EDIT

import eu.etaxonomy.cdm.common.URI;

 *

    /**

     * {@inheritDoc}

     */

    /**

     * @param state

     * @param next

     * @return

     */

    /**

     * @param ref

     * @return

     */

    /**

     * @param state

     * @param record

     * @return

     */

    /**

     * @param state

     * @param year

     * @param date

     */

    /**

     * @param state

     * @param da

     * @return

     */

    /**

     * @param state

     * @param py

     * @return

     */

    /**

     * @param state

     * @param list

     * @return

     */

    /**

     * @param state

     * @param risValue

     * @return

     */

    /**

     * @param state

     * @param list

     * @param tag

     */

    /**

     * @param state

     * @param next

     * @return

     */

    /**

     * {@inheritDoc}

     */

    /**

     * {@inheritDoc}

     */

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.reference;

import static org.junit.Assert.assertNotNull;

import java.io.FileNotFoundException;

import java.net.URISyntaxException;

import java.net.URL;

import org.junit.Assert;

import org.junit.Before;

import org.junit.Ignore;

import org.junit.Test;

import org.unitils.spring.annotation.SpringBeanByName;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.api.service.INameService;

import eu.etaxonomy.cdm.common.URI;

import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;

import eu.etaxonomy.cdm.io.common.IImportConfigurator;

import eu.etaxonomy.cdm.io.reference.endnote.in.EndnoteImportConfigurator;

import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;

/**

 * @author andy

 */

public class EndnoteRecordsImportTest extends CdmTransactionalIntegrationTest {

	@SpringBeanByName

	private CdmApplicationAwareDefaultImport<?> defaultImport;

	@SpringBeanByType

	private INameService nameService;

	private IImportConfigurator configurator;

	@Before

	public void setUp() {

		String inputFile = "/eu/etaxonomy/cdm/io/reference/EndnoteRecordImportTest-input.xml";

		URL url = this.getClass().getResource(inputFile);

		assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);

		try {

			configurator = EndnoteImportConfigurator.NewInstance(URI.fromUrl(url), null);

		} catch (URISyntaxException e) {

			e.printStackTrace();

			Assert.fail();

		}

		assertNotNull("Configurator could not be created", configurator);

	}

//***************************** TESTS *************************************//

	@Test

	public void testInit() {

//		assertNotNull("XXX should not be null", defaultImport);

		assertNotNull("nameService should not be null", nameService);

		assertNotNull("configurator should not be null", configurator);

	}

	@Test

	public void testDoInvokeWithoutExceptions() {

		defaultImport.invoke(configurator);

	}

	@Test

	@Ignore("Import does not fully work yet")

	public void testDoInvoke() {

		boolean result = defaultImport.invoke(configurator).isSuccess();

		//TODO result is still false

		logger.warn("No real testing for endnote import yet");

		Assert.assertTrue("Return value for import.invoke() should be true", result);

//		assertEquals("Number of TaxonNames should be 5", 5, nameService.count());

	}

    @Override

    public void createTestDataSet() throws FileNotFoundException {}

}

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.reference;

import static org.junit.Assert.assertNotNull;

import java.io.FileNotFoundException;

import java.net.URL;

import java.util.List;

import org.junit.Assert;

import org.junit.Before;

import org.junit.Test;

import org.unitils.dbunit.annotation.DataSet;

import org.unitils.spring.annotation.SpringBeanByName;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.api.service.IReferenceService;

//import eu.etaxonomy.cdm.common.DOI;

import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;

import eu.etaxonomy.cdm.io.common.ImportResult;

import eu.etaxonomy.cdm.io.reference.ris.in.RisReferenceImportConfigurator;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceType;

import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;

import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;

/**

 * @author a.mueller

 *

 */

public class RisReferenceImportTest extends CdmTransactionalIntegrationTest {

	@SpringBeanByName

	private CdmApplicationAwareDefaultImport<?> defaultImport;

	@SpringBeanByType

	private IReferenceService referenceService;

	private RisReferenceImportConfigurator configurator;

    private RisReferenceImportConfigurator configLong;

	@Before

	public void setUp() {

		String inputFile = "/eu/etaxonomy/cdm/io/reference/RisReferenceImportTest-input.ris";

        try {

            URL url = this.getClass().getResource(inputFile);

            assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);

            String inputFileLong = "/eu/etaxonomy/cdm/io/reference/Acantholimon.ris";

            URL urlLong = this.getClass().getResource(inputFileLong);

            assertNotNull("URL for the test file '" + inputFileLong + "' does not exist", urlLong);

			configurator = RisReferenceImportConfigurator.NewInstance(url, null);

			configLong = RisReferenceImportConfigurator.NewInstance(urlLong, null);

		} catch (Exception e) {

			e.printStackTrace();

			Assert.fail();

		}

		assertNotNull("Configurator could not be created", configurator);

	    assertNotNull("Configurator could not be created", configLong);

	    assertNotNull("nameService should not be null", referenceService);

	}

//***************************** TESTS *************************************//

	@Test

	@DataSet( value="/eu/etaxonomy/cdm/database/ClearDBDataSet.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)

	//@Ignore

    public void testShort() {

		ImportResult result = defaultImport.invoke(configurator);

		String report = result.createReport().toString();

		Assert.assertTrue(report.length() > 0);

		System.out.println(report);

		Integer expected = 2;

		Assert.assertEquals(expected, result.getNewRecords(Reference.class));

		List<Reference> list = referenceService.list(Reference.class, null, null, null, null);

		Assert.assertEquals("There should be 3 references, the article and the journal and the source reference",

		        3, list.size());

		for (Reference ref : list){

		    if (ref.equals(configurator.getSourceReference())){

		        continue;

		    }

		    Assert.assertTrue(ref.getType() == ReferenceType.Article || ref.getType() == ReferenceType.Journal);

		    if (ref.getType() == ReferenceType.Article){

		        //title

		        Assert.assertEquals("Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea",

		                ref.getTitle());

		        //author

		        TeamOrPersonBase<?> author = ref.getAuthorship();

		        Assert.assertNotNull(author);

		        Assert.assertTrue(author.isInstanceOf(Person.class));

		        Person person = CdmBase.deproxy(author, Person.class);

		        //this may change in future depending on the correct formatting strategy

		        Assert.assertEquals("Jongkind, C.C.H." ,person.getTitleCache());

		        Assert.assertEquals("Jongkind" ,person.getFamilyName());

		        Assert.assertEquals("Carel C. H." ,person.getGivenName());

		        //date

		        VerbatimTimePeriod date = ref.getDatePublished();

		        Assert.assertEquals(Integer.valueOf(2017) ,date.getStartYear());

		        //vol

		        Assert.assertEquals("47(1)" ,ref.getVolume());

                Assert.assertEquals("43-47" ,ref.getPages());

                //doi

                //Assert.assertEquals(DOI.fromString("10.3372/wi.47.47105"),ref.getDoi());

                //Abstract

                Assert.assertEquals("Abstract: A new species of Violaceae, Decorsella arborea Jongkind, is described and illustrated. The new species differs from the only other species in the genus, D. paradoxa A. Chev., by the larger size of the plants, smaller leaves, more slender flowers, and stamen filaments that are free for a much larger part. Both species are from the Guineo-Congolian forest of tropical Africa. The differences between Decorsella and Rinorea are discussed. Confirming recent reports, some species of Rinorea can have zygomorphic flowers and some of these can be almost equal in shape to Decorsella flowers. Citation: Jongkind C. C. H. 2017: Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea. ? Willdenowia 47: 43?47. doi: https://doi.org/10.3372/wi.47.47105 Version of record first published online on 13 February 2017 ahead of inclusion in April 2017 issue.",

                        ref.getReferenceAbstract());

                //TODO still missing Y1, Y2, M3, UR

		    }else if (ref.getType() == ReferenceType.Journal){

		        Assert.assertEquals("Willdenowia", ref.getTitle());

		        //or is this part of article?

		        Assert.assertEquals("Botanic Garden and Botanical Museum Berlin (BGBM)", ref.getPublisher());

		        //ISSN

                Assert.assertEquals("0511-9618" ,ref.getIssn());

		    }else{

		        Assert.fail("Only an article and a journal should exist");

		    }

		}

	}

	@Test

	//@Ignore

    public void testLongFile() {

        ImportResult result = defaultImport.invoke(configLong);

        String report = result.createReport().toString();

        System.out.println(report);

        Integer expected = 118;  //did not count yet

        Assert.assertEquals(expected, result.getNewRecords(Reference.class));

//        List<Reference> list = referenceService.list(Reference.class, null, null, null, null);

//        Assert.assertEquals("There should be 2 references, the article and the journal", 2, list.size());

//        for (Reference ref : list){

//            Assert.assertTrue(ref.getType() == ReferenceType.Article || ref.getType() == ReferenceType.Journal);

//            if (ref.getType() == ReferenceType.Article){

//                //title

//                Assert.assertEquals("Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea",

//                        ref.getTitle());

//                //author

//                TeamOrPersonBase<?> author = ref.getAuthorship();

//                Assert.assertNotNull(author);

//                Assert.assertTrue(author.isInstanceOf(Person.class));

//                Person person = CdmBase.deproxy(author, Person.class);

//                //this may change in future depending on the correct formatting strategy

//                Assert.assertEquals("Carel C. H. Jongkind" ,person.getTitleCache());

//                Assert.assertEquals("Jongkind" ,person.getFamilyName());

//                Assert.assertEquals("Carel C. H." ,person.getGivenName());

//                //date

//                TimePeriod date = ref.getDatePublished();

//                Assert.assertEquals(Integer.valueOf(2017) ,date.getStartYear());

//                //vol

//                Assert.assertEquals("47(1)" ,ref.getVolume());

//                Assert.assertEquals("43-47" ,ref.getPages());

//

//                //doi

//                Assert.assertEquals(DOI.fromString("10.3372/wi.47.47105"),ref.getDoi());

//

//                //Abstract

//                Assert.assertEquals("Abstract: A new species of Violaceae, Decorsella arborea Jongkind, is described and illustrated. The new species differs from the only other species in the genus, D. paradoxa A. Chev., by the larger size of the plants, smaller leaves, more slender flowers, and stamen filaments that are free for a much larger part. Both species are from the Guineo-Congolian forest of tropical Africa. The differences between Decorsella and Rinorea are discussed. Confirming recent reports, some species of Rinorea can have zygomorphic flowers and some of these can be almost equal in shape to Decorsella flowers. Citation: Jongkind C. C. H. 2017: Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea. ? Willdenowia 47: 43?47. doi: https://doi.org/10.3372/wi.47.47105 Version of record first published online on 13 February 2017 ahead of inclusion in April 2017 issue.",

//                        ref.getReferenceAbstract());

//

//                //TODO still missing Y1, Y2, M3, UR

//

//            }else if (ref.getType() == ReferenceType.Journal){

//                Assert.assertEquals("Willdenowia", ref.getTitle());

//                //or is this part of article?

//                Assert.assertEquals("Botanic Garden and Botanical Museum Berlin (BGBM)", ref.getPublisher());

//

//                //ISSN

//                Assert.assertEquals("0511-9618" ,ref.getIssn());

//

//            }else{

//                Assert.fail("Only an article and a journal should exist");

//            }

//        }

    }

    @Override

    public void createTestDataSet() throws FileNotFoundException {}

}

TY  - JOUR

AU  - Aguilar, J. F.

AU  - Feliner, G. N.

PY  - 2003

SP  - 430-447

ST  - Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae)

T2  - Molecular Phylogenetics and Evolution

TI  - Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae)

VL  - 28

ID  - 58

ER  - 

TY  - JOUR

AB  - A new species, Acantholimon karamanicum Akaychn & Dogan (Plumbaginaceae) is described and illustrated. The species grows on calcareous Mountain slopes in open Quercus sp. scrub, Astragalus sp. steppe, and inside Abies cilicica forest in Ermenek (Karaman). Diagnostic morphological characteristics from closely related species are discussed and conservation statuses of the species are given. A revised key to the Acantholimon species, with densely distichous spikes and outer bracts twice as long as the internodes, is also provided for the species found in Turkey.

AD  - Dogan, M

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

Middle E Tech Univ, Dept Sci Biol, TR-06531 Ankara, Turkey

AN  - WOS:000175945600008

AU  - Akaydin, G.

AU  - Doğan, M.

DO  - Doi 10.1092/54a2-0bep-Btyh-A3wc

IS  - 1

J2  - Isr J Plant Sci

LA  - English

N1  - 558bt

Times Cited:10

Cited References Count:12

PY  - 2002

SN  - 0792-9978

SP  - 67-71

ST  - A new species of Acantholimon Boiss. (Plumbaginaceae) from the western Taurus Mountains, Turkey

T2  - Israel Journal of Plant Sciences

TI  - A new species of Acantholimon Boiss. (Plumbaginaceae) from the western Taurus Mountains, Turkey

UR  - <Go to ISI>://WOS:000175945600008

VL  - 50

ID  - 17

ER  - 

TY  - JOUR

AU  - Aronne, G.

AU  - De Micco, V.

PY  - 2001

SP  - 789-794

ST  - Seasonal dimorphism in the Mediterranean Cistus incanus L. subsp. incanus

T2  - Annals of Botany

TI  - Seasonal dimorphism in the Mediterranean Cistus incanus L. subsp. incanus

VL  - 87

ID  - 44

ER  - 

TY  - CHAP

AU  - Assadi, M.

CY  - Tehran

PY  - 2005

SP  - XXX-XXX

ST  - Plumbaginaceae

T2  - Flora of Iran

TI  - Plumbaginaceae

VL  - 51

ID  - 53

ER  - 

TY  - JOUR

AU  - Assadi, M.

PY  - 2006

SP  - 114-120

ST  - Distribution patterns of the genus Acantholimon (Plumbaginaceae) in Iran

T2  - Iranian Journal of Botany

TI  - Distribution patterns of the genus Acantholimon (Plumbaginaceae) in Iran

VL  - 12

ID  - 51

ER  - 

TY  - JOUR

AB  - The new species Acantholimon doganii Y. Bagci, Dogu & Akaydin is described and illustrated. Diagnostic morphological characteristics in closely related species are discussed and the conservation status of the new species is analysed. A revised key to the Turkish Acantholimon species with persistent circinnate leaf basis is also provided.

AD  - Selcuk Univ, Dept Biol, Fac Sci & Art, TR-42031 Selcuklu, Konya, Turkey

Selcuk Univ, Dept Biol Educ, TR-42090 Meram, Konya, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06800 Ankara, Turkey

AN  - WOS:000267130000013

AU  - Bagci, Y.

AU  - Dogu, S.

AU  - Akaydin, G.

DO  - 10.1111/j.1756-1051.2008.00390.x

IS  - 3

J2  - Nord J Bot

LA  - English

N1  - 459sq

Times Cited:1

Cited References Count:14

PY  - 2009

SN  - 0107-055x

SP  - 228-231

ST  - Acantholimon doganii sp nov (Plumbaginaceae) with persistent circinnate leaf bases, from Turkey

T2  - Nordic Journal of Botany

TI  - Acantholimon doganii sp nov (Plumbaginaceae) with persistent circinnate leaf bases, from Turkey

UR  - <Go to ISI>://WOS:000267130000013

VL  - 27

ID  - 52

ER  - 

TY  - BOOK

AU  - Boissier, E.

PB  - Lipsiae Herrmann

PY  - 1846

SE  - 69-81

ST  - Diagnoses Plantarum Orientalium Novarum

TI  - Diagnoses Plantarum Orientalium Novarum

VL  - 7

ID  - 21

ER  - 

TY  - CHAP

A2  - de Candolle, A. P.

AU  - Boissier, E. 

CY  - Paris

PB  - Treuttel et Wurz

PY  - 1848

ST  - Plumbaginales

T2  - Prodromus systematis naturalis regni vegetabilis.

TI  - Plumbaginales

ID  - 22

ER  - 

TY  - BOOK

AU  - Boissier, Pierre-Edmond

CY  - Geneva

KW  - Africa

Angiospermas

Asia

Europa

Flora

Península Ibérica

PY  - 1859

ST  - Diagnoses plantarum Orientalium novarum [...] Series secunda. N.º 4

TI  - Diagnoses plantarum Orientalium novarum [...] Series secunda. N.º 4

UR  - http://www.biodiversitylibrary.org/item/142679

ID  - 43

ER  - 

TY  - BOOK

AU  - Boissier, Pierre-Edmond

CY  - Basileae, Genevae

KW  - Africa

Angiospermas

Asia

Europa

Flora

PB  - Apud H. Georg, Bibliopolam

PY  - 1879

ST  - Flora Orientalis [...] Volumen quartum. Fasciculus secundus

TI  - Flora Orientalis [...] Volumen quartum. Fasciculus secundus

UR  - http://www.biodiversitylibrary.org/item/142697

ID  - 24

ER  - 

TY  - THES

AU  - Bokhari, M. H. 

CY  - Edinburgh

PB  - The University of Edinburgh

PY  - 1970

ST  - Taxonomic studies in S.W. Asian Plumbaginaceae

T2  - Faculty of Science

TI  - Taxonomic studies in S.W. Asian Plumbaginaceae

ID  - 2

ER  - 

TY  - CHAP

A2  - H., Davis P.

AU  - Bokhari, M. H.

AU  - Edmondson, J. R.

CY  - Edinburgh

PB  - Edinburgh University Press

PY  - 1982

SP  - 478-502

ST  - Acantholimon Boiss.

T2  - Flora of Turkey and the east Aegean islands

TI  - Acantholimon Boiss.

ID  - 25

ER  - 

TY  - JOUR

AU  - Bunge, A.

PY  - 1872

SP  - 1-72

ST  - Die Gattung Acantholimon Boiss.

T2  - Mémoires de l'Académie impériale des sciences de St. Pétersbourg

TI  - Die Gattung Acantholimon Boiss.

VL  - VII

ID  - 23

ER  - 

TY  - JOUR

AN  - WOS:A1990CU44200009

AU  - Christodoulakis, N. S.

AU  - Tsimbani, H.

AU  - Fasseas, C.

DA  - Mar

IS  - 3

J2  - Ann Bot-London

LA  - English

N1  - Cu442

Times Cited:25

Cited References Count:21

PY  - 1990

SN  - 0305-7364

SP  - 291-296

ST  - Leaf structural peculiarities in Sarcopoterium spinosum, a seasonally dimorphic subshrub

T2  - Annals of Botany

TI  - Leaf structural peculiarities in Sarcopoterium spinosum, a seasonally dimorphic subshrub

UR  - <Go to ISI>://WOS:A1990CU44200009

VL  - 65

ID  - 45

ER  - 

TY  - JOUR

AB  - Agamospermous species account for a large proportion of the species of Limonium. Agamospermy is indicated by uneven polyploidy or aneuploidy, low pollen stainability and by the presence of monomorphic self-incompatible populations. The taxonomic treatment of agamospermous taxa varies from recognition of all of them at the same specific rank or by utilising a range of ranks in the taxonomic hierarchy. The influence of evolutionary hypotheses on taxonomic systems is considered. Molecular data provide a means of measuring the genetical relationships of taxa and establishing groups in a taxonomic hierarchy.

AD  - Univ London Birkbeck Coll, Dept Biol, London WC1E 7HX, England

Univ Oxford, Dept Plant Sci, Oxford OX1 3RB, England

AN  - WOS:000077957200009

AU  - Cowan, R.

AU  - Ingrouille, M. J.

AU  - Lledó, M. D.

IS  - 3

J2  - Folia Geobot

KW  - apomixis

hybridisation

taxonomic hierarchy

species concepts

DNA

markers

plants

rbcl

rapd

aflp

LA  - English

N1  - 155qe

Times Cited:16

Cited References Count:50

PY  - 1998

SN  - 0015-5551

SP  - 353-366

ST  - The taxonomic treatment of agamosperms in the genus Limonium Mill. (Plumbaginaceae)

T2  - Folia Geobotanica

TI  - The taxonomic treatment of agamosperms in the genus Limonium Mill. (Plumbaginaceae)

UR  - <Go to ISI>://WOS:000077957200009

VL  - 33

ID  - 38

ER  - 

TY  - JOUR

AB  - Two new genera are described to include six taxa commonly considered members of Limoniastrum Heist. ex Fabr. Saharanthus M.B. Crespo & M.D. Lledo nom, nov. is proposed on the basis of the illegitimate Lerrouxia Caball., for a woody species from western Sahara, also known as Caballeroa Font Quer. Ceratolimon M.B. Crespo & M.D. Lledo gen, nov. is proposed for a group of five taxa (four species and one additional variety) of dwarf shrubs with horned spikelets, which show a disjunct distribution on the edges of the Sahara Desert. This latter name applies to most species formerly placed in the illegitimate Bubania. Types are indicated for all taxa, and identification keys are also presented. (C) 2000 The Linnean Society of London.

AD  - Univ Alicante, Dept Ciencias Ambientales & Recursos Nat Bot, E-03080 Alicante, Spain

Royal Bot Gardens, Herbarium, Richmond TW9 3AB, Surrey, England

AN  - WOS:000086098300005

AU  - Crespo, M. B.

AU  - Lledó, M. D.

DA  - Feb

IS  - 2

J2  - Bot J Linn Soc

KW  - biogeography

bubania

caballeroa

nomenclature

taxonomy

typification

LA  - English

N1  - 297tg

Times Cited:3

Cited References Count:29

PY  - 2000

SN  - 0024-4074

SP  - 165-174

ST  - Two new North African genera related to Limoniastrum (Plumbaginaceae)

T2  - Botanical Journal of the Linnean Society

TI  - Two new North African genera related to Limoniastrum (Plumbaginaceae)

UR  - <Go to ISI>://WOS:000086098300005

VL  - 132

ID  - 36

ER  - 

TY  - JOUR

AU  - Daniela, I.

IS  - 27

J2  - Newslett. Int. Organ. Pl. Biosyst.

PY  - 1997

SP  - 14

ST  - Chromosome data 11

T2  - Newslett. Int. Organ. Pl. Biosyst.

TI  - Chromosome data 11

VL  - 26

ID  - 54

ER  - 

TY  - JOUR

AB  - This study explores the response of the Irano-Turanian flora to Quaternary glacial–interglacial cycles in SW Asia. We use new fossil pollen data to assess variation in abundance of Cousinia Cass. (Compositae), a large genus typical for the Irano-Turanian flora, during these cycles. The results are compared with modern topography, tectonic and palaeoclimatic history, and recent phylogenetic data to explain the extremely high speciation rate and level of endemism as well as the modern geographical distribution of the genus. Cousinia is consistently well-represented in glacial-age and late-glacial pollen assemblages of NW Iran and E Anatolia. In the ~ 200,000-year pollen sequence from Lake Urmia, NW Iran, Cousinia pollen shows significant values and is nearly continuously represented during both the last glacial (~ 70 ka to Holocene) and penultimate glacial periods (~ 190 to 130 ka). In contrast, its pollen is less frequent and occurs only sporadically during the last interglacial period and the Holocene. This pattern suggests that Cousinia could not only withstand Quaternary glaciations, but was a significant part of the glacial-age landscapes of the Irano-Turanian territory. We argue that the extremely high rate of speciation and endemism of Cousinia is due to (i) the continuous presence of a complex topography in the Middle East and Central Asia since Tertiary times, which created a wide range of environmental niches and facilitated the formation and persistence of isolated populations over long periods, (ii) relatively stable climate during the late Miocene–Pliocene compared to the Quaternary period that caused small species range shifts and gene flow, and (iii) a dampened impact of multiple glacial–interglacial cycles on the mountain regions of SW Asia compared to the higher latitude European mountain ranges. This left an extensive, non-glaciated altitudinal zone for the survival of Irano-Turanian species, thereby reducing extinction during glacial periods. During interglacial periods, many Cousinia species may have been geographically isolated in high mountain “interglacial refugia” of the Irano-Turanian region. Overall, the combination of the above factors during the Neogene resulted in geographical isolation and reduced gene flow, thereby fostering allopatric speciation in Cousinia and probably also in many other speciose Irano-Turanian plant taxa.

AU  - Djamali, Morteza

AU  - Baumel, Alex

AU  - Brewer, Simon

AU  - Jackson, Stephen T.

AU  - Kadereit, Joachim W.

AU  - López-Vinyallonga, Sara

AU  - Mehregan, Iraj

AU  - Shabanian, Esmaeil

AU  - Simakova, Aleksandra

DA  - 2/15/

DO  - http://dx.doi.org/10.1016/j.revpalbo.2012.01.005

KW  - Quaternary glaciations

allopatric speciation

topographical heterogeneity

interglacial refugia

tectonic history

SW Asia

PY  - 2012

SN  - 0034-6667

SP  - 10-20

ST  - Ecological implications of Cousinia Cass. (Asteraceae) persistence through the last two glacial–interglacial cycles in the continental Middle East for the Irano-Turanian flora

T2  - Review of Palaeobotany and Palynology

TI  - Ecological implications of Cousinia Cass. (Asteraceae) persistence through the last two glacial–interglacial cycles in the continental Middle East for the Irano-Turanian flora

UR  - http://www.sciencedirect.com/science/article/pii/S0034666712000061

VL  - 172

ID  - 3

ER  - 

TY  - JOUR

AB  - This study investigates the role of climate in determining phytogeographic regions, focusing particularly on the lrano-Turanian floristic region in SW and Central Asia. A set of simple climatic variables and bioclimatic indices were used to prepare climate-space scatter plots and climate diagrams. The climate data were also subjected to multivariate analyses (PCA and Regression tree) in order to develop a bioclimatic characterization of the Irano-Turanian region in comparison with the adjacent Mediterranean, Saharo-Sindian, Euro-Siberian, and Central-Asiatic regions. Phytogeographic regions of SW and Central Asia display distinct bioclimatic spaces with small overlaps. The Irano-Turanian region is differentiated from surrounding regions by continentality, winter temperature, and precipitation seasonality. Continentality is the most important bioclimatic factor in differentiating it from the Mediterranean and Saharo-Sindian regions and is responsible for floristic differences among sub-regions of the Irano-Turanian region. In our case study, the Irano-Turanian region is a nearly independent bioclimatic unit, distinct from its surrounding regions. Hence, it is suggested that the term "Irano-Turanian bioclimate" be used to describe the climate of most of the continental Middle East and Central Asia. Among different sub-regions, the west-central part of this floristic region ("IT2 sub-region") is a major center of speciation and endemism. Our case study demonstrates that climate is a primary determinant of phytogeographic regionalization. Although modern climate and topography are strong control parameters on the floristic composition and geographical delimitation of the Irano-Turanian region, the complex paleogeographic and paleoclimatic history of SW Asia has also influenced the Tertiary and Quaternary evolution of the Irano-Turanian flora, with additional impacts by the long-lasting historic and present land-use in this region. Many lrano-Turanian montane species are threatened by global warming, and particular conservation measures are needed to protect the Irano-Turanian flora in all sub-regions. (C) 2012 Elsevier GmbH. All rights reserved.

AD  - CNRS, UMR 7263, IMBE, IRD 237, F-13545 Aix En Provence 04, France

Univ Wyoming, Dept Bot 3165, Laramie, WY 82071 USA

Univ Bielefeld, Dept Ecol, D-33619 Bielefeld, Germany

Univ Wyoming, Berry Biodivers Conservat Ctr, Program Ecol 3622, Laramie, WY 82071 USA

AN  - WOS:000304898500001

AU  - Djamali, M.

AU  - Brewer, S.

AU  - Breckle, S. W.

AU  - Jackson, S. T.

DO  - 10.1016/j.flora.2012.01.009

IS  - 4

J2  - Flora

KW  - phytogeography

climate

continentality

flora

middle east

central asia

subtropical anticyclones

photosynthetic pathways

winter temperatures

late-quaternary

vegetation

dynamics

holocene

flora

east

precipitation

LA  - English

N1  - 953uk

Times Cited:8

Cited References Count:89

PY  - 2012

SN  - 0367-2530

SP  - 237-249

ST  - Climatic determinism in phytogeographic regionalization: A test from the Irano-Turanian region, SW and Central Asia

T2  - Flora

TI  - Climatic determinism in phytogeographic regionalization: A test from the Irano-Turanian region, SW and Central Asia

UR  - <Go to ISI>://WOS:000304898500001

VL  - 207

ID  - 50

ER  - 

TY  - JOUR

AB  - We describe the spatial distribution of the genus Acantholimon Boiss. (Plumbaginaceae) taxa in Turkey, and assess the role that environmental variables may be playing on this distribution. We collected a large number of specimens from 418 geo-referenced sampling sites between 2000 and 2004, and established a point database using geographic information systems (GIS) software. As a result, we identified and mapped 67 taxa; 43 of the determined taxa appear to be endemic. We re-evaluated the current conservation status of the taxa at a national level using recent IUCN Red List categories. In addition, we extracted the corresponding environmental variables of each determined point from the updated and available environmental raster map layers of Turkey and analysed the obtained taxa and environmental data by Hierarchical Clustering and Canonical Correspondence Analysis (CCA). Hierarchical Clustering delineated the subgroups, which have similarities at various levels in respect to environmental variables. The CCA results indicated that 8 environmental variables including longitude, distance to sea, maximum temperature, mean temperature, minimum temperature, potential evapotranspiration, elevation, and precipitation are the most effective in explaining the spatial distribution of the 18 Acantholimon taxa in Turkey.

AD  - Gaziosmanpasa Univ, Geog Informat Syst & Remote Sensing Unit, Dept Soil Sci, TR-60240 Tasliciftlik, Tokat, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06800 Ankara, Turkey

AN  - WOS:000289044300001

AU  - Doğan, H. M.

AU  - Doğan, M.

AU  - Akaydin, G.

AU  - Celep, F.

DO  - 10.3906/bot-0910-193

IS  - 2

J2  - Turk J Bot

KW  - acantholimon

anatolia

biodiversity

ecology

gis

mapping

spatial analysis

iucn

canonical correspondence-analysis

sect. staticopsis plumbaginaceae

boiss. plumbaginaceae

ecology

ankara

israel

LA  - English

N1  - 743un

Times Cited:3

Cited References Count:34

PY  - 2011

SN  - 1300-008x

SP  - 91-110

ST  - Mapping and analysing the diversity of the genus Acantholimon taxa in Turkey by geographic information systems (GIS)

T2  - Turkish Journal of Botany

TI  - Mapping and analysing the diversity of the genus Acantholimon taxa in Turkey by geographic information systems (GIS)

UR  - <Go to ISI>://WOS:000289044300001

VL  - 35

ID  - 8

ER  - 

TY  - JOUR

AB  - A new species, Acantholimon avanosicum Dogan & Akaydin in the Plumbaginaceae is described and illustrated. The species grows on argillaceaus slopes in Central Anatolia, Turkey. The diagnostic morphological characters that distinguish it from closely related taxa are discussed. A revised key to Acantholimon species in Turkey with densely distichous simple spikes is presented. (C) 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 138, 365-368.

AD  - Dogan, M

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000174806000008

AU  - Dogan, M.

AU  - Akaydin, G.

DA  - Mar

DO  - DOI 10.1046/j.1095-8339.2002.00027.x

IS  - 3

J2  - Bot J Linn Soc

KW  - conservation

distribution

LA  - English

N1  - 538gc

Times Cited:11

Cited References Count:10

PY  - 2002

SN  - 0024-4074

SP  - 365-368

ST  - A new species of Acantholimon Boiss. (Plumbaginaceae) from Turkey

T2  - Botanical Journal of the Linnean Society

TI  - A new species of Acantholimon Boiss. (Plumbaginaceae) from Turkey

UR  - <Go to ISI>://WOS:000174806000008

VL  - 138

ID  - 16

ER  - 

TY  - JOUR

AB  - A new species, Acantholimon birandii, is described and illustrated from Karaman, Turkey.

AD  - Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000176737100005

AU  - Doğan, M.

AU  - Akaydin, G.

DO  - DOI 10.1111/j.1756-1051.2001.tb00800.x

IS  - 5

J2  - Nord J Bot

LA  - English

N1  - 571ug

Times Cited:9

Cited References Count:13

PY  - 2001

SN  - 0107-055x

SP  - 481-484

ST  - A new species, Acantholimon birandii (Plumbaginaceae), from the Central Anatolian Steppe in Turkey

T2  - Nordic Journal of Botany

TI  - A new species, Acantholimon birandii (Plumbaginaceae), from the Central Anatolian Steppe in Turkey

UR  - <Go to ISI>://WOS:000176737100005

VL  - 21

ID  - 18

ER  - 

TY  - JOUR

AB  - Acantholimon anatolicum Dogan & Akaydin sp. nov. (Plumbaginaceae) is described and illustrated. The species grows on deep gypsum-rich sandy soil on eroded mountain slopes between Cayirhan and Nallihan in Ankara. Diagnostic morphological characters that discern it from closely related species are discussed and its conservation status is indicated. A revised key to Acantholimon species with dense terminal spikes and excurrent scapes is given for the species found in Turkey. (C) The Linnean Society of London.

AD  - Dogan, M

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000180083100008

AU  - Doğan, M.

AU  - Akaydin, G.

DA  - Dec

DO  - DOI 10.1046/j.1095-8339.2002.00095.x

IS  - 4

J2  - Bot J Linn Soc

KW  - central anatolia

conservation

distribution

LA  - English

N1  - 629zq

Times Cited:9

Cited References Count:20

PY  - 2002

SN  - 0024-4074

SP  - 443-448

ST  - A new species of Acantholimon Boiss. (Plumbaginaceae) from Ankara, Turkey

T2  - Botanical Journal of the Linnean Society

TI  - A new species of Acantholimon Boiss. (Plumbaginaceae) from Ankara, Turkey

UR  - <Go to ISI>://WOS:000180083100008

VL  - 140

ID  - 14

ER  - 

TY  - JOUR

AD  - Dogan, M

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000176896100009

AU  - Doğan, M.

AU  - Akaydin, G.

DA  - Jun

DO  - DOI 10.1046/j.1095-8339.2002.00059.x

IS  - 2

J2  - Bot J Linn Soc

LA  - English

N1  - 574nh

Times Cited:0

Cited References Count:1

PY  - 2002

SN  - 0024-4074

SP  - 223-223

ST  - A new species of Acantholimon Boiss. (Plumbaginaceae) from Turkey

T2  - Botanical Journal of the Linnean Society

TI  - A new species of Acantholimon Boiss. (Plumbaginaceae) from Turkey

UR  - <Go to ISI>://WOS:000176896100009

VL  - 139

ID  - 15

ER  - 

TY  - JOUR

AB  - A new species, Acantholimon turcicum Dogan & Akaydin (Plumbaginaceae), is described and illustrated. The species grows on calcareous mountain scree in Astragalus spp. steppe on Hazar Mountain above Sivrice (B7 Elazig). Diagnostic morphological characteristics from the closely related species are discussed and conservation status of the species is given, along with a discussion dealing with its taxonomic relationships. A revised key to the Acantholimon species with circinnate leaf basis is also provided for the species found in Turkey.

AD  - Dogan, M

Middle E Tech Univ, Dept Sci Biol, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Sci Biol, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Sci Biol, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000187835400010

AU  - Doğan, M.

AU  - Akaydin, G.

DO  - Doi 10.1560/Nugh-We3x-6f8p-6nt5

IS  - 3

J2  - Israel J Plant Sci

KW  - ankara

LA  - English

N1  - 760lq

Times Cited:5

Cited References Count:18

PY  - 2003

SN  - 0792-9978

SP  - 231-236

ST  - An undescribed species of Acantholimon Boiss. sect. Staticopsis (Plumbaginaceae) from Turkey, with some notes on its ecology, conservation status, and relationships

T2  - Israel Journal of Plant Sciences

TI  - An undescribed species of Acantholimon Boiss. sect. Staticopsis (Plumbaginaceae) from Turkey, with some notes on its ecology, conservation status, and relationships

UR  - <Go to ISI>://WOS:000187835400010

VL  - 51

ID  - 12

ER  - 

TY  - JOUR

AB  - Acantholimon koycegizicum Dogan & Akaydin sp. nova and A. goksunicum Dogan & Akaydin sp. nova (Plumbaginaceae) are described and illustrated from Anatolia, Turkey. Acantholimon koycegizicum grows on serpentine mountain slopes between Koycegiz and Kaplicalar (C2 Mugla) in South West Anatolia, and A. goksunicum grows on calcareous mountain steppe in Goksun (B6 Kahramanmaras) in SE Anatolia. The species are closely related to A. calvertii, an endemic confined to East Anatolia. Diagnostic morphological characters are discussed. A revised key to Turkish Acantholimon species with 2-5-branched terminal spikes and previous years' stem with persistent circinate leaf bases, is also presented along with notes on the ecology, biogeography and conservational status of the new species.

AD  - Dogan, M

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000182150700006

AU  - Doğan, M.

AU  - Akaydin, G.

IS  - 1

J2  - Ann Bot Fenn

KW  - acantholimon

plumbaginaceae

taxonomy

boiss. plumbaginaceae

LA  - English

N1  - 665zg

Times Cited:7

Cited References Count:18

PY  - 2003

SN  - 0003-3847

SP  - 53-58

ST  - Two new species in Acantholimon sect. Staticopsis (Plumbaginaceae) from Turkey

T2  - Annales Botanici Fennici

TI  - Two new species in Acantholimon sect. Staticopsis (Plumbaginaceae) from Turkey

UR  - <Go to ISI>://WOS:000182150700006

VL  - 40

ID  - 13

ER  - 

TY  - JOUR

AB  - Three new species, Acantholimon bashkaleicum sp. nov., Acantholimon artosense sp. nov. and Acantholimon hoshapicum sp. nov. (Plumbaginaceae) are described and illustrated. The species are all confined to B9/B10 Van Province in East Anatolia where they grow either on calcareous mountain slopes or on mountain steppes. Diagnostic morphological characteristics from the closely related species are given, along with a discussion dealing with their taxonomic relationships, and their conservation statuses are pointed out. A revised key to the Acantholimon species with heterophyllous leaves, two or more flowered and four or more bracteated spikelets is also provided. (C) 2004 The Linnean Society of London.

AD  - Dogan, M

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Univ Hacettepe, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000221045700009

AU  - Doğan, M.

AU  - Akaydin, G.

DA  - Apr

DO  - DOI 10.1111/j.1095-8339.2003.00267.x

IS  - 4

J2  - Bot J Linn Soc

KW  - conservation

sect. acantholimon

taxonomy

boiss. plumbaginaceae

ankara

LA  - English

N1  - 815mf

Times Cited:5

Cited References Count:22

PY  - 2004

SN  - 0024-4074

SP  - 497-505

ST  - Three new species with two flowered spikelets in Acantholimon (Plumbaginaceae) from East Anatolia, Turkey

T2  - Botanical Journal of the Linnean Society

TI  - Three new species with two flowered spikelets in Acantholimon (Plumbaginaceae) from East Anatolia, Turkey

UR  - <Go to ISI>://WOS:000221045700009

VL  - 144

ID  - 11

ER  - 

TY  - JOUR

AB  - A new species, Acantholimon evrenii sp. nov. is described and illustrated for the first time in sect. Glumaria from Turkey. The species is confined to B7 Elazig in East Anatolia where it grows on rocky mountain steppes. The diagnostic morphological characters from closely related species are given, along with a discussion dealing with its taxonomic relationship. Its conservation status is indicated. A revised key is also provided for the Acantholimon species with heterophyllous leaves, two or more flowered and four or more bracteated spikelets. (c) 2005 The Linnean Society of London.

AD  - Dogan, M

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06532 Ankara, Turkey

AN  - WOS:000233540200007

AU  - Doğan, M.

AU  - Akaydin, G.

DA  - Nov

DO  - DOI 10.1111/j.1095-8339.2005.00438.x

IS  - 3

J2  - Bot J Linn Soc

KW  - conservation

east anatolia

taxonomy

staticopsis plumbaginaceae

anatolia

ankara

LA  - English

N1  - 987tm

Times Cited:5

Cited References Count:26

PY  - 2005

SN  - 0024-4074

SP  - 351-356

ST  - A new species of Acantholimon Boiss. sect. Glumaria Boiss. (Plumbaginaceae) from Elazig, Turkey

T2  - Botanical Journal of the Linnean Society

TI  - A new species of Acantholimon Boiss. sect. Glumaria Boiss. (Plumbaginaceae) from Elazig, Turkey

UR  - <Go to ISI>://WOS:000233540200007

VL  - 149

ID  - 10

ER  - 

TY  - JOUR

AB  - A synopsis of Acantholimon in Turkey is given on the basis of a revisional study conducted in Turkey by the authors. An account of 52 species, ten subspecies, and 17 varieties is given, including keys to the species, subspecies, and varieties, and a general indication of their distribution, as well as their conservation status in Turkey. Seven new taxa, namely A. ekimii sp. nov., A. capitatum ssp. sivasicum ssp. nov., A. calvertii var. glabrum var. nov., A. huetii var. breviscapum var. nov., A. acerosum ssp. longibracteolorum ssp. nov., A. lycaonicum ssp. cappadocicum ssp. nov., and A. halophilum var. coloratum var. nov., are described, together with a few new combinations. A. wiedemannii, A. iconicum, and A. lycaonicum, described from Turkey in the past, but placed under other species as synonyms in the Flora of Turkey, are recognized once again as good species. A. multiflorum and A. parviflorum are given a species status. In Turkey, the presence of A. latifolium, A. araxanum, A. lepturoides, A. hohenackerii, A. senganense, A. fominii, A. petraeum, and A. tragacanthinum is also confirmed. (c) 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 397-419.

AD  - Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

Hacettepe Univ, Dept Biol Educ, TR-06800 Ankara, Turkey

AN  - WOS:000248372200010

AU  - Doğan, M.

AU  - Akaydin, G.

DA  - Jul

DO  - DOI 10.1111/j.1095-8339.2007.00663.x

IS  - 3