Chronospecies

Theoretical species concept and operational species criteria

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 will expand the meaning of the term “chronospecies” by applying it to the DNA-based species concept to be outlined below. 

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. One delimiting ages for species and subspecies are agreed upon, species-level taxonomies could be generated automatically by computer programs. 

 

References/Literature

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, 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(2), ukab014. (pdf) 

 

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(1), 489-522. (abstract)

 

Avise JC, Bowen BW, and Ayala FJ (2016), In the light of evolution X: comparative phylogeography (an introduction), Proc. Natl Acad. Sci. USA 113, 7957-7961. (pdf)

 

Baker RJ, and Bradley RD (2006), Speciation in mammals and the genetic species concept, J. Mammal. 87(4), 643-662. (pdf)

 

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)

 

Barrowclough TG (2019), The evolutionary origin of species, Oxford University Press. (link)

 

Barrowclough TG, 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)

 

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(pdf)

 

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)

 

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, 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 (2021), The genomic revolution and species delimitation in birds (and other organisms): why phenotypes should not be overlooked, Auk 138(2), ukaa069.  (abstract)

 

Carstens BC, Pelletier TA, Reid NM, and Satler JD (2013), How to fail at species delimitation, MolEcol. 22, 4369- 4383. (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(3), 1-25. (pdf)

 

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(2), ukab009. (abstract)

 

Collar NJ (2018), Taxonomy as tyranny, Ibis 160(2), 481-484. (pdf)

 

Collar NJ, Donald PF, and Kirwan GM (2021), Species, subspecies or morph - what was the Canary Islands Oystercatcher?, Ibis 163(4), 1500-1505. (pdf)

 

de Queiroz K (2007), Species concepts and species delimitation, SystBiol. 56(6), 879-886. (pdf)

 

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)

 

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, 6550-6557. (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(4), 748-759. (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)

 

Freudenstein JV, Broe MB, Folk RA, and Sinn BT (2017), Biodiversity and the species concept - lineages are not enough, SystBiol. 66(4), 644-656. (pdf)

 

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

 

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

 

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

 

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, e106962. (abstract)

 

Joseph L (2021), Species limits in birds: Australian perspectives on interrelated challenges of allopatry, introgression of mitochondrial DNA, recent speciation, and selection, Ornithology 138(2), ukab012. (pdf)

 

Knowles LL, and Carstens BC (2007), Delimiting species without monophyletic gene trees, SystBiol. 56(6), 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(7), 707-723. (abstract)

 

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(2), 162-167. (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)

 

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(1929), e20200683. (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)

 

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)

 

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(6), 1258-1270. (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(2), 731-751. (abstract)

 

Palumbi SR (1989), Rates of molecular evolution and the fractions of nucleotide positions free to vary, J. Mol. Evol. 29(2), 180-287. (abstract)

 

Pârâu LG, and Wink M (2021), Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review, J. Ornith., DOI: 10.1007/s10336-021-01893-x. (pdf)

 

Patten MA (2015), Subspecies and the philosophy of science, Auk 132, 481-485. (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(2), 155-172. (abstract)

 

Price T (2007/2008), Speciation in birds, Roberts & Company Publishers, Greenwood Village, CO, USA. (link)

 

Rannala (2015), The art of species delimitation, CurrZool. 61(5), 846-853. (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(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(2), ukab010.  (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(2), ukaa051. (pdf)

 

Sangster G (2013), The application of species criteria in avian taxonomy and its implications for the debate over species concepts, Biol. Rev. 89(1), 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)

 

Santana A, Marques Silva S, Francês do Nascimento N, 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, Avian Biol., DOI: 10.1111/jab.02723. (pdf)

 

Stankowski S, and Ravinet M (2021), Defining the species continuum, Evolution 75(6), 1256-1273. (pdf)

 

Stanley SM (1978), Chronospecies‘ longevities, the oigin of genera, and the punctuational model of evolution, Paleobiology 4, 26-40. (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, 428. (pdf)

 

Sukumaran J, Holder MT, and Knowles LL (2021), Incorporating the speciation process into species delimitation, PLoS Comput. Biol., e:1008924. (pdf)

 

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(2), ukab016. (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)

 

Winkler K (2021), An overview of speciation and species limits in birds, Auk 138(2), ukab006. (pdf) 

 

Winkler K, and Rasmussen PC (2021), Species limits and taxonomy in birds, Auk 138(2), ukab017. (abstract) 

 

Zink RM, and Barrowclough GF (2008), Mitochondrial DNA under siege in avian phylogeography, MolEcol. 17, 2107-2121. (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)