1,720,982 research outputs found
Figure 3 in Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird
No full textFigure 3. Scatterplot of hue and colour saturation (chroma) for the five Aphelocoma unicolor subspecies.Published as part of Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126 on page 7, DOI: 10.1093/biolinnean/bly156, http://zenodo.org/record/784888
Figure 5 in Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird
No full textFigure 5. Phylogenies of Aphelocoma unicolor based on mitochondrial DNA and ultraconserved elements (UCEs). For the Bayesian time-calibrated mitochondrial DNA phylogeny generated in BEAST, the mean estimated split dates are provided on the nodes, with the 95% highest probability density shown below in square brackets. For both phylogenies, nodes with perfect support are shown with black dots.Published as part of Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126 on page 9, DOI: 10.1093/biolinnean/bly156, http://zenodo.org/record/784888
Figure 6 in Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird
No full textFigure 6. Results of tests for strong niche divergence on multivariate niche axis in relationship to the phylogeny. Boxes show whether each niche axis was more divergent than background divergence (diverged), more similar than background divergence (conserved), or was similar to background divergence and therefore failed to reject the null hypothesis (null). Percentages indicate the amount of variation explained by that axis.Published as part of Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126 on page 10, DOI: 10.1093/biolinnean/bly156, http://zenodo.org/record/784888
Aphelocoma Cabanis 1851
No full text<i>APHELOCOMA OAXACAE</i> PITELKA, 1946 <p> <i>Type. Adult female, MLZ:</i> Bird:39121, collected by M. del Toro Avilés from Moctum, Oaxaca, Mexico on 18 October 1941. This species is smaller and is restricted to the state of Oaxaca, Mexico (Pitelka, 1946).</p>Published as part of <i>Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126</i> on page 12, DOI: 10.1093/biolinnean/bly156, <a href="http://zenodo.org/record/7848889">http://zenodo.org/record/7848889</a>
Aphelocoma Cabanis 1851
No full text<i>APHELOCOMA GUERRERENSIS</i> NELSON, 1903 <p> <i>Type. Adult male, USNM:</i> Bird:185539 collected by E. W. Nelson and E. A. Goldman from Omiltemi, Guerrero on 19 May 1903. This species is a saturated, purplish blue and has a very long tail and large bill. It is endemic to the cloud forests of Guerrero, Mexico (Pitelka, 1946).</p>Published as part of <i>Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126</i> on page 12, DOI: 10.1093/biolinnean/bly156, <a href="http://zenodo.org/record/7848889">http://zenodo.org/record/7848889</a>
Figure 4 in Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird
No full textFigure 4. Results of a discriminant function (DF) analysis and normal mixture models on all morphological and plumage traits. A, differences among all five Aphelocoma unicolor subspecies in the first two DF axes. B, differences between only the A. u. unicolor and A. u. griscomi subspecies in the third and fourth DF axes. C, D, results of normal mixture modelling to determine the objective number of phenotypic clusters among individuals west (C) and east (D) of the Isthmus of Tehuantepec, with inset showing the assignment of individuals to each cluster with respect to their a priori subspecies assignment.Published as part of Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126 on page 8, DOI: 10.1093/biolinnean/bly156, http://zenodo.org/record/784888
Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays
No full textComplex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (A. californica) and Woodhouse's Scrub-Jay (A. woodhouseii), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.Unfiltered SNPs called across all 115 samples are available as a gzipped vcf file called 'populations.snps_(1).vcf.gz'. Supplementary methods associated with the paper are contained in the file 'supplemental.material.may1.2022.docx'.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-155705
Aphelocoma Cabanis 1851
No full text<i>APHELOCOMA CONCOLOR</i> CASSIN, 1848 <p> <i>Type. An unsexed specimen, ANSP:</i> Bird:3039 labelled S. America, later determined probably to have originated near Xalapa, Veracruz (Phillips, 1986). This species is brighter blue than <i>A. u. oaxacae</i> and <i>A. u. guerrerensis</i> and has a larger wing and tail than <i>A. u. oaxacae</i>. It is found in cloud forests from Hidalgo south to Veracruz, Mexico (Pitelka 1946).</p>Published as part of <i>Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126</i> on page 12, DOI: 10.1093/biolinnean/bly156, <a href="http://zenodo.org/record/7848889">http://zenodo.org/record/7848889</a>
Aphelocoma unicolor Du Bus 1847
No full text<i>APHELOCOMA UNICOLOR</i> DU BUS, 1847 <p> <i>Type.</i> An unsexed specimen in the Brussels Museum labelled from Tabasco; however, this species does not occur in the state of Tabasco (van Rossem, 1942). The type locality was later designated as Ciudad de las Casas, Chiapas (Brodkorb, 1944). The nominate subspecies, <i>A. u. unicolor</i>, occurs in the highlands of Chiapas, Mexico and Guatemala. The larger-billed and generally more purplish <i>A. u. griscomi</i> is found in the highlands of Honduras, El Salvador, and northern Nicaragua (Pitelka, 1946).</p>Published as part of <i>Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M. & Mccormack, John E., 2019, Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, pp. 1-15 in Biological Journal of the Linnean Society 126</i> on page 12, DOI: 10.1093/biolinnean/bly156, <a href="http://zenodo.org/record/7848889">http://zenodo.org/record/7848889</a>
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