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10 results for “Aves: Alaudidae”
Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon
<p>This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus <em>Calandrella</em>, with the description of a range-restricted African relic taxon" by Stervander <em>et al</em>. </p> <p>For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript. </p> <p><strong>Phylogenetic analyses</strong></p> <ol> <li>Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa</li> <li>BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml</li> <li>BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log</li> <li>BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees</li> <li>TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk</li> </ol> <p><strong>Species delimitation</strong></p> <ol> <li>Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk</li> <li>mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt</li> <li>mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt</li> <li>mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg</li> </ol>
Figure 7 in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 7. Plots of the first two components of a linear discriminant analysis of songs among the six primary clades in the Corypha africana complex, excluding the type 2 song of C. a. athi (A) and songs among Corypha hypermetra (C. h. hypermetra and C. h. gallarum), C. h. kidepoensis, C. somalica and the 'type 2' song of C. a. athi (B).
Figure 8 in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 8. Summary of evidence. A, tree with support for different clades based on different datasets, labelled with the proposed new taxonomy. Symbols are explained at the top: black symbols = strong support; grey symbols = weak support; unfilled symbols = no support; white triangle with question mark = lack of data. *Restricted datasets were analysed for Corypha kidepoensis: only Cytb in the multilocus analyses, and a separate single nucleotide polymorphism (SNP)-based analysis not included in the principal component analysis (see main text). #Taxon featured in photograph. B, pairwise differentiation between all taxa, based on mitochondrial DNA, genome-wide SNPs, plumage, morphometrics, song and other behaviour. The full key and an example are at the top of the panel. For photograph credits, see Figure 4.
Figure 4 in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 4. Principal component analysis (PCA) based on seven morphometric variables: the lengths of wing, bill, tarsus, tail, hind claw and outermost primary, and the distance from the outermost primary to the wing tip. Ellipses indicate the 68% confidence interval (±1 SD) for each clade. Loadings for each trait, drawn with maps and their relative contributions across all principal components (PCs), can be viewed in the Supporting Information (Fig. S9). Photographs are by Nik Borrow (II, kidepoensis Kidepo National Park, Uganda, May; III, somalica Tuuyo Plains, Somaliland, September; VII, nyikae Nyika National Park, Malawi, December), Maans Booysen, Birding Weto, CC BY-SA 4.0 https:// creativecommons.org/licenses/by-sa/4.0, via Wikimedia Commons (VI, malbranti Longa, Angola), Paul F. Donald (Va, pallida, Caprivi Strip, Namibia, November), Emmanuel Barde Elisha (VIII, bamendae Mambilla Plateau, Nigeria), Stratton Hatfield (I, hypermetra Tsavo East National Park, Kenya, March), Peter Steward (IV, athi Nairobi National Park, Kenya, March) and The Trustees of The Natural History Museum, London (II, sharpii NHMUK, identity and collection information lacking). The taxa with photographs are also indicated by '#', and '*' for sharpii.
Figure 5 in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 5. Sonograms of songs of taxa treated as subspecies of Corypha africana, C. hypermetra and C. somalica. The strophes are numbered consecutively for precise reference in the text. Recordings: (1) Foumban-Tibati, Cameroon, BL 022A-W1CDR0000054 BD19 (Claude Chappuis); (2) Mambilla Plateau, Nigeria, ML274689 (Emmanuel Elisha); (3) Mambilla Plateau, Nigeria, ML274691 (Emmanuel Elisha); (4) Mambilla Plateau, Nigeria (Emmanuel Elisha); (5) Nyika National Park, Malawi, ML278996 (Peter Boesman); (6) Nyika National Park, Malawi, ML279004 (Peter Boesman); (7) Nyika National Park, Malawi, ML279005 (Peter Boesman); (8) Kipengere Plateau, Tanzania, ML562576011 (David Moyer); (9, 10) Kipengere Plateau, Tanzania, ML562576201 (David Moyer); (11) Minyanya plain, north-west Zambia, ML279942 = XC509007 (Peter Boesman); (12) Minyanya plain, north-west Zambia, ML279943 = XC509008 (Peter Boesman); (13) Minyanya plain, north-west Zambia, ML279957 = XC509010 (Peter Boesman); (14) Lékoni, Gabon, ML274685 (Nik Borrow); (15) south-east Gabon, Chappuis CD8 BD91 (P. Christy); (16) Lékoni, Gabon (Michael Mills); (17) Polokwane, Limpopo, South Africa, ML274677 (Per Alström); (18) Sandveld, South Africa, XC28667 (Patrik Åberg); (19) Free State, South Africa, XC536937 (Dawie de Swardt); (20) Polokwane, South Africa, ML274681 (Per Alström); (21) North West Province, South Africa, XC516080 (Frank Lambert); (22) Polokwane, Limpopo, South Africa, XC516146 (Frank Lambert); (23) Lusaka, Zambia, BL WS3371 C15 (Robert Stjernstedt); (24) Lusaka, Zambia, BL WS3371 C15 (Robert Stjernstedt); (25) Lusaka, Zambia, BL WS3371 C10 (Robert Stjernstedt); (26) Etosha National Park, Namibia, ML42945 (Linda Macaulay); (27) Etosha National Park, Namibia, ML61179 (Linda Macaulay); (28) Namutoni, Namibia, XC58667 (Charles Hesse); (29) Maasai Mara, Kenya, ML274675 (Stratton Hatfield); (30) Maasai Mara, Kenya, ML274674 (Stratton Hatfield); (31) Mara Triangle, Kenya, XC200107 (Rory Nefdt); (32) Entebbe, Uganda, ML8031 (Myles E. W. North); (33) Uganda, ML23453 (G. Stuart Keith); (34) Semliki Flats, Uganda, ML23454 (G. Stuart Keith); (35) Lake Nakuru, Rift valley, Kenya, ML8032 (Myles E. W. North); (36) Nairobi, Kenya, ML8034 (Myles E. W. North); (37) Nairobi, Kenya, ML274661 (Per Alström); (38) Lake Nakuru, Rift
Figure 3. Multilocus tree for the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 3. Multilocus tree for the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C. ashi complex based on Bayesian analysis (BEAST) of concatenated mitochondrial and nuclear loci (5,285 bp). Posterior probabilities (PPs) are indicated at the nodes, with an asterisk indicating a PP of 1.00. Clades that are discussed in the text are labelled I–VIII and with the name of the taxon that has priority in the respective clade. The names of C. africana s.l. are in black font; the other species are in other colours (the six outgroup species are all in pale blue). The three taxa that are not present in any other analyses are indicated by a red '§'. Topological incongruence compared with other phylogenetic trees is indicated by a red '#'. The blue lines indicate the divergence times of two of the outgroup species pairs.
Figure 2 in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 2. Phylogenies of the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C. ashi complex, with Corypha fasciolata as the outgroup (the more distant outgroup species Amirafra rufocinnamomea has been removed) based on the multi-species coalescent, produced within a Bayesian framework in SNAPP on 16,412 single nucleotide polymorphisms (SNPs) and single individuals per taxon (A) and with ASTRAL, summarising taxon quartets in maximum likelihood (ML) analyses of 32,000 SNPs across 626 unlinked windows for all samples (B). Node support values are posterior probabilities (PPs) for SNAPP and local PPs for ASTRAL, with an asterisk indicating a PP of 1.00. Clades that are discussed in the text are labelled I–VIII and with the name of the taxon that has priority in the respective clade. The names of C. africana s.l. are in black font; the other species are in other colours. Topological incongruence between these two trees, the Snapper species tree (Supporting Information, Fig. S3), the ML IQ-TREE tree (Supporting Information, Fig. S5) and/or the Bayesian multilocus tree (Fig. 3) are indicated by a red '#'.
Figure 6. A in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 6. A, mean and SD for eight song variables for the five primary clades in the Corypha africana complex (first song type, corresponding to Fig. 5: strophes 1–40). B, mean and SD for six song variables for type 2 song of C. a. athi, and song of Corypha hypermetra and C. somalica (corresponding to Fig. 5: strophes 41–57).
Figure 1 in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 1. Distribution of the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C. ashi complex based on BirdLife International and Handbook of the Birds of the World (2020) and Kennedy and Finch (in prep.), with type localities indicated by asterisks. Note that information on distribution should be regarded with caution, because further research is required for precision and accuracy. The distributions of specific taxa are listed in Table 2, but their boundaries (particularly within and between the two large continuous ranges in southern/southwestern Africa and East Africa) are unclear and in need of updating. For example, there have been records further east in southern Tanzania and northern Mozambique (Baker and Baker 2014; Supporting Information, Fig. S1B), indicated on the map by a question mark. Some additional information on distribution can be gleaned from Supporting Information, Figure S1, which shows localities for birds that have been sampled genetically or whose song has been recorded.
Data from: Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae)
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