title: Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate.
abstract: The squirrel monkey, Saimiri, is a pan-Amazonian Pleistocene radiation. We use statistical phylogeographic methods to create a mitochondrial DNA-based timetree for 118 squirrel monkey samples across 68 localities spanning all Amazonian centers of endemism, with the aim of better understanding (1) the effects of rivers as barriers to dispersal and distribution; (2) the area of origin for modern Saimiri; (3) whether ancestral Saimiri was a lowland lake-affiliated or an upland forest taxa; and (4) the effects of Pleistocene climate fluctuation on speciation. We also use our topology to help resolve current controversies in Saimiri taxonomy and species relationships. The Rondônia and Inambari centers in the southern Amazon were recovered as the most likely areas of origin for Saimiri. The Amazon River proved a strong barrier to dispersal, and squirrel monkey expansion and diversification was rapid, with all speciation events estimated to occur between 1.4 and 0.6Ma, predating the last three glacial maxima and eliminating climate extremes as the main driver of squirrel monkey speciation. Saimiri expansion was concentrated first in central and western Amazonia, which according to the "Young Amazon" hypothesis was just becoming available as floodplain habitat with the draining of the Amazon Lake. Squirrel monkeys also expanded and diversified east, both north and south of the Amazon, coincident with the formation of new rivers. This evolutionary history is most consistent with a Young Amazon Flooded Forest Taxa model, suggesting Saimiri has always maintained a lowland wetlands niche and was able to greatly expand its range with the transition from a lacustrine to a riverine system in Amazonia. Saimiri vanzolinii was recovered as the sister group to one clade of Saimiri ustus, discordant with the traditional Gothic vs. Roman morphological division of squirrel monkeys. We also found paraphyly within each of the currently recognized species: S. sciureus, S. ustus, and S. macrodon. We discuss evidence for taxonomic revision within the genus Saimiri, and the need for future work using nuclear markers.
authors.affiliation: Institute for Society and Genetics, University of California, Los Angeles, CA, United States; Department of Anthropology, University of California, Los Angeles, CA, United States. Electronic address: jlynchalfaro@ucla.edu.
authors.forename: Jessica W
authors.initials: JW
authors.lastname: Lynch Alfaro
authors.affiliation: School of Environment and Life Sciences, University of Salford, UK; Instituto Nacional de Pesquisas da Amazonia (INPA), Manaus, AM, Brazil. Electronic address: j.p.boubli@salford.ac.uk.
authors.forename: Jean P
authors.initials: JP
authors.lastname: Boubli
authors.affiliation: Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga 2584, CEP: 69470-000 Tefé, AM, Brazil. Electronic address: fernanda@mamiraua.org.br.
authors.forename: Fernanda P
authors.initials: FP
authors.lastname: Paim
authors.affiliation: Instituto Nacional de Pesquisas da Amazonia (INPA), Manaus, AM, Brazil. Electronic address: camilaribas@gmail.com.
authors.forename: Camila C
authors.initials: CC
authors.lastname: Ribas
authors.affiliation: Instituto Nacional de Pesquisas da Amazonia (INPA), Manaus, AM, Brazil. Electronic address: mndasilva@gmail.com.
authors.forename: Maria Nazareth F da
authors.initials: MN
authors.lastname: Silva
authors.affiliation: Laboratory of Mastozoology, Dept. Biology, Universidade Federal de Rondônia - UNIR - Porto Velho, Rondônia, RO, Brazil. Electronic address: messias.malu@gmail.com.
authors.forename: Mariluce R
authors.initials: MR
authors.lastname: Messias
authors.affiliation: Wildlife Conservation Society, Manaus, Brazil. Electronic address: fabio@gmail.com.
authors.forename: Fabio
authors.initials: F
authors.lastname: Röhe
authors.affiliation: Museu Paraense Emilio Goeldi, Belém, Brazil. Electronic address: michellemercesmasto@gmail.com.
authors.forename: Michelle P
authors.initials: MP
authors.lastname: Mercês
authors.affiliation: Museu Paraense Emilio Goeldi, Belém, Brazil. Electronic address: cazuza.junior@gmail.com.
authors.forename: José S
authors.initials: JS
authors.lastname: Silva Júnior
authors.affiliation: Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Amapá, AP, Brazil. Electronic address: crsilva.ap@gmail.com.
authors.forename: Claudia R
authors.initials: CR
authors.lastname: Silva
authors.affiliation: Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil. Electronic address: gabriela.m.pinho@gmail.com.
authors.forename: Gabriela M
authors.initials: GM
authors.lastname: Pinho
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States. Electronic address: gohark1989@ucla.edu.
authors.forename: Gohar
authors.initials: G
authors.lastname: Koshkarian
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States. Electronic address: mttn.pro@gmail.com.
authors.forename: Mai T T
authors.initials: MT
authors.lastname: Nguyen
authors.affiliation: Universidade Federal do Pará, Belém, PA, Brazil. Electronic address: harada@ufpa.com.br.
authors.forename: Maria L
authors.initials: ML
authors.lastname: Harada
authors.affiliation: Instituto Nacional de Pesquisas da Amazonia (INPA), Manaus, AM, Brazil; Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga 2584, CEP: 69470-000 Tefé, AM, Brazil. Electronic address: rmrabelo@gmail.com.
authors.forename: Rafael M
authors.initials: RM
authors.lastname: Rabelo
authors.affiliation: Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga 2584, CEP: 69470-000 Tefé, AM, Brazil. Electronic address: helder@mamiraua.org.br.
authors.forename: Helder L
authors.initials: HL
authors.lastname: Queiroz
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States. Electronic address: michaelalfaro@ucla.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Alfaro
authors.affiliation: Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil. Electronic address: izeni@evoamazon.net.
authors.forename: Izeni P
authors.initials: IP
authors.lastname: Farias
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000235:genetics; D017753:Ecosystem; D008957:Models, Genetic; D010802:Phylogeny; D058974:Phylogeography; D012453:Saimiri / Q000145:classification*; D017422:Sequence Analysis, DNA; D013020:South America
chemical_list: D004272:DNA, Mitochondrial
keywords: Cebidae; Phylogenetics; Pleistocene diversification; Refugia hypothesis; River barriers; South America