J. P. Rebman, K. E. Hasenstab-Lehman*, C. M. Guilliams*, and P. McConnell. 2013. Cryptantha wigginsii (Boraginaceae): A presumed extinct species rediscovered. Madroño 60(1): 24-34.

Simpson, M. G. and J. P. Rebman. 2013. A new species of Cryptantha (Boraginaceae) from the Sierra de San Pedro Mártir, Baja California, Mexico. Madroño 60(1): 35-45.

Starrett J, M Hedin, N Ayoub and CY Hayashi. 2013. Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae. Gene, In Press.

Yost, J. M., M. Bontrager, S. McCabe, D. Burton*, M. G. Simpson, K. M. Kay, and M. Ritter. In press. Phylogenetic relationships and evolution in Dudleya (Crassulaceae). Systematic Botany 38: 1096-1104.


Appeltans, W. and 100+ authors including A. Berta. 2012. The magnitude of global marine species diversity. Current Biology 22(23): 2189-2202.
Archibald, J. D. 2012. Darwin’s two competing phylogenetic trees: marsupials as ancestors or sister taxa? Archives of natural history 39:217-233.
Archibald, J. D. 2012. Dinosaur Extinction: Past and Present Perceptions. In Brett-Surman, M. K., Holtz, T. R., Farlow, J. O., and Walter, B, eds. Encyclopedia of Life Sciences. The Complete Dinosaur, Second Edition.  Bloomington: Indiana Press, pp. 1027-1038.
Archibald, J. D. 2012.  Eutheria (Placental Mammals).  In Encyclopedia of Life Sciences. London, Macmillan Publishers Ltd, Nature Publishing Group, www.elsnet, p. 1-4.
Archibald, J. D., and Averianov, A. O. 2012. Phylogenetic analysis, taxonomic revision, and dental ontogeny of the Cretaceous Zhelestidae (Mammalia: Eutheria). Zoological Journal of the Linnean Society 164:361-426.
Barroso, C.*, T.W. Cranford, and A. Berta. 2012. Shape analysis of odontocete mandibles: functional and evolutionary implications. Journal of Morphology 273:1021-1030.
Berta, A. 2012. Return to the Sea: the Life and Evolutionary Times of Marine Mammals, Univ. California Press, Berkeley, CA. 224 pp.
Bohonak, A. J. and E. T. Bauder. 2011. Accuracy of a hydrogeomorphic guidebook for functional assessment of vernal pools in Southern California. Pages 131-144 in D. Alexander, and R. Schlising, editors. Research and Recovery in Vernal Pool Landscapes. Studies from the Herbarium, Number 16. California State University, Chico. CA.
Burns, K. J. and A. J. Shultz.* 2012. Widespread cryptic dichromatism and ultravioloet reflectance in the largest radiation of Neotropical songbirds: implications of accounting for avian vision in the study of plumage evolution. The Auk 129: 211-221.
Burns, M., M. Hedin, and J.W. Shultz. 2012. Molecular phylogeny of the leiobunine harvestmen of eastern North America (Opiliones: Sclerosomatidae: Leiobuninae). Molecular Phylogenetics and Evolution 63, 291-298.
Bond, J.E., B.E. Hendrixson, C.A. Hamilton, and M. Hedin. 2012. A reconsideration of the classification of the spider infraorder Mygalomorphae based on three nuclear genes and morphology (Arachnida: Araneae). PLoS ONE 7(6): e38753. doi:10.1371/journal.pone.0038753.
Chester, S. G. B., Sargis, E. J., Szalay, F. S., Archibald, J. D., and Averianov, A. O. 2012. Therian femora from the Late Cretaceous of Uzbekistan. Acta Palaeontologca Polonica. 57:53-64.

Dodero, M. W.* and M. G. Simpson. 2012. Dudleya crassifolia (Crassulaceae), a new species from northern Baja California, Mexico. Madroño 59(4): 223–229.

Gatesy, J., J.H. Geisler, J. Changa, C. Buell, A. Berta, R.W. Meredith, M.S. Springer, and M. R. McGowen*. 2012. A phylogenetic blueprint for a modern whale. Mol. Phylog. Evol. 66:479-506.
Hasenstab-Lehman, K. E.* and M. G. Simpson. 2012. Cat’s eyes and popcorn flowers: Phylogenetic systematics of the genus Cryptantha s.l. (Boraginaceae). Systematic Botany 37: 738–757.
Hedin M., J Starrett, S Akhter, AL Schönhofer, JW Shultz. 2012. Phylogenomic resolution of Paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data. PLoS ONE, in press.
Hedin M., N. Tsurusaki, R. Macías-Ordóñez, and  J.W. Shultz.. 2012. Molecular systematics of sclerosomatid harvestmen (Opiliones, Phalangioidea, Sclerosomatidae): geography is better than taxonomy in predicting phylogeny. Molecular Phylogenetics and Evolution 62, 224-236.
Keith R. M.*, M. Hedin. 2012. Extreme mitochondrial population subdivision in southern Appalachian paleoendemic spiders (Araneae, Hypochilidae, Hypochilus), with implications for species delimitation. Journal of Arachnology, In Press.
Liwanag, H. E. M., A. Berta, D.P. Costa, M. Aubrey and T.M. Williams. 2012. Morphological and thermal properties of mammalian insulation: the evolution of fur for aquatic living. Biological Journal of the Linnean Society, 106 (4); 926-939.
Liwanag, H. E. M., A. Berta, D.P. Costa, S.M. Budge, and T.M. Williams. 2012 Morphological and thermal properties of mammalian insulation: the evolutionary transition to blubber in pinnipeds. Biological Journal of the Linnean Society 107 (4) 774-787.
Mallarino, R., O. Campàs, J. A. Fritz, K. J. Burns, O. G. Weeks, M. P. Brenner, and A. Abzhanov. 2012. Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. Proceedings of the National Academy of Sciences 109: 16222-16227.


Archibald, J. D. 2011. Extinction and Radiation: How the Death of the Dinosaurs Lead to the Rise of the Mammals. Baltimore: Johns Hopkins University Press, 120pp.
Archibald, J. D. 2011. Gould's real contribution.  Skeptic 16:12.
Archibald, J. D., Zhang, Y., Harper, T., and Cifelli, R. L. 2011.  Protungulatum, confirmed Cretaceous occurrence of an otherwise Paleocene eutherian (placental?) mammal.  Journal of Mammalian Evolution 18:153-161.
Baldo, L., A. de Queiroz, M. Hedin, C. Hayashi, and J. Gatesy. 2011. Nuclear-mitochondrial sequences as witnesses of past interbreeding and population diversity in the jumping bristletail Mesomachilis. Molecular Biology and Evolution 28, 195-210.

Berta, A. 2011. (Review of). Carnivoran Evolution (eds. A. Goswami and A. Friscia), Cambridge University Press, Systematic Biology 60(2): 241-243.

Berta, A. and M. Churchill*. 2011. Pinniped taxonomy: review of the evidence for description of currently recognized pinniped species and subspecies. Mammal Review doi: 10.1111/j.1365-2907.2011.00193.x
Bohonak, A. J. and E. T. Bauder.  In press.  Accuracy of a hydrogeomorphic guidebook for functional assessment of vernal pools in southern California.  in D. G. Alexander and R. A. Schlising (Editors), Research and Recovery in Vernal Pool Landscapes.  Studies from the Herbarium, Number 16.  California State University, Chico. CA.
Bohonak, A. J. and A. G. Vandergast. 2011. The value of DNA sequence data for studying landscape genetics. Molecular Ecology 20: 2477-2479.
Churchill, M.*, A. Berta, and T. Deméré. 2011. The systematics of right whales (Mysticeti: Balaenidae). Marine Mammal Science doi: 10.1111/j.1748-7692.2011.00504x.
Derkarabetian, S.*, J. Ledford, and M. Hedin. 2011. Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America. Molecular Phylogenetics and Evolution 61, 844-853.
Ekdale, E., A Berta, and T. Deméré. 2011. The comparative osteology of the petrotympanic complex in extant baleen whales (Cetacea: Mysticeti). PLoS ONE 6(6): e21311.doi:10.1371/journal.pone.0021311.
Galatius, A., A. Berta,  M.S. Frandsen, R. N. P. Goodall. 2011. Interspecific variation in ontogeny and paedomorphosis among phocoenids. Jour. Morphology 272(2): 136-148.
Guilliams, C. M.*, M. G. Simpson, and J. P. Rebman. 2011. Calyptridium parryi var. martirense (Montiaceae), a new taxon endemic to the Sierra San Pedro Mártir, Baja California, Mexico. Madroño 58: 258-266.

Hedin, M. and D. Carlson**. 2011. A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, nov sp), including consideration of mitochondrial phylogeographic structuring. Zootaxa 2963, 55-68.

Johnston, C.* and A. Berta. 2011. Comparative anatomy and evolutionary history of suction feeding in cetaceans. Marine Mammal Science 27(3): 493-513.
McKenna, M.F.*, T.W. Cranford. N.D. Peyenson, and A. Berta. 2011. Comparative morphology of the odontocete melon: implications for sound production and evolutionary interpretations. Marine Mammal Science doi: 10.1111/j.1748-7692.2011.00526.x
Robles-Sikisaka, R.*, A. J. Bohonak, L. McClenaghan and A. Dhar. 2010. Genetic signature of rapid IHHNV (Infectious Hypodermal and Hematopoeitic Necrosis Virus) expansion in wild Penaeus shrimp populations. PLoS ONE 5: e11799.

Satler, J.*, J. Starrett, C. Hayashi, and M. Hedin. 2011. Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus). PLoS ONE 6(9): e25355. doi:10.1371/journal.pone.0025355.

Walsh, B.* and A. Berta.  2011. Occipital ossification of balaenopteroid mysticetes. The Anatomical Record doi: 10.002/ar.21340.
Walsh, B.* and A. Berta.  2011. Occipital ossification of balaenopteroid mysticetes. The Anatomical Record doi: 10.002/ar.21340.


Archibald, J. D., et al. 2010.  Cretaceous extinctions: Multiple causes. Science 328:973.
Averianov, A. O., Archibald, J. D., and Ekdale, E. G. 2010.  New material of the Late Cretaceous deltatheroidan mammal Sulestes and a phylogenetic reassessment of the metatherian-eutherian dichotomy.  Journal of Systematic Palaeontology 8:301-330.

Benet-Pierce, N. and M. G. Simpson. 2010. Chenopodium littoreum (Chenopodiaceae): a new goosefoot from dunes of south-central coastal California. Madroño 57: 64–72.

Chester, S. G. B., Sargis, E. J., Szalay, F. S., Archibald, J. D., and Averianov, A. O. 2010.  Mammalian distal humeri from the Late Cretaceous of Uzbekistan. Acta Palaeontologca Polonica. 55:199-211.
Derkarabetian, S.*, D. B. Steinmann, and M. Hedin. 2010. Repeated and time-correlated morphological convergence in cave-dwelling harvestmen (Opiliones, Laniatores) from montane western North America. PLoS ONE, 5(5), e10388.
Hedin, M., S. Derkarabetian*, M. McCormack*, C. Richart*, and J.W. Shultz. 2010. The phylogenetic utility of the nuclear protein-coding gene EF-1a for resolving recent divergences in Opiliones, emphasizing intron evolution. Journal of Arachnology 38: 9-20.
Hedin, M. and S.M. Thomas*. 2010. Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves. Molecular Phylogenetics and Evolution 54: 107-121.
Johnston, C.*, T. Deméré, A. Berta, J. St. Leger, and J. Yonas. 2010. Observations on the musculoskeletal anatomy of the head of a neonate gray whale (Eschrichtius robustus). Marine Mammal Science, 26(1): 186-194.
Lovette, I. J., J. L. Pérez-Emán, J. Sullivan, R. C. Banks, I. Fiorentino, S. Córdoba-Córdoba, M. Echeverry-Galvis, F. K. Barker, K. J. Burns, J. Klicka, S. M. Lanyon,  and E. Bermingham.  2010. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves).  Molecular Phylogenetics and Evolution (in press).
Sanchez, A.* and A. Berta. 2010. The comparative anatomy and evolution of the odontocete flipper. Marine Mammal Science, 26(1): 140-160.
Sedano, R. E.* and Burns, K. J. 2010. Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini). Journal of Biogeography 37: 325-343.
Snowman, C.V., K.S. Zigler, and M. Hedin. 2010. Caves as Islands: Mitochondrial phylogeography of the cave-obligate spider species Nesticus barri (Araneae: Nesticidae). Journal of Arachnology 38, 49-57.

Simpson, M. G. 2010. Plant Systematics, 2nd edition. Elsevier-Academic Press. 

Simpson, M. G., M. Silveira*, and C. M. Guilliams.* 2010. Taxonomy of Calyptridium parryi (Montiaceae). Madroño 57: 154-160.