Temporal species delimitation

As discussed by Jarvis (2016) and recommended for allopatric species by Price (2008) and Hudson & Price (2014), I favour the idea that evolutionary age should be the sole criterion for species delimitation. This is also the underlying principle of species "detection" using COI barcoding, which is based on the fact that the mitochondrial COXI gene (like CYTB and ND2) evolved with relatively homogeneous base substitution rates, at least in passerines (Nguyen & Ho, 2016). 

Species status might be attributed to taxa that are at least two million years old (following Avise et al., 1998; Price, 2008, and Hudson & Price, 2014; Marki et al, 2018). Likewise, Alström et al. (2018b, Fig.2) included a two-million-years cutoff in their locustellid timetree to distinguish intra- from interspecific divergences. Species that are delimited by temporal thresholds may be referred to as “chronospecies”. It should be noted, however, that the term has previously been used by palaeontologists with a slightly different meaning (Stanley, 1978). 

Arguments against a universal age-based yardstick approach for species delimitation have been put forward (e.g. Halley et al., 2017), but I do not consider the arguments particularly convincing. 

References

Ahrens D (2024), Species diagnosis and DNA taxonomy, In: DNA barcoding: methods and protocols, Desalle R (ed.), pages 33-52. preprint (abstract)

Alambiaga I, González R, Vera P, Monrós JS, and Palermo F (2023), Genetic differentiation between two subspecies of Emberiza schoeniclus and open forest bunting’s evolution inferred from mitogenomes, J. Avian Biol., e:03087. (pdf)

Albrecht F, Hering J, Fuchs E, Illera JC, Ihlow F, Shannon TJ, Collinson JM, Wink M, Martens J, and Päckert M (2020), Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations, PLoS ONE 15, e:0230151. (pdf)

Aleixo A (2023), On species concepts, species delimitation criteria, taxonomy committees, and biases: a response to Lima (2022a), Ornithol. Res. 31, 62-70. (free pdf)

Aliabadian M, Alaei-Kakhki N, Mirshamsi O, Nijman V, and Roulin A (2016), Phylogeny, biogeography, and diversification of barn owls (Aves: Strigiformes), Biol. J. Linn. Soc. 119, 904-918. (free pdf)

Alström P, Barnes KN, Olsson U, Barker FK, Bloomer P, Khan AA, Qureshi MA, Guillaumet A, Crochet PA, and Ryan PG (2013), Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity, Mol. Phylogenet. Evol. 69, 1043-56. (abstract)

Alström P, Jønsson KA, Fjeldså J, Ödeen A, Ericson PGP, and Irestedt M (2015), Dramatic niche shifts and morphological change in two insular bird species, R. Soc. Open Sci. 2, e:140364. (pdf)

Alström P, Rasmussen PC, Zhao C, Xu J, Dalvi S, Cai T, Guan Y, Zhang R, Kalyakin MV, Lei F, and Olsson U (2016), Integrative taxonomy of the Plain-backed Thrush (Zoothera mollissima) complex (Aves, Turdidae) reveals cryptic species, including a new species, Avian Res. 7, e:1. (pdf)

Alström P, Rheindt FE, Zhang R, Zhao M, Wang J, Zhu X, Yin Gwee C, Hao Y, Ohlson J, Jia C, Prawiradilaga DM, Ericson PGP, Lei F, and Olsson U (2018a), Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation, Mol. Phylogenet. Evol. 126, 141-152. (abstract)

Alström P, Cibois A, Irestedt M, Zuccon D, Gelang M, Fjeldså J, Andersen MJ, Moyle RG, Pasquet E, and Olsson U (2018b), Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification, Mol. Phylogenet. Evol. 127, 367-375. (abstract)

Alström P, van Linschooten J, Donald PF, Sundev G, Mohammadi Z, Ghorbani F, Shafaeipour A, van den Berg A, Robb M, Aliabadian M, Wei C, Lei F, Oxelman B, and Olsson U (2021a), Multiple species delimitation approaches applied to the avian lark genus Alaudala, Mol. Phylogenet. Evol. 154, e:106994. (free viewing)

Alström P, Rasmussen PC, Xia C, Zhang L, Liu C, Magnusson J, Shafaeipour A, and Olsson U (2021b), Morphology, vocalizations, and mitochondrial DNA suggest that the Graceful Prinia is two species, Ornithol. 138, 1-23. (free pdf)

Alström P, Mohammadi Z, Donald PF, Nymark M, Enbody ED, Irestedt M, Elisha EB, Ndithia HK, Thieleman BI, Engelbrecht D, Olsson U, Rancilhac L, and Stervander M (2023), Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae), Zool. J. Linn. Soc. 20, 1-29. (free pdf)

 Anderson SAS, and Weir JT (2022), The role of divergent ecological adaptation during allopatric speciation in vertebrates, Science 378, 1214-18. (pdf)

Araújo-Silva LE, Miranda LS, Carneiro L, and Aleixo A (2017), Phylogeography and diversification of an Amazonian understorey hummingbird: paraphyly and evidence for widespread cryptic speciation in the Plio-Pleistocene, Ibis 159, 778-791. (abstract)

Arbabi T, Gonzalez J, Witt HH, Klein R, and Wink M (2014), Mitochondrial phylogeography of the Eurasian Reed Warbler Acrocephalus scirpaceus and the first genetic record of A. s. fuscus in Central Europe, Ibis 156, 799-811. (abstract)

Arbeláez-Cortés E (2019), Defining the phylogeographic relationship between cis- and trans-Andean populations of Dendrocincla fuliginosa and Xenopa minutus in Colombia, Rev. Mex. Biodivers. 91, e:912984. (pdf)

Areta JI, Benítez Saldívar MJ, Lentino M, Miranda J, Ferreira M, Klicka J, and Pérez-Emán J (2023), Phylogenetic relationships and systematics of the bamboo-specialist Amaurospiza blue seedeaters, Ibis 165, 844-861. (abstract)

Arnaiz-Villena A, Guillén J, Ruiz-del-Valle V, Lowy E, Zamora J, Varela P, Stefani D, and Allende LM (2001), Phylogeography of crossbills, bullfinches, grosbeaks, and rosefinches, Cell Mol. Life Sci. 58, 1159-66. (abbstract)

Arnaiz-Villena A, Areces C, Rey D, Enríquez-de-Salamanca M, Alonso-Rubio J, and Ruiz-del-Valle V (2012), Three different North American Siskin/Goldfinch evolutionary radiations (genus Carduelis): Pine Siskin green morphs and European siskins in America, Open Ornith. J. 5, 73-81. (pdf)

Avise JC, Walker D, and Johns GC (1998), Speciation durations and Pleistocene effects on vertebrate phylogeography, Proc. R. Soc. Lond. B 265, 1707-12. (pdf)

Azuaje-Rodríguez RA, Weckstein JD, Dispoto JH, Patel S, Cacioppo JA, Bates JM, Marques Silva S, and Aleixo A (2018), Molecular systematics of the Amazonian endemic genus Hylexetastes (Aves: Dendrocolaptidae): taxonomic and conservation implications, Ibis 162, 119-136. (abstract)

Barker FK, Burns KJ, Klicka J, Lanyon SM, and Lovette IJ (2015), New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, tanagers, warblers, and allies, Auk 132, 333-348. (free pdf)

Batalha-Filho H, Irestedt M, Fjeldsã J, Ericson PGP, Silveira LF, and Miyaki CY (2013), Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest, Mol. Phylogenet. Evol. 67, 86-94. (abstract)

Batalha-Filho H, Pessoa RO, Fabre PH, Fjeldså J, Irestedt M, Ericson PGP, Silveira LF, and Miyaki CY (2014), Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests, Mol. Phylogenet. Evol. 79, 422-432. (abstract)

Batista R, Olsson U, Andermann T, Aleixo A, Ribas CC, and Antonelli A (2020), Phylogenomics and biogeography of the world’s thrushes (Aves: Turdus): new evidence for a more parsimonious evolutionary history, Proc. R. Soc. B 287, e:20192400. (pdf)

Berryman AJ, and Collar NJ (2023), Subspeciation in the Ruby-throated Bulbul Rubigula dispar, Bull. B.O.C 143, 237-243. (free pdf)

Berv JS, and Prum RO (2014), A comprehensive multilocus phylogeny of the neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification, Mol. Phylogenet. Evol. 81, 120-136. (abstract)

Bolívar-Leguizamón SD, Silveira LF, Derryberry EP, Brumfield RT, and Bravo GA (2020), Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients, Mol. Phylogenet. Evol. 148, e:106810. (free reading)

Bowie RCK, Pasquet E, McEntee JP, Njilima F, and Fjeldså J (2017), The systematics and biogeography of African tailorbirds (Cisticolidae: Artisornis) with comment on the choice of Bayesian branch-length prior when analyzing heterogeneous data, Mol. Phylogenet. Evol. 118, 172-183. (abstract)

Brady SS, Moyle RG, Joseph L, and Andersen MJ (2022), Systematics and biogeography of the whistlers (Aves: Pachycephalidae) inferred from ultraconserved elements and ancestral area reconstruction, Mol. Phylogenet. Evol. 168, e:107379. (abstract)

Brower AVZ (2020), Dead on arrival: a postmortem assessment of “phylogenetic nomenclature”, 20+ years, Cladistics 36, 627-637. (pdf)

Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, and Thébaud C (2018), Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): implications for the biogeography and conservation of New Guinean lowland birds, Mol. Phylogenet. Evol. 120, 248-258. (abstract)

Bryson RW, Chaves J, Smith BT, Miller MJ, Winker K, Pérez-Emán JL, and Klicka J (2013), Diversification across the New World within the ‘blue’ cardinalids (Aves: Cardinalidae), J. Biogeogr. 41, 587-599. (abstract)

Buainain N, Maximiano MFA, Ferreira M, Aleixo A, Faircloth BC, Brumfield RT, Cracraft J, and Ribas CC (2021), Multiple species and deep genomic divergence despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae), Mol. Phylogenet. Evol. 162, e:107206. (abstract)

Buainain N, Ferreira M, Avendaño JE, Cadena CD, Faircloth BC, Brumfield RT, Cracraft J, and Ribas CC (2022), Biogeography of a neotropical songbird radiation reveals similar diversification dynamics between montane and lowland clades, J. Biogeogr. 49, 1260-73. (abstract)

Bukowski B, Campagna L, Cabanne GS, Tubaro PL, and Lijtmaer DA (2024), Genetic and phenotypic differentiation in Thamnophilus ruficapillus, a Neotropical passerine with disjunct distribution in the Andean and Atlantic forests, J. Avian Biol. , e:0393. (free pdf)

Cabanne GS, Campagna L, Trujillo-Arias N, Naoki K, Gómez I, Miyaki CY, Santos FR, Dantas GPM, Aleixo A, Claramunt S, Rocha A, Caparroz R, Lovette IJ, and Tubaro PL (2019), Phylogeographic variation within the Buff-browed Foliage-gleaner (Aves: Furnariidae: Syndactyla rufosuperciliata) supports an Andean-Atlantic forests connection via the Cerrado, Mol. Phylogenet. Evol. 133, 198-213. (abstract)

Cadena CD, Pérez-Emán JL, Cuervo AM, Céspedes LN, Epperly KL, and Klicka JT (2019), Extreme genetic structure and dynamic range evolution in a montane passerine bird: implications for tropical diversification, Biol. J. Linn. Soc. 126, 487-506. (free pdf)

Cadena CD, Cuervo AM, Céspedes LN, Bravo GA, Krabbe N, Schulenberg TS, Derryberry GE, Silveira LF, Derrybery EP, Brumfield RT, and Fjeldså J (2021), Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds, Ornithology 138, e:ukaa024. (free pdf)

Cadena CD, and Zapata F (2021), The genomic revolution and species delimitation in birds (and other organisms): gene flow matters, but what about other evolutionary forces?, Ornithology 138, e:ukaa059. (free pdf)

Cai T, Fjeldså J, Wu Y, Shao S, Shen Y, Quan Q, Li X, Song X, Qu Y, Qiao G, and Lei F (2017), What makes the Sino-Himalayan mountains the major diversity hotspot for pheasants?, J. Biogeogr. 45, 640-651. (abstract)

Cai T, Cibois A, Alström P, Moyle RG, Kennedy JD, Shao S, Zhang R, Irestedt M, Ericson PGP, Gelang M, Qu Y, Lei F, and Fjeldså J (2019), Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes), Mol. Phylogenet. Evol. 130, 346-356. (abstract)

Cai T, Wu G, Sun L, Zhang Y, Peng Z, Guo Y, Liu X, Pan T, Chang J, Sun Z, and Zhang B (2021), Biogeography and diversification of Old World buntings (Aves: Emberizidae): radiation in open habitats, J. Avian Res. 52, e:02672. (free reading)

Campbell CR, Poelstra JW, and Yoder AD (2018), What is speciation genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species, Biol. J. Linn. Soc. 124, 561–583. (free pdf)

Campillo LC, Barley AJ, and Thomson RC (2020), Model-based species delimitation: are coalescent species reproductively isolated?, Syst. Biol. 69, 708-721. (free pdf)

Carmi O, Witt CC, Jaramillo A, and Dumbacher JP (2019), Phylogeography of the Vermillion Flycatcher species concept: multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird, Mol. Phylogenet. Evol. 102, 152-173. (abstract)

Carneiro L, Bravo GA, Aristizábal N, Cuervo AM, and Aleixo A (2018), Molecular systematics and biogeography of lowland antpittas (Aves, Grallariidae): the role of vicariance and dispersal in the diversification of a widespread Neotropical lineage, Mol. Phylogenet. Evol. 120, 375-389. (free reading)

Carneiro L, Burlamaqui TCT, Aleixo A, Oren DC, and Da Silva JMC (2022), Biogeography and diversification of bare-eyes, an endemic Amazonian clade, J. Biogeogr. 49, 1110-23. (abstract)

Chen D, Liu Y, Davison G, Li Yong D, Gao S, Hu J, Li SH, and Zhang Z (2020), Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences, Mol. Phylogenet. Evol. 151, e:106895. (abstract)

Chesser RT, Harvey MG, Brumfield RT, and Derryberry EP (2020), A revised classification of the Xolmiini (Aves: Tyrannidae: Fluvicolinae), including a new genus for Muscisaxicola fluviatilis, Proc. Biol. Soc. Wash. 133, 35-48. (abstract)

Christidis L, Horton P, and Norman JA (2008), Subspeciation in the Short-tailed Grasswren (Amytornis merrotsyi, Maluridae), Emu 108, 275-282. (abstract)

Cibois A, Thibault JC, Bonillo C, Filardi CE, Watling D, and Pasquet E (2014), Phylogeny and biogeography of the fruit doves (Aves: Columbidae), Mol. Phylogenet. Evol. 70, 442-453. (abstract)

Cibois A, Thibault JC, Bonillo C, Filardi C, and Pasquet E (2017), Phylogeny and biogeography of the imperial pigeons (Aves: Columbidae) in the Pacific Ocean, Mol. Phylogenet. Evol. 110, 19-26. (abstract)

Cibois A, Gelang M, Alström P, Pasquet E, Fjeldså J, Ericson PGP, and Olsson U (2018), Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy, Zool. Scr. 47, 428-440. (abstract)

Cicero C, Mason NA, Jiménez RA, Wait DR, Wang-Claypool CY, and Bowie RCK (2021), Integrative taxonomy and geographic sampling underlie successful species delimitation, Ornithology 138, 1-15. (free pdf)

Conix S, Cuypers V, Zachos FE, Artois T, and Monnens M (2023), A plea for preregistration in taxonomy, Megataxa 10, 1-14. (pdf)

Cummings MP, Neel MC, and Shaw KL (2008), A genealogical approach to quantifying lineage divergence, Evolution 62, 2411-22. (pdf)

Dalton DL, Nupen LJ, Mwale M, Pretorius C, Kropff AS, Monchusi BA, Labuschagne K, and Osinubi ST (2022), First steps to success: identification of divergence among the northern and the southern lineages of African Pygmy Kingfisher (Ispidina picta) (Coraciiformes: Alcedinidae), J. Ornithol. 163, 931-943. (abstract)

Dantas SM, Weckstein JD, Bates JM, Krabbe NK, Cadena CD, Robbins MB, Valderrama E, and Aleixo A (2016), Molecular systematics of the new world screech-owls (Megascops: Aves, Strigidae): biogeographic and taxonomic implications, Mol. Phylogenet. Evol. 94, 626-634. (free reading)

Dantas SM, Weckstein JD, Bates J, Oliveira JN, Catanach TA, and Aleixo A (2021), Multi-character taxonomic review, systematics, and biogeography of the Black-capped/ Tawny-bellied Screech Owl (Megascops atricapilla – M. watsoni) complex (Aves: Strigidae), Zootaxa 4949, 401-444. (pdf)

De Queiroz K (2007), Species concepts and species delimitation, Syst. Biol. 56, 879-886. (free pdf)

De Queiroz K 2011), Branches in the lines of descent: Charles Darwin and the evolution of the species concept, Biol. J. Linn. Soc. 103, 19-35. (free pdf)

Dejtaradol A, Renner SC, Karajan S, Bates PJJ, Moyle RG, and Päckert M (2015), Indochinese-Sundaic faunal transition and phylogeographical divides north of the Isthmus of Kra in Southeast Asian bulbuls (Aves: Pycnonotidae), J. Biogeogr. 43, 471-483. (abstract)

de Melo Moura CC, de Araujo HFP, Aleixo A, Wink M, and Fernandes AM (2018), The role of landscape change and paleoclimatic events in shaping the evolutionary history of the Polioptila gnatcatchers (Passeriformes, Polioptilidae) with emphasis on species associated with open habitats, J. Avian Biol. 49, 1-12. (free reading)

de Melo Moura CC, Bastian HV, Bastian A, Wang E, Wang X, and Wink M (2019), Pliocene origin, ice ages and postglacial population expansion have influenced a panmuctic phylogeography of the European Bee-eater Merops apiaster, Diversity 11, e:12. (free pdf)

de Melo Moura CC, Fernandes AM, Aleixo A, Pereira de Araújo HF, de Freitas Mariano E, and Wink M (2020), Evolutionary history of the Pectoral Sparrow Arremon taciturnus: evidence for diversification during the Late Pleistocene, Ibis 162, 1198-210. (pdf)

Després L (2019), One, two or more species? Mitonuclear discordance and species delimitation, Mol. Ecol. 28, 3845-47. (pdf)

D’Horta FM, Cuervo AM, Ribas CC, Brumfield RT, and Miyaki CY (2012), Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists, J. Biogeogr. 40, 37-49. (abstract)

Dickens JK, Bitton PP, Bravo GA, and Silveira LF (2021), Species limits, patterns of secondary contact and a new species in the Trogon rufus complex (Aves: Trogonidae), Zool. J. Linn. Soc. 193, 499-540. (free pdf)

Dietz L, Eberle J, Mayer C, Kukowka S, Bohacz C, Baur H, Espeland M, Huber BA, Hutter C, Mengual X, Peters RS, Vences M, Wesener T, Willmott K, Misof B, Niehuis O, and Ahrens D (2023a), Standardized nuclear markers improve and homogenize species delimitation in Metazoa, Methods Ecol. Evol. 14, 543-555. (pdf)

Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Posiadlowski L, Niehuis O, and Ahrens D (2023b), Metazoa-level USCOs as markers in species delimitation and classification, Mol. Ecol. Resour. 24, e:13921. (pdf)

Dong F, Li SH, Zou FS, Lei FM, Liang W, Yang JX, and Yang X J (2014), Molecular systematics and plumage coloration evolution of an enigmatic babbler (Pomatorhinus ruficollis) in East Asia, Mol. Phylogenet. Evol. 70, 76-83. (abstract)

dos Santos Barbosa WE, Ferreira M, de Deus Schultz E, Luna LW, Laranjeiras TO, Aleixo A, and Ribas CC (2021), Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains, J. Biogeogr. 49, 1683-95. (abstract)

Drovetski SV, Fadeev IV, Rakovic M, Lopes RJ, Boano G, Pavia M, Koblik EA, Lohman YV, Red’kin YA, Aghayan SA, Reis S, Drovetskaya SS, and Voelker G (2018), A test for the European Pleistocene refugial paradigm, using a Western Palaearctic endemic bird species, Proc. R. Soc. B 285, e:20181606. (pdf)

Dubois A, Ohler A, and Pyron A (2021), New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia), Megataxa 5, 1-738. (free pdf)

Dussex N, Sainsbury J, Moorhouse R, Jamieson IG, and Robertson BC (2015), Evidence for Bergmann’s rule and not allopatric subspeciation in the threatened Kaka (Nestor meridionalis), J. Hered. 106, 679-691. (free pdf)

Eberle J, Ahrens D, Mayer C, Niehuis O, and Misof B (2020), A plea for standardized nuclear markers in metazoan DNA taxonomy, Trends Ecol. Evol. 35, 336-345. (abstract)

Ericson PGP, Qu Y, Rasmussen PC, Blom M, Rheindt FE, and Irestedt M (2019), Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex, BMC Evol. Biol. 19, e:151. (pdf)

Fernandes AM, Wink M, and Aleixo A (2012), Phylogeography of the chestnut-tailed antbird (Myrmeciza hemimelaeana) clarifies the role of rivers in Amazonian biogeography, J. Biogeogr. 39, 1524-35. (abstract)

Fernandes AM, Gonzalez J, Wink M, and Aleixo S (2013), Multilocus phylogeography of the Wedge-billed Woodcreeper Glyphorynchus spirurus (Aves, Furnariidae) in lowland Amazonia: widespread cryptic diversity and paraphyly reveal a complex diversification pattern, Mol. Phylogenet. Evol. 66, 270-282. (abstract)

Fernandes AM, Wink M, Sardelli CH, and Aleixo A (2014), Multiple speciation across the Andes and throughout Amazonia: the case of the spot-backed antbird species complex (Hylophylax naevius/Hylophylax naevioides), J. Biogeogr. 41, 1094-104. (abstract)

Ferreira M, Aleixo A, Ribas CC, and Santos MPD (2017), Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate, J. Biogeogr. 44, 748-759. (abstract)

Ferreira M, Fernandes AM, Aleixo A, Antonelli A, Olsson U, Bates JM, Cracraft J, and Ribas CC (2018), Evidence for mDNA capture in the jacamar Galbula leucogastra/ clalcothorax species complex and insights on the evolution of white-sand ecosystems in the Amazon basin, Mol. Phylogenet. Evol. 129, 149-157. (free reading)

Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González-Solís J, Rozas J, Welch AJ, and Riutort M (2022), Palaeoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds, J. Biogeogr. 49, 171-188. (pdf)

Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, and González-Solis J (2023), Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of peagic seabirds, Mol. Phylogenet. Evol. 179, e:107671. (free reading)

Ford J (1978), Subspeciation, hybridization and relationships in the Little Shrike-thrush Colluricincla megarhyncha of Australia and New Guinea, Emu 79, 195-210. (abstract)

Ford J (1979) Speciation or subspeciation in the Yellow Robins?, Emu 79, 103-106. (abstract)

Fuchs J, Alström P, Yosef R, and Olsson U (2019), Miocene diversification of an open-habitat predatorial passerine radiation, the shrikes (Aves: Passeriformes: Laniidae), Zool. Scr. 48, 571-588. (abstract)

Fujisawa T, Aswad A, and Barraclough TG (2016), A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and root triplets, Syst. Ent. 65, 759-771. (free pdf)

Fujita MK, Leaché AD, Burbrink FT, McGuire JA, and Moritz C (2012), Coalescent-based species delimitation in an integrative taxonomy, Trends Ecol. Evol. 27, 480-488. (abstract)

Galla SJ, and Johnson JA (2015), Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus), Mol. Phylogenet. Evol. 84, 1-13. (abstract)

Garcia-R JC, Lemmon EM, Lemmon AR, and French N (2020), Phylogenomic reconstruction sheds light on new relationships and timescale of rails (Aves: Rallidae) evolution, Diversity 12, e:70. (pdf)

Ghorbani F, Aliabadian M, Olsson U, Donald PF, Khan AA, and Alström P (2019), Mitochondrial phylogeography of the genus Eremophila confirms underestimated species diversity in the Palearctic, J. Ornithol. 161, 297-312. (free pdf)

Ghorbani F, Aliabadian M, Zhang R, Irestedt M, Hao Y, Sundev G, Lei F, Ma M, Olsson U, and Alström P (2020), Densely sampled phylogenetic analyses of the Lesser Short-toed Lark (Alaudala rufescens) – Sand Lark (A. raytal) species complex (Aves, Passeriformes) reveal cryptic diversity, Zool. Scr. 49, 427-439. (abstract)

González-Rubio C, García De León FJ, and Rodríguez-Estrella R (2018), Phylogeography of endemic Xantus’ hummingbird (Hylocharis xantusii) show a different history of vicariance in the Baja California Peninsula, Mol. Phylogenet. Evol. 102, 265-277. (abstract)

Halley MR, Klicka JC, Sesink Clee PR, Weckstein JD (2017), Restoring the species status of Catharus maculatus (Aves: Turdidae), a secretive Andean thrush, with a critique of the  yardstick approach to species delimitation, Zootaxa 4276, 387-404. (pdf)

Harris RB, Birks SM, and Leaché SD (2014), Incubator birds: biogeographical origins and evolution of underground nesting in megapodes (Galliformes: Megapodiidae), J. Biogeogr. 41, 2045-56. (abstract)

Harvey MG, Bravo GA, Claramunt S, Cuervo AM, Derryberry GE, Battilana J, Seeholzer GF, McKay JS, O’Meara BC, Faircloth BC, Edwards SV, Peréz-Emán J, Moyle RG, Sheldon FH, Aleixo A, Smith BT, Chesser RT, Silveira LF, Cracraft J, Brumfield RT, and Derryberry EP (2020), The evolution of a tropical biodiversity hotspot, Science 370, 1343-48. (pdf) (hi-res tree)

Helbig AJ, Knox AG, Parkin DT, Sangster G, and Collinson M (2002), Guidelines for assigning species rank, Ibis 144, 518-525. (pdf)

Holt BG, and Jønsson KA (2014), Reconciling hierarchical taxonomy with molecular phylogenies, Syst. Biol. 63, 1010-17. (free pdf)

Hosner PA, Nyári ÁS, and Moyle RG (2013), Water barriers and intra-island isolation contribute to diversification in the insular Aethopyga sunbirds (Aves: Nectariniidae), J. Biogeogr. 40, 1094-106. (abstract)

Hosner PA, Campillo LC, Andersen MJ, Sánchez-González LA, Oliveros CH, Urriza RC, and Moyle RG (2018), An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago, Conservation Genet. 19, 1153-68. (abstract)

Huang JP (2020) Is population subdivision different from speciation?, Ecol. Evol. 10, 6890-96. (pdf)

Hudson EJ, and Price TD (2014), Pervasive reinforcement and the role of sexual selection in biological speciation, J. Hered. 105, 821-833. (free pdf)

Huntley JW, Harvey JA, Pavia M, Boano G, and Voelker G (2017), The systematics and biogeography of the Bearded Greenbuls (Aves: Criniger) reveals the impact of Plio-Pleistocene forest fragmentation of Afro-tropical avian diversity, Zool. J. Linn. Soc. 183, 672-686. (free pdf)

Imfeld TS, Barker FK, and Brumfield RT (2020), Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chorophonia finches (Passeriformes: Fringillidae), Auk 137, 1-25. (free pdf)

Irestedt M, Fabre PH, Batalha-Filho H, Jønsson KA, Roselaar CS, Sangster G, and Ericson PGP (2013), The spatio-temporal colonization and diversification across the Info-Pacific by a ‘great speciator’ (Aves, Erythropitta erythrogaster), Proc. R. Soc. B 280, e:20130309. (abstract)

Irestedt M, Batalha-Filho H, Roselaar CS, Christidis L, and Ericson PGP (2016), Contrasting phylogeographic signatures in two Australo-Papuan bowerbird species complexes (Aves: Ailuroedus), Zool. Scr. 45, 365-379. (abstract)

Jackson ND, Morales AE, Carstens BC, and O’Meara BC (2017), PHRAPL: phylogenetic inference using approximate likelyhoods, Syst. Biol. 66, 1045-53. (free pdf)

Jagannathan M, and Yamashita YM (2021), Defective satellite DNA clustering into chromocenters underlies hybrid incompatibility in Drosophila, Mol. Biol. Evol. 38, 4977-86. (free pdf)

Jetz W, Thomas GH, Joy JB, Hartmann K, and Mooers AO (2012), The global diversity of birds in space and time, Nature 491, 444-448. (abstract)

Jønsson KA, Fabre PH, Kennedy JD, Holt BG, Borregaard MK, Rahbek C, and Fjeldså J (2016), A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides), Mol. Phylogenet. Evol. 94, 87-94. (abstract)

Jønsson KA, Blom MPK, Marki PZ, Joseph L, Sangster G, Ericson PGP, and Irestedt M (2019a), Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): out of Australasia and return, Mol. Phylogenet. Evol. 137, 200-209. (abstract)

Jønsson KA, Reeve AH, Blom MPK, Irestedt M, and Marki PZ (2019b), Unrecognised (species) diversity in New Guinean passerine birds, Emu 119, 233-241. (abstract)

Johansson US, Nylinder S, Ohlson JI, and Tietze DT (2018), Reconstruction of the late Miocene biogeographical history of tits and chickadees (Aves: Passeriformes: Paridae): a comparison between discrete area analyses and probabilistic diffusion approach, J. Biogeogr. 45, 14-25. (abstract)

Johnson O, Howard JT, and Brumfield RT (2021), Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla), Mol. Phylogenet. Evol. 154, e:106962. (abstract)

Jukema J, van Rhijn JG, and Piersma T (2016), Geographic variation in morphometrics, molt and migration suggests ongoing subspeciation in Pacific golden-plovers (Pluvialis fulva), Auk 132, 647-656. (free pdf)

Kakhki NA, Aliabadian M, Förschler MI, Ghasempouri SM, Kiabi BH, Verde Arregoitia LD, and Schweizer M (2017), Phylogeography of the Oenanthe hispanica–pleschanka –cypriaca complex (Aves, Muscicapidae: Saxicolinae): diversification history of open-habitat specialists based on climate niche models, genetic data, and morphometric data, J. Zool. Res. Evol. Syst. 56, 408-427. (abstract)

Kamp L, Pasinelli G, Milanesi P, Drovetski SV, Kosiński Z, Kossenko S, Robles H, and Schweizer M (2019), Significant Asia-Europe divergence in the middle spotted woodpecker (Aves, Picidae), Zool. Scr. 48, 17-32. (abstract)

Kearns AM, Restani M, Szabo I, Schrøder-Nielsen A, Ah Kim J, Richardson HM, Marzluff JM, Fleischer RC, Johnsen A, and Omland KE (2018), Genomic evidence of speciation reversal in ravens, Nature Comm. 9, e:906. (pdf)

Kryukow AP, Goroshko OA, Arkhipov VY, Red’kin YA, Lee SI, Dorda BA, Kryukov KA, Kapun M, and Haring E (2022), Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations, Org. Divers. Evol. 22, 1037-64. (pdf)

Kryukov AP, Kryukov KA, Collier K, Fang B, and Edwards S (2023), Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation, Curr. Zool. e:zoad048. (free pdf)

Leaché AD, Zhu T, Rannala B, and Yang Z (2019), The spectre of too may species, Syst. Biol. 68, 168-181. (free pdf)

Lefébure T, Douady CJ, Gouy M, and Gibert J (2006), Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation, Mol. Phylogenet. Evol. 40, 435-447. (abstract)

Lerner HRL, Meyer M, James HF, Hofreiter M, and Fleischer RC (2011), Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers, Curr. Biol. 21, 1838-44. (free reading)

Li J, Song G, Chen G, Liu N, Dong L, and Bao X (2023), A new bunting species in South China revealed by an integrative taxonomic investigation of the Emberiza godlewskii complex (Aves, Emberidae [sic]), Mol. Phylogenet. Evol. 180, e:107697. (abstract)

Li SH, Li JW, Han LX, Yao CT, Shi H, Lei FM, and Yen C (2006), Species delimitation in the Hwamei Garrulax canorus, Ibis 148, 698-706. (abstract)

Li X, Huang Y, and Lei F (2015), Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae, Galliformes), BMC Genomics 16, e:42. (pdf)

Lima RD, Bocalini F, and Silveira LF (2023), Integrative revision of species limits in the genus Schiffornis (Aves: Tityridae) reveals cryptic diversity in the Neotropics, Zool. J. Linn. Soc. 200, 1048-79. (abstract)

Liu B, Alström P, Olsson U, Fjeldså J, Quan Q, Roselaar KCS, Saitoh T, Yao C, Hao Y, Wang W, Qu Y, and Lei F (2017), Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family, Ecol. Evol. 7, 6346-57. (pdf)

Liu T, Xu Y, Xia C, Edwards D, Hu X, Su Y, Xie J, and Zhang W (2022), Multiple lines of evidence confirm that the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) is an independent species, Avian Res. 13, e:100022. (free reading)

Liu Y, Chen G, Huang Q, Jia C, Carey G, Leader P, Li Y, Zou F, Yang X, Olsson U, and Alström P (2016), Species delimitation of the white-tailed rubythroat Calliope pectoralis complex (Aves, Muscicapidae) using an integrative taxonomic approach, J. Avian Biol. 47, 899-910. (free reading)

Llanes-Quevedo A, Mastretta-Yanes A, Sánchez-González LA, Castillo-Chora VJ, and Navarro-Sigüenza AG (2022), The tangled evolutionary history of a long-debated Mesoamerican taxon: the Velazquez Woodpecker (Melanerpes santacruzi, Aves: Picidae), Mol. Phylogenet. Evol. 170, e:107445. (abstract)

Luo A, Ling C, Ho SYW, and Zhu CD (2018), Comparison of methods for molecular species delimitation across a range of speciation scenarios, Syst. Biol. 67, 830-846. (free pdf)

Lutz HL, Weckstein JD, Patané JSL, Bates JM, and Aleixo A (2013), Biogeography and spatio-temporal diversification of Selenidera and Andigena toucans (Aves: Ramphastidae), Mol. Phylogenet. Evol. 69, 873-883. (abstract)

Mallet J (2013), Species, concepts of, In: “Encyclopedia of biodiversity” (Levin SA, ed.), vol. 6 (pp. 679-691). Academic Press, Waltham, MA, USA. (authors personal copy)

Manawatthana S, Laosinchai P, Onparn N, Brockelman WY, and Round PD (2017), Phylogeography of bulbuls in the genus Iole (Aves: Pycnonotidae), Biol. J. Linn. Soc. 120, 931-944. (free pdf)

Marki PZ, Jønsson KA, Irestedt M, Nguyen MT, Rahbek C, and Fjeldså J (2017), Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes), Mol. Phylogenet. Evol. 107, 516-529. (abstract)

Marki PZ, Fjeldså J, Irestedt M, and Jønsson KA (2018), Molecular phylogenetics and species limits in a cryptically coloured radiation of Australo-Papuan passerine birds (Pachycephalidae: Colluricincla), Mol. Phylogenet. Evol. 124, 100-105. (abstract)

Martins FC, Cox SC, Irestedt M, Prŷs-Jones RP, and Day JJ (2020), A comprehensive molecular phylogeny of Aftrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history, Mol. Phylogenet. Evol. 149, e:106843. (abstract)

Matos MV, Borges SH, d’Horta FM, Cornelius C, Latrubesse E, Cohn-Haft M, and Ribas CC (2016), Comparative phylogeography of two bird species, Tachyphonus phoenicius (Thraupidae) and Polytmus theresiae (Trochilidae), specialised in Amazonian white-sand vegetation, Biotropica 48, 110-120. (abstract)

Mayr E (1968), Theory of biological classification, Nature 220, 545-548. (link)

Mays HL, McKay B, Tietze DT, Yao CT, Miller LN, Moreland KN, and Lei F (2015), A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla), Avian Res. 6, e:17. (pdf)

McKay BD, and Zink RM (2010), The causes of mitochondrial DNA gene tree paraphyly in birds, Mol. Phylogenet. Evol. 54, 647-650. (abstract)

Milá B, Bruxaux J, Friis G, Sam K, Ashari H, and Thébaud C (2021), A new, undescribed species of Melanocharis berrypecker from western New Guinea and the evolutionary history of the family Melanocharitidae, Ibis 163, 1310-29. (pdf)

Mirarab S, Nakhleh L, and Warnow T (2021), Multispecies coalescent: theory and applications in phylogenetics, Annu. Rev. Ecol. Evol. Syst. 52, 247-268. (pdf)

Moncrieff AE, Faircloth BC, and Brumfield RT (2022), Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers, Mol. Phylogenet. Evol. 173, e:107525. (abstract)

Moura dos Santos Soares L, Bates J, Carneiro LS, Dantas Santos MP, and Aleixo S (2019), Molecular systematics, biogeography, and taxonomy of forest-falcons in the Micrastur ruficollis species complex (Aves: Falconidae), J. Avian Biol. 50, e:01943. (free reading)

Naka LN, and Brumfield RT (2018), The dual role of Amazonian rivers in the generation and maintenance of avian diversity, Sci. Adv. 4, e:eaar8575. (pdf)

Norman JA, Rheindt FE, Rowe DL, and Christidis L (2007), Speciation dynamics in the Australian-Papuan honeyeaters, Mol. Phylogenet. Evol. 42, 80-91. (abstract)

Olsson U, Leader P, Carey G, Khan AA, Svensson L, and Alström P (2013), New insights into the intricate taxonomy and phylogeny of the Sylvia curruca complex, Mol. Phylogenet. Evol. 67, 72-85. (abstract)

Olsson U, and Alström P (2020), A comprehensive phylogeny and taxonomy of the waxbills (Aves: Estrildidae), Mol. Phylogenet. Evol. 146, e:106757. (free reading)

Ortiz-Ramírez MF, Andersen MJ, Zaldívar-Riverón A, Ornelas JF, and Navarro-Sigüenza AG (2015), Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush (Catharus frantzii; Aves: Turdidae), Mol. Phylogenet. Evol. 94, 74-86. (abstract)

Oswald JA, Harvey MG, Remsen RC, Foxworth DU, Cardiff SW, Dittmann DL, Megna LC, Carling Mad, and Brumfield RT (2016), Willet he one species or two? A genomic view of the evolutionary history of Tringa semipalmata, Auk 133, 593-614. (free pdf)

Oswald JA, Harvey MG, Remsen RC, Foxworth DU, Dittmann DL, Cardiff SW, and Brumfield RT (2018), Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World, Mol. Ecol. 28, 1675-91. (abstract)

Päckert M, Bader-Blukott M, Künzelmann B, Sun YH, Hsu YC, Kehlmaier C, Albrecht F, Illera JC, and Martens J (2020a), A revised phylogeny of nuthatches (Aves, Passeriformes, Sitta) reveals insight in intra- and interspecific diversification patterns in the Palearctic, Vertebr. Zool. 70, 241-262. (pdf)

Päckert M, Favre A, Schnitzler J, Martens J, Sun YH, Tietze DT, Hailer F, Michalak I, and Strutzenberger P (2020b), “In and out” of the Qinghai-Tibet Plateau and the Himalayas: centers of origin and diversification across five clades of Eurasian montane and alpine passerine birds, Ecol. Evol. 10, 9283-300. (pdf)

Päckert M, Hering J, Aït Belkacem A, Sun YH, Hille S, Lkhagvasuren D, Islam S, and Martens J (2021), A revised multilocus phylogeny of Old World sparrows (Aves: Passeridae), Vertebr. Zool. 71, 353-366. (free pdf)

Parau LG, and Wink M (2021), Common patterns in the molecular phylogeography of western Palearctic birds: a comprehensive review, J. Ornithol. 162, 937-959. (pdf)

Pasquet E, Barker FK, Martens J, Tillier A, Cruaud C, and Cibois A (2014), Evolution within the nuthatches (Sittiche: Aves, Passeriformes): molecular phylogeny, biogeography, and ecological perspectives, J. Ornithol. 155, 755-765. (abstract)

Pedersen MP, Irestedt M, Joseph L, Rahbek C, and Jønsson KA (2018), Phylogeography of a “great speciator” (Aves: Edolisoma tenuirostre) reveals complex dispersal and diversification dynamics across the Info-Pacific, J. Biogeogr. 45, 826-837. (abstract)

Pentzold S, Tritsch C, Martens J, Tietze DT, Giacalone G, Lo Valvo M, Nazarenko AA, Kvist L, and Päckert M (2013), Where is the line? Phylogeography and secondary contact of western Palearctic coal tits (Periparus ater: Aves, Passeriformes, Paridae), Zool. Anz. 252, 367-382. (abstract)

Persons NW, Hosner PA, Meiklejohn KA, Braun EL, and Kimball RT (2016), Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences, Mol. Phylogenet. Evol. 98, 123-132. (abstract)

Pertierra LR, Segovia NI, Noll D, Martinez PA, Pliscoff P, Barbosa A, Aragón P, Raya Rey A, Pistorius P, Trathan P, Polanowski A, Bonadonna F, Le Bohec C, Bi K, Wang-Claypool CY, González-Acuña D, Dantas GPM, Bowie RCK, Poulin E, and Vianna JA (2020), Cryptic speciation in gentoo penguins is driven by geographic isolation and regional marine conditions: unforeseen vulnerabilities to global change, Divers. Distrib. 26, 958-975. (pdf)

Phillimore AB (2010), Subspecies origination and extinction in birds, Ornithol. Monogr. 67, 42-53. (abstract)

Pons JM, Campión D, Chiozzi G, Ettwein A, Grangé JL, Kajtoch Ł, Mazgajski T, Rakovic M, Winkler H, and Fuchs J (2020), Phylogeography of a widespread Palaearctic forest bird species: the White-backed Woodpecker (Aves, Picidae), Zool. Scr. 50, 155-172. (abstract)

Pourebrahimi S, Mirshamsi O, Ghasempouri SM, Moghaddam FY, and Aliabadian M (2022), Phylogeny and evolutionary history of the Sombre Tit, Poecile lugubris in the western Palearctic (Aves, Paridae), Mol. Phylogenet. Evol. 167, e:107343. (abstract)

Price TD, and Bouvier MM (2002), The evolution of F1 postzygotic incompatibilities in birds, Evolution 56, 2083-89. (abstract)

Puillandre N, Lambert A, Brouillet S, and Achaz G (2011), ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Mol. Ecol. 21, 1864-77. (abstract)

Pulido-Santacruz P, Bornschein MR, Belmonte-Lopes R, and Bonatto SL (2016), Multiple evolutionary units and demographic stability during the last glacial maximum in the Scytalopus speluncae complex (Aves: Rhinocryptidae), Mol. Phylogenet. Evol. 102, 86-96. (abstract)

Rakovič M, Neto JM, Lopes RJ, Koblik EA, Fadeev IV, Lohman YV, Aghayan SA, Boano G, Pavia M, Perman Y, Kiat Y, Ben Dov A, Collinson JM, Voelker G, and Drovetski SV (2019), Geographic patterns of mtDNA and Z-linked sequence variation in the Common Chiffchaff and the ‘chiffchaff complex’, PLoS ONE 14, e:0210268. (pdf)

Ramirez JL, Miyaki CY, Frederick PC, and Del Lama SN (2014), Species delimitation in the genus Eudocimus (Threskiornithidae: Pelecaniformes): first genetic approach, Waterbirds 37, 419-425. (abstract)

Rannala B, and Yang Z (2003), Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci, Genetics 164, 1645-56. (free pdf)

Rannala B, and Yang Z (2017), Efficient Bayesian species tree inference under the multispecies coalescent, Syst. Biol. 66, 823-842. (free pdf)

Rannala B, and Yang Z (2020), Species delimitation, In: “Phylogenetics in the genomic era” (Scornavacca C, Delsuc F, and Galtier N, eds.), pp 5.5.1-18, Authors open access book. (pdf)

Recuerda M, Illera JC, Blanco G, Zardoya R, and Milá B (2021), Sequential colonization of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs), Mol. Phylogenet. Evol. 164, e:107291. (free reading)

Reeve AH, Blom MPK, Marki PZ, Batista R, Olsson U, Edmark VN, Irestedt M, and Jønsson KA (2022) The Sulawesi Thrush (Cataponera turdoides; Aves: Passeriformes) belongs to the genus Turdus, Zool. Scr. 51, 32-40. (free reading)

Reyes P, Bates JM, Naka LN, Miller MJ, Caballero I, Gonzalez-Quevedo C, Parra JL, Rivera-Gutierrez HF, Bonaccorso E, and Tello JG (2023), Phylogenetic relationships and biogeography of the ancient genus Onychorhynchus (Aves: Onychorhynchidae) suggest cryptic Amazonian diversity, J. Avian Biol. e:03159. (pdf)

Ribas CC, Aleixo A, Nogueira ACR, Miyaki CY, and Cracraft J (2012), A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years, Proc. R. Soc. B 279, 681-689. (abstract)

Ritter CD, Coelho LA, Capurucho JMG, Borges SH, Cornelius C, and Ribas CC (2021), Sister species, different histories: comparative phylogeography of two species associated with Amazonian open vegetation, Biol. J. Linn. Soc. 132, 161-173. (free pdf)

Rivera-Arroyo RC, Escalante-Pliego P, Aguilar-Torres D, and Úbeda-Olivas MF (2022), Phylogeography of the white-crowned parrot (Pionus senilis), Biota Neotrop. 22, e:20221382. (pdf)

Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, and Navarro-Sigüenza AG (2018), Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae), ZooKeys 809, 125-148. (pdf)

Ross HA (2014), The incidence of species-level paraphyly in animals: a re-assessment, Mol. Phylogenet. Evol. 76, 10-16. (abstract)

Sánchez-Nivicela M, Avendaño JE, Sánchez-Nivicela JC, Torres A, Fuchs J, Bird B, and Bonaccorso E (2021), A taxonomic assessment of Chlorospingus flavopectus phaeocephalus and Chlorospingus semifuscus (Passeriformes: Passerellidae), including the description of a new subspecies, Zootaxa 5057, 151-180. (abstract)

Sandoval L, Epperly KL, Klicka J, and Mennill DJ (2017), The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae), Mol. Phylogenet. Evol. 110, 50-59. (abstract)

Sangster G (2014), The application of species criteria in avian taxonomy and its implications for the debate over species concepts, Biol. Rev. 89, 199-214. (abstract)

Sangster G, Roselaar CS, Irestedt M, and Ericson PGP (2016), Sillem’s Mountain Finch Leucosticte sillemi is a valid species of rosefinch (Carpodacus, Fringillidae), Ibis 158, 184-189. (abstract)

Sangster G (2018), Integrative taxonomy of birds: the nature and delimitation of species, In: “Bird species – How they arise, modify and vanish” (Tietze DT, ed.), chapter 2, Springer Open, Cham, Switzerland. (pdf)

Santana A, Silva SM, Do Nascimento NF, Sampaio I, and Aleixo A (2021), Phylogeography of the Dendrocolaptes picumnus (Aves: Dendrocolaptidae) species complex: new insights on the diversification of a trans-American lineage, J. Avian Biol. 52, e:02723. (pdf)

Schultz ED, Burney CW, Brumfield RT, Polo EM, Cracraft J, and Ribas CC (2017), Systematics and biogeography of the Automolus infuscatus complex (Aves; Furnariidae): cryptic diversity reveals western Amazonia as the origin of a transcontinental radiation, Mol. Phylogenet. Evol. 107, 503-515. (free reading)

Schultz E, Pérez-Emán J, Aleixo A, Miyaki C, Brumfield R, Cracraft J, and Ribas C (2019), Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): insights from broad geographic sampling, Mol. Phylogenet. Evol. 140, e:106581. (abstract)

Schweizer M, Shirihai H, Schmaljohann H, and Kirwan GM (2018), Phylogeography of the House Bunting complex: discordance between species limits and genetic markers, J. Ornithol. 159, 47-61. (abstract)

Schweizer M, Liu Y, Olsson U, Shirihai H, Huang Q, Leader PJ, Copete JL, Kirwan GM, and Svensson L (2018), Contrasting patterns of diversification in two sister species of martins (Aves: Hirundinidae): the Sand Martin Riparia riparia and the Pale Martin R. diluta, Mol. Phylogenet. Evol. 125, 116-126. (abstract)

Schweizer M, Marques DA, Olsson U, and Crochet PA (2023), The Howard & Moore complete checklist of the birds of the world: framework for species delimitation, Avian Syst. 1, 35-41. (pdf)

Singh A, Gupta SK, Alström P, Mohan D, Hooper DM, Kumar RS, Bhatt D, Singh P, and Price TD (2019), Taxonomy of cryptic species in the Cyornis rubeculoides complex in the Indian subcontinent, Ibis 162, 924-935. (abstract)

Sites JW, and Marshall JC (2004), Operational criteria for delimiting species, Annu. Rev. Ecol. Evol. Syst. 35, 199-227. (abstract)

Stanton DWG, Frandsen P, Waples RK, Heller R, Russo IRM, Orozco-terWengel PA, Tingskov Pedersen CE, Siegismund HR, and Bruford MW (2019), More grist for the mill? Species delimitation in the genomic era and its implications for conservation, Conserv. Genet. 20, 101-113. (pdf)

Stelbrink B, von Rintelen T, Richter K, Finstermeier K, Frahnert S, Cracraft J, and Hofreiter M (2022), Insights into the geographical origin and phylogeographical patterns of Parasidaea birds-of-paradise, Zool. J. Linn. Soc. 196, 1394-407. (free pdf)

Stervander M, Hansson B, Olsson U, Hulme MF, Ottosson U, and Alström P (2020), 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, e:428. (free pdf)

Stopiglia R, Barbosa W, Ferreira M, Raposo MA, Dubois A, Harvey MG, Kirwan GM, Forcato G, Bockmann FA, and Ribas CC (2021), Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae), Zool. J. Linn. Soc. 195, 65-87. (free pdf)

Sweet AD, and Johnson KP (2014), Patterns of diversification in small New World ground doves are consistent with major geologic events, Auk 132, 300-312. (free pdf)

Sweet AD, Maddox JD, and Johnson KP (2017), A complete molecular phylogeny of Claravis confirms its paraphyly within small New World ground-doves (Aves: Peristerinae) and implies multiple plumage state transitions, J. Avian Biol. 48, 459-464. (free pdf)

Thom G, and Aleixo A (2015), Cryptic speciation in the White-shouldered Antshrike (Thamnophilus aethiops, Aves – Thamnophilidae): the tale of a transcontinental radiation across rivers in lowland Amazonia and the northeastern Atlantic Forest, Mol. Phylogenet. Evol. 82, 95-110. (abstract)

Tietze DT, Päckert M, Martens J, Lehmann H, and Sun YH (2013), Complete phylogeny and historical biogeography of true rose finches (Aves: Carpodacus), Zool. J. Linn. Soc. 169, 215-234. (free pdf)

Tilston Smith B, Bryson RW, Mauck WM, Chaves J, Robbins MB, Aleixo A, and Klicka J (2018), Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae), Mol. Phylogenet. Evol. 126, 45-57. (abstract)

Töpfer D, Haring E, Birkhead TR, Lopes RJ, Severinghaus LL, Martens J, and Päckert M (2011) A molecular phylogeny of bullfinches Brisson 1760 (Aves: Fringillidae), Mol. Phylogenet. Evol. 58, 271-282. (abstract)

Van Doren BM, Freeman BG, Aristizabal N, Alvarez-R M, Pérez-Emán J, Cuervo AM, and Bravo GA (2018), Species limits in the Rusty-breasted Antpitta (Grallaricula ferrugineipectus) complex, Wilson J. Ornithol. 130, 152-167. (abstract)

Vaux F, Trewick SA, and Morgan-Richards M (2016), Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary, Biol. J. Linn. Soc. 117, 165-176. (free pdf)

Vences M, Miralles A, and Dufresnes C (2024), Next-generation species delimitation: Implications for biogeography, J. Biogeogr. 51, 1709-22. (pdf)

Venkatraman MX, DeRaad DA, Tsai WLE, Zarza E, Zellmer AJ, Maley JM, and McCormack JE (2019), Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird, Biol. J. Linn. Soc. 126, 1-15. (free pdf)

Voelker G, Tobler M, Prestridge HL, Duijm E, Groenenberg D, Hutchinson MR, Martin AD, Nieman A, Roselaar CS, and Huntley JW (2017), Three new species of Stiphrornis (Aves: Muscicapidae) from the Afrotropics, with a molecular phylogenetic assessment of the genus, Syst. Biodiv. 15, 87-104. (abstract)

Wei C, Dong L, Li SH, Alström P, Liu Y, Xia C, Yao CT, and Zhang Y (2019), From the Himalayas to a continental Island: integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex, Mol. Phylogenet. Evol. 131, 219-227. (abstract)

Wei C, Sangster G, Olsson U, Rasmussen PC, Svensson L, Yao CT, Carey GJ, Leader PJ, Zhang R, Chen G, Song G, Lei F, Wilcove DS, Alström P, and Liu Y (2022), Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species, Mol. Phylogenet. Evol. 175, e:107580. (view pdf)

Winker K, and Rasmussen PC (2021), Species limits and taxonomy in birds, Ornithology 138, e:ukab017. (free pdf)

Zink RM, and Klicka LB (2022), The taxonomic basis of subspecies listed as threatened under the endangered species act, Front. Conserv. Sci. 3, e:971280. (free pdf)

Zink RM, Spellman GM, Canales-del-Castillo R, Epperly K, and Klicka J (2023), Mitochondrial DNA phylogeography of the Bushtit (Psaltriparus minimus), Wilson J. Ornithol. 135, 22-30. (abstract)