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RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea).

Iguchi A, Yoshioka Y, Forsman ZH, Knapp ISS, Toonen RJ, Hongo Y, Nagai S, Yasuda N.

BMC Evol Biol. 2019 Oct 15;19(1):187. doi: 10.1186/s12862-019-1522-0.


Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora.

Cunha RL, Forsman ZH, Belderok R, Knapp ISS, Castilho R, Toonen RJ.

BMC Evol Biol. 2019 Jul 24;19(1):153. doi: 10.1186/s12862-019-1476-2.


A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri.

Ylitalo H, Oliver TA, Fernandez-Silva I, Wood JB, Toonen RJ.

PeerJ. 2019 Jun 7;7:e6927. doi: 10.7717/peerj.6927. eCollection 2019.


Annotated checklist for stony corals of American Sāmoa with reference to mesophotic depth records.

Montgomery AD, Fenner D, Toonen RJ.

Zookeys. 2019 May 21;849:1-170. doi: 10.3897/zookeys.849.34763. eCollection 2019.


Shared genomic outliers across two divergent population clusters of a highly threatened seagrass.

Phair NL, Toonen RJ, Knapp I, von der Heyden S.

PeerJ. 2019 Apr 29;7:e6806. doi: 10.7717/peerj.6806. eCollection 2019.


Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans.

Jury CP, Toonen RJ.

Proc Biol Sci. 2019 May 15;286(1902):20190614. doi: 10.1098/rspb.2019.0614.


Evidence of local adaptation in a waterfall-climbing Hawaiian goby fish derived from coupled biophysical modeling of larval dispersal and post-settlement selection.

Moody KN, Wren JLK, Kobayashi DR, Blum MJ, Ptacek MB, Blob RW, Toonen RJ, Schoenfuss HL, Childress MJ.

BMC Evol Biol. 2019 Apr 11;19(1):88. doi: 10.1186/s12862-019-1413-4.


Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean.

Vicente J, Ríos JA, Zea S, Toonen RJ.

PeerJ. 2019 Feb 5;7:e6371. doi: 10.7717/peerj.6371. eCollection 2019.


A coalescent sampler successfully detects biologically meaningful population structure overlooked by F-statistics.

Crandall ED, Toonen RJ; ToBo Laboratory, Selkoe KA.

Evol Appl. 2018 Oct 15;12(2):255-265. doi: 10.1111/eva.12712. eCollection 2019 Feb.


High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata.

Barshis DJ, Birkeland C, Toonen RJ, Gates RD, Stillman JH.

J Exp Biol. 2018 Dec 10;221(Pt 24). pii: jeb188581. doi: 10.1242/jeb.188581.


Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species.

Copus JM, Montgomery WL, Forsman ZH, Bowen BW, Toonen RJ.

PeerJ. 2018 Sep 27;6:e5605. doi: 10.7717/peerj.5605. eCollection 2018.


Modeled larval connectivity of a multi-species reef fish and invertebrate assemblage off the coast of Moloka'i, Hawai'i.

Conklin EE, Neuheimer AB, Toonen RJ.

PeerJ. 2018 Sep 28;6:e5688. doi: 10.7717/peerj.5688. eCollection 2018.


Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model.

Schuster A, Vargas S, Knapp IS, Pomponi SA, Toonen RJ, Erpenbeck D, Wörheide G.

BMC Evol Biol. 2018 Jul 18;18(1):114. doi: 10.1186/s12862-018-1230-1.


Complex signatures of genomic variation of two non-model marine species in a homogeneous environment.

Nielsen ES, Henriques R, Toonen RJ, Knapp ISS, Guo B, von der Heyden S.

BMC Genomics. 2018 May 9;19(1):347. doi: 10.1186/s12864-018-4721-y.


The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages.

Dudoit ', Iacchei M, Coleman RR, Gaither MR, Browne WE, Bowen BW, Toonen RJ.

PeerJ. 2018 Mar 6;6:e4409. doi: 10.7717/peerj.4409. eCollection 2018.


A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora.

Johnston EC, Forsman ZH, Toonen RJ.

PeerJ. 2018 Feb 8;6:e4355. doi: 10.7717/peerj.4355. eCollection 2018.


Coral calcification mechanisms facilitate adaptive responses to ocean acidification.

Schoepf V, Jury CP, Toonen RJ, McCulloch MT.

Proc Biol Sci. 2017 Dec 6;284(1868). pii: 20172117. doi: 10.1098/rspb.2017.2117.


Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean.

Capel KCC, Toonen RJ, Rachid CTCC, Creed JC, Kitahara MV, Forsman Z, Zilberberg C.

PeerJ. 2017 Oct 5;5:e3873. doi: 10.7717/peerj.3873. eCollection 2017.


The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

Deck J, Gaither MR, Ewing R, Bird CE, Davies N, Meyer C, Riginos C, Toonen RJ, Crandall ED.

PLoS Biol. 2017 Aug 3;15(8):e2002925. doi: 10.1371/journal.pbio.2002925. eCollection 2017 Aug.


A genomic glance through the fog of plasticity and diversification in Pocillopora.

Johnston EC, Forsman ZH, Flot JF, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ.

Sci Rep. 2017 Jul 20;7(1):5991. doi: 10.1038/s41598-017-06085-3.


Life-history predicts past and present population connectivity in two sympatric sea stars.

Puritz JB, Keever CC, Addison JA, Barbosa SS, Byrne M, Hart MW, Grosberg RK, Toonen RJ.

Ecol Evol. 2017 Apr 23;7(11):3916-3930. doi: 10.1002/ece3.2938. eCollection 2017 Jun.


Species boundaries in the absence of morphological, ecological or geographical differentiation in the Red Sea octocoral genus Ovabunda (Alcyonacea: Xeniidae).

McFadden CS, Haverkort-Yeh R, Reynolds AM, Halàsz A, Quattrini AM, Forsman ZH, Benayahu Y, Toonen RJ.

Mol Phylogenet Evol. 2017 Jul;112:174-184. doi: 10.1016/j.ympev.2017.04.025. Epub 2017 Apr 30.


Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa.

Forsman ZH, Knapp ISS, Tisthammer K, Eaton DAR, Belcaid M, Toonen RJ.

Mol Phylogenet Evol. 2017 Jun;111:132-148. doi: 10.1016/j.ympev.2017.03.023. Epub 2017 Mar 31.


Coral reef grazer-benthos dynamics complicated by invasive algae in a small marine reserve.

Stamoulis KA, Friedlander AM, Meyer CG, Fernandez-Silva I, Toonen RJ.

Sci Rep. 2017 Mar 9;7:43819. doi: 10.1038/srep43819.


Modeled Population Connectivity across the Hawaiian Archipelago.

Wren JL, Kobayashi DR, Jia Y, Toonen RJ.

PLoS One. 2016 Dec 8;11(12):e0167626. doi: 10.1371/journal.pone.0167626. eCollection 2016.


Population genetic structure between Yap and Palau for the coral Acropora hyacinthus.

Cros A, Toonen RJ, Davies SW, Karl SA.

PeerJ. 2016 Aug 18;4:e2330. doi: 10.7717/peerj.2330. eCollection 2016.


The implementation of rare events logistic regression to predict the distribution of mesophotic hard corals across the main Hawaiian Islands.

Veazey LM, Franklin EC, Kelley C, Rooney J, Frazer LN, Toonen RJ.

PeerJ. 2016 Jul 6;4:e2189. doi: 10.7717/peerj.2189. eCollection 2016.


Comparative phylogeography of the ocean planet.

Bowen BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, Toonen RJ, Briggs JC.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):7962-9. doi: 10.1073/pnas.1602404113.


The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages.

Selkoe KA, Gaggiotti OE, Treml EA, Wren JL, Donovan MK; Hawai‘i Reef Connectivity Consortium, Toonen RJ.

Proc Biol Sci. 2016 Apr 27;283(1829). pii: 20160354. doi: 10.1098/rspb.2016.0354.


Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover.

Forsman ZH, Page CA, Toonen RJ, Vaughan D.

PeerJ. 2015 Oct 20;3:e1313. doi: 10.7717/peerj.1313. eCollection 2015.


Survivorship and feeding preferences among size classes of outplanted sea urchins, Tripneustes gratilla, and possible use as biocontrol for invasive alien algae.

Westbrook CE, Ringang RR, Cantero SM; HDAR & TNC Urchin Team, Toonen RJ.

PeerJ. 2015 Sep 15;3:e1235. doi: 10.7717/peerj.1235. eCollection 2015.


Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific.

Knapp IS, Forsman ZH, Williams GJ, Toonen RJ, Bell JJ.

PeerJ. 2015 Aug 6;3:e1170. doi: 10.7717/peerj.1170. eCollection 2015.


The unnatural history of Kāne'ohe Bay: coral reef resilience in the face of centuries of anthropogenic impacts.

Bahr KD, Jokiel PL, Toonen RJ.

PeerJ. 2015 May 12;3:e950. doi: 10.7717/peerj.950. eCollection 2015.


Demystifying computer science for molecular ecologists.

Belcaid M, Toonen RJ.

Mol Ecol. 2015 Jun;24(11):2619-40. doi: 10.1111/mec.13175. Epub 2015 May 7. Review.


Demystifying the RAD fad.

Puritz JB, Matz MV, Toonen RJ, Weber JN, Bolnick DI, Bird CE.

Mol Ecol. 2014 Dec;23(24):5937-42. doi: 10.1111/mec.12965.


Large-scale introduction of the Indo-Pacific damselfish Abudefduf vaigiensis into Hawai'i promotes genetic swamping of the endemic congener A. abdominalis.

Coleman RR, Gaither MR, Kimokeo B, Stanton FG, Bowen BW, Toonen RJ.

Mol Ecol. 2014 Nov;23(22):5552-65. doi: 10.1111/mec.12952. Epub 2014 Oct 30.


Emergent patterns of population genetic structure for a coral reef community.

Selkoe KA, Gaggiotti OE, Bowen BW, Toonen RJ; ToBo Laboratory.

Mol Ecol. 2014 Jun;23(12):3064-79. doi: 10.1111/mec.12804.


Archaeological evidence of validity of fish populations on unexploited reefs as proxy targets for modern populations.

Longenecker K, Chan YL, Toonen RJ, Carlon DB, Hunt TL, Friedlander AM, Demartini EE.

Conserv Biol. 2014 Oct;28(5):1322-30. doi: 10.1111/cobi.12287. Epub 2014 Mar 25.


ezRAD: a simplified method for genomic genotyping in non-model organisms.

Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE.

PeerJ. 2013 Nov 19;1:e203. doi: 10.7717/peerj.203. eCollection 2013.


One size does not fit all: the emerging frontier in large-scale marine conservation.

Toonen RJ, Wilhelm T', Maxwell SM, Wagner D, Bowen BW, Sheppard CR, Taei SM, Teroroko T, Moffitt R, Gaymer CF, Morgan L, Lewis N, Sheppard AL, Parks J, Friedlander AM; Big Ocean Think Tank.

Mar Pollut Bull. 2013 Dec 15;77(1-2):7-10. doi: 10.1016/j.marpolbul.2013.10.039. Epub 2013 Nov 15.


Between tide and wave marks: a unifying model of physical zonation on littoral shores.

Bird CE, Franklin EC, Smith CM, Toonen RJ.

PeerJ. 2013 Sep 19;1:e154. doi: 10.7717/peerj.154. eCollection 2013.


Polyphyly and hidden species among Hawai'i's dominant mesophotic coral genera, Leptoseris and Pavona (Scleractinia: Agariciidae).

Luck DG, Forsman ZH, Toonen RJ, Leicht SJ, Kahng SE.

PeerJ. 2013 Aug 13;1:e132. doi: 10.7717/peerj.132. eCollection 2013.


Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra).

Keever CC, Puritz JB, Addison JA, Byrne M, Grosberg RK, Toonen RJ, Hart MW.

Biol Lett. 2013 Aug 7;9(5):20130551. doi: 10.1098/rsbl.2013.0551. Print 2013 Oct 23.


Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.

Iacchei M, Ben-Horin T, Selkoe KA, Bird CE, García-Rodríguez FJ, Toonen RJ.

Mol Ecol. 2013 Jul;22(13):3476-94. doi: 10.1111/mec.12341.


Population structure in the native range predicts the spread of introduced marine species.

Gaither MR, Bowen BW, Toonen RJ.

Proc Biol Sci. 2013 Apr 17;280(1760):20130409. doi: 10.1098/rspb.2013.0409. Print 2013 Jun 7.


The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers.

Andrews KR, Perrin WF, Oremus M, Karczmarski L, Bowen BW, Puritz JB, Toonen RJ.

Mol Ecol. 2013 May;22(9):2408-23. doi: 10.1111/mec.12193. Epub 2013 Apr 2.


Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses.

Fernandez-Silva I, Toonen RJ.

Methods Mol Biol. 2013;1006:101-20. doi: 10.1007/978-1-62703-389-3_7.


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