Research Article |
Corresponding author: Adolfo G. Navarro-Sigüenza ( adolfon@ciencias.unam.mx ) Academic editor: Knud Jønsson
© 2018 Alberto Rocha-Méndez, Luis A. Sánchez-González, Enrique Arbeláez-Cortés, Adolfo G. Navarro-Sigüenza.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG (2018) Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae). ZooKeys 809: 125-148. https://doi.org/10.3897/zookeys.809.28743
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The White-naped Brushfinch (Atlapetes albinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A. albinucha and A. gutturalis), but they are presently considered as one polytypic species. Previous studies in the genus Atlapetes have shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography of A. albinucha was analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations of A. albinucha in spite of the species’ ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.
allotypy, coalescent, Last Glacial Maximum, mtDNA, montane forest, Pleistocene, phylogeography, plumage differentiation
Phylogeographic analyses of widespread Neotropical montane forest bird species have indicated different levels of geographic structure in the variation of mitochondrial DNA (mtDNA) among populations (
The genus Atlapetes comprises a group of Neotropical finches inhabiting mainly humid montane forests from Mexico to northern Argentina (
Atlapetes albinucha (White-naped Brushfinch) is a widely distributed species found in montane regions from eastern Mexico to Colombia (
Atlapetes albinucha distribution shown in green stapled lines, based on
Here, using an extensive sampling for A. albinucha (39 individuals from 24 localities in four countries), we tested: a) if yellow- and gray-plumaged groups are reciprocally monophyletic, b) if there is phylogeographic structure in this widespread taxon across their range, and c) if past reconstructions of the environmental conditions were A. albinucha ranges at present indicate distributional changes that may be related with their genetic-geographic variation. These questions were approached using a mtDNA assessment of populations included within this complex, as well as environmental niche modelling analyses based on records of voucher specimens in biological collections.
Tissue and blood samples of A. albinucha were obtained from different museum collections in Mexico, USA, and Colombia, spanning the whole distribution of the species (Table
Tissue and blood samples used in this study. Samples of A. albinucha species were grouped in five geographic groups: Northern Chiapas (NC, n = 11), Southern Chiapas (SC, n = 11), El Salvador (Sal, n = 7), Honduras (Hon, n = 1), and Colombia (Col, n = 9). One sample of Atlapetes pileatus tissue was also obtained and added to the analysis.
Sample source | Catalog number | Voucher specimen | State/ Department | Locality | Latitude | Longitude | GenBank Accession Number | Geographic Group | |
---|---|---|---|---|---|---|---|---|---|
ND2 | Cyt b | ||||||||
Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, UNAM | BONA 33 | BONA 33 | Chiapas | Carretera estatal Coapilla-Ocotepec km 29 a 5.4 km N de Coapilla | 17.31388, -93.2 | MH938475 | MH938514 | NC | |
BONA 39 | BONA 39 | Chiapas | Volcán Tacaná ladera, vereda a Tapalapa, Rancho Chiquihuite | 15.0666, -92.08333 | MH938476 | MH938515 | SC | ||
BONA 52 | BONA 52 | Chiapas | Volcán Tacaná ladera, vereda a Tapalapa, Rancho Chiquihuite | 15.0666, -92.08333 | MH938474 | MH938513 | SC | ||
BONA 89 | BONA 89 | Chiapas | Volcán Tacaná ladera, vereda a Tapalapa, Rancho Chiquihuite | 15.0666, -92.08333 | MH938479 | – | SC | ||
BONA 94 | BONA 94 | Chiapas | Volcán Tacaná ladera, vereda a Tapalapa, Rancho Chiquihuite | 15.0666, -92.08333 | MH938477 | MH938516 | SC | ||
BMM 577 | BMM 577 | Chiapas | 6 km NE de Pueblo Nuevo; camino a Aurora-Ermita | 17.18333, -92.08333 | MH938478 | MH938517 | NC | ||
BMM 582 | BMM 582 | Chiapas | 6 km NE de Pueblo Nuevo; camino a Aurora-Ermita | 17.18333, -92.08333 | MH938464 | MH938503 | NC | ||
BMM 834 | BMM 834 | Chiapas | Volcán Tacaná ladera, vereda a Tapalapa, Rancho Chiquihuite | 15.0666, -92.08333 | KM360517 | MH938498 | SC | ||
MOL 13001 | MOL 13001 | Chiapas | San Nicolás Buenavista, Cerro Huitepec | 16.73805, -92.68805 | MH938468 | MH938507 | NC | ||
MOL 13061 | MOL 13061 | Chiapas | San Nicolás Buenavista, Cerro Huitepec | 16.73805, -92.68805 | MH938467 | MH938506 | NC | ||
MOL 13130 | MOL 13130 | Chiapas | San Nicolás Buenavista, Cerro Huitepec | 16.73805, -92.68805 | MH938466 | MH938505 | NC | ||
SIT 105 | SIT 105 | Chiapas | CarreteraCopainalá-Ocotepec km 38 a 95.5 km N de Coapilla | 17.16891, -93.14533 | MH938481 | MH938519 | NC | ||
SIT 146 | SIT 146 | Chiapas | Coapilla a 6.5 km N | 17.17413, -93.14636 | MH938463 | MH938502 | NC | ||
SIT 147 | SIT 147 | Chiapas | Coapilla a 6.5 km N | 17.17413, -93.14636 | MH938472 | MH938511 | NC | ||
SIT 157 | SIT 157 | Chiapas | Coapilla a 6.5 km N | 17.17413, -93.14636 | MH938462 | MH938501 | NC | ||
SIT 158 | SIT 158 | Chiapas | Coapilla a 6.5 km N | 17.17413, -93.14636 | MH938480 | MH938518 | NC | ||
EAGT 806 | EAGT 806 | Chiapas | Cerro Mozotal, en la cima | 15.4294, -92.3411 | MH938458 | MH938495 | SC | ||
EAGT 817 | EAGT 817 | Chiapas | Cerro Mozotal, en la cima | 15.4294, -92.3411 | MH938457 | MH938494 | SC | ||
EAGT 844 | EAGT 844 | Chiapas | Cerro Boqueron, en la cima | 15.23541, -92.30463 | MH938473 | MH938512 | SC | ||
ZRH 407 | ZRH 407 | Chiapas | Cerro Mozotal, en la cima | 15.4294, -92.3411 | MH938460 | MH938499 | SC | ||
Museo de Zoología Facultad de Ciencias “Alfonso L. Herrera” UNAM | 130332 | 130332 | Chiapas | Reserva Ecológica el Triunfo | 14.81278, -92.40594 | MH938456 | MH938492 | SC | |
130345 | 130345 | Chiapas | Reserva Ecológica el Triunfo | 14.81278, -92.40594 | KM360516 | MH938493 | SC | ||
QRO0272 | QRO0272 | Querétaro | El Pemoche | 21.2263, -99.109694 | MH938455 | MH938491 | |||
OVMP227 | OVMP227 | Jalisco | – | – | – | FJ547292 | FJ547251 | ||
University of Kansas, Natural History Museum | EAGT 21 | KU 4907 | San Miguel | San Miguel | 13.48138, -88.1775 | GU377050 | MH938497 | Sal | |
EAGT 74 | KU 5017 | Chalatenango | Concepción Quezaltepec | 14.08333, -88.95 | MH938459 | MH938496 | Sal | ||
OK 56 | KU 4961 | Morazan | Chilanga | 13.71666, -88.11666 | MH938465 | MH938504 | Sal | ||
CMZF 120 | KU 6448 | San Vicente | Nuevo Tepetitán | 13.64527, -88.78416 | MH938471 | MH938510 | Sal | ||
LR 58 | KU 7704 | Chalatenango | La Laguna | 14.0666, -88.8666 | MH938470 | MH938509 | Sal | ||
SLA 165 | KU 7775 | San Vicente | Nuevo Tepetitán | 13.64527, -88.78416 | MH938461 | MH938500 | Sal | ||
MBR 6584 | KU 9400 | Santa Ana | Metapán | 13.98333, -89.5333 | MH938469 | MH938508 | Sal | ||
Instituto de Investigación de Recursos Biológicos “Alexander von Humboldt” | IAvH-CT-01158 | IAvH-11694 | Pereira | Parque regional Ucumarí Entre Peña Bonita y Peñas Blancas | 4.709233, -75.4907 | MH938483 | MH938521 | Col | |
IAvH-CT-01726 | IAvH-11946 | Aranzazu | Vereda El Laurel, Cuenca Alta del Río Hacienda Termopilas | 5.230944, -75.48841 | MH938484 | – | Col | ||
IAvH-CT-02391 | IAvH-12363 | Yotoco | Yotoco | 3.87975, -76.443 | MH938485 | MH938522 | Col | ||
IAvH-CT-04519 | IAvH-13101 | Santa Rosa de Cabal | Vereda La Linda, Parque Municipal de Campoalegre | 4.8675, -75.54666 | MH938486 | MH938523 | Col | ||
IAvH-CT-04835 | IAvH-CT-04835 | Anorí | Vereda Santa Gertrudis, Finca La Estrella margen derecha de la Quebrada Santa Gertrudis | 7.135444, -75.15527 | MH938487 | – | Col | ||
IAvH-CT-07844 | IAvH-CT-07844 | Amalfi | Vereda Cajamarca, Finca Canales Cuenca de la quebrada Cajamarca | 6.8235, -75.15527 | MH938488 | MH938524 | Col | ||
IAvH-CT-09344 | ICN 34591 | Amalfi | Vereda El Encanto, La Secreta | 6.909167, -75.0766 | MH938489 | MH938525 | Col | ||
IAvH-CT-09695 | IAvH-CT-09695 | Pereira | P. Ucumarí, La Pastora | 4.814278, -75.69455 | MH938490 | MH938526 | Col | ||
IAvH-CT-18248 | ICN 38086 | Santander | Serranía de los Yariguies, Carmen de Chucurí | 6.68333, -73.4333 | MH938482 | MH938520 | Col | ||
Marjorie Barrick Museum of Natural History | GAV 1374 | MBM 6640 | Copán | Copán Ruinas, 10 km ENE | 14.86667, -89.05 | GU377047 | DQ459625 | Hon | |
DAB1706 | MBM 4600 | Managua | Chocoyero, Volcán Mombacho, 48km SE Managua | 11.829, -85.963 | EF529823 | EF529932 |
Extraction of DNA from tissue samples was carried out in two laboratory facilities in Mexico and Colombia using the DNeasy Blood & Tissue Kit (Qiagen Inc., Valencia, CA) following manufacturer’s protocols. We amplified two mtDNA genes fragments comprising the NADH dehydrogenase subunit 2 (ND2) and Cytochrome b (Cyt b), which have been shown to successfully assess phylogenetic relationships due to its high probability for tracking recent diversification events (
We conducted analyses using an alignment with both mtDNA loci (ND2 and Cyt B) concatenated. Nucleotide substitution model parameters and partition schemes were estimated for each gene in PARTITIONFINDER (
Divergence times were estimated through calculation of a maximum clade credibility tree (MCCT) using a Yule speciation process (
Finally, to complement the visualization of the relationships among haplotypes, a haplotype network was constructed using NETWORK 4.6.1.1 (Fluxus Engineering, www.fluxus-engineering.com), through a Median-joining method, assigning equal weights to all variable sites and an epsilon parameter with default values (Ɛ = 0). This method estimates evolutionary relationships among sequences when divergences are recent (
To analyze the molecular information in the framework of population genetics, we clustered individuals of A. albinucha into four groups considering subspecific membership as well as geographic proximity and evidence of montane forest continuity (Table
To test if there is evidence of genetic structure among the four geographic groups, we performed a hierarchical analysis of molecular variance (AMOVA) using pairwise differences. In addition, to test if phenotypic divergence is related to genetic structure we also performed an AMOVA between gray-plumaged subspecies and yellow-plumaged subspecies. Genetic divergence between groups was also measured using FST fixation index values (
To test for evidence of recent demographic changes in A. albinucha, we estimated demographic dynamics experienced by the whole taxon through the calculation of neutrality tests corresponding to Fu's FS statistic (
We tested the hypotheses that the ecological/environmental conditions in which A. albinucha ranges at present may have allowed for population connectivity at least since the Last Interglacial (120,000 ya) using ecological niche models (ENM). We compiled a total of 475 geographical records, representing 176 localities, of the species through the Global Biodiversity Information Facility (GBIF, http://www.gbif.org) and museum vouchers (see Acknowledgements). GBIF records were filtered for elimination of both duplicates and records lacking geographic data. ENMs were obtained using 19 bioclimatic variables with a cell resolution of 2.5 arc-minutes (ca. 4.5 km2) generated by the Community Climate System Model (CCSM) downloaded through WorldClim (http://www.worldclim.org/bioclim;
Phylogenetic reconstruction analyses were conducted using the substitution models HKY+I+G for the first position of ND2 and the second position of Cyt b, F81+I for ND2 second position and third Cyt b position and HKY+G for the third and first positions of ND2 and Cyt b respectively. Both phylogenetic reconstruction methods (ML and IB) rendered similar topologies. The Bayesian tree topology (Figure
A Dated Bayesian maximum clade credibility tree showing phylogenetic relationships among members of Atlapetes albinucha species. Node bars depict 95% HDP interval, scale bar represents millions of years. Nodal values above branches indicate posterior probabilities/ bootstrap supports of BI/ML. Capital letters depict haplotypes. An asterisk (*) indicate birds representing yellow morphs B Median-joining haplotype network for the concatenated dataset. Each color depicts the geographic provenance of samples: green-northern Chiapas (subspecies albinucha), red-southern Chiapas (subspecies griseipectus), blue-El Salvador (subspecies griseipectus), yellow-Honduras (subspecies fuscipygius) and light blue-Colombia (subspecies gutturalis). Each branch represents a single nucleotide change, transversal black lines along branches depict the occurrence of three mutations. Gray dots indicate median vectors inferred for the data.
Overall, genetic diversity values for the geographic groups showed a low nucleotide diversity (π < 0.008), but high haplotype diversity (Hd > 0.71; Table
Genetic diversity measures and demographic fluctuation measured at the species and population level within the concatenated data set. Abbreviations: N Sample size, Hd Haplotype diversity, π nucleotide diversity, SD standard deviation.
N | Hd (SD) | π (SD) | Tajima's D | Fu's Fs | |
Northern Chiapas | 11 | 0.982 (0.046) | 0.00264 (0.0015) | -1.49107 | -2.654 |
Southern Chiapas | 11 | 0.727 (0.144) | 0.007674 (0.0041) | -1.037 | -0.905 |
El Salvador | 7 | 0.714 (0.181) | 0.00077 (0.00028) | -1.023 | -0.538 |
Colombia | 9 | 0.722 (0.159) | 0.004313 (0.0026) | -1.37093 | 0.81161 |
Honduras | 1 | – | – | – | – |
Total | 39 | 0.835 (0.047) | 0.00652 (0.0007) | -1.267 | -5.08 |
Analyses of molecular variance (AMOVA) between gray- and yellow-plumaged morphs and between geographical groups.
AMOVA: gray- and yellow-plumaged morphs | ||||
Source of variation | Sum of squares | Variance components | Percentage of variation | P |
Among morphs | 70.621 | 4.00944 | 35.48 | 0.001 |
Within morphs | 269.815 | 7.29230 | 64.52 | 0.00098 |
AMOVA: geographic groups | ||||
Source of variation | Sum of squares | Variance components | Percentage of variation | P |
Among geographic groups | 170.961 | 5.13057 | 50.72 | 0.001 |
Within geographic groups | 169.475 | 4.98455 | 49.28 | 0.001 |
The haplotype network showed three non-shared high frequency haplotypes: one including most samples from Colombia (gutturalis); a second one where most samples from northern Chiapas (albinucha) are located; and a third high frequency haplotype that was shared by most samples corresponding to northern Central America, which includes subspecies griseipectus and fuscipygius (Figure
Despite relatively low bootstrap values, molecular dating of the divergence between A. albinucha and A. pileatus yielded a time estimate during the Late Pliocene-Early Pleistocene about 2.5 Mya (HPD range 1.94–3.28 Mya), whereas differentiation between major clades of A. albinucha apparently occurred around 1.5 Mya (HDP range 1.01–1.61 Mya), during the Early Pleistocene (Figure
Historical demography in A. albinucha as estimated from the Tajima's D and Fu's FS tests showed in most cases negative values, except for the FS in the Colombian population. Both demographic tests did not depart from neutrality given that values were not significant neither at the species nor at the geographic group level; therefore, demographic fluctuations are difficult to suggest based on these values (Table
Bayesian skyline plot derived from the concatenated gene dataset of Atlapetes albinucha species. Time in millions of years. Population size change (Ne*generation time) in the Y axis. Mean estimate is shown as a thick solid line, and the 95% HDP limits are shown in solid purple color area surrounding the mean estimate.
All of our ENM analyses performed better (AUC > 0.94) than a random non-predictive model (AUC = 0.5), indicating that the models obtained may reflect, relatively well, the past distribution of environmental conditions where A. albinucha inhabits at present. ENMs suggested a scenario of geographically fragmented environmental conditions for populations in Mexico, Central America, and Colombia during three of the modeled timeframes: LIG (ca. 120,000 ya, P-ROC, min = 0.998, max = 1.972; Figure
The major result of our analyses using mtDNA sequence data for individuals of A. albinucha is that this taxon exhibits an incomplete genetic differentiation along their range in the Neotropical Montane Forest. The lack of clear phylogeographic structure in this montane bird taxon is in sharp contrast with expectations based on plumage differentiation which has resulted in the recognition of up to eight subspecies (
Population pairwise comparisons using the concatenated data set. Above the diagonal is found the number of migrants per generation estimates (Nm value). Below the diagonal FST index. FST values with * depict significant values p < 0.05. Numbers depict geographic group correspondence.
1 | 2 | 3 | 4 | 5 | |
1-Northern Chiapas | 0.70586 | 0.20016 | 0.2547 | 0.45921 | |
2-Southern Chiapas | 0.41464* | 10.47426 | 0.67099 | – | |
3-El Salvador | 0.71412* | 0.04556 | 0.24878 | – | |
4-Colombia | 0.66252* | 0.42699* | 0.66775* | 0.75137 | |
5-Honduras | 0.52126 | 0 | 0 | 0.39956 |
The phylogeographic pattern of A. albinucha is consistent with allotypy, a term used to denote a stage in intermediate polyphyly (
In the case of A. albinucha, BSP (Figure
Causes of differentiation in plumage coloration in A. albinucha remain elusive in our analysis, as both plumage coloration patterns appeared intermixed in the tree topology, which suggest different processes for the configuration of the genetic variation and the phenotypic plumage differentiation. Therefore, the clear phenotypic differentiation between yellow-colored birds in northern Chiapas and gray-colored birds in the rest of the distributional range suggests that plumage may be under natural selection. Similar results have been obtained for other groups of birds in different geographical and ecological settings, such as in the Tropical Pacific islands (
Results in this paper are not conclusive in terms of the currently accepted taxonomy for A. albinucha. Genetic divergence as a result of allotypy is apparent, suggesting that these taxa are likely at allotypy (
Genetic patterns found in A. albinucha were unexpected given previous findings in birds and other taxa codistributed in montane forests throughout the region (see
The phylogeography of A. albinucha is consistent with allotypy, which has been suggested to represent an intermediate stage in the path to reciprocal monophyly (
Environmental factors may have played a major role in shaping the evolution of morphological traits by natural selection that have been considered taxonomically relevant (
This contribution is part of AR-M Undergraduate Thesis and was supported by a scholarship from PAPIIT. Financial support was obtained from CONACyT 152060 and PAPIIT 215515 to AGN-S, and from Vicerrectoría de Investigación y Extensión of Universidad Industrial de Santander, Colombia, under Grant Proyecto de investigación capital semilla 2300 to EA-C. We thank the University of Kansas (M. B. Robbins & A. T. Peterson), the Colección de Tejidos del Instituto de Investigación de Recursos Biológicos “Alexander von Humboldt”, and the Museo de Zoología de la Facultad de Ciencias “Alfonso L. Herrera” and their respective staff for kindly providing tissue samples used in this study; a special acknowledgment to all the scientific collectors that obtained and deposited samples and voucher specimens of A. albinucha in these collections. We thank Natural Earth (http://www.naturalearthdata.com) for providing the raster data that was used in this study to map our species distribution models. Logistic help was obtained from Jano Núñez, Fanny Rebón, and Alejandro Gordillo (at UNAM), and by Diana Espitia Reina and Claudia A. Medina Uribe (at IAvH). Comments to early versions of this paper were obtained from Laura Márquez, Leticia Ochoa, and Erick García-Trejo. We are deeply indebted to Jon Fjeldså and Knud Jønsson for their comments, which greatly improved our manuscript.