(Chrono-) Species delimitation

"After all, if we can adopt meters and kilograms, perhaps we could agree on units of biodiversity in a similar way…  (Mallet, 2013, p. 680)


Determining temporal threshold values

Primary ranks (species and genera) need to be defined by temporal thresholds to objectively assign species status and genus affiliation, respectively. Secondary and tertiary ranks (subspecies and infrasubspecies) must also be taken into account, since species often exhibit substantial intraspecific diversification. Infrasubspecies are not regulated by the ICZN-Code, but article 45.5 states that "a fourth name published as an addition to a trinomen automatically denotes an infrasubspecific entity".

To delimit taxa, a continuous series of ever-splitting lineages has to be divided into individual sections, i.e. taxonomic ranks. However, in the search for suitable threshold values (cutoffs), utmost caution is required to ensure that existing taxon compositions are preserved as far as possible to minimise nomenclatural disruptions. To guarantee overall nomenclatural stability, a wealth of taxonomic information must be compiled, evaluated and implemented. Predictably, it will take a long time until taxonomists will agree on adopting temporal threshold values (cutoffs) to delimit categorial ranks. 

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). Likewise, Alström et al. (2018b, Fig.2) included a two-million-years cutoff in their locustellid timetree to distinguish intra- from interspecific divergences. 

Based on the evaluation of numerous papers on avian phylogeography and systematics, I propose temporal threshold values (cutoffs) to delimit species, subspecies and infrasubspecies, in the following way: 

  • species rank: 2 Ma
  • subspecies rank: 1 Ma
  • infrasubspecies rank: 0.5 Ma

Exemplary infrasubspecies-level timetree depicting the relationships among eight extant taxa whose ranks have been delimited by the temporal threshold values that are favoured here. Note that infrasubspecific names are put in brackets to distinguish them from subspecific names. 

 

Comment

When long-established genera finally turn out to be non-monophyletic, taxonomists are left alone with the decision to either break up large non-monophyletic genera into several smaller genera (thus proliferating new genus names), or to merge several non-monophyletic genera to one large genus (thus eliminating familiar genus names). Both camps, the “lumpers” and the “splitters”, should be considered victims of taxonomic codes that refuse to provide clear guidelines for delimitation. 

Additional problems are encountered on the species-level rank. Shall newly discovered low-level taxa be treated as species, subspecies, or infrasubspecies? Again, there are no guidelines. Instead, the ICZN-Code proudly claims to ensure the freedom of scientists to classify animals according to taxonomic judgements. But what is the benefit of regulating the naming of taxa without defining them? Isn’t that taking the second step without the first?

It is to the great credit of Kevin de Queiroz (2007, 2011) that he disclosed several shortcomings of current taxonomy. However, Kevin de Queiroz himself failed at providing a sound alternative. His statement (de Queiroz, 2011, p. 28) that „species are simply separately evolving lineages at the inclusive end of the population level continuum“ has two weaknesses: first, species are taxa, not lineages, and secondly, species have to be unequivocally distinguished from close sister species and infraspecific taxa, respectively. The phrase "inclusive end of the population level continuum” is deliberately kept vague and needs to be specified to become meaningful. In its present form, the statement merely corresponds to a species concept that is still devoid of an accompanying species-delimitation approach. Likewise the PhyloCode, developed by Kevin de Queiroz and colleagues, is no step forward, since it depends upon the traditional Codes and their Types, and does not solve the species problem (Brower, 2020). 

In view of the general discontent with existing approaches of delimiting individual species, a number of theoretical proposals and software tools for computer-assisted species delimitation have been put forward to address the "species problem", e.g.:

  • Genealogical sorting index (Cummings et al., 2008)
  • Genealogical divergence index (Jackson et al., 2017)
  • Multispecies coalescent model (Rannala & Yang, 2003, 2017)

References/Literature

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)

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 reading)

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)

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) 

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)  

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 pdf)

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. (link)

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. (abstract)

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, 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. (open manuscript)

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)

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 pdf)

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. (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)

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)

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

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. (pdf) 

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. (free pdf)

De Queiroz K (2007), Species concepts and species delimitation, SystBiol. 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)

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. (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. (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)

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, MolPhylogenetEvol. 129, 149-157. (pdf)

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)

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)

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, 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. (pdf)

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) 

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. (abstract) (hi-res tree)

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)

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)

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. (pdf)

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. (open manuscript)

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)

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)

Leaché AD, Zhu T, Rannala B, and Yang Z (2021), 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. (pdf)

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)

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 pdf)

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)

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. (abstract)

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

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) (free pdf)

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. (view open manuscript) 

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)

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)

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 - 5.5.18, 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 pdf)

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 TurdusZool. Scr. 51, 32-40. (free reading) 

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)

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 (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 pdf)

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)

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. (abstract)

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. (abstract) 

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)

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)

Vázquez-López M, Córtes-Rodríguez N, Robles-Bello SM, Bueno-Hernández A, Zamudio-Beltrán LE, Ruegg K, and Hernández-Baños BE (2021), Phylogeography and morphometric variation in the Cinnamon Hummingbird complex: Amazilia rutila (Aves: Trochilidae), Avian Res. 12, e:61. (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 (2016), Three new species of Stiphrornis (Aves: Muscicapidae) from the Afro-tropics, with a molecular phylogenetic assessment of the genus, Syst. Biodivers. 15, 87-104. (abstract)

Wang N, Kimball RT, Braun EL, Liang B, and Zhang Z (2017), Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling in Phasianidae, J. Biogeogr. 44, 122-135. (abstract)

Wei C, Sangster G, Olsson U, Rasmussen PC, Svensson L, Yao CT, Carey GH, 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 Robbins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species, Mol. Phylogenet. Evol. 175, e:107580. (free pdf)

Winker K (2021), An overview of speciation and species limits in birds, Ornithology 138, e:ukab006. (free pdf)

Yan C, Mou B, Meng Y, Tuv F, Fan Z, Price M, Yue B, and Zhang X (2016), A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history, PLoS ONE 12, e:0181649. (pdf) 

Younger JL, Strozier L, Maddox JD, Nyári ÁS, Bonfitto MT, Raherilalao MJ, Goodman SM, and Reddy S (2018), Hidden diversity of forest birds in Madagascar revealed using integrative taxonomy, Mol. Phylogenet. Evol. 124, 16-26. (open manuscript) for