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Revista Brasileira de Ornitologia 25(1): 60–66. ARTICLE March 2017 Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) indicates a history of demographic decline 1 1 2 3 Leilton Willians Luna , Thainara Olive ira Souza , Weber Andrade de Girão e Silva , Horacio Schneider , Iracilda 3 1 1,4 Sampaio , Juliana Araripe & Péricles Sena do Rêgo Laboratório de Genética e Conservação, Instituto de Estudos Costeiros, Universidade Federal do Pará, Alameda Leandro Ribeiro s/n, Aldeia, CEP 68600-000, Bragança, PA, Brazil. Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, CEP 61627-610, Caucaia, CE, Brazil. Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Alameda Leandro Ribeiro s/n, Aldeia, CEP 68600-000, Bragança, PA, Brazil. Corresponding author: email@example.com Received on 10 May 2016. Accepted on 22 April 2017. ABSTRACT: The Araripe Manakin (An tilophia bokermanni) is a “Critically Endangered” bird species endemic to northeastern Brazil. The habitat of the species has suffered intense fragmentation and degradation in recent years, resulting in a decline in population numbers. The present study evaluated t he genetic diversity and structure of this population through the analysis of the Hypervariable Domain I of the mitochondrial Control Region and two nuclear introns (I7BF and G3PDH). Results revealed an absence of population substructuring and population decline beginning during the late Pleistocene, approximately 50,000 years ago. The evidence indicates that the effective population size of the Araripe Manakin has declined gradually over time ever since, a process that may have been intensified as a result of the recent anthropogenic impacts on the habitat of the species. KEY-WORDS: coalescent theory, conservation, control region, Pipridae, population genetics. INTRODUCTION and may lead to a loss of fitness (Frankham 2005). A recent study of the Araripe Manakin revealed slightly lower The Araripe Manakin (An tilophia bokermanni) is the genetic diversity in comparison with its sister species, A. world's most threatened species of manakin, according to galeata (Rêgo et al. 2010). Historical evolutionary processes are generally the International Union for the Conservation of Nature (BirdLife International 2016). This species is endemic to underestimated during the development of conservation a small tract of humid forest on the slopes of the Araripe policies for threatened species (Chaves et al. 2011), Plateau in Ceará state in northeastern Brazil. The principal despite the importance of understanding the demographic threats to the survival of the species are the ongoing history of threatened populations, such as those of A. bokermanni, for the development of reliable conservation anthropogenic degradation and loss of habitat, which is thought to contain less than one thousand individuals programs (Cornetti et al. 2014). In this context, genetic (Silva et al. 2011, BirdLife International 2016). data can support a better understanding of demographic The risks faced by A. bokermanni highlight the need for processes that contributed to the current genetic diversity the collection of reliable data for the effective management of the species (Chaves et al. 2011). In the present study, the genetic diversity of A. and conservation of the remaining populations, including insights into the evolutionary history of the species. Silva et bokermanni populations was analyzed based on sequences al. (2011) estimated that the numbers of individuals have of the mitochondrial control region and two nuclear declined by more than a third over the past twenty years. introns. Based on analyses of coalescent theory, the data This may have intensified t he process of genetic drift, were used to detect possible signs of historical demographic variation, and describe the spatial distribution of the further reducing the genetic variability of its populations, while also increasing the probability of inbreeding, which genetic variation of the present-day population of the favors the appearance of genetic anomalies and diseases, Araripe Manakin. Revista Brasileira de Ornitologia 25(1): 2017 Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) Luna et al. METHODS Beta-Fibrinogen (I7BF) and intron of the glycerol-3- phosphate dehydrogenase 11 gene (G3PDH). Primers used were Dloop H-739 (Sorenson et al. 1999) and Population sampling and laboratory procedures CytB-End (Bensch & Harlid 2000) for HDI, FIB-BI7H Samples of blood or feathers were obtained from 37 and FIB-BI7L (Prychitko & Moore 1997) for I7BF, Araripe Manakins obtained from 12 sites distributed and G3PDH13b and G3PDH14b (Fjeldså et al. 2003) for G3PDH. Amplification condition consisted of an throughout the geographic range of the species (Fig. initial denaturation at 94°C for 3 min, followed by 35 1A, B). Samples were stored in 95% ethanol at -20°C. Total genomic DNA was isolated using a Wizard cycles of denaturarion at 94°C for 30 s, hybridization Genomic DNA Purification kit (Promega) accor ding at locus specific temperatures and times (HDI, 52°C to the manufacturer's instructions. Polymerase Chain for 30 s; I7BF, 50°C for 35 s and G3PDH, 55°C for 30 s), extension at 72°C for 1 min and a final extension Reaction (PCR) was used to amplify Hypervariable at 72°C for 10 min. PCR products were purified using Domain I (HDI) of the mitochondrial Control Region, which is widely used for the evaluation of diversity in Polyethylene Glycol 8000 (PEG, 1 g/mL), sequenced studies of population genetics (e.g. Sammler et al. 2012, using BigDye Terminator v. 3.1 Cycle Sequencing Jackson et al. 2013). We also selected two unlinked kit (Applied Biosystems™) and run in an ABI3500 XL automatic sequencer (Applied Biosystems™). nuclear introns for multilocus analyses, intron 7 of the Figure 1. (A) Location of the Araripe Plateau in Ceará state, northeastern Brazil. (B) Distribution of Antilophia bokermanni and sites at which samples were collected in upland rainforest. (C) Haplotype network, only for HDI control region, and the number of individuals per haplotype. Genetic computational analysis the introns were established using the Phase algorithm (Stephens & Donnelly 2003), with posterior probabilities Sequences were aligned in Clustal-W (Thompson et al. of at least 0.6 were considered to be resolved (Harrigan et 1994) and edited in Bioedit 7.2 (Hall 1999). Best-fit al. 2008). A hierarchical analysis of molecular variance models of nucleotide evolution were determined in Mega (AMOVA) was run in Arlequin 18.104.22.168 (Excoffier & 6 (Tamura et al. 2013), based on the Bayesian Information Lischer 2010), for which we inferred the presence of Criterion (BIC) with the HKY model being chosen for two groups, one located in the northwestern portion of mtDNA, and the T93 model for the two nuclear introns, the distribution of the species (sites 1–7), and the other which were used in the Bayesian Skyline Plot analyses in the southeastern portion (sites 8–12), based on the (see below). The possible recombination of the markers discontinuity in the distribution of the humid forest was verified using the phi test (Bruen et al. 2006), run (Table 1; Fig. 1) (see Rêgo et al. 2010, Silva et al. 2011). in Splits Tree 4 4.14.4 (Huson & Bryant 2006). Genetic The number of independent A. bokermanni populations, diversity was estimated based on the indices of haplotype based on the assumption of non-spatially hierarchical (h) and nucleotide (π) diversity, which were calculated in genetic mixing at an individual level, was inferred from Dnasp 5.1 (Librado & Rozas 2009). Gametic phases of the mitochondrial database using the Bayesian Analysis Revista Brasileira de Ornitologia 25(1): 2017 Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) Luna et al. of Population Structure software (Baps 6; Corander et an Extended Bayesian Skyline Plot (EBSP) was used al. 2008). A haplotype network was also inferred using for a simultaneous analysis of the three markers (Heled the maximum likelihood approach in Haploviewer & Drummond 2008) to test historical fluctuations in population size. These analyses were run for 200 × 10 (Salzburger et al. 2011) to provide a visual representation of the relationships among haplotypes. generations with sample genealogies being sampled every Two approaches were used to evaluate the occurrence 10,000 generations, in a strict molecular clock model, of historic changes in the size of the A. bokermanni in which the first 10% of generations were discar ded as population. Firstly, deviations from neutral evolution burn-in. The calibration of the molecular clock was based on the intraspecific mutation rate estimated by Norman was based on three tests, Fu's F (Fu 1997), Tajima D (Tajima 1989), and R2 (Ramos-Onsins & Rozas 2002), et al. (2014) for the HDI (0.0348 substitutions per site followed by a mismatch distribution analysis, in order per lineage per million years), and 0.0135 substitutions to evaluate whether the A. bokermanni population is per site per lineage per million years for nuclear introns in equilibrium, expansion or has suffered a bottleneck (Ellegren 2007). One year was assumed as generation time in the calculation of the effective number of (Rogers & Harpending 1992). These tests were computed in Dnasp 5.1. Secondly, Beast 1.8 software (Drummond females (Nef). The BSP/EBSP and t he Effective Sample & Rambaut 2007) was used to estimate a Bayesian Sizes (ESS) were determined in Tracer 1.6 (Rambaut & Skyline Plot (BSP) for the mitochondrial data, while Drummond 2007). Table 1. Sample sites and their geographic coordinates, number of samples analyzed, and the haplotypes observed for HDI control region only, on Araripe Manakin (Antilophia bokermanni). Sample No. of Geographic coordinates Hap1Hap2Hap3Hap4Hap5Hap6 sites samples 1 39°28'28''W; 7°13'48''S 6 - - - 2 4 - 2 39°28'20''W; 7°14'18''S 2 1 - - - 1 - 3 39°28'14''W; 7°15'41''S 2 1 - - 1 - - 4 39°26'21''W; 7°17'01''S 2 - 1 - - 1 - 5 39°23'51''W; 7°18'43''S 3 1 - - 1 1 - 6 39°24'29''W; 7°19'42''S 1 ----- 1 7 39°24'45''W; 7°19'58''S 2 - - - 2 - - 8 39°21'36''W; 7°22'49''S 1 ---- 1 - 9 39°18'48''W; 7°21'57''S 6 2 - 1 2 1 - 10 39°13'37''W; 7°24'46''S 2 ----- 2 11 39°10'01''W; 7°24'24''S 3 1 - - - 2 - 12 39°12'23''W; 7°24'34''S 5 - - - 2 3 - Total 35 6 1 1 10 14 3 RESULTS of 0.0161. By contrast, introns presented lower levels of genetic diversity, with only three haplotypes for Population genetic diversity and structure each marker (Table 2), and lower levels of haplotype and nucleotide diversity for both I7BF (0.080 and 0.00008, respectively) and G3PDH (0.210 and 0.00055, Total dataset length and individual count was 348 bp respectively). Non-significant F values (Table 2) were for mitochondrial HDI from 35 specimens, 961 bp st for I7BF from 37 specimens and 393 bp for G3PDH obtained between the northwestern and southeastern intron from 31 specimens, with no evidence of indels. segments of the population, indicating a lack of genetic GenBank accession numbers for the sequences of the sub-structuring in both mitochondrial (-0.007) and nuclear (-0.008) markers. The AMOVA indicated t hat all different molecular markers analyzed: HDI (KY788006 (100%) the molecular variability was contained within – KY788011), G3PDH (KY788012, Hap1 n = 24; KY788013, Hap2 n = 3; KY788014 Hap3, n = 4) and the population as a whole, rather than in the different I7BF (KY788015, Hap1 n = 34; KY788016, Hap2 n subpopulations. The structural analysis in Baps indicated = 1; KY788017 Hap3, n = 2). The phi test found no the existence of two groups (k = 2, marginal probability = -108.6688), but without independent lineages when the evidence of any significant recombination in this marker northwestern and southeastern groupings were included (P > 0.9). A total of 15 polymorphic sites was identified for the control region, with six haplotypes (Table 1), and in the analysis (Appendix I). The haplotype network, haplotype diversity of 0.741 and nucleotide diversity represented only for HDI (Fig. 1C) shows that the most Revista Brasileira de Ornitologia 25(1): 2017 Southeast Northwest Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) Luna et al. common haplotypes (Hap1, Hap4, Hap5) are found mitochondrial marker, presented a bimodal pattern (Fig. throughout the population (Table 1). 2), which was consistent with the haplotype network, but distinct from that of a population in equilibrium. Historical demography The evaluation of historic changes in population size based on the inferences derived from the EBSP found low Significant positive results were obtained from t he data ESS values (< 200) in the different simulations. On the for the HDI for D (1.7591; P < 0.05), F (5.368; P < other hand, the demographic pattern outlined by the 0.01) and R2 (0.1868; P < 0.01), rejecting the equilibrium BSP (Fig. 3), focusing exclusively on the mitochondrial population hypothesis. For the nuclear markers, the locus, indicates that mean values of effective size of the A. neutrality and population change tests did not return bokermanni population (females only) has been declining significant values (Table 2), and did not allow any steadily over the past 50,000 years. However, the 95% reliable interpretation based on coalescence inferences. confidence intervals indicated a scenario of relative The mismatch distribution, performed only for the stability or possibly, a recent expansion. Table 2. Numbers of individuals and haplotypes sampled and summary statistics of indices of genetic diversity and population neutrality estimated for Antilophia bokermanni. n – number of samples; NH – number of haplotypes; S – variables sites; h – haplotype diversity; π – nucleotidic diversity, SD – standard deviation; D and Fs –Tajima and Fu tests, respectively; R2 – Ramos & Rozas test. * P < 0.05 (significant); ** P < 0.02 (significant). Size of Marker n NH S h ± SD π ± SD DF R2 F s st sequences Control Region-DHI 348 35 6 15 0.741 ± 0.044 0.0161 ± 0.0027 1.7591* 5.368** 0.1868* -0.007 I7BF 961 37 3 2 0.080 ± 0.043 0.0008 ± 0.00005 -1.3130 -2.853 0.0592 -0.008 G3PDH 393 31 3 2 0.210 ± 0.067 0.00055 ± 0.00018 -0.8350 -1.129 0.0541 DISCUSSION Genetic diversity and structure Despite being among the world's most threatened bird species (BirdLife International 2016), the genetic diversity reported here for the mitochondrial marker of the Araripe Manakin (HDI h = 0.741) is much higher than that found typically in the other threatened species of this group, such as Aquila adalberti (h = 0.321, Martínez-Cruz et al. 2004), Pomarea dimidiata (h = 0.000, Chan et al. 2011), Figure 2. Mismatch distribution of the sequences of the HDI Control and Ardeotis nigriceps (h = 0.261, Ishtiaq et al. 2011). region of Antilophia bokermanni, based on the equilibrium population The significantly lower levels of diversity in these species model. Expected (Exp) and observed (Obs) values are marked, appear to have been produced by severe population respectively. bottlenecks, which do not appear to have occurred in A. bokermanni, suggesting that population size has been maintained above 500 individuals (Jackson et al. 2013). The unexpectedly high levels of genetic diversity found in the Araripe Manakin may be related to the retention of an ancestral polymorphism, associated with its relatively recent, and as yet incomplete separation from its sister species, A. galeata (Rêgo et al. 2010). Overall, then, the genetic diversity found in A. bokermanni is not consistent with any drastic reduction in population size (Jackson et al. 2013), but that there has been a slow and recent decline over the course of the evolutionary history of the species. Figure 3. Bayesian Skyline Plot (for mitochondrial only) representing Despite the substantial fragmentation of the habitat the effective size of the A. bokermanni population over time. The curve found in the central portion of the range of this species, represents a gradual and constant decline beginning 50,000 years the results of F and the homogeneous distribution of st before present. The solid dark blue line represents the mean and the haplotypes within the population (Table 1) indicate blue shaded area represents the 95% confidence interval of the historic effective size of the female population (Nef ). a lack of substructuring. A similar pattern was also Revista Brasileira de Ornitologia 25(1): 2017 Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) Luna et al. observed by Rêgo et al. (2010), in their analysis of size using this current method. It is also important to note the pseudo-control region. This may reflect either the that the mutation rate of the genetic marker analyzed in relatively recent process of fragmentation, which has yet the present study, while adequate for the evaluation of to affect the genetic structure of this type of marker, or recent demographic events on an evolutionary time scale the migration of individuals among fragments of forest. (Zink & Barrowclough 2008), would not be sensitive The latter hypothesis would be related to the behavior of enough to assess the effects of more recent anthropogenic the adult males of this species, which normally expel the impacts. juvenile offspring from t heir territories, obliging them to The possible recent reduction in the size of occupy new areas (Silva et al. 2011). This would result population of the Araripe Manakin, within the last in high levels of gene flow, which would contribute to a 50,000 years, corresponds to the late Pleistocene. This reduction in the potential for inbreeding, and tends to epoch is characterized by successive periods of climate increase in smaller, fragmented populations. This type change (wet and dry cycles), which had a profound effect of behavior also enhances the probability of adaptation on the dynamics of the Neotropical biotas (Vuilleumier to fragmented habitats (Canales-Delgadillo et al. 2012), 1971), especially in the more rainforest and open biomes, although the exact genetic consequences of this dispersal such as the Cerrado and Caatinga (Werneck 2011), in pattern in A. bokermanni are still unclear. which the species of the genus Antilophia are found. The subsequent periods of glaciations and inter- Historical demography glacials characterized by significant cooling, interspersed with shorter periods of intensely humid climate, resulted Despite the reduced resolution of the EBSP analysis, in the expansion and retraction of the majority of the the demographic history of this species derived from the gallery and scarp forests in northeastern Brazil (Behling HDI sequence of the Control Region (derived from the et al. 2000), the type of habitat which the Araripe BSP analysis) indicates a possible reduction in the A. Manakin is associated. These climatic fluctuations may bokermanni population approximately 50,000 years ago. have provoked adverse conditions for the A. bokermanni The BSP derived from this analysis revealed a general population, which may have suffered a reduction in its trend of population decline, although the confidence genetic diversity during the adaptation process (Frankham intervals are also consistent with a stable population, 2005). In this context, the reduction and fragmentation or even a recent expansion. However, the lack of of forest habitats may have led to a decrease in effective information derived from the low diversity of these loci population size (Croteau et al. 2007), as observed in A. limits phylogenetic estimates of the genealogy (Heled & bokermanni. This indicates that the present-day genetic Drummond 2008), and precludes reliable interpretation diversity of this population may have been determined of the demographic events that have occurred in the primarily by past environmental and climatic events, Araripe Manikin population using only this approach. during the evolutionary history of the species, rather Complementing these results, and supporting the than ongoing anthropogenic pressures, and the resulting assumption of a constant decline in the population size reduction in population numbers (Silva et al. 2011). of the species, the demographic model presented in the As in A. bokermanni, studies of other passeriform mismatch distribution shows a pattern which may reflect populations in the forests of northeastern Brazil have the mixing of lineages that have separated recently or also found evidence of a historical decline in population that have suffered a recent decline in numbers, with only size during the same period. The ranges of species the most common haplotypes surviving. The significant such as Sclerurus scansor cearensis (d'Horta et al. 2011), neutrality found in the HDI of the Control Region is also Conopophaga lineata cearae (Batalha-Filho et al. 2014), compatible with a historical reduction in population size. and Pipra fasciicauda scarlatina (Ferraz 2016), which are Assuming that the Araripe Manakin has had a relatively currently restricted to enclaves of humid cloud forest stable demographic history or has undergone a recent within the Caatinga, may have contracted progressively expansion, we would conclude that the considerable through the successive fluctuations in climate occurring variation observed in the Nef values of the BSP resulted during this period. from the retention of ancestral polymorphisms. This feature is typical of the species of the genus Antilophia, Conservation implications as indicated by the recent separation of its lineages (Rêgo et al. 2010). This effect may generate false evidence of Based on the most recent census data, the population of changes in population size, which emphasizes the need this species may have suffered a loss of up to 36% over for caution in the interpretation of results (Grant et al. the past two decades, resulting from the deforestation of 2012, Heller et al. 2013). This restricts the potential for riparian zones, and the illegal catchment of springs, which the inference of reliable estimates of effective population typically results in the desiccation of the prime riparian Revista Brasileira de Ornitologia 25(1): 2017 Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) Luna et al. statistical test for detecting the presence of recombination. breeding habitat of the species (Silva et al. 2011). This Genetics 172: 2665–2681. type of impact, together with the historic decline in the Canales-Delgadillo J.C., Scott-Morales L. & Korb J. 2012. The A. bokermanni population, may have severe consequences influence of habitat fragmentation on genetic diversity of a rare in genetic terms, such as mating between closely-related bird species that commonly faces environmental fluctuations. Journal of Avian Biology 43: 168–176. individuals and increasing effects of inbree ding depression Chan C.-H., Robertson H.A., Saul E.K., Nia L.V., Luong V.P., Kong (Keller & Waller 2002). X., Zhao Y. & Chambers G.K. 2011. Genetic variation in the The results of the present study emphasize the need Kakerori (Pomarea dimidiata), an endangered endemic bird for the preservation of the remaining genetic variability successfully recovering in the Cook Island. Conservation Genetics and the prevention of further losses, given the importance 12: 441–447. Chaves P.B., Alvarenga C.S, Possamai C.B., Dias L.G., Boubli J.P., of this diversity for the adaptation of these organisms to Strier K.B., Mendes S.L. & Fagundes V. 2011. Genetic diversity random changes in the environment (Frankham 2005). and population history of a critically endangered primate, the These findings also reinforce need for the understanding Northern Muriqui (Brachyteles hypoxanthus). PLoS ONE 6: of the genetic diversity of the A. bokermanni population. e20722. The main factor determining the loss of this diversity has Corander J., Marttinen P., Sirén J. & Tang J. 2008. Enhanced Bayesian modelling in BAPS software for learning genetic structures of yet to be identified. Further genetic analyses, based on populations. BMC Bioinformatics 9: 539. more detailed methods and analyses (e.g. microsatellites Cornetti L., Menegon M., Giovine G., Heulin B. & Vernesi C. 2014. and SNPs) may provide more conclusive answers for this Mitochondrial and nuclear DNA survey of Zootoca vivipara across problem and other important questions. 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APPENDIX I Hierarchical clustering from Bayesian Analysis of Population Structure. The individual level mixture analysis resulted in two groups in the optimal partition, but not suitable when placed geographically (northwest and southeast of the Antilophia bokermanni distribution). Revista Brasileira de Ornitologia 25(1): 2017
Ornithology Research – Springer Journals
Published: Mar 1, 2017
Keywords: coalescent theory; conservation; control region; Pipridae; population genetics
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