Phylogenetic Relationships and Historical Biogeography of Neotropical Parrots (Psittaciformes: Psittacidae: Arini) Inferred from Mitochondrial and Nuclear DNA Sequences
ABSTRACT Previous hypotheses of phylogenetic relationships among Neotropical parrots were based on limited taxon sampling and lacked support for most internal nodes. In this study we increased the number of taxa (29 species belonging to 25 of the 30 genera) and gene sequences (6388 base pairs of RAG-1, cyt b, NADH2, ATPase 6, ATPase 8, COIII, 12S rDNA, and 16S rDNA) to obtain a stronger molecular phylogenetic hypothesis for this group of birds. Analyses of the combined gene sequences using maximum likelihood and Bayesian methods resulted in a well-supported phylogeny and indicated that amazons and allies are a sister clade to macaws, conures, and relatives, and these two clades are in turn a sister group to parrotlets. Key morphological and behavioral characters used in previous classifications were mapped on the molecular tree and were phylogenetically uninformative. We estimated divergence times of taxa using the molecular tree and Bayesian and penalized likelihood methods that allow for rate variation in DNA substitutions among sites and taxa. Our estimates suggest that the Neotropical parrots shared a common ancestor with Australian parrots 59 Mya (million of years ago; 95% credibility interval (CrI) 66, 51 Mya), well before Australia separated from Antarctica and South America, implying that ancestral parrots were widespread in Gondwanaland. Thus, the divergence of Australian and Neotropical parrots could be attributed to vicariance. The three major clades of Neotropical parrots originated about 50 Mya (95% CrI 57, 41 Mya), coinciding with periods of higher sea level when both Antarctica and South America were fragmented with transcontinental seaways, and likely isolated the ancestors of modern Neotropical parrots in different regions in these continents. The correspondence between major paleoenvironmental changes in South America and the diversification of genera in the clade of amazons and allies between 46 and 16 Mya suggests they diversified exclusively in South America. Conversely, ancestors of parrotlets and of macaws, conures, and allies may have been isolated in Antarctica and/or the southern cone of South America, and only dispersed out of these southern regions when climate cooled and Antarctica became ice-encrusted about 35 Mya. The subsequent radiation of macaws and their allies in South America beginning about 28 Mya (95% CrI 22, 35 Mya) coincides with the uplift of the Andes and the subsequent formation of dry, open grassland habitats that would have facilitated ecological speciation via niche expansion from forested habitats.
[Show abstract] [Hide abstract]
- "animals (Pereira et al. 2002; Tavares et al. 2006). Six haplotypes were identified (Supplementary Table S1 online). "
ABSTRACT: Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: email@example.com.The Journal of heredity 01/2015; 106 Suppl 1. DOI:10.1093/jhered/esv035 · 1.97 Impact Factor
[Show abstract] [Hide abstract]
- "ND2 sequences were taken from GenBank or generated using the primers MetL and ASNH for PCR amplification and sequencing from both sides (Tavares et al. 2006). The laboratory methods followed Schweizer et al. (2010) using the PCR Protocol of Tavares et al. (2006) for ND 2 with the annealing temperature set to 53°C. The alignment of the sequences was done manually with BioEdit 22.214.171.124 (Hall 1999). "
ABSTRACT: Specialization to nectarivory is associated with radiations within different bird groups, including parrots. One of them, the Australasian lories, were shown to be unexpectedly species-rich. Their shift to nectarivory may have created an ecological opportunity promoting species proliferation. Several morphological specializations of the feeding tract to nectarivory have been described for parrots. However, they have never been assessed in a quantitative framework considering phylogenetic non-independence. Using a phylogenetic comparative approach with broad taxon sampling and 15 continuous characters of the digestive tract, we demonstrate that nectarivorous parrots differ in several traits from the remaining parrots. These trait-changes indicate phenotype-environment correlations and parallel evolution, and may reflect adaptations to feed effectively on nectar. Moreover, the diet shift was associated with significant trait shifts at the base of the radiation of the lories, as shown by a newly developed statistical approach. Their diet shift might be considered as an evolutionary key innovation which promoted significant non-adaptive lineage diversification through allopatric partitioning of the same new niche. The lack of increased rates of cladogenesis in other nectarivorous parrots indicates that evolutionary innovations need not be associated one-to-one with diversification events.Ecology and Evolution 07/2014; 4(14). DOI:10.1002/ece3.1131 · 1.66 Impact Factor
[Show abstract] [Hide abstract]
- "Weir, 2006; Hoorn et al., 2010). This diversification may have occurred as a result of niche expansion and ecological speciation , or as a result of vicariance events between isolated habitat patches (Tavares et al., 2006; Schweizer et al., 2011). Arini are a good clade in which to explore continentalscale diversification, and should permit us to assess the relative importance of the classical model of adaptive radiation on the one hand – which involves the filling of a fixed set of niches after an initial colonization event – and the more continuous process of diversification driven by dynamic and changing environments on the other. "
ABSTRACT: The Neotropical parrots (Arini) are an unusually diverse group which colonized South America in the Oligocene. The newly invaded Neotropics may have functioned as an underused adaptive zone and provided novel ecological opportunities that facilitated diversification. Alternatively, diversification may have been driven by ecological changes caused by Andean uplift and/or climate change from the Miocene onwards. Our aim was to find out whether Arini diversified in a classical adaptive radiation after their colonization of South America, or whether their diversification occurred later and was influenced by more recent environmental change. Neotropics. We generated a time-calibrated phylogeny of more than 80% of all Arini species in order to analyse lineage diversification. This chronogram was also used as the basis for the reconstruction of morphological evolution within Arini using a multivariate ratio analysis of three size measurements. We found a concentration of size evolution and partitioning of size niches in the early history of Arini consistent with the process of adaptive radiation, but there were no signs of an early burst of speciation or a decrease in speciation rates through time. Although we detected no overall temporal shifts in diversification rates, we discovered two young, unexpectedly species-rich clades. Arini show signs of an early adaptive radiation, but we found no evidence of the slowdown in speciation rate generally considered a feature of island or lake radiations. Historical processes and environmental change from the Miocene onwards may have kept diversification rates roughly constant ever since the colonization of the Neotropics. Thus, Arini may not yet have reached equilibrium diversity. The lack of diversity-dependent speciation might be a general feature of adaptive radiations on a continental scale, and diversification processes on continents might therefore not be as ecologically limited as in isolated lakes or on oceanic islands.Journal of Biogeography 07/2014; 41(7). DOI:10.1111/jbi.12293 · 4.97 Impact Factor