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Cryptic Species in a Neotropical Parrot: Genetic Variation Within the Amazona Farinosa Species Complex and Its Conservation Implications

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Cryptic Species in a Neotropical Parrot: Genetic Variation Within the Amazona Farinosa Species Complex and Its Conservation Implications Conserv Genet DOI 10.1007/s10592-012-0364-8 SHORT COMMUNICATION Cryptic species in a Neotropical parrot: genetic variation within the Amazona farinosa species complex and its conservation implications Theodore J. Wenner • Michael A. Russello • Timothy F. Wright Received: 7 December 2011 / Accepted: 9 May 2012 Ó Springer Science+Business Media B.V. 2012 Abstract The application of genetic approaches has cytochrome-b (3.5–5.4 % corrected distance). Our data enhanced the identification of cryptic species in a wide support recognizing Central American and South American variety of taxa, often with immediate conservation impli- Mealy Amazons as separate species worthy of independent cations. Here, we employed multilocus DNA analyses to conservation management. Furthermore, our results suggest assess genetic variation and its correspondence to taxonomy recognition of two separate management units within the within the Mealy Amazon (Amazona farinosa), a parrot South American clade, although further study is required. species found in Central and South America. DNA sequence These findings have important conservation implications as data from four mitochondrial regions and two nuclear introns Central American A. farinosa are under increased pressure were used to infer relationships among all five named sub- from habitat destruction and collection for the pet trade, species in this species complex. Two reciprocally mono- yet are listed as of Least Concern due to their current clas- phyletic groups with strong nodal support were found; one sification as subspecies’ subsumed within the species comprised of the two Central American subspecies guate- complex. malae and virenticeps and one including all three South American subspecies farinosa, chapmani, and inornata. Keywords Cryptic species Á Mealy Amazon Á Molecular characters diagnosed distinct Central American Neotropics Á Parrots Á Species complex and South American lineages, with an estimated divergence time of 1.75–2.70 million years ago as inferred from Introduction Electronic supplementary material The online version of this Accurate scientific taxonomy is a foundation for effective article (doi:10.1007/s10592-012-0364-8) contains supplementary conservation efforts, particularly those focusing on indi- material, which is available to authorized users. vidual species as representatives of distinct evolutionary T. J. Wenner Á T. F. Wright histories (Hazevoet 1996; Mace 2004). However, species Department of Biology, MSC 3AF, New Mexico State status is not always definitively known, especially in University, Las Cruces, NM 88003, USA morphologically conserved species or within variable e-mail: [email protected] species complexes that may conceal genetically distinct Present Address: species. Application of genetic approaches has enhanced T. J. Wenner (&) the identification of such cryptic species in a wide variety School of Zoology, University of Tasmania, Private Bag 5, of taxa, often with immediate conservation implications Hobart, TAS 7001, Australia e-mail: [email protected] (Bickford et al. 2007; Russello et al. 2005). These suc- cesses include several notable examples from the parrots M. A. Russello (Order Psitacciformes; Eberhard and Bermingham 2004; Department of Biology, The University of British Columbia, Murphy et al. 2011; Russello et al. 2010), which is one of Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada the most endangered large orders of birds (Birdlife Inter- e-mail: [email protected] national 2004). 123 Conserv Genet Parrots of the genus Amazona are highly prized in the populations. It is important to note however that a small exotic pet trade due to their colorful plumage and ability to sample size, incomplete taxon sampling and lack of vou- mimic human speech. As a consequence, a majority of chered A. farinosa specimens limit the conclusions of Amazona species are listed by the IUCN under some cat- Russello and Amato (2004). In the present study, we used egory of conservation concern (e.g., near threatened, vul- multilocus DNA sequence analyses derived exclusively nerable, endangered or critically endangered; IUCN 2011). from vouchered specimens to explicitly test whether Cen- However, the Mealy Amazon (Amazona farinosa) is listed tral and South American A. farinosa constitute distinct as a species of Least Concern due to an extensive range and phylogenetic species (Cracraft 1983) in order to resolve large population, even though the species has a declining taxonomic uncertainty within this complex and address population trend (IUCN 2011). Central American popula- associated conservation implications. tions are under particular pressure from habitat loss and collection for the pet trade (Juniper and Parr 1998; J Gilardi pers. comm.) Methods The A. farinosa species complex consists of five rec- ognized subspecies (farinosa, chapmani, inornata, viren- We sampled all five recognized subspecies of A. farinosa ticeps, and guatemalae) ranging from southern Mexico as well as A. kawalli; Amazona auropalliata and Amazona through Central America and Panama, and through the amazonica were included as outgroups. We only used Amazon basin to southern Brazil and along the Atlantic vouchered samples from museum collections and excluded Coastal Forest (Fig. 1). Morphological variation has lead to the four specimens from Russello and Amato (2004) due to numerous revisions of this species complex with the Cen- their undocumented origins. Most samples came from tral American forms A. f. guatemalae and A. f. virenticeps frozen tissues, but five originated from toe pads of study once treated as full species before being subsumed as skins and one from a bone fragment of a study skeleton subspecies of A. farinosa (Juniper and Parr 1998; Salvadori (Online Resource 1). 1891). Amazona kawalli was once recognized as an aber- For frozen tissue samples, total genomic DNA was rant form of A. farinosa but is now recognized as a distinct isolated using a DNeasy extraction kit following manu- species (Collar and Pittman 1996; Stresemann 1924). facturer’s protocol (Qiagen, Valencia, CA). Four mito- Russello and Amato’s (2004) molecular phylogeny of chondrial DNA fragments [12 s rDNA (12S); 16 s rDNA the genus Amazona included one representative each of (16S); cytochrome oxidase subunit I (COI); cytochrome- four of the five subspecies of A. farinosa. They found that b (CYTB)] and two non-coding nuclear introns [tropomy- Central American and South American subspecies formed osin alpha-subunit intron 5 (TROP); transforming growth sister clades but the distance between the two groups factor b-2 intron 1 (TGFB2)] were PCR amplified (primers of subspecies was as pronounced as divisions between in Online Resource 2). Bone and toe pad extractions were other long-recognized Amazona species (Russello and conducted in a UV hood in a lab where no vertebrate PCR Amato 2004). Such a division could have important con- products have ever been present. Negative extraction and servation implications, particularly for Central American PCR controls were conducted alongside to monitor for Fig. 1 Sampling localities and ranges of currently recognized subspecies with median-joining network based on 1,157 bp of COI and CYTB summarizing the relationships among subspecies. Size of circle is proportional to the number of individuals sharing that haplotype. Branches represent number of mutational steps between haplotypes and are proportional in length to the number of changes from one to six mutations, or otherwise are denoted by numbers on branches 123 Conserv Genet contamination. DNA isolation was conducted with modi- Net between group mean genetic distances were calcu- fications to the DNeasy protocol following Boessenkool lated using MEGA 5.05 (Tamura et al. 2011) and the et al. (2009) for both bone and toe pad samples. Only COI Kimura 2-Parameter model (Kimura 1980) with gamma and CYTB fragments were amplified from these samples distribution of rates among sites, to account for intra using primers that amplified overlapping fragments. population variation before calculating inter population All PCRs were cleaned using QiaQuick 96 PCR purifi- distances. Standard deviation estimates were calculated cation kit (Qiagen, Valencia, CA) and manufacturer’s using 1,000 bootstrap replicates. protocols. Products were sequenced at the University of Chicago CRC DNA sequencing facility, with the same primers used for PCR. Resulting bi-directional sequences Results were checked and edited using Sequencher 4.10.1 (Gene Codes Corporation, Ann Arbor, MI) and consensus A total of 3,463 bp was obtained for the full dataset including sequences were aligned in Clustal X 2.1 (Larkin et al. both nuclear and mtDNA: 393 bp of 12S, 526 bp of 16S, 2007) employing default settings for gap opening and 528 bp or 422 bp of COI (some toepads failed to amplify a extension. section), 868 bp or 776 bp of CYTB (some toepads failed to Unique haplotypes were identified using DnaSP 5.10 amplify a section), 523 bp of TROP, and 625 bp of TGFB2 (Librado and Rozas 2009) for a combined data set of (sequences deposited in GenBank Online Resource 1). Evi- CYTB and COI. We constructed a median joining haplo- dence we sequenced from mitochondria include: (1) long type network using Network 4.6.0.0 (Fluxus Technology amplifications or highly specific internal primers with sig- Ltd., Clare, England) to estimate relationships among nificant overlap; (2) lack of indels or stop codons observed in haplotypes. Nuclear and mtDNA sequence alignments for coding
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