am sorry for any inconvenience, but this page is still in preparation. At present, it is no more than an extensive collection of putatively relevant literature and first fragmented ideas…

When populations of one and the same species evolve independently from each other for a longer period of time, they are inevitably going to differentiate. This is a gradual and continuous process. But at which point should divergent populations be considered separate species? The answer to this question is still a matter of debate…


Correlation between “Theoretical species concepts” and “Operational species delimitation criteria”

Phylogeography, speciation, species delimitation. species limits,

Genetic divergence versus morphological, plumage or song differentiation, 

Genetic differentiation (divergence, distance) should be translated to divergence time…

comparing a small number of specific DNA sequences (or ‘markers’) was not informative for distinguishing (delimiting) taxa.

Biodiversity conservation has historically focused on species; however, how species are conceptualised and delimitated are topics which continue to be

Due to evolutionary processes like incomplete lineage sorting and introgression through hybridization, several independent DNA markers are essential to resolve closely related species.

Biological species concept - the foundation of integrative taxonomy

initial empirical investigation/determination of reliable species boundaries provide the basis for subsequent a posteriori taxonomic generalisations of reliable species-divergence thresholds 

Since a comparison of a multitude of independent integrative taxonomic studies resulted in largely concordant results, the data obtained should be taken as a framework allowing general conclusions to be drawn. 

Identification, delimitation, definition

DNA sequence-based species delimitation

Divergence events between either species- or subspecies-level taxa demand thresholds to be definede to be able to distinguish between them. 

Reproductive isolation is a by-product of genetic differentiating following prolonged spatial separation (isolation). 


Guided by the idea that DNA should be informative at all taxonomic levels, I conclude that the delimitation of species and subspecies should also be based on differences in DNA sequences (as discussed in Jarvis, 2016 and recommended for allopatric species by Price, 2008 and Hudson & Price, 2014). This pragmatic approach is based on the widely accepted assumption that the speciation process represents a continuum that can only be arbitrarily divided. It ultimately follows that species cannot be detected but have to be defined. Originally established in palaeontology (Stanley, 1978), I expand the meaning of the term “chronospecies” by applying it to the DNA-based species concept to be outlined below. 

Selecting an appropriate threshold of sequence divergence for species delimitation, and thus cannot be criticised for not taking into account evolutionary processes. 

First, differences in the DNA signature of independent lineages need to be quantified. Next, the observed differences need be translated into divergence times. Finally, the putative divergence times are used to delimit species and subspecies according to the putative times of divergence. Species status might be attributed to lineages that are at least two million years old (following Price, 2008; and Hudson & Price, 2014), and subspecies status to lineages that are at least one million years old ( new suggestion). 

Age should be the sole operating criterion in defining species and subspecies. At present, however, avian taxonomists integrate everything - except time. Other traits (morphology, acoustics, behaviour, habitat preference, distribution, and possibly others) are still required to investigate the underlying evolutionary processes of speciation. 

Relying exclusively on age substantially reduces the level of subjectivity in species-delimitation decisions. Once delimiting ages for species and subspecies are agreed upon, species-level taxonomies could be generated automatically by computer programs. 

When considering closely related populations of organisms, it can be difficult to decide where to draw the line between species and subspecies. The problem is exacerbated by the fact that many distinct species inter-breed to some extent, blurring the lines between species and subspecies further.  


Abbott R, Albach D, Ansell S, Arntzen W, Baird SJE, Bierne N, Boughman J, Brelsford A, Buerkle CA, Buggs R, Butlin RK, Dieckmann U, Eroukhmanoff F, Grill A, Cahan SA, Hermansen JS, Hewitt G, Hudson AG, Jiggins C, Jones J, Keller B, Marczewski T, Mallet J, Martinez-Rodriguez P, Möst M, Mullen S, Nichols R, Nolte AW, Parisod C, Pfennig K, Rice AM, Ritchie MG, Seifert B, Smadja CM, Stelkens R, Szymura JM, Väinölä R, Wolf JBW, and Zimmer D (2013), Hybridization and speciation, J. Evol. Biol. 26, 229-246. (pdf)

Ahrens D, Ahyong ST, Ballerio A, Barclay MVL, Eberle J, Espeland M, Huber BA, Mengual X, Pacheco TL, Peters RS, Rulik B, Vas-de-Mello F, Wesener T, and Krell FT (2021), Is it time to describe new species without diagnoses? - A comment on Sharkey et al. (2021), Zootaxa 5027, 151-159. (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 Iberia-Maghrebian and Cyrenaican populations, PLOS ONE 15, e:0230151. (pdf)


Alcaide M, Scordato ESC, Price DT, and Irwin DE (2014), Genomic divergence in a ring species complex, Nature 511, 83-85. (abstract)


Aldhebiani AY (2018), Species concept and speciation, Saudi J. Biol. Sci. 25, 437-440. (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, Gwee CY, Hao Y, Ohlson J, Jia C, Prawiradilaga DM, Ericson PGP, Lei F, and Olsson U (2018), Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation, Mol. Phylogenet. Evol. 126, 141-152. (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 AlaudalaMolPhylogenetEvol. 154, e:106994(pdf) 


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


Alvarez S, Salter JF, McCormack JE, and Milá B (2015), Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black-capped siekin complex, J. Avian Biol. 47, 335-345. (abstract)


Andersen MJ, Nyári AS, Mason I, Joseph L, Dumbacher JP, Filardi CE, and Moyle RG (2014), Molecular systematics of the world’s most polytypic bird: the Pachycephala pectoralis/melanura (Aves: Pachycephalidae) species complex, Zool. J. Linn. Soc. 170, 566-588. (pdf)


Andersen MJ, Shult HT, Cibois A, Thibault JC, Filardi CE, and Moyle RG (2015), Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae: Todiramphus), R. Soc. open Sci. 2, e:140375. (pdf)


Arato J, and Fitch WT (2021), Phylogenetic signal in the vocalizations of vocal learning and vocal non-learning birds, Phil. Transact. Roy. Soc. B 376, e:20200241. (pdf)


Arbeláez-Cortés E (2020), Defining the phylogeographic relationship between cis- and trans-Andean populations of Dendrocincla fuliginosa and Xenops minutus in Colombia, Revista Mex. Biodiv. 91, e:912984. (pdf)


Arguedas N, and Parker PG (2000), Seasonal migration and genetic population structure in house wrens, Condor 102, 517-528. (pdf)


Arnaiz-Villena A, Ruiz-del-Valle V, Moscoso J, Serrano-Vela JI, and Zamora J (2007), mtDNA phylogeny of North American Carduelis pina group, Ardeola 54, 1-14. (pdf)


Arnaiz-Villena A, Areces C, Rey D, Enríquez-de-Salamanca M, Alsonso-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)


Avendaño JE, Arbeláez-Cortés E, and Cadena CD (2017), On the importance of geographic and taxonomic sampling in phylogeography: a reevaluation of diversification and species limits in a Neotropical thrush (Aves, Turdidae), Mol. Phylogenet. Evol. 111, 87-97. (abstract)


Avendaño JE, Cuervo AM, Montoya P, Pulgarín-R PC, and Stiles FG (2021), A new subspecies in the Turdus nudigenis complex (Aves: Turdidae) from the Cauca River valley of Colombia, Zootaxa 5060, 105-123. (abstract)


Avise JC (2000), Phylogeography: the history and formation of species, Harvard Univ. Press, Cambridge, MA. 447 pp. (link)


Avise JC (2009), Phylogeography: retrospect and prospect, J. Biogeogr. 36, 3-15. (abstract)


Avise JC (2014), Conceptual breakthroughs in evolutionary genetics: a brief history of shifting paradigms, Elsevier, New York. 164 pp. (link)


Avise JC, Arnold J, Ball RM, and Bermingham E (1987), Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics, AnnuRev. Ecol. Syst. 18, 489-522. (link)


Avise JC, Bowen BW, and Ayala FJ (2016), In the light of evolution X: comparative phylogeography (an introduction), Proc. Natl Acad. Sci. USA 113, 7957-61. (pdf)


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


Baker AJ, Pereira SL, Rogers DI, Elbourne R, and Hassell CJ (2007), Mitochondrial-DNA evidence shows the Australian Painted Snipe is a full species, Rostratula australis, Emu 107, 185-189. (abstract)


Baker RJ, and Bradley RD (2006), Speciation in mammals and the genetic species concept, J. Mammal. 87, 643-662. (pdf)


Bamberger S, Xu J, and Hausdorf B (2021), Evaluating species delimitation methods in radiations: the land snail Albinaria cretensis complex on Crete, Syst. Biol., e:syab050. (abstract)


Barani-Beiranwand H, Aliabadian M, Irestedt M, Qu Y, Darvish J, Szekely T, van Dijk RE, and Ericson PGP (2017), Phylogeny of penduline tits inferred from mitochondrial and microsatellite genotyping, J. Avian Biol. 48, 932-940. (abstract)


Barbosa WES, Ferreira M, Schultz ED, 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)


Barley AJ, Brown JM, and Thomson RC (2018), Impact of model violations on the inference of species boundaries under the multispecies coalescent, Syst. Biol. 67, 269-284. (pdf)


Barrera-Guzmán AO, Aleixo A, Shawkey MD, and Weir JT (2017), Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird, PNAS 115, E218-E225. (pdf)


Barraclough TG, and Nee S (2001), Phylogenetics and speciation, Trends Ecol. Evol. 16, 391-399. (abstract)

Barraclough TG (2019), The evolutionary biology of species, Oxford University Press. (link)


Barrowclough GF, Cracraft J, Klicka J, and Zink RM (2016), How many kinds of birds are there and why does it matter? PLOS ONE 11, 1-15. (pdf)


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)


Beam JK, Funk ER, and Taylor SA (2021), Genomic and acoustic differences separate Lilian‘s Meadowlark (Sturnella magna lilianae) from Eastern (S. magna) and Western (S. neglecta) meadowlarks, Ornithology 138, e:ukab004. (abstract)


Benz BW, and Robbins MB (2010), Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae), Mol. Phylogenet. Evol. 61, 29-44. (abstract)


Berv JS, Campagna L, Feo TJ, Castro-Astor I, Ribas CC, Prum RO, and Lovette IJ (2021), Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes, Mol. Phylogenet. Evol. 164, e:107205. (pdf)


Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker  K, Ingram KK, and Das zi (2007), Cryptic species as a window on diversity and conservation, Trends Ecol. Evol. 22, 148-155. (abstract)

Bininda-Emons ORP (2007), Fast genes and slow clades: comparative rates of molecular evolution in mammals, Evol. Bioinform. 3, 59-85. (pdf)


Bocalini F, Bolívar-Leguizamón SD, Silveira LF, and Bravo GA (2021), Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic forest, Mol. Phylogenet. Evol. 154, e:106973. (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. (pdf)


Bowie RCK, Pasquet E, McEntee JP, Njilima F, and Fjeldså J (2018), 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)


Brelsford A, and Irwin DE (2009), Incipient speciation despite little assortative mating: the Yellow-rumped Warbler hybrid zone, Evolution 63, 3050-60. (pdf)


Brelsford A (2011), Hybrid speciation in birds: allopatry more important than ecology?, Mol. Ecol. 20, 3705-07. (abstract)


Brower AVZ (2010), Alleviating the taxonomic impediment of DNA barcoding and setting a bad precedent: names for ten species of ‘Astraptes fulgerator’ (Lepidoptera: Hesperiidae: Eudaminae) with DNA-based diagnoses, Syst. Biodivers. 4, 127-132. (abstract)


Brown RM, Techow N, Wood AG, and Phillips RA (2015), Hybridization and back-crossing in giant petrels (Macronectes giganteus and M. halli) at Bird Island, South Georgia, and a summary of hybridization in seabirds, PLoS ONE 10, e:0121688. (pdf)

Buainain N, Assis C, and Raposo MA (2017), Geographic variation and taxonomy of the Arremon taciturnus (Hermann, 1783) species complex (Aves: Passerellidae), J. Ornith. 158, 631-650. (abstract)


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


Burbrink FT, and Ruane S (2021), Contemporary philosophy and methods for studying speciation and delimiting species, Ichthyol. Herpetol. 109, e:3. (pdf)


Cadena CD, and Cuervo AM (2010), Molecules, ecology, morphology, and songs in concert: how many species is Arremon torquatus (Aves: Emberizidae)?, Biol. J. Linn. Soc. 99, 152-176. (pdf)


Cadena CD, Zapata F, and Jiménez I (2018), Issues and perspectives in species delimitation using phenotypic data: Atlantean evolution of Darwin’s finches, Syst. Biol. 67, 181-194. (pdf)


Cadena CD, Cuervo AM, Céspedes LN, Bravo GA, Krabbe N, Schulenberg TS, Derryberry GE, Silveira LF, Derryberry EP, Brumfeld RT, and Fjeldså J (2020), Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds, Auk 137, 1-30. (pdf)


Cadena CD, and Zapata F (2020), The genomic revolution and species delimitation in birds (and other organisms): gene flow matters, but what about other evolutionary forces?, EcoEvoRxiv, (pdf)


Cadena CD, and Zapata F (2021), The genomic revolution and species delimitation in birds (and other organisms): why phenotypes should not be overlooked, Ornithology 138, 1-18.  (abstract)


Camargo A, and Sites J (2013), Species delimitation: a decade after the renaissance, In: Pavlinov I, “The species problem”, chapter 9, eBook. (pdf)


Carmi O, Witt CC, Jaramillo A, and Dumbacher JP (2016) Phylogeography of the Vermilion Flycatcher species complex: multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species, Mol. Phylogenet. Evol. 102, 152-173. (abstract)


Carneiro de Melo Moura C, Fernandes AM, Aleixo A, Farias Pereira de Araújo H, 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, 1198-1220. (pdf)


Caro LM, Caycedo-Rosales PC, Bowie RCK, Slabbekoorn H, and Cadena CD (2013), Ecological speciation along an elevational gradient in a tropical passerine bird?, J. Evol. Biol. 26, 357-374. (pdf)


Carstens BC, Pelletier TA, Reid NM, and Satler JD (2013), How to fail at species delimitation, MolEcol. 22, 4369- 4383. (pdf)


Cate CT (2021), Re-evaluating vocal production learning in non-oscine birds, Phil. Trans. Roy. Soc. B 376, e:20200249. (pdf)


Cellinese N, Conix S, and Lapp H (2021), Phyloreferences: tree-native, reproducible, and machine-interpretable taxon concepts, EcoEvoRxiv (pdf)


Chesser RT, Isler ML, Cuervo AM, Cadena D, Galen SC, Bergner LM, Fleischer RC, Bravo GA, Lane DF, and Hosner PA (2020), Conservative plumage masks extraordinary phylogenetic diversity in the Grallaria rufula (Rufous Antpitta) complex of the humid Andes, Auk 137, 1-25. (pdf)


Chou MH, Tseng WZ, Sang YD, Morgan B, de Vivo M, Kuan YH, Wang LJ, Chen WY, and Huang JP (2021), Incipient speciation and its impact on taxonomic decision: a case study using a sky island sister-species pair of stag beetles (Lucanidae: Lucanus), Biol. J. Linn. Soc. 134, 745-759. (abstract)


Chua VL, Phillipps Q, Lim HC, Taylor SS, Gawin DF, Rahman MA, Moyle RG, and Sheldon FH (2015), Phylogeography of three endemic birds of Marathua Island, a potential archive of Bornean biogeography, Raffles Bull. Zool. 63, 259-269. (pdf)


Cibois A, Gelang M, Alström P, Pasquet E, Fjeldså J, Ericson PGP, and Olsson U (2018), Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiotrichidae) 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, e:ukab009. (pdf)


Clegg SM, Degnan SM, Moritz C, Estoup A, Kikkawa J, and Owens IPF (2002), Microevolution in island forms: the roles of drift and directional selection in morphological divergence of a passerine bird, Evolution 56, 2090-2099. (pdf)


Coates DJ, Byrne M, and Moritz C (2018), Genetic diversity and conservation units: dealing with the species-population continuum in the age of genomics, Front. Ecol. Evol. 6, e:165. (pdf)


Collar NJ (2018), Taxonomy as tyranny, Ibis 160, 481-484.  (pdf)


Collar NJ, Donald PF, and Kirwan GM (2021), Species, subspecies or morph - what was the Canary Islands Oystercatcher?, Ibis 163, 1500-1505. (pdf)


Conix S (2018), Integrative taxonomy and the operationalization of evolutionary independence, Eur. J. Phil. Sci. 8, 587-603. (pdf)


Cooper JC, Maddox JD, McKague K, and Bates JM (2021), Multiple lines of evidence indicate ongoing allopathic and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi), Ornithology 138, e:ukaa081. (abstract)


Coyne JA, and Orr HA (2004), Speciation, Sinauer Associates, Sunderland, MA, USA. (link)


Cracraft J (2005), The species of the birds-of-paradise (Paradisaeidae) - applying the phylogenetic species concept to a complex pattern of diversification, Cladistics 8, 1-43. (pdf)


Dai C, Dong F, and Yang C (2020), Morphospecies or distinct species? A multilocus assessment of two East Asian scimitar babblers (Aves: Timaliidae), Zool. Scr. 49, 265-279. (abstract)


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)


Dejtaradol A, Renner SC, Karapan S, Bates PJ, Moyle RG, and Päcker 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)


Dellicour S, and Flot JF (2018), The hitchhiker‘s guide to single-locus species delimitation, Mol. Ecol. Resour. 18, 1234-1246. (abstract)


den Tex RJ, and Leonard JA (2013), A molecular phylogeny of Asian barbets: speciation and extinction in the tropics, Mol. Phylogenet. Evol. 68, 1-23. (abstract)


d’Horta F, Cuervo AM, Ribas CC, and Brumfield RT (2013), 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)


De Salle R, Egan MG, and Siddall M (2005), The unholy trinity: taxonomy, species delimitation and DNA barcoding, Phil. Trans. R. Soc. B 360, e:1462. (abstract)

de Queiroz K (2007), Species concepts and species delimitation, SystBiol. 56, 879-886. (pdf)


Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, and Hedin M (2019), A demonstration of unsupervised machine learning in species delimitation, Mol. Phylogenet. Evol. 139, e:106562. (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(abstract)


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 (2021), Standardized nuclear markers advance metazoan taxonomy, bioRxiv (pdf)


dos Santos Soares LM, Bates J, Carneiro LS, Santos MPD, and Aleixo A (2019), Molecular systematics, biogeography and taxonomy of forest-falcons in the Micrastur ruficollis species complex (Aves: Falconidae), J. Avian Biol. 50, (abstract)


Dowton M, Meiklejohn K, Cameron SL, and Wallman J (2017), A preliminary framework for DNA barcoding, incorporating the multispecies coalescent, Syst. Biol. 63, 639-644. (pdf)

Eberhard JR, and Bermingham E (2005), Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans, MolPhylogenetEvol. 36, 288-304. (abstract)


Eberle J, Fabrizi S, Bazzato E, Rossi M, Stella Columba M, Cillo D, Uliana M, Sparacio I, Sabatinelli G, Warnock RCM, Carpaneto GM, and Ahrens D (2019), Sex-biased dispersal obscures species boundaries in integrative species delimitation approaches, Syst. Biol. 68, 441-459. (pdf)


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


Eda M, Yamasaki T, Izumi H, Tomita N, Konno S, Konno M, Murakami H, and Sato F (2020), Cryptic species in a Vulnerable seabird: shorttailed albatross consists of two species, Endang. Species Res. 43, 375-386. (pdf)


Edwards DL, and Knowles LL(2014), Species detection and individual assignment in species delimitation: can integrative data increase efficacy?, Proc. R. Soc. 281, e:20132765. (pdf)


Edwards SV, Kingan SB, Calkins JD, Balakrishnan CN, Jennings WB, Swanson WJ, and Sorenson MD (2005), Speciation in birds: genes, geography, and sexual selection, Proc. Natl Acad. Sci. USA 102, 6550-57. (pdf)


Edwards S (2008), Bird speciation: selection and the origin of species, Evolution 62, 991-995. (pdf)


Ellegren H (2009), Is genetic diversity really higher in large populations?, J. Biol. 8, e:41. (pdf)

Engler JO, Lawrie Y, Cabral JS, Lens L, and Martínez-Meyer E (2021), Niche evolution reveals disparate signatures of speciation in the ‘great speciator’ (white-eyes, Aves: Zosterops), J. Biogeogr. 48, 1981-1993. (pdf)


Everson KM, McLaughlin JF, Cato IA, Evans MM, Gastaldi AR, Mills KK, Shink KG, Wilbur SM, and Winker K (2019), Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves: Turdidae), Mol. Phylogenet. Evol. 139, e:106564. (abstract)


Feder JL, Egan SP, and Nosil P (2012), The genomics of speciation-with-gene-flow, Trends Genet. 28, 342-350. (abstract)


Feder JL, Flaxman SM, Egan SP, Comeault AA, and Nosil P (2013), Geographic mode of speciation and genomic divergence, Annu. Rev. Ecol. Evol. Syst. 44, 73-97. (abstract)


Fernandes AM, Wink M, and Aleixo A (2012), Phylogeography of the chestnut-tailed antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography, J. Biogeogr. 39, 1524-1535. (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, 1094-1104. (abstract)


Ferreira GG, Aleixo A, and Silva SM (2016), Systematic review of the cinnamon-throated wood creeper Dendrexetastes rufigula (Aves: Dendrocolaptidae) based on multilocus phylogeography, Ornithol. Research 24, 358-469. (pdf)


Ferreira M, Aleixo A, Ribas CC, and Santos MPD (2016), 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)


Firneno TJ, O’Neill JR, Itgen MW, Kihneman TA, Townsend JH, and Fujita MK (2021), Delimitation despite discordance: evaluating the species limits of a confounding species complex in the face of mitonuclear discordance, Ecol. Evol. 11, 12739-53. (pdf)

Fišer C, Robinson CT, and Malard F (2018), Cryptic species as a window into the paradigm shift of the species concept, Mol. Ecol. 27, 613-625. (pdf)

Flot JF (2015), Species delimitation’s coming of age, Syst. Biol. 64, 897-899. (pdf)

Fontaneto D, Flot JF, and Tang CQ (2015), Guidelines for DNA taxonomy, with a focus on the meiofauna, Marine Biodivers. 45, 433-451. (abstract)

Forcina G, Boesman P, and Jowers MJ (2021), Cryptic diversity in a neotropical avian species complex untangled by neglected genetic evidence, Stud. Neotrop. Fauna Environ.  (abstract) 


Fraser DJ, and Bernatchez L (2002), Adaptive evolutionary conservation: towards a unified concept for defining conservation units, Mol. Ecol. 10, 2741-52. (pdf)


Freudenstein JV, Broe MB, Folk RA, and Sinn BT (2017), Biodiversity and the species concept - lineages are not enough, SystBiol. 66, 644-656. (pdf)


Friis G, Aleixandre P, Rodríguez-Estrella R, Navarro-Sigüenza AG, and Milá B (2018a), Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence, Mol. Ecol. 25, 6175-95. (abstract)


Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, and Milá B (2018b), Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird, Mol. Ecol. 27, 5137-53. (abstract)


Fuchs J, Ericson PG, Bonillo C, Couloux A, and Pasquet E (2015), The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putative new ring species complex, Mol. Ecol. 24, 5460-74. (abstract)


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)


Funk DJ, and Omland KE (2003), Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA, Annu. Rev. Ecol. Evol. Syst. 34, 397-423. (abstract)


Galtier N, Nabholz B, Glémin S, and Hurst GD (2009), Mitochondrial DNA as a marker of molecular diversity: a reappraisal, Mol. Ecol. 18, 4541-50. (pdf)


Garnett ST, and Christidis L (2017), Taxonomy anarchy hampers conservation, Nature 546, 25-27. (pdf)


Garnett ST, Christidis L, Conix S, Costello MJ, Zachos FE, Bánki OS, Bao Y, Barik SK, Buckeridge JS, Hobern D, Lien A, Montgomery N, Nikolaeva S, Pyle RL, Thomson SA, van Dijk PP, Whalen A, Zhang ZQ, and Thiele KR (2020), Principles for creating a single authoritative list of the world‘s species, PLoS Biol. 18, e:3000736. (pdf)


Ghorbani F, Aliabadian F, 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. Scri. 49, 427-439. (pdf)


Gill FB (2014), Species taxonomy of birds: which null hypothesis? Auk 131, 150-161. (pdf)


Gutiérrez-Pinto N, McCracken KG, Tubaro P, Kopuchian C, Astie A, and Cadena CD (2019), Molecular and morphological differentiation among Torrent Duck (Merganetta armata) populations in the Andes, Zool. Scr. 48, 589-604. (abstract)


Halley MR, Klicka JC, Sesink Clee PR, and 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)


Harvey MG, and Brumfield RT (2015), Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow, Mol. Phylogenet. Evol. 83, 305-316. (abstract)


Heethoff M (2018), Cryptic species - conceptual or terminological chaos? A response to Struck et al., Trends Ecol. Evol. 33, e:310. (abstract)

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


Heled J, and Drummond AJ (2009), Bayesian inference of species trees from multilocus data, Mol. Biol. Evol. 27, 570-580. (pdf)


Henderson EC, and Brelsford A (2020), Genomic differentiation across the speciation continuum in three hummingbird species pairs, BMC Evol. Biol. 20, e:113. (pdf)

Hey J (2006), Recent advances in assessing gene flow between diverging populations and species, Curr. Opin. Genet. Dev. 16, 592-596. (abstract)


Hey J, Waples RS, Arnold ML, Butlin RK, and Harrison RG (2003), Understanding and confronting species uncertainty in biology and conservation, Trends Ecol. Evol. 18, 597-603. (abstract)


Hill GE, and Powers M (2021), Ecomorphs are not species: the case of locally adapted populations of red crossbills, J. Avian Biol. (pdf)


Hillis DM (2019), Species delimitation in herpetology, J. Herpetol. 53, 3-12. (pdf)


Hogner S, Laskemoen T, Lifjeld JT, Porkert J, Kleven O, Albayrak T, Kabasakal B, and Johnsen A (2012), Deep sympatric mitochondrial divergence without reproductive isolation in the common red-start Phoenicurus phoenicurus, Ecol. Evol. 2, 2974-88. (pdf)


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, Conserv. Genet. 19, 1153-1168. (abstract)


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


Hung CH, Hung HY, Yeh CF, Fu YQ, Chen D, Lei F, Yao CT, Yao CJ, Yang XJ, Lai YT, and Li SH (2014), Species delimitation in the Chinese bamboo partridge Bambusicola thoracica (Phasianidae; Aves), Zool. Scr. 43, 562-575. (abstract)


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


Irestedt M, Jønsson KA, and Ericson PGP (2009), An unexpectedly long history of sexual selection in birds-of-paradise, BMC Evol. Biol. 9, e:235. (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, Ericson PGP, Christidis L, and Schodde R (2017), Phylogeny, biogeography and taxonomic consequences in a bird-of-paradise species complex, Lophorina-Ptiloris (Aves: Paradisaeidae), Zool. J. Linn. Soc. 181, 439-470. (pdf)


Isler ML, Bravo GA, and Brumfield RT (2014), Systematics of the obligate ant-following clade of antbirds (Aves: Passeriformes: Thamnophilidae), Wilson J. Ornith. 126, 635-648. (abstract)


Isler ML, and Maldonado-Coelho M (2017), Calls distinguish species of Antbirds (Aves: Passeriformes: Thamnophilidae) in the genus Pyriglena, Zootaxa 4291, 275-294. (abstract)


Jackson DU, dos Remedios N, Maher KH, Zefania S, Haig S, Oyler-McCance S, Blomqvist D, Burke T, Bruford MW, and Székely T (2017), Polygamy slows down population divergence in shorebirds, Evolution 71, 1313-1326. (pdf)

Jackson ND, Carstens BC, Morales AE, O’Meara BC (2017), Species delimitation with gene flow, Syst. Biol. 66, 799-812. (pdf)

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


Jarvis ED (2016), Perspectives from the avian phylogenomic project: questions that can be answered with sequencing all genomes of a vertebrate class, Annu. Rev. Anim. Biosc. 4, 45-59. (abstract)


Jønsson KA, Bowie RCK, Moyle RG, Christidis L, Norman JA, Benz BW, and Fjeldså J (2010), Historical biogeography of an Indo-Pacific passerine bird family (Pachycephalidae): different colonization patterns in the Indonesian and Melanesian archipelagos, J. Biogeogr. 37, 245-257. (abstract) 


Jønsson KA, Bowie RCK, Moyle RG, Christidis L, Filardi CE, Norman JA, and Fjeldså J (2008), Molecular phylogenetics and diversification within one of the most geographically variable bird species complexes Pachycephala pectoralis/melanura, J. Avian Biol. 39, 473-478. (abstract)


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


Johansson US, Alström P, Olsson U, Ericson PGP, Sundberg P, and Price TD (2007), Build-up of the Himalayan avifauna through immigration: a biogeographical analysis of the Phylloscopus and Seicercus warblers, Evolution 61, 324-333. (pdf)


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)


Jones G (2017), Algorithmic improvements to species delimitation and phylogeny estimation under the multi species coalescent, J. Math. Biol. 74, 447-467. (abstract)


Jones G, Aydin Z, and Oxelman B (2015), DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent, Bioinformatics 31, 991-998. (pdf)

Jordan EA, Tello JG, Benítez-Saldívar MJ, and Areta JI (2020), Molecular phylogenetics of Doraditos (Aves: Pseudocolopterxy): evolution of cryptic species, vocal and mechanical sounds, Zool. Scr. 50, 173-192. (abstract)


Joseph L (2018), Phylogeography and the role of hybridization in speciation, In: “Bird species - how they arise, modify and vanish“ (Tietze DT, ed.), chapter 10, Springer Open. (pdf)


Joseph L (2021), Species limits in birds: Australian perspectives on interrelated challenges of allopatry, introgression of mitochondrial DNA, recent speciation, and selection, Ornithology 138, e:ukab012. (abstract)


Joseph L, Wilke T, Bermingham T, Alpers D, and Ricklefs R (2004), Towards a phylogenetic framework for the evolution of shakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae), Mol. Phylogenet. Evol. 31, 139-152. (pdf)


Joseph L, Toon A, Nyári ÅS, Longmore NW, Rowe KMC, Haryoko T, Trueman J, and Gardner JL (2014a), A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical and ecological complexity of a spect isle avian radiation, Zool. Scr. 43, 325-348. (abstract)


Joseph L, Nyári ÁS, and Andersen MJ (2014b), Taxonomic consequences of cryptic speciation in the Golden Whistler Pachycephala pectoralis complex in mainland southern Australia, Zootaxa 3900, (abstract)


Joseph L, and Wilke T (2016), When DNA throws a spanner in the taxonomic works: testing for monophyly in the Dusky-capped Flycatcher, Myiarchus tuberculifer, and its South American subspecies M.t. atriceps, Emu 104, 197-204. (abstract)


Joseph L, Drew A, Mason IJ, and Peters JL (2019), Introgression between non-sister species of honeyeaters (Aves: Meliphagidae) several million years after speciation, Biol, J. Linn. Soc. 128, 583-591. (pdf)


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


Kennedy JB, Kukla R, Paterson T (2005), Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration, In: Ludäscher B, and Raschid L (eds), Data integration in the life sciences, DILS 2005, Lecture notes in Computer Science, vol. 3615, pp. 80-95, Springer. (abstract)


Kimura M (1980), A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol. 16, 111-120. (abstract)

Kingman JFC (1982), On the genealogy of large populations, J. Appl. Probab. 29, 27-43. (pdf)


Klimov PB, Skoracki M, and Bochkov AV (2019), Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes, Parasites Vectors 12, e:8. (pdf)

Knowles LL, and Carstens BC (2007), Delimiting species without monophyletic gene trees, SystBiol. 56, 887-895. (pdf)


Koblik EA, Red‘kin YA, Volkov SV, and Mosalov AA (2020), The concept of bird species: theory and practice, Biol. Bull. 47, 707-723. (abstract)

Korshunova T, Picton B, Furfaro G, Mariottini P, Pontes M, Prkić J, Fletcher K, Malmberg K, Lundin K, and Martynov A (2019), Multilevel fine-scale diversity challenges the ‘cryptic species’ concept, Sci. Rep. 9, e:6732. (pdf)

Leaché AD, Fujita MK, Minin VN, and Bouckaert RR (2014), Secies delimitation using genome-wide SNP data, Syst. Biol. 63, 534-542. (pdf)


Leaché AD, David HR, Singhal S, Fujita K, Lahti ME, and Zamudio KR (2021), Phylogenetic assessment of biodiversity using a reference-based taxonomy: an example with horned lizards (Phrynosoma), Front. Ecol. Evol. 9, e:678110. (pdf)


Leite RN, Kimball RT, Braun EL, Derryberry EP, Hosner PA, Derryberry GE, Anciães M, McKay J, Meyer D, Aleixo A, Ribas CC, Brumfield RT, and Cracraft J (2021), Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness, Mol. Phylogenet. Evol. 155, e:207030. (abstract)


Lerner HR, 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. 31, 1838-1844. (pdf)


Lim HC, Shakya SB, Harvey MG, Moyle RG, Fleischer RC, Braun MJ, and Sheldon FH (2020), Opening the door to greater phylogeographic inference in Southeast Asia: comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA, Ecol. Evol. 10, 3222-47. (pdf)


Lipscomb D, Platnick N, and Wheeler Q (2003), The intellectual content of taxonomy: a comment on DNA taxonomy, Trends Ecol. Evol. 18, 65-66. (abstract)


Lipshutz SE, Overcast IA, Hickerson MJ, Brumfield RT, and Derryberry EP (2017), Behavioral response to song and genetic divergence in two subspecies of white-crowned sparrows (Zonotrichia leucophrys), Mol. Ecol. 26, 3011-27. (abstract)


Liu JN, Jiang JM, Song SL, Tornabene L, Chabarria R, Naylor GJP, and Li CH (2017), Multilocus DNA barcoding - species identification with multilocus data, Sci. Rep. 7, e:16601. (pdf)

Liu Y, Keller I, and Heckel G (2012), Breeding site fidelity and winter admixture in a long-distance migrant, the tufted duck (Aythya fuligula), Heredity 109, 108-116. (pdf)


Lohman DJ, Ingram KK, Prawiradilaga DM, Winker K, Sheldon FH, Moyle RG, Ng PK. Ong PS, Wang LK, Braille TM, and Astuti D (2010), Cryptic genetic diversity in ‘widespread’ Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated, Biol. Conserv, 143, 1885-1890. (abstract)


Luna LW, Ribas CC, and Aleixo A (2021), Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species, J. Biogeogr. (pdf)


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. (pdf)

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


Maclean N, Collinson M, and Newell RG (2005), Taxonomy for birders: a beginner’s guide to DNA and species problems, Brit. Birds 98, 512-537. (pdf)


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. (pdf)


Mandiwana-Neudani TG, Crowe TM, Little RM, and Bowie RCK (2021), The importance of adopting an integrative taxonomy framework in species delimitation: response to Hunter et al. (2021), Ostrich 92, 162-167. (abstract)


Manthey JD, Klicka J, and Spellman GM (2021), The genomic signature of allopatric speciation in a songbird is shaped by genome architecture (Aves: Certhia americana), Genome Biol. Evol. 13, e:evab120. (pdf)


Marcaigh FO, Kelly DJ, O’Connell DP, Dunleavy D, Clark A, Lawless N, Karya A, Analuddin K, and Marples NM (2021), Evolution in the understorey: the Sulawesi babbler Pellorneum celebense (Passeriformes: Pellorneidae) has diverged rapidly on land-bridge islands in the Wallacean biodiversity hotspot, Zool. Anz. 293, 314-325. (pdf)


Marcondes RS, and Brumfield RT (2019), Fifty shades of brown: macroevolution of plumage brightness in a large clade of Neotropical passerines, Evolution 73, 704-719. (abstract)


Marki PZ, Fjeldså J, 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)


Marques Silva S, Ribas CC, and Aleixo A (2021), Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests, EcolEvol(pdf)


Martin BT, Chafin TK, Douglas MR, Placyk JS, Birkhead RD, Phillips CA, and Douglas ME (2021), The choices we make and the impacts they have: machine learning and species delimitation in North American box turtles (Terrapene spp.), Mol. Ecol. Resour. 21, 2801-17. (abstract)


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


Mason NA, Burns KJ, Tobias JA, Claramunt S, Seddon N, and Derryberry EP (2017), Song evolution, speciation, and vocal learning in passerine birds, Evolution 71, 786-796. (abstract)


Mason NA, Fletcher NK, Gill BA, Funk WC, and Zamudio KR  (2020), Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance, Syst. Biodivers. 18, 269-280. (pdf)


Masters BC, Fan V, and Ross HA (2010), Species delimitation -a geneious plugin for the exploration of species boundaries, Mol. Ecol. Resour. 11, 154-157. (abstract)


Mata H, Fontana CS, Mauricio GN, Bornschein MR, Ferreira de Vasconcelos M, and Bonatto SL (2009), Molecular phylogeny and biogeography of the eastern Tapaculos (Aves: Rhinocryptidae: Scytalopus, Eleoscythalopus): cryptic diversification in Brazilian Atlantic Forest, Mol. Phylogenet. Evol. 53, 450-462. (pdf)


Mayr E (1996), What is a species, and what is not?, Philos. Sci. 63, 262-277. (preview)

McClure CJW, Lepage D, Dunn L, Anderson DL, Schulwitz SE, Camacho L, Robinson BW, Christidis L, Schulenberg TS, Iliff MJ, Rasmussen PC, and Johnson J (2020), Towards reconciliation of the four world bird lists: hotspots of disagreement in taxonomy of raptors, Proc. Roy. Soc. B 287, e:20200683. (pdf)


McCormack JE, and Maley JM (2015), Interpreting negative results with taxonomic and conservation implications: another look at the distinctness of coastal California Gnatcatchers, Auk 132, 380-388. (pdf)


McEntee JP, Tobias jA, Sheard C, and Burleigh JG (2018), Tempo and timing of ecological trait divergence in birds, Nat. Ecol. Evol. 2, 1120-1127. (abstract)


Meier R, Blaimer BB, Buenaventura E, Hartop E, von Rintelen T, Srivathsan A, and Yeo D (2021), A re-analysis of the data in Sharkey et al.‘s (2021) minimalist revision reveals that BINS do not deserve names, but BOLD Systems needs a stronger commitment to open science, Cladistics (pdf)


Meier-Kolthoff JP, Auch AF, Klenk HP, and Göker M (2013), Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinform. 14, 1-14. (pdf)

Meierotto S, Sharkey MJ, Janzen DH, Hallwachs W, Hebert PDN, Chapman EG, and Smith MA (2019), A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment, DtschEntomol. Z. 66, 119-145. (pdf)


Mettler RD, and Spellman GM (2009), A hybrid zone revisited: molecular and morphological analysis of the maintenance, movement, and evolution of a Great Plains avian (Cardinalidae: Pheuticus) hybrid zone, Mol. Ecol. 18, 3256-67. (pdf) 


Miller MP, Gratto-Trevor C, Haig SM, Mizrahi DS, Mitchell MM, and Mullins TD (2013), Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla), Waterbirds 36, 166-178. (pdf)


Miranda LS, Prestes BO, and Aleixo A (2021), Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary, Biol. J. Linn. Soc. 132, 431-450. (abstract)


Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glace F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, and Vences M (2020), Repositories for taxonomic data: where we are and what is missing, Syst. Biol. 69, 1231-1253. (pdf)


Monaghan MT, and Sartori M (2009), Genetic contributions to the study of taxonomy, ecology, and evolution of mayflies (Ephemeroptera): review and future perspectives, Aquat. Insects 31 (suppl.1), 19-39. (pdf)


Moyle RG, Schilthuizen M, Rahman MA, and Sheldon FH (2005), Molecular phylogenetic analysis of the white-crowned forktail Enicurus leschenaulti in Borneo, JAvian Biol. 36, 96-101. (abstract)


Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, and Nielsen R (2008), Statistical assignment of DNA sequences using Bayesian phylogenetics, Syst. Biol. 57, 750-757. (pdf) 


Musher LJ, and Cracraft J (2018), Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus), MolPhylogenetEvol. 118, 204-221.  (open manuscript)


Neate-Clegg MHC, Blount JD, and Sekercioglu ÇH (2021), Ecological and biogeographical predictors of taxonomic discord across the world‘s birds, GlobEcolBiogeogr. 30, 1258-1270.  (abstract) 


Nguembock B, Fjeldså J, Couloux A, and Pasquet E (2009), Molecular phylogeny of Carduelinae (Aves, Passeriformes, Fringillidae) proves polyphyletic origin of the genera Serinus and Carduelis and suggests redefined generic limits, Mol. Phylogenet. Evol. 51, 169-181. (abstract)


Nielsen R, and Wakeley J (2001), Distinguishing migration from isolation: a Markov Chain Monte Carlo approach, Genet. 158, 885-896. (pdf)


Nielsen R, and Matz M (2006), Statistical approaches for DNA barcoding, Syst. Biol. 55, 162-269. (pdf)


Nosil P, and Feder JL (2012), Genomic divergence during speciation: causes and consequences, Philos. Trans. Roy. Soc. B 367, 332-342. (pdf)

Núñez-Zapata J, Peterson AT, and Navarro- Sigüenza AG (2016), Pleistocene diversification and speciation of White-throated Thrush (Turdus assimilis; Aves: Turdidae), J. Ornithol. 157, 1073-1085. (abstract)

Nyári ÁS (2007), Phylogeographic patterns, molecular and vocal differentiation, and species limits in Schiffornis turdina (Aves), Mol. Phylogenet. Evol. 44, 154-164. (abstract)

O’Connell DP, Kelly DJ, Lawless N, Karya A, Analuddin K, and Marples NM (2018), Diversification of a ‘great speciator’ in the Wallacea region: differing responses of closely related resident and migratory kingfisher species (Aves: Alcedinidae: Todiramphus), Ibis 161, 806-823. (abstract)

O’Connell DP, Kelly D, Lawless N, and O’Brien K (2019), A sympatric pair of undescribed white-eye species (Aves: Zosteropidae: Zosterops) with different origins, Zool. J. Linn. Soc. 186, 701-724. (pdf)

Olave M, Solà E, and Knowles LL (2014), Upstream analyses create problems with DNA-based species delimitation, Syst. Biol. 63, 263-271.(pdf)

Olsson U, Alström P, Ericson PGP, and Sundberg P (2005), Non-monophyletic taxa and cryptic species - evidence from a molecular phylogeny of leaf-warblers (Phylloscopus, Aves), Mol. Phylogenet Evol. 36, 261-276. (abstract)

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

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

Oswald JA, Harvey MG, Remsen RC, Foxworth DPU, Dittmann DL, Cardiff SW, and Brumfield RT (2019), Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World, Mol. Ecol. 28, 1675-1691. (abstract)

Ottenburghs J (2019), Multispecies hybridization in birds, Avian Research 10, e:20. (pdf)

Ottenburghs J, Megens HJ, Kraus RHS, Madsen O, van Hooft P, van Wieren SE, Crooijmans RPMA, Ydenberg RC, Groenen MAM, and Prints HHT (2016), A tree of geese: a phylogenomic perspective on the evolutionary history of true geese, Mol. Phylogenet. Evol. 101, 303-313. (abstract)

Päckert M, Martens J, and Sun YH (2010), Phylogeny of long-tailed tits and allies inferred from mitochondrial and nuclear markers (Aves: Passeriformes, Aegithalidae), Mol. Phylogenet. Evol. 55, 952-967. (abstract)


Päckert M, Martens J, Sun YH, Severinghaus LL, Nazarenko AA, Ting J, Töpfer T, and Tietze DT (2012), Horizontal and elevational phylogeographic patterns of Himalayan and Southeast Asian forest passerines (Aves: Passeriformes), J. Biogeogr. 39, 556-573. (abstract)

Padial JM, and de la Riva I (2021), A paradigm shift in our view of species drives current trends in biological classification, Biol. Rev. 96, 731-751. (abstract)


Palumbi SR (1989), Rates of molecular evolution and the fractions of nucleotide positions free to vary, J. Mol. Evol. 29, 180-287. (abstract)


Palumbi SR, Cipriano F, and Hare M0 (2001), Predicting nuclear gene coalescence from mitochondrial data: the three-times rule, Evolution 55, 859-868. (abstract)


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

Parkin DT (2005), Birding and DNA: species for the new millennium, Bird Study 50, 223-242. (pdf)


Patten MA (2015), Subspecies and the philosophy of science, Auk 132, 481-485. (pdf) 


Patten MA, and Pruett C (2009), The Song Sparrow, Melospiza melodia, as a ring species: patterns of geographic variation, a revision of subspecies, and implications for speciation, System. Biodivers., 7, 33-62. (abstract)

Pavlinov IY (2013), The species problem, why again?, In: Pavlinov I, “The species problem”, chapter 1, eBook. (open access)

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


Peede D, d’Agostino E, and Ottenburghs J (2019), Digest: species delimitation in the face of demographic processes, Evolution 74, 499-500. (pdf)

Pereira SL, and Baker AJ (2004), Vicariant speciation of curassows (Aves: Cracidae): a hypothesis based on mitochondrial DNA phylogeny, Auk 121, 682-694. (pdf)


Perktas U, and Quintero E (2012), A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex, Dendrocopos major (Aves: Picidae), Biol. J. Linn. Soc. 108, 173-188. (abstract)


Perktas U, Groth JG, and Barrowclough GF (2020), Phylogeography, species limits, phylogeny, and classification of the turacos (Aves: Musophagidae) based on mitochondrial and nuclear DNA sequences, Am. Mus. Novit. 3934, 1-61. (abstract)


Petit RJ, and Excoffier L (2009), Gene flow and species delimitation, Trends Ecol. Evol. 24, 386-393. (abstract)


Pons J, Barroclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, and Vogler AP (2006), Sequence-based species delimitation for the DNA taxonomy of undescribed insects, Syst. Biol. 55, 595-609. (pdf)


Pons JM, Campión D, Chiozzi G, Ettwein A, Grangé JJ, Kajtoch L, Mazgaski TD, Rakovic M, Winkler H, and Fuchs J (2021), Phylogeography of a widespread Palaearctic forest bird species: the White-backed Woodpecker (Aves, Picidae), ZoolScr. 50, 155-172. (abstract)


Pourebrahimi S, Mirshamsi O, Ghasempouri SM, Moghaddam FY, and Aliabadian M (2021), Phylogeny and evolutionary history of the Sombre Tit, Poecile lugubris in the western Palearctic (Aves: Paridae), Mol. Phylogenet. Evol., e:107343. (abstract)

Prager M, Johansson EIA, and Andersson S (2008), A molecular phylogeny of the African widowbirds and bishops, Euplectes spp. (Aves: Passeridae: Ploceinae), Mol. Phylogenet. Evol. 46, 290-302. (abstract)


Price T (2008), Speciation in birds, Roberts & Company Publishers, Greenwood Village, CO, USA. (link)


Quintero E, and Perktas U (2019), Phylogeny of Thripophagini  ovenbirds (Aves: Synallaxinae: Furnariidae), Biol. J. Linn. Soc. 127, 826-846. (pdf)


Rabosky DL, and Matute DR (2013), Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds, PNAS 110, 15354-59. (pdf)

Ramírez-Barrera SM, Hernández-Baños BE, Jaramillo-Correa JP, and Klicka J (2018), Deep divergence of Red-crowned Ant Tanager (Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica, PeerJ 6, e:5469. (free reading)

Rannala (2015), The art of species delimitation, CurrZool. 61, 846-853. (pdf)


Rannala B, and Yang Z (2007), Inferring speciation times under an episodic molecular clock, Syst. Biol. 56, 453-466. (pdf)


Rannala B, and Yang Z (2020), Species delimitation, In: Scornavacca C, Delsuc F, and Galtier N (eds) “Phylogenetics in the genomic era”, chapter 5.5, authors open access book. (pdf)


Raposo MA, Stopiglia R, Brito GRR, Bockmann FA, Kirwan GM, Gayon J, and Dubois A (2017), What really hampers taxonomy and conservation? A riposte to Garnett and Christidis (2017), Zootaxa 4317, 179-184. (pdf)


Recuerda M, Illera Cobo JC, Blanco G, Zardoya R, and Milá B (2021), Sequential colonisation of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs), MolPhylogenetEvol. 164, e:107291. (pdf)


Reddy S (2008), Systematics and biogeography of the shrike-babblers (Pteruthius): species limits, molecular phylogenetics, and diversification patterns across southern Asia, Mol. Phylogenet. Evol. 47, 54-72. (abstract)


Reddy S, and Moyle RG (2011), Systematics of the scimitar babblers (Pomatorhinus: Timaliidae): phylogeny, biogeography, and species limits of four species complexes, Biol. J. Linn. Soc. 102, 846-869. (pdf)


Reeve AH, Blom MPK, Marki PZ, Batista R, Olsson U, Edmark VN, Irestedt M, and Jønsson KA (2021), The Sulawesi Thrush (Cataponera turdoides; Aves: Passeriformes) belongs to the genus Turdus, Zool. Scr. (abstract)


Reid NM, and Carstens BC (2012), Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model, BMC Evol. Biol. 12, e:196. (pdf)


Reilly SB, Stubbs AL, Arida E, Karin BR, Arifin U, Kaiser H, Bi K, Iskandar DT, and McGuire JA (2021), Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda flying lizards (genus Draco), Syst. Biol., e:sysb043. (abstract)


Rheindt FE, Szekely T, Edwards SV, Lee PLM, Burke T, Kennerley PR, Bakewell DN, Alrashidi M, Kosztolányi A, Weston MA, Liu WT, Lei WP, Shigeta Y, Javed S, Zefania S, and Küpper C (2011), Conflict between genetic and phenotypic differentiation: the evolutionary history of a ‘lost and rediscovered’ shorebird, PLOS ONE 6, e:26995. (pdf)


Rheindt FE, Christidis L, Norman JA, Eaton JA, Sadanandan KR, and Schodde R (2017), Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex, Zootaxa 4250, 401-433. (abstract)


Rheindt FE, and Ng EYX (2021), Avian taxonomy in turmoil: the 7-point rule is poorly reproducible and may overlook substantial cryptic diversity, Ornithology 138, e:ukab010. (abstract)


Reis CA, Dias C, Araripe J, Aleixo A, Anciães M, Sampaio I, Schneider H, and do Rego PS (2019), Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance, Zool. Scr. 49, 129-144. (abstract)


Renner SS (2016), A return to Linnaeus’s focus on diagnosis, not description: the use of DNA characters in the formal naming of species, Syst. Biol. 65, 1085-1095. (pdf)


Ribas CC, Aleixo A, Gubili C, d’Horta FM, Brumfield RT, and Cracraft J (2018), Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): implications for the evolution of Amazonian landscapes during the Quaternary, J. Biogeogr. 45, 917-928. (abstract)


Rocha AV, Rivera LO, Martinez J, Prestes NP, and Caparroz R (2014), Biogeography of speciation of two sister species of Neotropical Amazona (Aves, Psittaciformes) based on mitochondrial sequence data, PLOS ONE 9, e:108096. (pdf)


Rojas-Soto OR, Navarro-Sigüenza AG, and Espinosa de los Monteros A (2010), Systematics and bird conservation policies: the importance of species limits, Bird Conserv. Int. 20, 176-185. (pdf)

Roux C, Fraïsse C, Romiguier J, Anciaux Y, Galtier N, and Bierne N (2016), Shedding light on the grey zone of speciation along a continuum of genomic divergence, PLoS Biol. 14, e:2000234. (pdf)

Ruane S, Bryson RW, Pyron RA, and Burbrink FT (2014), Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses, Syst. Biol. 63, 231-250. (pdf)


Rubinoff D, and Holland BS (2005), Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference, Syst. Biol. 54, 952-961. (pdf)


Ruegg KC, Brinkmeyer M, Bossu CM, Bay RA, Anderson EC, Boal CW, Dawson RD, Eschenbauch A, McClure CJW, Miller KE, Morrow L, Morrow J, Oleyar MD, Ralph B, Schulwitz S, Swem T, Therrien JF, van Buskirk R, Smith TB, and Heath JA (2021), The American Kestrel (Falco sparverius) genoscape: implications for monitoring, management, and subspecies boundaries, Ornithology 138, e:ukaa051. (abstract)


Rull V (2008), Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence, Mol. Evol. 17, 2722-29. (abstract)


Rundle HD, and Nosil P (2005), Ecological speciation, Ecol. Lett. 8, 336-352. (free reading)


Saitoh T, Sugita N, Someya S, Iwami Y, Kobayashi S, Kamigaichi H, Higuchi A, Asai S, Yamamoto Y, and Nishiumi I (2014), DNA barcoding reveals 24 distinct lineages as cryptic species candidates in and around the Japanese Archipelago, Mol. Ecol. Resour. 15, 177-186. (pdf)


Sánchez-González LA, and Moyle RG (2011), Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura), Mol. Phylogenet. Evol. 61, 290-299. (abstract)


Sandoval L, Bitton PP, Demko AD, Doucet SM, and Mennill DJ (2017), Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-Sparrows (Cabanis) (Aves: Passerellidae), Zootaxa 4291, 155-170. (abstract)


Sangster G (2009), Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation, Proc. R. Soc. B 276, 3185-91. (pdf)


Sangster G (2013), 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.), pp. 9-38. (pdf)


Sangster G, Cancino KM, and Hutchinson RO (2021), Taxonomic revision of the Savannah Nightjar (Caprimulgus affinis) complex based on vocalizations reveals three species, Avian Res. 12, e:54. (pdf)


Santana A, Silva SM, Batista R, Sampaio I, and Aleixo A (2021a), Molecular systematics, species limits, and diversification of the genus Dendrocolaptes (Aves: Furnariidae): insights on biotic exchanges between dry and humid forest types in the Neotropics, J. Zool. Syst. Evol. Res. 59, 277-293. (pdf)


Santana A, Marques Silva S, Francês do Nascimento N, Sampaio I, and Aleixo A (2021b), Phylogeography of the Dendrocolaptes picumnus (Aves: Dendrocolaptidae) species complex: new insights on the diversification of a trans-American lineage, Avian Biol. 52, e:02723. (pdf)


Schield DR, Scordato ESC, Smith CCR, Carter JK, Cherkaoui SI, Gombobaatar S, Hajib S, Hanane S, Hund AK, Koyama K, Liang W, Liu Y, Magri N, Rubtsov A, Sheta B, Turbek SP, Wilkins MR, Yu L, and Safran RJ (2021), Sex-linked genetic diversity and differentiation in a globally distributed avian species complex, Mol. Ecol. 30, 2313-32. (abstract)


Schlick-Steiner BC, Steiner FM, Seifert B, Stauffer C, Christian E, and Crozier RH (2010), Integrative taxonomy: a multisource approach to exploring biodiversity, Annu. Rev. Ent. 55, 421-438. (abstract)


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. (pdf)


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


Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, and Brännström Å (2014), Genomics and the origin of species, Nat. Rev. Genet. 15, 176-192. (abstract)


Seeholzer GF,and Brumfield RT (2018), Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis, Line-cheeked Spinetail) despite near three-fold body size change across an environmental gradient, Mol. Ecol. 27, 279-296. (abstract)


Settlecowski AE, Cuervo AM, Tello JG, Harvey MG, Brumfield RT, and Derryberry EP (2020), Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae), Mol. Phylogenet. Evol. 147, e:106779. (abstract)


Sharkey MJ, Janzen DH, Hallwachs W, Chapman EG, Smith MA, Dapkey T, Brown A, Ratnasingham S, Naik S, Manjunath R, Perez K, Milton M, Hebert P, Shaw SR, Kittel RN, Solis MA, Metz MA, Goldstein PZ, Brown JW, Quicke DLJ, van Achterberg C, Brown BV, and Burns JM (2021a), Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species, ZooKeys 1013, 1-665. (pdf)


Sharkey M, Brown B, Baker A, and Mutanten M (2021b), Response to Zamani et al. (2020): the omission of critical data in the pursuit of “revolutionary” methods to accelerate the description of species, ZooKeys 1033, 191-201. (pdf)


Shaw KL, and Mullen SP (2014), Speciation continuum, J. Hered. 105, 741-742. (pdf)

Sheldon FH, Lohman DJ, Lim HC, Zou F, Goodman SM, Prawiradilaga DM, Winker K, Braile TM, and Moyle RG (2009), Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier and unusual dispersal patterns in the Indian Ocean and Southeast Asia, J. Biogeogr. 36, 1070-1083. (abstract)


Shipham A, Schmidt DJ, Joseph L, and Hughes JM (2015), Phylogenetic analysis of the Australian rosella parrots (Platycercus) reveals discordance among molecules and plumage, Mol. Phylogenet. Evol. 91, 150-159. (abstract)


Silva SM, Ribas CC, and Aleixo A (2021), Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests, Ecol. Evol. 11, 11826-38. (pdf)


Simões CC, Vieira Cerqueira P, Peloso P, and Aleixo A (2021), Integrative taxonomy of Flatbill Flycatchers (Tyrannidae) reveals a new species from the Amazonian lowlands, Zool. Scr. (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)

Singhal S, and Bi K (2017), History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone, Evolution 71, 1888-1899. (abstract)

Singhal S, Hoskin C, Couper P, Potter S, and Moritz C (2018), A framework for resolving cryptic species: a case study from the lizards of the Australian wet tropics, Syst. Biol. 67, 1061-1075. (pdf)

Singhal S, and Moritz C (2013), Reproductive isolation between phylogeographic lineages scales with divergence, Proc. R. Soc. B 280, e:20132246. (pdf)

Sites JW, and Marshall JC (2003), Delimiting species: a renaissance issue in systematic biology, Trends Ecol. Evol. 18, 462-470. (abstract)


Smith BT, Bryson RW, Mauck WM, Chavez 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)


Smith ML, Ruffley M, Rankin AM, Espíndola A, Tank DC, Sullivan J, and Carstens BC (2018), Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data, Biol. J. Linn. Soc. 124, 518-532. (pdf)


Smith ML, and Carstens BC (2020), Process-based species delimitation leads to identification of more biologically relevant species, Evolution 74, 216-229. (abstract)


Solís-Semus C, Knowles LL, and Ané C (2015), Bayesian species delimitation combining multiple genes and traits in a unified framework, Evolution 69, 492-507. (abstract)


Sousa-Neves T, Aleixo A, and Sequestrationen F (2013), Cryptic patterns of diversification of a widespread Amazonian Woodcreeper species complex (Aves: Dendrocolaptidae) inferred from multilocus phylogenetic analysis: implications for historical biogeography and taxonomy, Mol. Phylogenet. Evol. 68, 410-424. (abstract)


Srivathsan A, Hartop E, Puniamoorthy J, Lee WT, Kutty SN, Kurina O, and Meier R (2019), Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing, BMC Biol. 17, e:69. (pdf)


Stankowski S, and Ravinet M (2021a), Defining the species continuum, Evolution 75, 1256-1273. (pdf)


Stankowski S, and Ravinet M (2021b), Quantifying the use of species concepts, Curr. Biol. 31, R428-R429. (abstract)


Stanley SM (1978), Chronospecies‘ longevities, the oigin of genera, and the punctuational model of evolution, Paleobiology 4, 26-40. (abstract)


Stervander M, Alström P, Olsson U, Hansson B, and Bensch S (2016), Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae), Mol. Phylogenet. Evol. 102, 233-245. (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. (pdf)

Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, Kistenich S, Larsson KH, Liow LH, Nowak MD, Stedje B, Bachmann L, and Dimitrov D (2018), Finding evolutionary processes hidden in cryptic species, Trends Ecol. Evol. 33, 153-163. (abstract)

Sukumaran J, and Knowles LL (2017), Multispecies coalescent delimits structure, not species, Proc. Natl Acad. Sci. USA 114, 1607-1612. (pdf) 


Sukumaran J, Holder MT, and Knowles LL (2021), Incorporating the speciation process into species delimitation, PLoS Comput. Biol. 17, e:I008924(pdf)


Taberlet P, Coissac E, Pompanon F, Brochmann C, and Willerslev E (2012), Towards next-generation biodiversity assessment using DNA metabarcoding , Mol. Ecol. 21, 2045-2050. (abstract)


Tautz D, Arctander P, Minelli A, Thomas RH, and Vogler AP (2003), A plea for DNA taxonomy, Trends Ecol. Evol. 18, 70-74. (abstract)


Thomson SA, Pyle RL, Ahyong ST, Alonso-Zarazaga M, Ammirati J, Francisco Araya J, Ascher JS, Lynn Audisio T,  Azevedo-Santos VM, Bailly N, Baker WJ, Balke M, Barclay MVL, Russell RL, Benine RC, Bickerstaff JRM, Bouchard P, Bour R, Bourgoin T, Boyko CB, Breure ASH, Brothers DJ, Byng JW, Campbell D, Ceríaco LMP, Cernák I, Cerretti P, Chang CH, Cho S, Copus JM, Costello MJ, Cseh A, Csuzdi C, Culham A, d‘Elía G, d‘Udekem d‘Acoz C, Daneliya ME, Dekker R, Dickinson EC, Dickinson TA, van Dijk PP, Dijkstra KDB, Dima B, Dmitriev DA, Duistermaat L, Dumbacher JP, Eisenhardt WL, Ekrem T, Evenhuis NL, Faille A, Fernández-Triana JL, Fiesler E, Fishbein M, Fordham BG, Freitas AVL, Friol NR, Fritz U, Frøslev T, Funk VA, Gaimari SD, Garbino GST, Garraffoni ARS, Geml J, Gill AC, Gray A, Grazziotin FG, Greenslade P, Gutiérrez EE, Harvey MS, Hazevoet CJ, He K, He X, Helfer S, Helgen KM, van Heteren AH, Hita Garcia F, Holstein N, Horváth MK, Hovenkamp PH, Song Wang W, Hyvönen J, Islam MB, Iverson JB, Ivie MA, Jaafar Z, Jackson MD, Jayat JP, Johnson NF, Kaiser H, Klitgård BB, Knapp DG, Kojima J, Kōljag U, Kontschán J, Krell FT, Krisai-Greilhuber I, Kullander S, Latella L, Lattke JE, Lencioni V, Lewis GP, Lhano MG, Lujan NK, Luksenburg JA, Mariaux J, Marinho-Filho J, Marshall CJ, Mate JF, McDonough MM, Michel E, Miranda VFO, Mitroiu MD, Molinari J, Monks S, Moore AJ, Moratelli R, Murányi D, Nakano T, Nikolaeva S, Noyes J, Ohl M, Oleas NH, Orrell T, Páll-Gergely B, Pape T, Papp V, Parenti LR, Patterson D, Pavlinov IY, Pine RH, Poczai P, Prado J, Prathapan D, Rabeler RK, Randall JE, Rheindt FE, Rhodin AGJ, Rodríguez SM, Rogers DC, Roque FO, Rowe KC, Ruedas LA, Salazar-Bravo J, Salvador RB, Sangster G, Sarmiento CE, Schigel DS, Schmidt S, Schueler FW, Segers H, Snow N, Souza-Dias PGB, Stals R, Stenroos S, Douglas Stone R, Sturm CF, Štys P, Teta P, Thomas DC, Timm RM, Tindall BJ, Todd JA, Triebel D, Valdecasas AG, Vizzini A, Vorontsova MS, de Vos JM, Wagner P, Watling L, Weakley A, Welter-Schultes F, Whitmore D, Wilding N, Will K, Williams J, Wilson K, Winston JE, Wüster W, Yanega D, Yeates DK, Zaher H, Zhang G, Zhang ZQ, and Zhou HZ (2018), Taxonomy based on science is necessary for global conservation, PLOS Biol. 16, e:2005075. (pdf)

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. (pdf)


Tobias JA, Ottenburghs J, and Pigot AL (2020), Avian diversity: speciation, macroevolution, and ecological function, Annu. Rev. Ecol. Evol. Syst. 51, 533-560. (abstract)


Tobias JA, Donald PF, Martin RW, Butchart SHM, and Collar NJ (2021), Performance of a points-based scoring system for assessing species limits in birds, Ornithology 138, e:ukab016. (abstract)


Toews DPL, and Brelsford A (2012), The biogeography of mitochondrial and nuclear discordance in animals, Mol. Ecol. 21, 3907-3930. (pdf)

Uy JAC, Irwin DE, and Webster MS (2018), Behavioral isolation and incipient speciation in birds, Annu. Rev. Ecol. Evol. Syst. 49, 1-24. (abstract)


Vázquez-López M, Morrone JJ, Ramirez-Barrera SM, Lòpez-López A, Robles-Bello SM, and Hernández-Baños BE (2020), Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves: Fringillidae), ZooKeys 952, 129-157. (pdf)


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)


Vázquez-Miranda H, and Barker FK (2021), Autosomal, sex-linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus, Mol. Phylogenet. Evol. 163, e:107242. (abstract)


Vences M (2020), The promise of next-generation taxonomy, Megataxa 1, 35-38. (pdf)


Vilaça ST, and Santos FR (2010), Biogeographic history of the species complex Basileuterus culicivorus (Aves: Parulidae) in the Neotropics, Mol. Phylogenet. Evol. 57, 585-597. (pdf)


Voelker G (1999), Dispersal, vicariance and clocks: historical biogeography and speciation in a cosmopolitan passerine genus (Anthus: Motacillidae), Evolution 53, 1536-1552. (pdf)


Voelker G, Bowie RCK, Wilson B, and Anderson C (2012), Phylogenetic relationships and speciation patterns in an African savanna dwelling bird genus (Myrmecocichla), Biol. J. Linn. Soc. 106, 180-290. (pdf)


Voelker G, Peñalba JV, Huntley JW, and Bowie RCK (2014), Diversification in an Afro-Asian songbird clade (Erythropygia-Copychus) reveals founder-event speciation via trans-oceanic dispersals and a southern to northern colonization pattern in Africa, Mol. Phylogenet. Evol. 73, 97-105. (abstract)


Voelker G, Tobler M, Prestridge HL, Duijm E, Groenenberg D, Hutchinson MR, Martín AD, Nieman A, Roselaar CS, and Huntley JW (2016), Three new species of Stiphornis (Aves: Muscicapidae) from the Afro-tropics, with a molecular phylogenetic assessment of the genus, Syst. Biodiv. 15, 87-104. (abstract)


Voelker G, Wogan GOU, Huntley JW, and Bowie RCK (2021), Comparative phylogeography of southern African bird species suggests an ephemeral speciation model, Diversity 13, e:434. (pdf)

Wallace SJ, Morris-Pocock JA, González-Solís J, Quillfeldt P, and Friesen VL (2017), A phylogenetic test of sympatric speciation in the Hydrobatinae (Aves: Procellariiformes), Mol. Phylogenet. Evol. 107, 39-57. (abstract)


Wang E, Zhang D, Braun MS, Hotz-Wagenblatt A, Pärt T, Arlt D, Schmaljohann H, Bairlein F, Lei F, and Wink M (2020), Can mitogenomes of the Northern Wheatear (Oenanthe oenanthe) reconstruct its phylogeography and reveal the origin of migrant birds?, Sci. Rep. 10, e:9290. (pdf)


Wang X, Maher KH, Zhang N, Que P, Zheng C, Liu S, Wang B, Huang Q, Chen D, Yang X, Zhang Z, Székely T, Urrutia AO, and Liu Y (2019a), Demographic histories and genome-wide patterns of divergence in incipient species of shorebirds, Front. Genet. 10, e:919. (pdf)

Wang X, Que P, Heckel G, Hu J, Zhang X, Chiang CY, Zhang N, Huang Q, Liu S, Martinez J, Pagani-Núñez E, Dingle C, Leung YY, Székely T, Zhang Z, and Liu Y (2019b), Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast, BMC Ecol. Evol. 19, e:135. (pdf)


Watson DM (2005), Diagnosable versus distinct: evaluating species limits in birds, BioScience 5, 60-68. (pdf)


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)


Weir JT, and Price TR (2011), Limits to speciation inferred from times to secondary sympatry and ages of hybridizing  species along a latitudinal gradient, Am. Natur. 177, 462-467. (abstract)


Wiens JJ (2007), Species delimitation: new approaches for discovering diversity, Syst. Biol. 56, 875-878. (pdf)


Winger BM, Hosner PA, Bravo GA, Cuervo AM, Aristizábal N, Cueto LE, and Bates JM (2015), Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s.l.), Mol. Ecol. 24, 6256-77. (abstract)


Winker K (2010), Subspecies represent geographically partitioned variation, a goldmine of evolutionary biology, and a challenge for conservation, Ornithol. Monogr. 67, 6-23. (pdf)


Winker K (2016), An examination of species limits in the Aulacorhynchus “prasinus” toucanet complex (Aves: Ramphastidae), PeerJ 4, e:2381. (pdf)


Winker K (2021), An overviews of speciation and species limits in birds, Ornithology 138, 1-27. (pdf)


Winker K, McCracken KG, Gibson DD, and Peters JL (2013), Heteropatric speciation in a duck, Anas crecca, Mol. Ecol. 22, 5922-35. (abstract)


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


Wolf JB, and Ellegren H (2017), Making sense of genomic islands of differentiation in light of speciation, Nat. Rev. Genet. 18, e:87. (abstract)


Wu HC, Lin RC, Hung HY, Yeh CF, Chu JH, Yang CJ, Yao CJ, Zou FS, Yao CT, Li SH, and Lei FM (2011), Molecular and morphological evidences reveal a cryptic species in the Vinaceous Rosefinch Carpodacus vinaceus (Fringillidae; Aves), Zool. Scr. 40, 468-478. (abstract)


Yamaguchi R, and Iwasa Y (2013), First passage time to allopatric speciation, Interface Focus 3, e:20130026. (pdf)


Yang M, He Z, Shi S, and Wu CI (2017), Can genomic data alone tell us whether speciation happened with gene flow?, Mol. Ecol. 26, 2845-49. (pdf)


Yang Z (2014), Molecular evolution: a statistical approach, Oxford University Press. (link)


Yang Z (2015), The BPP program for species tree estimation and species delimitation, Curr. Zool. 61, 854-865. (pdf)


Yang Z, and Rannala B (2010), Bayesian species delimitation using multilocus sequence data, Proc. Natl Acad. Sci. 107, 9264-69. (pdf)


Yang Z, and Rannala B (2014), Unguided species delimitation using DNA sequence data from multiple loci, Mol. Biol. Evol. 31, 3125-35. (pdf)


Yeates DK, Seago A, Nelson L, Cameron SL, Joseph L, and Trueman WH (2011), Integrative taxonomy, or iterative taxonomy?, Syst. Ent. 36, 209-217. (pdf)


Yin Gwee CY, Eaton JA, Garg KM, Alström P, van Balen S, Hutchinson RO, Prawiradilaga DM, Hung Le M, and Rheindt FE (2019), Cryptic diversity in Cyornis (Aves: Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches, Zool.  J. LinnSoc. 186, 725-741. (pdf)


Zachos FE (2018a), (New) Species concepts, species delimitation and the inherent limitations of taxonomy, J. Genet. 97, 811-815. (abstract)

Zachos FE (2018b), Species concepts in biology, Springer Nature. (link)

Zamani A, Vahtera V, Sääksjärvi IE, and Scherz MD (2021), The omission of critical data in the pursuit of ‚revolutionary‘ methods to accelerate the description of species, Syst. Ent. 46, 1-4. (pdf)

Zamudio-Beltrán LE, and Hernández-Baños BE (2018), Genetic and morphometric divergence in the Garnet-throated Hummingbird Lamprolaima rhami (Aves: Trochilidae), PeerJ 6, e:5733. (free reading)

Zamudio-Beltrán LE, Ornelas JF, Malpica A, and Hernández-Baños BE (2020), Genetic and morphological differentiation among populations of the Rivoli’s Hummingbird (Eugenes fulgens) species complex (Aves: Trochilidae), Auk 137, e:ukaa032. (pdf)

Zhang D, Tang L, Cheng Y, Hao Y, Xiong Y, Song G, Qu Y, Rheindt FE, Alström P, Jia C, and Lei F (2019), “Ghost introgression” as a cause of deep mitochondrial divergence in a bird species complex, Mol. Biol. Evol. 36, 2375-86. (pdf)

Zhang J, Kapli P, Pavlidis P, and Stamatakis A (2013), A general species delimitation method with applications to phylogenetic placements, Bioinformatics 29, 2869-76. (pdf)

Zhen Y, Harrigan RJ, Ruegg KC, Anderson EC, Ng TC, Lao S, Lohmueller KE, and Smith TB (2021), Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens), Mol. Ecol. 26, 4966-77. (abstract)


Zink RM (2012), The geography of speciation: case studies from birds, EvolEduc. Outreach 5, 541-546. (pdf)


Zink RM, and Barrowclough GF (2008), Mitochondrial DNA under siege in avian phylogeography, MolEcol. 17, 2107-21. (pdf)


Zink RM, Groth JG, Vázquez-Miranda H, and Barrowclough GF (2013), Phylogeography of the California Gnatcatcher (Polioptila californica) using multilocus DNA sequences and ecological niche modeling: implications for conservation, Auk 130, 449-458. (pdf)


Zink RM, Groth JG, Vázquez-Miranda H, and Barrowclough GF (2016), Geographic variation, null hypotheses, and subspecies limits in the California Gnatcacher: a response to McCormack and Maley, Auk 133, 59-68. (pdf)

Zink RM, and Vázquez-Miranda H (2019), Species limits and phylogenomic relationships of Darwin’s finches remain unresolved: potential consequences of a volatile ecological setting, Syst. Biol. 68, 347-357. (pdf)


Zucker MR, Harvey MG, Oswald JA, Cuervo AM, Derryberry EP, and Brumfield RT (2016), The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck, MolPhylogenet. Evol. 101, 294-302. (abstract)