AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
Powered by AMiner. Clicking this button will take you away from SciOpen.
Home Avian Research Article
PDF (6.8 MB)
Cite
EndNote(RIS) BibTeX
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Research Article | Open Access

Systematics of the avian family Alaudidae using multilocus and genomic data

Per Alströma,b( ), Zeinolabedin Mohammadic, Erik D. Enbodyd,e, Martin Irestedtf, Derek Engelbrechtg, Pierre-André Crocheth, Alban Guillaumeti, Loïs Rancilhaca, B. Irene Tielemanj, Urban Olssonk,l, Paul F. Donaldm,n, Martin Stervandero( )
Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
Department of Biology, Faculty of Sciences, Golestan University, Gorgan, Golestan, Iran
Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden
Department of Biomolecular Engineering, University of California, Santa Cruz, 95060, Santa Cruz, CA, USA
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
Department of Biodiversity, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa
CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
Department of Biological & Environmental Sciences, Troy University, Troy, AL, 36082, USA
Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, SE-405 30, Gothenburg, Sweden
Gothenburg Global Biodiversity Centre, P.O. Box 461, SE-405 30, Gothenburg, Sweden
BirdLife International, The David Attenborough Building, Pembroke St, Cambridge, CB2 3QZ, UK
Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
Bird Group, Natural History Museum, Akeman Street, Tring, Hertfordshire, HP23 6AP, United Kingdom
Show Author Information

Abstract

The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ~80% of the species, revealed multiple cases of parallel evolution and large variation in rates of morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct the phylogeny of the larks, using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species (in total 133 taxa; not all loci available for all species). We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling (in total 51 samples of 44 taxa across 40 species). Our results confirm the previous findings of rampant morphological convergence and divergence, and reveal new cases of paraphyletic genera. We propose a new subfamily classification, and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae. Our study supports recently proposed species splits as well as some recent lumps, while also questioning some of the latter. This comprehensive phylogeny will form an important basis for future studies, such as comparative studies of lark natural history, ecology, evolution and conservation.

Keywords

TaxonomyMultispecies coalescentPhylogenomicsPhylogenyLarkParaphylySubfamily description

References

 
Ali, S., Ripley, S.D., 1973. Handbook of the Birds of India and Pakistan. vol. 9. Oxford University Press, Bombay.
 

Alström, P., 1998. Taxonomy of the Mirafra assamica complex. Forktail 13, 97-107.
Google Scholar
 
Alström, P., 2020a. Tibetan Lark (Melanocorypha maxima), version 1.0. In: del Hoyo, J., Elliott, A., Sargatal, J., Christie, D.A., de Juana, E. (Eds.), Birds of the World. Cornell Lab of Ornithology, Ithaca. https://doi.org/10.2173/bow.tiblar1.01.
Crossref
 
Alström, P., 2020b. Mongolian Lark (Melanocorypha mongolica), version 1.0. In: del Hoyo, J., Elliott, A., Sargatal, J., Christie, D.A., de Juana, E. (Eds.), Birds of the World. Cornell Lab of Ornithology, Ithaca. https://doi.org/10.2173/bow.monlar1.01.
Crossref
 
Alström, P., Donald, P.F., 2022. Sharpe’s Lark (Mirafra sharpii), version 1.0. In: Keeney, B.K. (Ed.), Birds of the World. Cornell Lab of Ornithology, Ithaca. https://doi.org/10.2173/bow.runlar2.01.
Crossref
 

Alström, P., Sundev, G., 2021. Mongolian Short-toed Lark Calandrella dukhunensis, an overlooked East Asian species. J. Ornithol. 162, 165-177. https://doi.org/10.1007/s10336-020-01819-z.
Crossref Google Scholar
 
Alström, P., Mohammadi, Z., Donald, P.F., Nymark, M., Enbody, E.D., Irestedt, M., et al. Integrative Taxonomy Reveals Unrecognised Species Diversity in African Corypha Larks (Aves: Alaudidae). (Submitted manuscript).
 

Alström, P., Ericson, P.G.P., Olsson, U., Sundberg, P., 2006. Phylogeny and classification of the avian superfamily Sylvioidea. Mol. Phylogenet. Evol. 38, 381-397. https://doi.org/10.1016/j.ympev.2005.05.015.
Crossref Google Scholar
 

Alström, P., Barnes, K.N., Olsson, U., Barker, F.K., Bloomer, P., Khan, A.A., et al., 2013a. Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity. Mol. Phylogenet. Evol. 69, 1043-1056. https://doi.org/10.1016/j.ympev.2013.06.005.
Crossref Google Scholar
 

Alström, P., Olsson, U., Lei, F., 2013b. A review of the recent advances in the systematics of the avian superfamily Sylvioidea. Chinese Birds 4, 99-131. https://doi.org/10.5122/cbirds.2013.0016.
Crossref Google Scholar
 

Alström, P., van Linschooten, J., Donald, P.F., Sundev, G., Mohammadi, Z., Ghorbani, F., et al., 2021. Multiple species delimitation approaches applied to the avian lark genus Alaudala. Mol. Phylogenet. Evol. 154, 106994. https://doi.org/10.1016/j.ympev.2020.106994.
Crossref Google Scholar
 
Andrews, S., 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
 

Ash, J.S., Miskell, J.E., 1998. Birds of Somalia. Pica Press, Robertsbridge.
 
Bianchi, V.L., 1905. Дополнительныя замітки о палеарктическихь жаворонкахъ (Alaudidae) [Notices supplémentaires sur les alouettes paléarctiques (Alaudidae)]. Bulletin de l’Académie impériale des sciences de St.-Pétersbourg XXIII, 205–240, 5esérie.
 
Bianchi, V., 1906. Catalogue of the known species of Alaudidae or family of Larks, with aTable showing the geographical distribution and a Key to the genera. Bulletin del’Académie impériale des sciences de St.-Pétersbourg. 5e série XXV, 1–98.
 

Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duchene, S., Fourment, M., Gavryushkina, A., et al., 2019. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650. https://doi.org/10.1371/journal.pcbi.1006650.
Crossref Google Scholar
 
Bradley, J., 2021. Friedmann’s Lark (Mirafra pulpa), version 2.0. In: Kirwan, G.M., Keeney, B.K. (Eds.), Birds of the World. Cornell Lab of Ornithology, Ithaca. https://doi.org/10.2173/bow.frilar1.02.
Crossref
 

Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N.A., RoyChoudhury, A., 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29, 1917-1932.
Crossref Google Scholar
 

Burbrink, F.T., Gehara, M., 2018. The biogeography of deep time phylogenetic reticulation. Syst. Biol. 67, 743-755.
Crossref Google Scholar
 

Chen, S., Zhou, Y., Chen, Y., Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890. https://doi.org/10.1093/bioinformatics/bty560.
Crossref Google Scholar
 
Clements, J.F., Schulenberg, T.S., Iliff, M.J., Fredericks, T.A., Gerbracht, J.A., Lepage, D., et al., 2022. The eBird/Clements checklist of Birds of the World: v2022. https://www.birds.cornell.edu/clementschecklist/download.
 
Cramp, S., 1988. In: The Birds of the Western Palearctic, vol. V. Oxford University Press, Oxford.
 

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., et al., 2011. 1000 Genomes Project Analysis Group, The variant call format and VCFtools. Bioinformatics 27, 2156-2158.
Crossref Google Scholar
 

Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M.O., et al., 2021. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008. https://doi.org/10.1093/gigascience/giab008.
Crossref Google Scholar
 

Darriba, D., Taboada, G.L., Doallo, R., Posada, D., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat. Method. 9, 772. https://doi.org/10.1038/nmeth.2109.
Crossref Google Scholar
 
de Juana, E., Suárez, F., Ryan, P., Alstrom, P., Donald, P., 2004. Family Alaudidae (larks).In: del Hoyo, J., Elliott, A., Christie, D.A. (Eds.), Handbook of the Birds of the World, vol. 9. Lynx Edicions, Barcelona, pp. 496–601.
 

Degnan, J.H., Rosenberg, N.A., 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2, 762-768.
Crossref Google Scholar
 
Dement’ev, G.P., Gladkov, N.A., 1968. Birds of the Soviet Union, vol. 5. Israel Program forScientific Translations.
 

Donald, P.F., Christodoulides, S., 2018. The 2007 record of ‘Dunn’s Lark’ on Cyprus revisited, with notes on the separation of Dunn’s Lark Eremalauda dunni and Arabian Lark E. eremodites. Sandgrouse 40, 17-24.
Google Scholar
 

Donald, P.F., Collar, N.J., 2011. Notes on the structure and plumage of Beesley’s Lark Chersomanes [albofasciata] beesleyi. Bull. Afr. Bird Club 18, 168-173.
Crossref Google Scholar
 

Donald, P., Alström, P., Engelbrecht, D., 2017. Possible mechanisms of substrate colour-matching in larks (Alaudidae) and their taxonomic implications. Ibis 159, 699-702. https://doi.org/10.1111/ibi.12487.
Crossref Google Scholar
 

Drovetski, S.V., Raković, M., Semenov, G., Fadeev, I.V., Red’kin, Y.A., 2014. Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecologically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila. PLoS One 9, e87570. https://doi.org/10.1371/journal.pone.0087570.
Crossref Google Scholar
 

Edwards, S.V., Liu, L., Pearl, D.K., 2007. High-resolution species trees without concatenation. P. Natl. Acad. Sci. USA 104, 5936-5941.
Crossref Google Scholar
 

Edwards, S.V., Potter, S., Schmitt, C.J., Bragg, J.G., Moritz, C., 2016. Reticulation, divergence, and the phylogeography-phylogenetics continuum. P. Natl. Acad. Sci. USA 113, 8025-8032.
Crossref Google Scholar
 

Finch, B.W., Hatfield, R.S., Colombo, S., Kennedy, A.S., te Raa, M., Irestedt, M., et al., 2023. Disjunct resident population of Melodious Lark Mirafra cheniana discovered in East Africa. J. Ornithol. 164, 55-71. https://doi.org/10.1007/s10336-022-02013-z.
Crossref Google Scholar
 
Fjeldså, J., Alström, P., Olsson, U., Cibois, A., Johansson, U., 2020a. Superfamily Sylvioidea, the old world warblers and their allies. In: Fjeldså, J., Ericson, P.G.P., Christidis, L. (Eds.), The Largest Avian Radiation: the Evolution of Perching Birds, or the Order Passeriformes. Lynx Edicions, Barcelona, pp. 191–236.
 
Fjeldså, J., Christidis, L., Ericson, P.G.P., Stervander, M., Ohlson, J.I., Alström, P., 2020b. An updated classification of passerine birds. In: Fjeldså, J., Ericson, P.G.P., Christidis, L. (Eds.), The Largest Avian Radiation: the Evolution of Perching Birds, or the Order Passeriformes. Lynx Edicions, Barcelona, pp. 45–64.
 

Freed, D., Aldana, R., Weber, J.A., Edwards, J.S., 2017. The Sentieon Genomics Tools - A fast and accurate solution to variant calling from next-generation sequence data. BioRxiv, 115717. https://doi.org/10.1101/115717.
Crossref Google Scholar
 

Fregin, S., Haase, M., Olsson, U., Alström, P., 2012. New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers. BMC Evol. Biol. 12, 157. https://doi.org/10.1186/1471-2148-12-157.
Crossref Google Scholar
 
Ganpule, P., Varu, M., Trivedi, B., Raina, A.D., 2022. A Field Guide to the Birds of Gujarat.Bird Conservation Society, Gujarat, Ahmedabad.
 

Ghorbani, F., Aliabadian, M., Zhang, R., Irestedt, M., Yan, H., Sundev, G., et al., 2020a. Densely sampled phylogenetic analyses of the Lesser Short-toed Lark Alaudala rufescens-Sand Lark A. raytal species complex (Aves, Passeriformes) reveal cryptic diversity. Zool. Scripta 49, 427-439. https://doi.org/10.1111/zsc.12422.
Crossref Google Scholar
 

Ghorbani, F., Aliabadian, M., Olsson, U., Donald, P.F., Khan, A.A., Alström, P., 2020b. Mitochondrial phylogeography of the genus Eremophila confirms underestimated species diversity in the Palearctic. J. Ornithol. 161, 297-312. https://doi.org/10.1007/s10336-019-01714-2.
Crossref Google Scholar
 
Gill, F., Donsker, D., Rasmussen, P., 2022. IOC world bird list (v12.2). https://doi.org/10.14344/IOC.ML.12.0.
Crossref
 
Gray, G.R., 1840. A List of the Genera of Birds, with an Indication of the Typical Species ofEach Genus. Richard and John E. Taylor, London.
Crossref
 

Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., et al., 2010. A draft sequence of the Neandertal genome. Science 328, 710-722.
Crossref Google Scholar
 

Guillaumet, A., Crochet, P.A., Godelle, B., 2005. Phenotypic variation in Galerida larks in Morocco: the role of history and natural selection. Mol. Ecol. 14, 3809-3821.
Crossref Google Scholar
 

Guillaumet, A., Pons, J.M., Godelle, B., Crochet, P.A., 2006. History of the Crested Lark in the Mediterranean region as revealed by mtDNA sequences and morphology. Mol. Phylogenet. Evol. 39, 645-656.
Crossref Google Scholar
 

Guillaumet, A., Crochet, P.A., Pons, J-M., 2008. Climate-driven diversification in two widespread Galerida larks. BMC Evol. Biol. 8, 32.
Crossref Google Scholar
 

Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95⁄98⁄NT. Nucleic Acids Symp. Ser. 41, 95-98.
Google Scholar
 

Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q., Vinh, L.S., 2018. UFBoot2: improving the Ultrafast Bootstrap Approximation. Mol. Biol. Evol. 35, 518-522.
Crossref Google Scholar
 

Hodgson, B.H., 1844. Catalogue of Nipalese birds, collected between 1824 and 1844. Zoological Miscellany (J.E. Gray), 81–86.
Google Scholar
 

Horsfield, T., 1821. Systematic arrangement and description of birds from the island of Java. Trans. Linn. Soc. London 13, 133–200.
Crossref Google Scholar
 

Horsfield, T., 1840. List of Mammalia and Birds collected in Assam by John McClelland, Esq., Assistant-Surgeon in the service of the East India Company, Bengal Establishment, Member of the late deputation which was sent into that country for the purpose of investigating the nature of the Tea Plant. Proc. Zool. Soc. Lond. 7, 146–167.
Google Scholar
 
ICZN (International Commission on Zoological Nomenclature), 1999. International Codeof Zoological Nomenclature, fourth ed. International Trust for ZoologicalNomenclature, London, p. 335.
 

ICZN (International Commission on Zoological Nomenclature), 2012. Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to Expand and Refine Methods of Publication. ZooKeys 219, 1-10. https://doi.org/10.3897/zookeys.219.3944.
Crossref Google Scholar
 

Irestedt, M., Thorn, F., Muller, I., Joensson, K.A., Ericson, P.G.P., 2022. A guide to avian museomics: insights gained from resequencing hundreds of avian study skins. Mol. Ecol. Res. 22, 2672-2684. https://doi.org/10.1111/1755-0998.13660.
Crossref Google Scholar
 

Junier, T., Zdobnov, E.M., 2010. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 29, 1669-1670.
Crossref Google Scholar
 

Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., Jermiin, L.S., 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Method. 14, 587-589. https://doi.org/10.1038/nmeth.4285.
Crossref Google Scholar
 

Kubatko, L.S., Degnan, J.H., 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56, 17-24.
Crossref Google Scholar
 
Le Maout, J.E.M., 1852. Histoire naturelle des oiseaux: suivant la classification de M.Isidore Geoffroy-Saint-Hilaire, avec l’indication de leurs moeurs et de leurs rapportsavec les arts, le commerce et l’agriculture. L. Curmer, Paris.
Crossref
 
Li, H., 2013. Aligning sequence reads, clone sequences and assembly contigs with BWAMEM. arXiv, 1303.3997. https://doi.org/10.48550/arXiv.1303.3997.
 
Linnaeus, C., 1758. Systema Naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Editio decima, reformata, Vol. 1. Laurentius Salvius, Holmiae.
Crossref
 

MMason, N.A., Pulgarin, P., Cadena, C.D., Lovette, I.J., 2020. De novo assembly of a high-quality reference genome for the Horned Lark (Eremophila alpestris). G3: Genes Genomes Genet. 10, 475–478. https://doi.org/10.1534/g3.119.400846.
Crossref Google Scholar
 

Mason, N.A., Riddell, E.A., Romero, F.G., Cicero, C., Bowie, R.C.K., 2023. Plumage balances camouflage and thermoregulation in Horned Larks (Eremophila alpestris). Am. Nat. 201, E23-E40. https://doi.org/10.1086/722560.
Crossref Google Scholar
 

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., et al., 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303. https://doi.org/10.1101/gr.107524.110.
Crossref Google Scholar
 

Meyer, M., Kircher, M., 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocals 2010(6), 1-10. https://doi.org/10.1101/pdb.prot5448.
Crossref Google Scholar
 

Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von Haeseler, A., et al., 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530-1534. https://doi.org/10.1093/molbev/msaa015.
Crossref Google Scholar
 

Nguyen, L.-T., Schmidt, H.A., von Haeseler, A., Minh, B.Q., 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268-274.
Crossref Google Scholar
 

Oliveros, C.H., Field, D.J., Ksepka, D.T., Barker, F.K., Aleixo, A., Andersen, M.J., et al., 2019. Earth history and the passerine superradiation. P. Nat. Acad. Sci. USA 116, 7916-7925. https://doi.org/10.1073/pnas.1813206116.
Crossref Google Scholar
 
Peters, J.L., 1960. Family Alaudidae. In: Mayr, E., Greenway Jr., J.C. (Eds.), Check-list ofBirds of the World, vol. IX. Museum of Comparative Zoology, pp. 3–80. Cambridge, Mass.
 
Rambaut, A., 2016. FigTree. Version 1.4.3. http://tree.bio.ed.ac.uk/software/figtree/.(Accessed 4 October 2016).
 
Rambaut, A., Drummond, A.J., 2015. TreeAnnotator. Version 2.2.1. http://www.beast2.bio.ed.ac.uk.
 

Rambaut, A., Drummond, A.J., Xie, D., Baele, G., Suchard, M.A., 2018. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901-904. https://doi.org/10.1093/sysbio/syy032.
Crossref Google Scholar
 

Rancilhac, L., Irisarri, I., Angelini, C., Arntzen, J.W., Babik, W., Bossuyt, F., et al., 2021. Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders. Mol. Phylogenet. Evol. 155, 106967. https://doi.org/10.1016/j.ympev.2020.106967.
Crossref Google Scholar
 

Rannala, B., Yang, Z., 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645-1656.
Crossref Google Scholar
 
Rasmussen, P.C., Anderton, J.C., 2012. In: Birds of South Asia: the Ripley Guide, 2ndrevised edition, vol. 2. Smithsonian Institution and Michigan State University, LynxEdicions, Barcelona.
 
Roberts, T.J., 1992. In: The Birds of Pakistan, vol. 2. Oxford University Press, Karachi.
 

Ryan, P.G., Bloomer, P., 1999. The Long-billed Lark complex: a species mosaic in south-western Africa. Auk 116, 194-208.
Crossref Google Scholar
 

Ryan, P.G., Hood, I., Bloomer, P., Komen, J., Crowe, T.M., 1998. Barlow’s Lark: a new species in the Karoo Lark Certhilauda albescens complex of southwest Africa. Ibis 140, 605-619.
Crossref Google Scholar
 
Shirihai, H., Svensson, L., 2018. In: Handbook of Western Palearctic Birds, vol. 1.Passerines to Larks. Helm, London.
 

Sigeman, H., Ponnikas, S., Hansson, B., 2020. Whole-genome analysis across 10 songbird families within Sylvioidea reveals a novel autosome-sex chromosome fusion. Biol. Lett. 16, 20200082. https://doi.org/10.1098/rsbl.2020.0082.
Crossref Google Scholar
 

Spottiswoode, C.N., Olsson, U., Mills, M.S.L., Cohen, C., Francis, J.E., Toye, N., et al., 2013. Rediscovery of a long-lost lark reveals the conspecificity of endangered Heteromirafra populations in the Horn of Africa. J. Ornithol. 154, 813-825. https://doi.org/10.1007/s10336-013-0948-1.
Crossref Google Scholar
 

Stange, M., Sanchez-Villagra, M.R., Salzburger, W., Matschiner, M., 2018. Divergence-time estimation with genome-wide single-nucleotide polymorphism data of sea catfishes (Ariidae) supports miocene closure of the Panamanian Isthmus. Syst. Biol. 67, 681-699.
Crossref Google Scholar
 

Stervander, M., Alström, P., Olsson, U., Ottosson, U., Hansson, B., Bensch, S., 2016. Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae). Mol. Phylogenet. Evol. 102, 233-245. https://doi.org/10.1016/j.ympev.2016.05.032.
Crossref Google Scholar
 

Stervander, M., Hansson, B., Olsson, U., Hulme, M.F., Ottosson, U., Alström, P., 2020a. Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon. Diversity 12, 428. https://doi.org/10.3390/d12110428.
Crossref Google Scholar
 
Stervander, M., Fjeldså, J., Christidis, L., Ericson, P.G.P., Ohlson, J.I., Alström, P., 2020b.An updated chronology of passerine birds. In: Fjeldså, J., Christidis, L., Ericson, P.G.P.(Eds.), The Largest Avian Radiation: the Evolution of Perching Birds, or the OrderPasseriformes. Lynx Edicions, Barcelona, pp. 387–396.
 

Swainson, W., 1827. On several groups and forms in ornithology, not hitherto defined. Zoological Journal 3, 343–363.
Google Scholar
 

Taylor, S.A., Larson, E.L., 2019. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat. Ecol. Evol. 3, 170-177.
Crossref Google Scholar
 

Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specifc gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
Crossref Google Scholar
 

Vigors, N.A., 1825. Sketches in ornithology; or, observations on the leading affinities of some of the more extensive groups of birds. Zoological Journal 2, 368–405.
Google Scholar
 

Zhang, C., Rabiee, M., Sayyari, E., Mirarab, S., 2018. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19, 153.
Crossref Google Scholar
 

Zhang, D., Tang, L., Cheng, Y., Yao, H., Xiong, Y., Song, G., et al., 2019. ‘Ghost introgression’ as a cause of deep mitochondrial divergence in a bird species complex. Mol. Biol. Evol. 36, 2375-2386. https://doi.org/10.1093/molbev/msz170.
Crossref Google Scholar
 

Zhang, D., Rheindt, F.E., She, H., Cheng, Y., Song, G., Jia, C., et al., 2021. Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow. Syst. Biol. 70, 961-975. https://doi.org/10.1093/sysbio/syab024.
Crossref Google Scholar
Avian Research
Volume 14 Issue 2,
June 2023
Article number: 100095
DOI: 10.1016/j.avrs.2023.100095
Cite this article:
Alström P, Mohammadi Z, Enbody ED, et al. Systematics of the avian family Alaudidae using multilocus and genomic data. Avian Research, 2023, 14(2): 100095. https://doi.org/10.1016/j.avrs.2023.100095

381

Views

21

Downloads

9

Crossref

0

Web of Science

4

Scopus

0

CSCD

Altmetrics
Received: 03 December 2022
Revised: 10 March 2023
Accepted: 12 March 2023
Published: 21 March 2023
© 2023 The Authors.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Return