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Chlorospingus semifuscus semifuscus “ Chimborazo ” morph Plumage and iris coloration (n = 6, 5 males and 1 unsexed). — Throat color and pattern: in general, it can be perceived as something between light buff (f. 17) and cream color (f. 19) mixture; some feathers are pale smoke gray (C.44) and drab-gray (C.119D), with olive-yellow (C.52) scattered barbules with the presence of glaucous (C.79) speckles. Malar region: some olive-yellow (C.52) barbules with a slight glaucous (C.79) moustachial stripe can be seen from lateral view. Pectoral band: close to spectrum yellow (C.55) and partially olive-yellow (C.52) on flanks near shoulder. Belly: transition from whitish plumage with light neutral gray (C.85) and pale neutral gray (C.86) presenting some olive-yellow (C.52) scattered barbules. Iris coloration: In the field, the iris of this population is generally pale yellow. However, the specimen collected during this research (MECN 9637) presented a combination of iris colors, from pale yellowish in the inner border of the iris, changing to very pale yellow-pinkish in the outer border of the iris, to red in the ciliary margin. When thoracic compression was applied, the entire iris turned a color similar to flesh ocher (C.132D). However, the labels of four specimens collected by Stolzmann and Siemiradski in 1883 contained the species epithet “ erythrops,” which means red eye, and three red color-related descriptive terms when collected, such as: brick-red (NHMUK 1885.6.12.855), flesh color (MNHN 1999-2693, USNM 159864), and blood-red (USNM97741). Postmortem iris colors were described as “flesh or ocher-red,” while in juveniles were described as grayish-brown (Berlepsch & Taczanowski 1884). Breeding.—A juvenile female was collected in Cayandeled or Chimbo junction by J. Stolzmann and J. Siemiradski, but the specific date of that skin is difficult to discern. They collected in January, February, March, and September 1883 (Berlepsch & Taczanowski 1884). Distribution.—Along the Chimbo River headwaters and tributaries, in Bolívar and Chimborazo provinces, southwards the junction and drainage of the Chimbo and Chanchán rivers (Fig. 1). This population could be restricted to the remaining suitable habitat in this region, which is surrounded by agricultural land, farms, and cattle pasture. According to the skin label (NHMUK 1885.6.12.856), the site where the first individual of this population was collected is Chillanes, in Bolívar Province. This locality is at a higher elevation, but not distant from the Chimbo-Chanchán river junction and Pallatanga town in Chimborazo Province, where L. Fraser spent a fair time during his expedition in Ecuador. It is difficult to elucidate the exact original locality of this specimen, since no other details are specified by Sclater & Salvin (1877). However, it may be located in the same general region and habitat where other similar individuals of C. “ Chimborazo ” have been found later in the same province. After two field expeditions visiting suitable habitat in the Cañar River drainage and Molleturo-Naranjal road area, we did not find representatives of this population or any of the Chlorospingus populations reviewed here (Fig. 1). This population might be restricted on its southern limit by the Cañar River drainage. We cannot estimate the altitudinal range of this population precisely. Still, the altitudes where specimens of this group were collected are Cayandeled (1372 m), Surupata (1128 m) (Berlepsch & Taczanowski 1884), and Santa Rosa de Chilicay (this study ~ 1217–1227 m; Fig. 1). We consider this population uncommon and very localized. Taxonomic status.—Given the uncertainties about the origin and nature of C. “ Chimborazo ” and the results of phylogenetic analyses, this population could be treated as a variant of C. s. semifuscus with yellow-olive breast band, and different iris colorations from pale yellow to variations of red. On the other hand, based on its distribution between C. s. semifuscus and C. “ El Oro,” it might comprise a stable hybrid population between these two. However, until further studies are conducted, we are inclined to support the treatment as a morph of C. s. semifuscus. A complementary taxonomic history review is available in Supplementary Material A9., Published as part of Sánchez-Nivicela, Manuel, Avendaño, Jorge Enrique, Sánchez-Nivicela, Juan C., Torres, Ana, Fuchs, Jérôme, Bird, Bentley & Bonaccorso, Elisa, 2021, A taxonomic assessment of Chlorospingus flavopectus phaeocephalus and Chlorospingus semifuscus (Passeriformes: Passerellidae), including the description of a new subspecies, pp. 151-180 in Zootaxa 5057 (2) on page 165, DOI: 10.11646/zootaxa.5057.2.1, http://zenodo.org/record/5588075, {"references":["Berlepsch, H. & Taczanowski, L. (1884) Deuxieme liste des oiseaux recueillis dans l'Ecuadeur occidental par MM. Stolzmann et Siemiradski. Proceedings of the Zoological Society of London, 52 (3), 281 - 313.","Sclater, P. L. & Salvin, O. (1877) Descriptions of six new species of South-American birds. Proceedings of the Zoological Society of London, 1887 (3), 521 - 522."]}

Chlorospingus semifuscus semifuscus “ Chimborazo ” morph Plumage and iris coloration (n = 6, 5 males and 1 unsexed). — Throat color and pattern: in general, it can be perceived as something between light buff (f. 17) and cream color (f. 19) mixture; some feathers are pale smoke gray (C.44) and drab-gray (C.119D), with olive-yellow (C.52) scattered barbules with the presence of glaucous (C.79) speckles. Malar region: some olive-yellow (C.52) barbules with a slight glaucous (C.79) moustachial stripe can be seen from lateral view. Pectoral band: close to spectrum yellow (C.55) and partially olive-yellow (C.52) on flanks near shoulder. Belly: transition from whitish plumage with light neutral gray (C.85) and pale neutral gray (C.86) presenting some olive-yellow (C.52) scattered barbules. Iris coloration: In the field, the iris of this population is generally pale yellow. However, the specimen collected during this research (MECN 9637) presented a combination of iris colors, from pale yellowish in the inner border of the iris, changing to very pale yellow-pinkish in the outer border of the iris, to red in the ciliary margin. When thoracic compression was applied, the entire iris turned a color similar to flesh ocher (C.132D). However, the labels of four specimens collected by Stolzmann and Siemiradski in 1883 contained the species epithet “ erythrops,” which means red eye, and three red color-related descriptive terms when collected, such as: brick-red (NHMUK 1885.6.12.855), flesh color (MNHN 1999-2693, USNM 159864), and blood-red (USNM97741). Postmortem iris colors were described as “flesh or ocher-red,” while in juveniles were described as grayish-brown (Berlepsch & Taczanowski 1884). Breeding.—A juvenile female was collected in Cayandeled or Chimbo junction by J. Stolzmann and J. Siemiradski, but the specific date of that skin is difficult to discern. They collected in January, February, March, and September 1883 (Berlepsch & Taczanowski 1884). Distribution.—Along the Chimbo River headwaters and tributaries, in Bolívar and Chimborazo provinces, southwards the junction and drainage of the Chimbo and Chanchán rivers (Fig. 1). This population could be restricted to the remaining suitable habitat in this region, which is surrounded by agricultural land, farms, and cattle pasture. According to the skin label (NHMUK 1885.6.12.856), the site where the first individual of this population was collected is Chillanes, in Bolívar Province. This locality is at a higher elevation, but not distant from the Chimbo-Chanchán river junction and Pallatanga town in Chimborazo Province, where L. Fraser spent a fair time during his expedition in Ecuador. It is difficult to elucidate the exact original locality of this specimen, since no other details are specified by Sclater & Salvin (1877). However, it may be located in the same general region and habitat where other similar individuals of C. “ Chimborazo ” have been found later in the same province. After two field expeditions visiting suitable habitat in the Cañar River drainage and Molleturo-Naranjal road area, we did not find representatives of this population or any of the Chlorospingus populations reviewed here (Fig. 1). This population might be restricted on its southern limit by the Cañar River drainage. We cannot estimate the altitudinal range of this population precisely. Still, the altitudes where specimens of this group were collected are Cayandeled (1372 m), Surupata (1128 m) (Berlepsch & Taczanowski 1884), and Santa Rosa de Chilicay (this study ~ 1217–1227 m; Fig. 1). We consider this population uncommon and very localized. Taxonomic status.—Given the uncertainties about the origin and nature of C. “ Chimborazo ” and the results of phylogenetic analyses, this population could be treated as a variant of C. s. semifuscus with yellow-olive breast band, and different iris colorations from pale yellow to variations of red. On the other hand, based on its distribution between C. s. semifuscus and C. “ El Oro,” it might comprise a stable hybrid population between these two. However, until further studies are conducted, we are inclined to support the treatment as a morph of C. s. semifuscus. A complementary taxonomic history review is available in Supplementary Material A9.

Chlorospingus semifuscus livingstoni Bond & Meyer de Schauensee, 1940 Plumage and iris coloration (n = 31; 20 males, 8 females, and 5 unsexed).—Some variations in adult individuals may be related to sex and age. Throat in adult males (holotype ANSP 141967, and specimens ICN 37437, ICN 37438, and IAvH A12532): dark neutral gray (C.83) with scarce dark quaker drab (k. 1) or dark mouse gray (k. 15) speckles. Malar region: a combination of light neutral gray (C.85) and glaucous (C.79, C.80); a weak dark neutral gray (C.83) moustachial stripe can be perceived depending on view angle. Throat region in females and subadults: lighter or pale neutral gray (C.86), some barbules with olive-yellow (C.52). Pectoral band: absent in adults, but a hint of olive-yellow (C.52) or citrine (C.51) feathers on some chest barbules, and on both flanks on shoulders, can be seen; subadults have a major presence of olive-yellow (C.52) barbules/feathers over this body part giving the impression of an inconspicuous band (e.g., IAvH A12508). Belly: in adult males has a combination of olive-gray (C.42), medium neutral gray (C.84), and dark olive-gray (i.23); in juveniles or subadults, all these colors are present with white, some pearl gray (C.81), pale neutral gray (C.86), and olive-yellow (C.52) or citrine (c.51) scattered on belly and flanks. Iris coloration: usually silvery-yellow; certain individuals can present reddish coloration in and near the outer rim of the iris. Breeding.—A juvenile was observed and photographed giving begging calls and following its parents in the Montezuma region (Tatamá National Park), Risaralda Department, Colombia, on 26 June 2019. Begging calls were recorded by MSN (XC 607806). Distribution.—West slope of Western Cordillera of Colombia, from the headwaters of San Juan River on Cerro Tatamá, Risaralda Department south to Cerro Munchique, Cauca Department at 900‒2400 m (Hilty & Brown 1986; Hilty 2020b). The southern limit of this Colombian endemic may be in the Patía River drainage at a place named “Hoz del Minamá” (F. Ayerbe-Quiñones pers. comm.). This Colombian endemic subspecies does not overlap geographically with C. s. semifuscus., Published as part of Sánchez-Nivicela, Manuel, Avendaño, Jorge Enrique, Sánchez-Nivicela, Juan C., Torres, Ana, Fuchs, Jérôme, Bird, Bentley & Bonaccorso, Elisa, 2021, A taxonomic assessment of Chlorospingus flavopectus phaeocephalus and Chlorospingus semifuscus (Passeriformes: Passerellidae), including the description of a new subspecies, pp. 151-180 in Zootaxa 5057 (2) on page 164, DOI: 10.11646/zootaxa.5057.2.1, http://zenodo.org/record/5588075, {"references":["Bond, J. & Meyer de Schauensee, R. (1940) On some birds from southern Colombia. Proceedings of the Academy of Natural Sciences of Philadelphia, 92, 153 - 169.","Hilty, S. L. & Brown, W. L. (1986) A Guide to the Birds of Colombia. Princeton University Press, Princeton, New Jersey, 836 pp.","Hilty, S. (2020 b) Dusky Chlorospingus (Chlorospingus semifuscus), version 1.0. In: J. del Hoyo, Elliott, A., Sargatal, J., Christie, D. A. & de Juana, E. (Eds.), Birds of the World. Cornell Lab of Ornithology, Ithaca. Available from: https: // doi. org / 10.2173 / bow. dubtan 1.01 (accessed 8 May 2020)"]}

Chlorospingus “ El Oro ” We suggest the treatment of this population as a new subspecies of the Chocó-Andean Chlorospingus semifuscus group, endemic of southwest Ecuador, as follows., Published as part of Sánchez-Nivicela, Manuel, Avendaño, Jorge Enrique, Sánchez-Nivicela, Juan C., Torres, Ana, Fuchs, Jérôme, Bird, Bentley & Bonaccorso, Elisa, 2021, A taxonomic assessment of Chlorospingus flavopectus phaeocephalus and Chlorospingus semifuscus (Passeriformes: Passerellidae), including the description of a new subspecies, pp. 151-180 in Zootaxa 5057 (2) on page 165, DOI: 10.11646/zootaxa.5057.2.1, http://zenodo.org/record/5588075

Chlorospingus flavopectus phaeocephalus Sclater & Salvin, 1877 Plumage and iris coloration (n = 20; 13 males, 4 females, and 3 unsexed).—Throat color and pattern: whitish or buff cream color (C.54) with some spectrum yellow (C.55) barbules and some scattered glaucous (C.79) speckles. Chin and lower throat including malar region: hints of glaucous (C.79) n some individuals. Moustachial stripe: weak glaucous (C.79) in adult can be perceived depending on the view angle. Pectoral band: a fairly bright lemon chrome (b. 21) in center, with more olive-yellow (C.52) on the sides. Belly: whitish silvery, light olive-gray (d. 23) in some individuals. Iris coloration: silvery yellow. Some labels in Spanish refer to iris as “cream color,” meaning pale yellow. Breeding. — Cadena et al. (2007) reported nests from 1 March to 5 June 2001, in the Cosanga area, near San Isidro Lodge, Napo Province. At San Isidro Lodge, MSN observed a juvenile accompanying its parents on 12 January 2019, a family group with two young on 17 June, and an adult collecting food (beetles and moths) on 17 August. On 16 February 2020, a juvenile was observed catching moths. Distribution.—Montane evergreen forest and forest borders in the eastern slope of the Andes (Amazon basin), from the Colombian massif region in Putumayo (Avendaño et al. 2013; Chavez-Paz et al. 2017; Felix & Coral-Jaramillo 2017), through the Ecuadorian east Andean slope—from north to south— entering the Cajamarca Department in far northeast Peru. Its altitudinal distribution in Ecuador is 1500–2700 m (Freile & Restall 2018). A complementary taxonomic history review is given in Supplementary Material A9., Published as part of Sánchez-Nivicela, Manuel, Avendaño, Jorge Enrique, Sánchez-Nivicela, Juan C., Torres, Ana, Fuchs, Jérôme, Bird, Bentley & Bonaccorso, Elisa, 2021, A taxonomic assessment of Chlorospingus flavopectus phaeocephalus and Chlorospingus semifuscus (Passeriformes: Passerellidae), including the description of a new subspecies, pp. 151-180 in Zootaxa 5057 (2) on page 163, DOI: 10.11646/zootaxa.5057.2.1, http://zenodo.org/record/5588075, {"references":["Sclater, P. L. & Salvin, O. (1877) Descriptions of six new species of South-American birds. Proceedings of the Zoological Society of London, 1887 (3), 521 - 522.","Cadena, C. D., Cordoba-Cordoba, S., Londono, G. A., Calderon, F. D., Martin, T. E. & Baptiste, M. P. (2007) Nesting and singing behavior of Common Bush-Tanagers (Chlorospingus ophthalmicus) in South America. Ornitologia Colombiana, 5, 54 - 63.","Avendano, J. E., Stiles, F. G. & Cadena, C. D. (2013) A new subspecies of Common Bush-Tanager (Chlorospingus flavopectus, Emberizidae) from the east slope of the Andes of Colombia. Ornitologia Colombiana, 13, 45 - 58.","Chavez-Paz, L. F., Rosero-Chates, E. B. & Munoz-Garcia, J. (2017) eBird Checklist: ebird: An online database of bird distribution and abundance. Web Application. eBird, Ithaca, New York. Available from: https: // ebird. org / checklist / S 38825296 (accessed 30 September 2019)","Freile, J. F. & Restall, R. (2018) Birds of Ecuador. Bloomsbury Publishing, London, 656 pp."]}

Chlorospingus semifuscus xanthothorax (subspecies nova) Diagnosis.—Similar to C. f. phaeocephalus (Fig. 1) but inhabits the cloud forest of the southwestern Andes of Ecuador. The type series is presented in Figure 7. The color of the pectoral band of C. f. phaeocephalus is somewhat more yellowish than in C. s. xanthothorax, as supported by Zimmer´s (1947) review. The pectoral band in C. s. xanthothorax is a rather bright combination between spectrum yellow (C.55) and olive-yellow (C.52), with more olive yellow on flanks, whereas the pectoral band in C. f. phaeocephalus is a brighter lemon chrome (b. 21) on the center with more olive-yellow (C.52), mainly on the flanks. Both C. s. xanthothorax and C. f. phaeocephalus present pale silvery yellow iris. In examined specimens, the relevant plumage difference between adult individuals in these two populations might be the throat pattern coloration. In C. f. phaeocephalus, the throat is more buff-white or whitish with some grayish or glaucous speckles (see holotype description below), but this feature is age variable and difficult to distinguish in the field given the poor light conditions of cloud forests. In both taxa, postocular spots on adults are related to ontogeny and probably sex (females). Both sexes of C. s. xanthothorax are smaller than the other members of C. f. phaeocephalus and the C. semifuscus group (Fig. 5). Description of Holotype MECN 9592 (in life).—Adult. Weight 22 g. Culmen, lores, fore crown, supercilium and lower auricular region blackish neutral gray (C.82) with weak hints of yellowish olive-green (C.50) randomly distributed on some barbules. Crown and back of the head are dark neutral gray (C.83). Nape, back, rump, wing-coverts, and upper tail coverts are yellowish olive-green (C.50). On upper-wings, primaries, secondaries, tertials inner webs, and under wings are brownish olive (C.29), better diagnosed when wings are folded, mainly at the end of the primary projection. Bill: upper mandible, matte black, with some hints of pale russet vinaceous (C.221D) near the gape. Lower mandible is a mixture of matte black with some light russet vinaceous (C.221D). The malar transitions from a very pale cream color (C.54) near the base of the bill reaching the throat to a light neutral gray (C.85) with some hints of yellowish olive-green (C.50) barbules. It presents a thin blackish neutral gray (C.82) moustachial stripe. Chin is buffy-white. Throat center presents the same transition between pale cream color and dark neutral gray. In the field, the throat plumage can be perceived as a mixture of speckled dark gray and buff. The pectoral band is a fairly bright combination between spectrum yellow (C.55) and olive-yellow (C.52), with more olive-yellow (C.52) on flanks. Center of belly is a pale pearl gray (C.81) and/or silvery-white that narrows in the vent. Flanks are bright spectrum yellow (C.55) with some pale neutral gray (C.86) on middle flanks. Tail from above is yellowish olive-green (C.50). Outer webs spectrum yellow and inner webs are dull yellowish olive-green (C.50), with black rachises. Tail from below dull yellowish olive-green (C.50). Under-tail coverts are spectrum yellow (C.55). Iris: silvery yellow. The iris can vary, and is perceived as pale-yellow in the field. Tarsometatarsus, flesh color (C.5). Tarsi and toes light neutral gray with hints of flesh color. Specimen measurements MECN 9592 (Fig. 7); wing chord mean 86.7 mm, tarsus mean 22.3 mm, tail 56.0 mm, bill length from the distal edge of the nostril to the tip of the bill 8.5 mm, bill depth at the center of nostrils 5.4 mm and bill width at center of nostrils 4.5 mm. Empty stomach. Showing molt at both P10 (primaries). Type locality: Sambotambo road (boundaries of Buenaventura Reserve; 03° 39’ 07.32” S, 79° 44’ 36.32” W; 969 m elevation; Fig. 1), El Oro Province, Ecuador; collected on 8 September 2017, by MSN and JSN; prepared by Hernando Román; field catalog number EOC 002; GenBank accession number provided in Appendix I. Paratypes.— Two female specimens complete the type series (Fig. 7), as follows. Study skin MECN 9214; wing chord mean 64.00 mm, tarsus mean 28.72 mm, tail 60.00 mm, bill length from the distal edge of the nostril to the tip of the bill 8.10 mm, bill depth at the center of nostrils 5.32 mm and bill width at center of nostrils 4.83 mm. Locality: Buenaventura Reserve at 1090 m; collected on 2 January 2017, by MSN and JSN. MECN 9593; wing chord mean 65.00 mm, tarsus mean 27.70 mm, tail 52.00 mm, bill length from the distal edge of the nostril to the tip of the bill 8.18 mm, bill depth at the center of nostrils 5.14 mm and bill width at center of nostrils 4.79 mm; collection site is the same as holotype. Both skins prepared by Hernando Román; field catalog numbers EOC 001 and EOC 003, GenBank Accession numbers provided in Appendix I. Dawn song.—Two complete dawn songs of this taxon by MECN 9592 (XC607786, XC607789) are deposited at xeno-canto.org. For description per element see Table 3; for spectrograms, see Figure 6, and Supplementary Material A2. A single, sharp, high-pitched element (note “a”) repeated several times before pre-trill notes and dry staccato trill similar than C. s. semifuscus; but pre-trill notes “b” and “c” delivered in different order and post-trill notes different than nominal. Etymology.—We choose an epithet that matches the obvious field diagnostic feature of this new member of the C. semifuscus group, which is its olive-yellow breast band. Xanthothorax combines two Greek words, xanthos meaning yellow and thorax meaning breast (Jobling 2010). Distribution and habitat.—Mainly found in the borders of humid subtropical lower montane cloud forests in El Oro Province and in similar ecosystems in adjacent Loja Province (Ridgely & Greenfield 2001). To our knowledge, this subspecies is restricted in its northern limit by the arid Jubones River valley. The southernmost record is from Vicentino south of Puyango River, in Loja Province (Best et al. 1993). Its southern distribution might be limited by the transition from the Chocoan humid to Tumbesian dry ecosystems, between Puyango and Catamayo rivers. Its elevation range is ~ 800‒1700 m. Uncommon and localized, in general, but frequently found in Buenaventura Reserve (Robbins & Ridgely 1990) and in suitable habitat and elevation in El Oro province (Garzón-Santomaro et al. 2019) and adjacent Loja province. Breeding.—Juveniles were reported begging for food on 26 February (vocalization recorded by MSN, XC 607791) and 9 September 2017. Both breeding records were within the area where we collected the holotype., Published as part of Sánchez-Nivicela, Manuel, Avendaño, Jorge Enrique, Sánchez-Nivicela, Juan C., Torres, Ana, Fuchs, Jérôme, Bird, Bentley & Bonaccorso, Elisa, 2021, A taxonomic assessment of Chlorospingus flavopectus phaeocephalus and Chlorospingus semifuscus (Passeriformes: Passerellidae), including the description of a new subspecies, pp. 151-180 in Zootaxa 5057 (2) on pages 166-167, DOI: 10.11646/zootaxa.5057.2.1, http://zenodo.org/record/5588075, {"references":["Zimmer, J. T. (1947) Studies of Peruvian birds no. 52. The genera Sericossypha, Chlorospingus, Cnemoscopus, Hemispingus, Conothraupis, Chlorornis, Lamprospiza, Cissopis and Schistochlamys. American Museum Novitates, 1367, 4 - 5.","Jobling, J. A. (2010) The Helm Dictionary of Scientific Bird Names from Aalge to Zusii. Helm, London, 432 pp.","Ridgely, R. S. & Greenfield, P. J. (2001) The Birds of Ecuador. Status, Distribution and Taxonomy. Cornell University Press, Ithaca, New York, 848 pp.","Best, B. F., Clarke, C. T., Checker, M., Broom, A. L., Thewlis, R. M., Duckworth, W. & McNab, A. (1993) Distributional records, natural history notes, and conservation of some poorly known birds from southwestern Ecuador and northwestern Peru. Bulletin British Ornithologists' Club, 113 (2), 108 - 119.","Robbins, M. B. & Ridgely, R. S. (1990) The avifauna of an upper tropical cloud forest in southwestern Ecuador. Proceedings of the Academy of Natural Sciences of Philadelphia, 142, 59 - 71.","Garzon-Santomaro, C., Pozo-Zamora, G., Sornoza-Molina, F. & Mena-Valenzuela, P. (2019) Aves del Paramo al Manglar. In: MECN-INB-GADPEO, Anfibios, Reptiles y Aves de la Provincia de El Oro. Una Guia para la Identificacion de Especies del Paramo al Manglar. Segunda Edicion. Publicacion Miscelanea N ° 11. GADPEO-INABIO, Quito, pp. 121 - 218."]}

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363genomes from 92.4% of bird families-including 267newly sequenced genomes produced for phaseII of the Bird 10,000Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

We report here the genome sequence of a circular virus isolated from samples of an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract. The genome is 2,152bp in length and is most similar (30 to 44.5% amino acid identity) to the genome sequences of other single-stranded DNA (ssDNA) circular viruses belonging to the gemycircularvirus group.

The Resplendent Quetzal Pharomachrus mocinno is a rare Neotropical bird included in the IUCN red list as Near Threatened. Fragmentation of its habitat, the cloud forest, is considered as the principal threat. Two subspecies are currently recognised but genetic and morphometric studies suggested they could be considered as full species. We assessed whether male vocalisation would support a species delimitation hypothesis. We recorded in the field and downloaded from sound archives vocalisation of 57 individuals from 30 different localities distributed in 11 countries. We estimated the acoustic differences of all the Pharomachrus taxa with multivariate analyses and machine learning techniques. Our results show vocal differences between P. m. mocinno and P. m. costaricensis that could have a molecular basis, potentially due to genetic drift developed during the more than three million years of separation of P. m. mocinno (from Mexico to Nicaragua) and P. m. costaricensis (Costa Rica and Panama). We therefore suggest that P. mocinno could potentially be divided into two species. A possible separation of these taxa into two species could have important consequences for the conservation status of the Resplendent Quetzals, and redirect conservation efforts for these taxa.

The Resplendent Quetzal Pharomachrus mocinno is a rare Neotropical bird included in the IUCN red list as Near Threatened. Fragmentation of its habitat, the cloud forest, is considered as the principal threat. Two subspecies are currently recognised but genetic and morphometric studies suggested they could be considered as full species. We assessed whether male vocalisation would support a species delimitation hypothesis. We recorded in the field and downloaded from sound archives vocalisation of 57 individuals from 30 different localities distributed in 11 countries. We estimated the acoustic differences of all the Pharomachrus taxa with multivariate analyses and machine learning techniques. Our results show vocal differences between P. m. mocinno and P. m. costaricensis that could have a molecular basis, potentially due to genetic drift developed during the more than three million years of separation of P. m. mocinno (from Mexico to Nicaragua) and P. m. costaricensis (Costa Rica and Panama). We therefore suggest that P. mocinno could potentially be divided into two species. A possible separation of these taxa into two species could have important consequences for the conservation status of the Resplendent Quetzals, and redirect conservation efforts for these taxa.