Show simple item record

dc.contributor.advisorStone, Graham
dc.contributor.advisorRichardson, James
dc.contributor.authorValderrama Escallon, Eugenio
dc.date.accessioned2017-12-20T15:54:55Z
dc.date.available2017-12-20T15:54:55Z
dc.date.issued2016-06-28
dc.identifier.urihttp://hdl.handle.net/1842/25791
dc.description.abstractThe well-known high species richness of the tropical forests is not uniform through its different regions; Africa is species-poor when compared to Southeast Asia and the Neotropical region. One of the hypotheses for differences between the richness in the Neotropics and Africa points to the importance of recent speciation in the Neotropics. This is considered in particular in Andean-centred taxa that probably diversified in response to the opportunities for speciation offered by the final uplift of the tropical Andes (during the past c. 25 million years [Ma] to the present, with higher rates on the past 10 Ma to the present). The aim of this thesis is to test this hypothesis in the genus Renealmia L.f. (Zingiberaceae), an Andean centred lineage (c. 64 Neotropical spp.) that also occurs in Africa (c. 17 spp.). A taxonomic account of the Colombian species (c. 32; the country with the most species) is presented, and three species new to science were discovered and are described in an updated revision. I designed a new approach for obtaining nuclear phylogenetic markers for estimating species-level phylogenies using transcriptomes for recent diversification that could be applied to samples from herbarium specimens. I generated de-novo transcriptomes for two Renealmia species and a relative in the subfamily Alpinioideae that were combined with data available in repositories to target low copy number and potentially orthologous genes with short introns. I obtained sequence data for eight introns (ranging from 219 to 924 bp) and an rRNA (ITS1 & ITS2) marker for 40 species and at least one marker for 64 species, comprising a total of 137 accessions of which 67.9%(93) were sampled from herbarium specimens. Gene and species-trees were estimated for the genus. I found that most of the subgroups based on morphological characters are supported by the molecular data but a possible combination of incomplete lineage sorting (related to recent radiations or large population sizes) and/or introgression through hybridisation makes difficult to solve the relationships among these subgroups. Finally I estimated and compared diversification rates of the Neotropical and African lineages using dated phylogenies based on the trees estimated. I used available and customized methods that take into account incomplete taxon sampling, the uncertainty in the phylogenetic relationships and the stochasticity inherent to diversifications processes. Differences in diversification rates between Africa and the Neotropics indicate increased speciation attributable to the Andean orogeny in the Neotropical lineages of Renealmia.en
dc.contributor.sponsorotheren
dc.language.isoenen
dc.publisherThe University of Edinburghen
dc.relation.hasversionArmstrong K.E., Stone G.N., Nicholls J.A., Valderrama E., Anderberg A.A., Smedmark J., Gautier L., Naciri Y., Milne R., & Richardson J.E. (2014) Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae. Frontiers in genetics, 5, 1–13.en
dc.relation.hasversionSteege ter H., Pitman N.C.A., Sabatier D., Baraloto C., Salomão R.P., Guevara J.E., Phillips O.L., Castilho C.V., Magnusson W.E., Molino J.-F., Monteagudo A., Núñez Vargas P., Montero J.C., Feldpausch T.R., Coronado E.N.H., Killeen T.J., Mostacedo B., Vasquez R., Assis R.L., Terborgh J., Wittmann F., Andrade A., Laurance W.F., Laurance S.G.W., Marimon B.S., Marimon B.-H., Guimarães Vieira I.C., Amaral I.L., Brienen R., Castellanos H., Cárdenas López D., Duivenvoorden J.F., Mogollón H.F., Matos F.D. de A., Dávila N., García-Villacorta R., Stevenson Diaz P.R., Costa F., Emilio T., Levis C., Schietti J., Souza P., Alonso A., Dallmeier F., Montoya A.J.D., Fernandez Piedade M.T., Araujo-Murakami A., Arroyo L., Gribel R., Fine P.V.A., Peres C.A., Toledo M., Aymard C G.A., Baker T.R., Cerón C., Engel J., Henkel T.W., Maas P., Petronelli P., Stropp J., Zartman C.E., Daly D., Neill D., Silveira M., Paredes M.R., Chave J., Lima Filho D. de A., Jørgensen P.M., Fuentes A., Schöngart J., Cornejo Valverde F., Di Fiore A., Jimenez E.M., Peñuela Mora M.C., Phillips J.F., Rivas G., van Andel T.R., Hildebrand von P., Hoffman B., Zent E.L., Malhi Y., Prieto A., Rudas A., Ruschell A.R., Silva N., Vos V., Zent S., Oliveira A.A., Schutz A.C., Gonzales T., Trindade Nascimento M., Ramirez-Angulo H., Sierra R., Tirado M., Umaña Medina M.N., van der Heijden G., Vela C.I.A., Vilanova Torre E., Vriesendorp C., Wang O., Young K.R., Baider C., Balslev H., Ferreira C., Mesones I., Torres-Lezama A., Urrego Giraldo L.E., Zagt R., Alexiades M.N., Hernandez L., Huamantupa-Chuquimaco I., Milliken W., Palacios Cuenca W., Pauletto D., Valderrama Sandoval E., Valenzuela Gamarra L., Dexter K.G., Feeley K., Lopez- Gonzalez G., & Silman M.R. (2013) Hyperdominance in the Amazonian tree flora. Science, 342, 1243092.en
dc.subjectNeotropical radiationsen
dc.subjectAfricaen
dc.subjectRenealmiaen
dc.subjectAndean orogenyen
dc.subjectdiversification ratesen
dc.subjectde-novo transcriptomesen
dc.subjecttranscriptome miningen
dc.subjectspecies treesen
dc.subjectColombiaen
dc.titleExplaining the differences in African and Neotropical species richness by comparing diversification rates in Renealmia L.f. (Zingiberaceae).en
dc.typeThesis or Dissertationen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD Doctor of Philosophyen
dc.rights.embargodate2100-12-31en
dcterms.accessRightsRestricted Accessen


Files in this item

This item appears in the following Collection(s)

Show simple item record