Laboratories of Analytical Biology Publications from 2014 Publications listed in alphabetical order.

Andrade, SCS, H Montenegro, M Strand, M Schwartz, H Kajihara, JL Norenburg, JM Turbeville, P Sundberg, & G Giribet. 2014. Phylogenomics of ribbon worms (phylum Nemertea). Molecular Biology & Evolution. doi:10.1093/molbev/msu253

Appelhans, MS, J Wen & WL Wagner. 2014. A molecular phylogeny of Acronychia, Euodia, Melicope and relatives (Rutaceae) reveals polyphyletic genera and key innovations for species richness. Molecular Phylogenetics & Evolution: in press.

Appelhans, MS, J Wen , KR Wood, GJ Allan, EA Zimmer & WL Wagner. 2014. Molecular phylogenetic analysis of Hawaiian Rutaceae (Melicope, Platydesma & Zanthoxylum) and their different colonization patterns. Botanical Journal of the Linnean Society 174(3): 425-448. doi:10.1111/boj.12123

Baeza, JA, RT Bauer, J Okuno & M Thiel. 2014. Molecular phylogeny of hinge-beak shrimps (Decapoda: Caridea: Rhynchocinetes and Cinetorhyncus) and allies: a formal test of familiar and generic monophyly using a multilocus phylogeny. Zoological Journal of the Linnean Society: in press.

Baldwin, CC & GD Johnson. 2014. Connectivity across the Caribbean Sea: DNA barcoding and morphology unite an enigmatic fish larva from the Florida Straits with a new species of sea bass from deep reefs off Curaçao. PLoS ONE 9(5): e97661.

Baldwin, CC & DR Robertson. 2014. A new Liopropoma sea bass (Serranidae: Epinephelinae: Liopropomini) from deep reefs off Curaçao, southern Caribbean, with comments on depth distributions of western Atlantic liopropomins. Zookeys 409: 71-92.

Betancur-R R & G Ortí. 2014. Molecular evidence for the monophyly of flatfishes (Carangimorpharia: Pleuronectiformes). Molecular Phylogenetics & Evolution 73: 18-22. doi:10.1016/j.ympev.2014.01.006

Betancur-R R, G Naylor, & G Ortí. 2014. Conserved genes, sampling error, and phylogenomic inference. Systematic Biology. doi: 10.1093/sysbio/syt073

Bowen, BW, K Shanker, N Yasuda, MCMD Malay, S von der Heyden, G Paulay, LA Rocha, KA Selkoe, PH Barber, ST Williams, HA Lessios, ED Crandall, G Bernardi, CP Meyer , KE Carpenter & RJ Toonen. 2014. Phylogeography unplugged: comparative surveys in the genomic era. Bulletin of Marine Science 90(1): 13-46.

Bracken-Grissom, HD, ST Ahyong, RD Wilkinson, RM Feldmann, CE Schweitzer, JW Breinholt, M Bendall, F Palero, T-Y Chan, DL Felder, R Robles, K-H Chu, L-M Tsang, D Kim, JW Martin, & KA Crandall. 2014. The emergence of lobsters: Phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida). Systematic Biology 63(4):457-479. doi:10.1093/sysbio/syu008

Brady, SG, BL Fisher, TR Schultz, & PS Ward. 2014. The rise of the army ants: Diversification of the specialized predatory doryline ants. BMC Evolutionary Biology 14:e93. doi: 10.1186/1471-2148-14-93 Brix, S, F Leese, T Riehl & TC Kihara. 2014. A new genus and new species of Desmosomatidae Sars, 1897 (Isopoda) from the east South-Atlantic abyss described by means of integrative taxonomy. Marine Biodiversity: online 3 May 2014. DOI: 10.1007/s12526-014-0218-3.

Buffington, ML, E Perkovsky, & SG Brady . 2014. The description of Rovnoeucoila typanomorphaBuffington & Perkovsky, a new genus and species of fossil eucoiline, with observations on the asynchronous evolution of Diglyphosematini (Hymenoptera: Figitidae: Eucoilinae). Proceedings of the Entomological Society of Washington 116: 243–254. doi: 10.4289/0013-8797.116.3.243

Callicrate, T, RB Dikow, JW Thomas, JC Mullikin, ED Jarvis, RC Fleischer & NISC Comparative Sequencing Program. 2014. Genomic resources for the endangered Hawaiian honeycreepers. BMC Genomics 15: 1098. doi: 10.1186/1471-2164-15-1098.

Chen, H, S Sun, JL Norenburg, & P Sundberg. 2014. Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea). PLoS ONE 9: e85631. doi:10.1371/journal.pone.0085631

Chen, J, J Zhao, DL Erickson, N Xia & WJ Kress. 2014. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China. Molecular Ecology Resources: early view. doi: 10.1111/1755-0998.12319.

Chin, S-W, J Shaw, R Haberle, J Wen & D Potter. 2014. Diversification of almonds, peaches, plums and cherries - molecular systematics and biogeographic history of Prunus (Rosaceae). Molecular Phylogenetics & Evolution 76: 34-48. doi:10.1016/j.ympev.2014.02.024

Cialdella, AM, SM Sede, K Romaschenko, PM Peterson, RJ Soreng, FO Zuloaga & O Morrone. 2014. Phylogeny of Nassella (Stipeae, Pooideae, Poaceae) based on analyses of chloroplast and nuclear ribosomal DNA and morphology. Systematic Botany 39: 814−828. dx.doi.org/10.1600/036364414X681419

Cochran, AT, J Prado & E Schuettpelz. 2014. Tryonia, a new taenitidoid fern genus segregated from Jamesonia and Eriosorus (Pteridaceae). PhytoKeys 35: 23–43.

Connolly, SR, MA MacNeil, MJ Caley, E Cripps, M Hisano, LM Thibaut, BD Bhattacharya, L Benedetti- Cecchi, RE Brainard, A Brandt, F Bulleri, KE Ellingsen, S Kaiser, N Knowlton, I Kröncke, K Linse, E Maggi, TD O'Hara, L Plaisance, GCB Poore, SK Sarkar, KK Satpathy, U Schückel, A Williams & RS Wilson. 2014. Commonness and rarity in the marine biosphere. Proceedings of the National Academy of Sciences, USA: in press.

Conway, KW, CC Baldwin & MD White. 2014. Cryptic diversity and venom glands in western Atlantic clingfishes of the genus Acyrtus (Teleostei: Gobiesocidae). PLoS ONE 9(5): e97664.

Davies, N, D Field, L Amaral-Zettler, MS Clark, J Deck, A Drummond, DP Faith, J Geller, J Gilbert, FO Glockner, PR Hirsch, J-A Leong, CP Meyer , et al & GOs-COS. 2014. The founding charter of the Genomic Observatories Network. GigaScience 3:2.

Deeds, JR, SM Handy, F Fry Jr., H Granade, JT Williams, M Powers, R Shipp & LA Weigt. 2014. Protocol for building a reference standard sequence library for DNA-based seafood identification. Journal of AOAC International 97(6): 1-14. doi: 10.5740/jaoacint.14-111 Delrieu-Trottin, E, JT Williams & S Planes. 2014. Macropharyngodon pakoko, a new species of wrasse (Teleostei: Labridae) endemic to the Marquesas Islands, French Polynesia. Zootaxa 3857 (3): 433– 443. https://dx.doi.org/10.11646/zootaxa.3857.3.6

Erickson, DL, FA Jones, NG Swenson, N Pei, N Bourg, W Chen, SJ Davies, X Ge, Z Hao, RW Howe, C-L Huang, A Larson, S Lum, JA Lutz, K Ma, M Meegaskumbura, X Mi, JD Parker, I Fang-Sun, J Wright, AT Wolf, W Ye, D Xing, JK Zimmerman & WJ Kress. 2014. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach. Frontiers in Genetics: doi: 10.3389/fgene.2014.00358.

Escovar, JE, R González, ML Quiñones, RC Wilkerson, F Ruiz, BA Harrison. 2014. Morphology of the larvae, male genitalia and DNA sequences of Anopheles (Kerteszia) pholidotus (Diptera: Culicidae) from Colombia. Mem Inst Oswaldo Cruz, Rio de Janeiro: 1-7, 2014.

Faircloth, BC, MG Branstetter, ND White & SG Brady . 2014. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Molecular Ecology Resources DOI: 10.1111/1755-0998.12328.

Faulde, MK, LM Rueda & BA Kaireh. 2014. First record of the Asian malaria vector Anopheles stephensi and its possible role in resurgence of malaria in Djibouti, Horn of Africa (Diptera, Culicidae). Acta Tropica 139: 39-43.

Foley, DH, M-Y Linton, JF Ruiz-Lopez, JE Conn, MAM Sallum, MM Póvoa, E Bergo, I Sucupira & RC Wilkerson. 2014. Using occurrence data to explore the evolution and disease importance of species within the Neotropical Anopheles albitarsis group (Diptera, Culicidae). Journal of Vector Ecology 39(1): 168-181. doi:10.1111/j.1948-7134.2014.12084.x

Funk, VA, G Sancho, N Roque, CL Kelloff, I Ventosa-Rodríguez, M Diazgranado, JM Bonifacino & R Chan. 2014. A Phylogeny of the Gochnatieae: Understanding a critically placed tribe in the Compositae. Taxon. 63(4): 859–882.

Geller, J, CP Meyer , M Parker & H Hawk. 2014. Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Molecular Ecology Resources: In press.

Grossmann MM, AG Collins & DJ Lindsay. 2014. Description of the eudoxid stages of Lensia havock and Lensia leloupi (Cnidaria: Siphonophora: Calycophorae), with a review of all known Lensia eudoxid bracts. Biodiversity & Systematics: in press.

Gunay, F, B Alten, F Simsek, A Aldemir & Y-M Linton. 2014. Barcoding Turkish Culex mosquitoes to facilitate arbovirus vector incrimination studies reveals hidden diversity and new potential vectors. Acta Tropica; (available online). DOI: 10.1016/j.actatropica.2014.10.013

Harasewych, MG. 2014. Systematics and phylogeography of Cerion sensu stricto (Mollusca: Gastropoda: Pulmonata: Cerionidae) from Aruba, Curaçao and Bonaire. Journal of Molluscan Studies: in press.

Harasewych, MG & RE Petit. 2014. Morphology and systematic relationships of Brocchinia clenchiPetit, 1986 (Mollusca, Caenogastropoda, Cancellariidae) from the Azores. In: Martins, AMF (ed.) The Marine Fauna and Flora of the Azores (Proceedings of the 4rd International Workshop of Malacology and Marine Biology, São Miguel, 2011). Açoreana, Supplement: in press.

Horn, JW, Z Xi, R Riina, JA Peirson, Y Yang, BL Dorsey, PE Berry, CC Davis & KJ Wurdack. 2014. Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway. Evolution 68(12): 3485-3504. doi:10.1111/evo.12534

Hubert, N, B Espiau, C Meyer & S Planes. 2014. Identifying ichtyoplankton of a coral reef using DNA barcoding. Molecular Ecology Resource. doi: 10.1111/1755-0998.12293

Jarvis, ED, et al., A Driskell, et al., M Braun, et al., W Johnson, et al., GR Graves, et al. 2014. Whole- genome analyses resolve early branches in the tree of life of modern birds. Science346(6215): 1320- 1331.

Keyse, J, ED Crandall, RJ Toonen, CP Meyer , EA Treml & C Riginos. 2014. The scope of published population genetic data for Indo-Pacific marine fauna and future research opportunities in the region. Bulletin of Marine Science 90(1): 47-78.

Kingston, SE, AG Navarro-Sigüenza, EA García-Trejo, H Vázquez-Miranda, WF Fagan, & MJ Braun. 2014. Genetic differentiation and habitat connectivity across towhee hybrid zones in Mexico. Evolutionary Ecology 28(2): 277-297.

Kress, WJ, C García-Robledo, M Uriarte & DL Erickson. 2014. DNA Barcodes for Ecology, Evolution, and Conservation. TREE 30: 25-35. https://dx.doi.org/10.1016/j.tree.2014.10.008.

Lasky, JR, M Uriarte, V Boukili, DL Erickson, WJ Kress, RL Chazdon.. 2014. The relationship between tree biodiversity and biomass dynamics changes with tropical forest succession. Ecology Letters 17: 1158- 1167.

Leasi F, & JL Norenburg. 2014. The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea. PLoS ONE 9: e104385. DOI: 10.1371/journal.pone.0104385

Lemer, S, GY Kawauchi, SC Andrade, SC, VL González, MJ Boyle & G Giribet. 2014. Re-evaluating the phylogeny of Sipuncula through transcriptomics. Molecular Phylogenetics & Evolution 83C:174-183. doi: 10.1016/j.ympev.2014.10.019

Liu, Q, B Jiang, J Wen & PM Peterson. 2014. Low-copy nuclear gene and McGISH resolves polyploid history of Eleusine coracana and morphological character evolution in Eleusine. Turkish Journal of Botany 38: 1-12. doi:10.3906/bot-1305-12

Liu, Q, H Liu, J Wen & PM Peterson. 2014. Infrageneric phylogeny and temporal divergence of Sorghum (Andropogoneae, Poaceae) based on low-copy nuclear and plastid sequences. PLoS ONE9(8): 1−14. doi.org/10.1371/journal.pone.0104933

Mandel, JR, RB Dikow, VA Funk, R. Masalia, SE Staton, A Kozik, RW Michelmore, LH Rieseberg, & JM Burke. 2014. Target enrichment for next-gen sequencing and phylogenetic analyses: Lessons from the Compositae. Applications in Plant Sciences (APPS): 2(2): 1300085. doi:10.3732/apps.1300085 Martin, AR, DL Erickson, WJ Kress & SC Thomas. 2014. Wood nitrogen concentrations in tropical trees: phylogenetic patterns and ecological correlates. New Phytologist: doi: 10.1111/nph.12943

Martin, MD, EA Zimmer, MT Olsen, AD Foote, MTP Gilbert & GS Brush. 2014. Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance. Molecular Ecology 23: 1701–1716. doi: 10.1111/mec.12675

Masiulionis, VE, C Rabeling, HH De Fine Licht, T Schultz, M Bacci Jr, CM Santos Bezerra & FC Pagnocca. 2014. The asexual fungus-growing ant Mycocepurus smithii (Formicidae, Myrmicinae, Attini) cultivates morphologically and genetically diverse fungal symbionts with gongylidia-like structures. PLoS ONE 9(8): e103800. doi: 10.1371/journal.pone.0103800.

Morrone, O, K Romaschenko, M Giusanni & PM Peterson. 2014. Phylogeny of Nassella (Poaceae: Stipeae) based on four plastid and nuclear DNA ITS regions. Systematic Botany 39(2): xxx-xxx. (in press)

Mulcahy, DG, JE Martínez-Gómez, G Aguirre-León, JA Cervantes Pasqualli & GR Zug. 2014. Rediscovery of an endemic vertebrate from the remote Islas Revillagigedo in the eastern Pacific Ocean: The Clarión Nightsnake, with conservation and systematic implications. PLoS ONE: 9(5): e97682. doi:10.1371/journal.pone.0097682

Muscarella, R, M Uriarte, DL Erickson, NG Swenson, JK Zimmerman & WJ Kress. 2014. A well-resolved phylogeny of the trees of Puerto Rico on DNA barcode sequence data. PLoS ONE 9(11): e112843. doi: 10.1371/journal.pone.0112843

Pérez-Losada M, JT Høeg, N Simon-Blecher, Y Achituv, D Jones, KA Crandall. 2014. Molecular phylogeny, systematics and morphological evolution of the acorn barnacles (Thoracica: Sessilia: Balanomorpha). Molecular Phylogenetics & Evolution 81:147–158.

Peterson, PM, K Romaschenko & Y Herrera Arrieta. 2014. A molecular phylogeny and classification of the Cteniinae, Farragininae, Gouiniinae, Gymnopogoninae, Perotidinae, and Trichoneurinae (Poaceae: Chloridoideae: Cynodonteae). Taxon 63: 275−286. doi.org/10.12705/632.35

Peterson, PM, K Romaschenko, Y Herrera Arrieta & JM Saarela. 2014. A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae). Taxon63(6): 1212−1243. doi.org/10.12705/636.19

Peterson, PM, K Romaschenko, Y Herrera Arrieta & JM Saarela. 2014. (2332) Proposal to conserve the name Sporobolus against Spartina, Crypsis, Ponceletia, and Heleochloa (Poaceae, Chloridoideae, Sporobolinae). Taxon 63(6): 1373−1374. doi.org/10.12705/636.23

Peterson, P M, K Romaschenko & RJ Soreng. 2014. A laboratory guide for generating DNA barcodes in grasses: A case study of Leptochloa s.l. (Poaceae: Chloridoideae). Webbia 69(1): 1−12. doi.org/10.1080/00837792.2014.927555

Pons, J-M, S. Sonsthagen, C. Dove, and P-A Crochet. 2014. Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact. Heredity 2013: 1- 14. Doi:10.1038/hdy.2013.98

Puebla O, E Bermingham, WO McMillan. 2014. Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp, Serranidae). Molecular Ecology 23: 5291–5303. doi:10.1111/mec.12926 Puillandre, N, TF Duda, C Meyer, BM Olivera & P Bocuhet. 2014. One, four or 100 genera? Classification of the cones. Journal of Molluscan Studies. eyu055

Puillandre, N, P Bouchet, TF Duda, S Kauferstein, AJ Kohn, BM Olivera, M Watkins & CG Meyer. 2014. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea). Molecular Phylogenetics & Evolution 78: 290-303. doi:10.1016/j.ympev.2014.05.023

Rabeling, CR, TR Schultz, NE Pierce & M Bacci, Jr. 2014. A social parasite evolved reproductive isolation from its fungus-growing ant host in sympatry. Current Biology 24: 1-6.doi:10.1016/j.cub.2014.07.048.

Riehl, T, N Brenke, S Brix, A Driskell, S Kaiser & A Brandt. 2014. Field and laboratory methods for DNA studies on deep-sea isopod crustaceans. Polish Polar Research 35(2): 203-224.

Robinson, H & VA Funk. 2014. Dysaster cajamarcensis, a new shrubby genus and species of Astereae from Peru (Asteraceae). PhytoKeys 36: 35-40. doi: 10.3897/phytokeys.36.7393

Robinson, H & VA Funk. 2014. Gymnanthemum koekemoeri (Compositae: Vernonieae), a new species from South Africa. PhytoKeys 36: 59-65.

Robison, HW, CT McAllister, JW Breinholt & K.A. Crandall. 2014. Status, distribution and genetics of Blair's fencing crayfish, Faxonella blairi (Decapoda: Cambaridae). The Southwestern Naturalist59(2):185- 191.

Romaschenko, K, N Garcia-Jacas, PM Peterson, RJ Soreng, R Vilatersana & A Susanna. 2014. Miocene– Pliocene speciation, introgression, and migration of Patis and Ptilagrostis (Poaceae: Stipeae). Molecular Phylogenetics & Evolution 70: 244−259. doi.org/10.1016/j.ympev.2013.09.018

Rosenthal, MA, SR Rosenthal, G Johnson, WC Taylor & EA Zimmer. 2014. Isoetes viridimontana: a previously unrecognized quillwort from Vermont, USA. Amer. Fern Jnl.: in press.

Rothfels, CJ & E Schuettpelz. 2014. Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection. Systematic Biology 63: 31–54.

Scarpa, F, P Cossu, D Sanna, T Lai, JL Norenburg, M Curini-Galletti, & M Casu. 2014. An 18S and 28S- based clock calibration for marine Proseriata (Platyhelminthes). Journal of Experimental Marine Biology and Ecology 463: 22-31. doi:10.1016/j.jembe.2014.10.020.

Schuettpelz, E, A Davila, J Prado, RY Hirai & G Yatskievych. 2014. Molecular phylogenetic and morphological affinities of Adiantum senae (Pteridaceae). Taxon 63: 258–264.

Ssymank, A & X Mengual. 2014. Paragus caligneus sp. nov., a new Afrotropical species of flower fly (Diptera: Syrphidae). Acta Entomologica Musei Nationalis Pragae: in press.

Thompson, AW, R Betancur-R, H Lopez-Fernandez, & G Ortí. 2014. A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods. Molecular Phylogenetics & Evolution 81: 242-257.

Todaro MA, Leasi F, Hochberg R. 2014. A new species, genus and family of marine Gastrotricha from Jamaica, with a phylogenetic analysis of Macrodasyida based on the 18S rDNA gene. Systematics and Biodiversity 12: 473-488. DOI: 10.1080/14772000.2014.942718 Toledo-Hernández, C, X Vélez-Zuazo, CP Ruiz-Diaz, AR Patricio, P Mège, M Navarro, AB Sabat, R Betancur-R & R Papa. 2014. Population ecology and genetics of the invasive lionfish in Puerto Rico. Aquatic Invasions 9: 227-237. https://dx.doi.org/10.3391/ai.2014.9.2.12

Valcárcel, V, O Fiz-Palacios & J Wen. 2014. The origin of the early differentiation of Ivies (HederaL.) and the radiation of the Asian Palmate group (Araliaceae). Molecular Phylogenetics & Evolution70: 492- 503. doi:10.1016/j.ympev.2013.10.016

Ward, PS, SG Brady , BL Fisher, & TR Schultz. 2014. The evolution of myrmicine ants: Phylogeny and biogeography of a hyperdiverse ant clade. Systematic Entomology 40: 61–81. doi: 10.1111/syen.12090

Wen, J, J-Q Zhang, Z-L Nie, Y Zhong & H Sun. 2014. Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau. Frontiers in Genetics 5. doi:10.3389/fgene.2014.00004

Windsor, AM & DL Felder. 2014. Molecular phylogenetics and taxonomic reanalysis of the family Mithracidae MacLeay (Decapoda: Brachyura: Majoidea). Invertebrate Systematics 28(2): in press.

Zarowiecki, M, YM Linton, RJ Post, MJ Bangs, PT Htun, T Hlaing, CM Seng, V Baimai, DH Ding, T Sochantha & C Walton. 2014. Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo-Oriental Region. Molecular Ecology 23: 2573–2589. doi: 10.1111/mec.12761