Molecular Biology and Genetics
Statistics of barcoding coverage
Specimens with Sequences:1047
Specimens with Barcodes:1022
Species With Barcodes:154
Darwin's finches (also known as the Galápagos finches) are a group of about fifteen species of passerine birds. They are often classified as the subfamily Geospizinae or tribe Geospizini. It is still not clear to which bird family they belong, but they are not related to the true finches. They were first collected by Charles Darwin on the Galápagos Islands during the second voyage of the Beagle. Apart from the Cocos finch, which is from Cocos Island, the others are found only on the Galápagos Islands.
The term "Darwin's finches" was first applied by Percy Lowe in 1936, and popularised in 1947 by David Lack in his book Darwin's Finches. David Lack based his analysis on the large collection of museum specimens collected by the 1905–06 Galápagos expedition of the California Academy of Sciences, to whom Lack dedicated his 1947 book. The birds vary in size from 10 to 20 cm and weigh between 8 and 38 grams. The smallest are the warbler-finches and the largest is the vegetarian finch. The most important differences between species are in the size and shape of their beaks, and the beaks are highly adapted to different food sources. The birds are all dull-coloured.
During the survey voyage of HMS Beagle, Darwin had no idea of the significance of the birds of the Galápagos. He had learned how to preserve bird specimens while at the University of Edinburgh and had been keen on shooting, but he had no expertise in ornithology and by this stage of the voyage concentrated mainly on geology. In Galápagos he mostly left bird shooting to his servant Syms Covington. Nonetheless, these birds were to play an important part in the inception of Darwin's theory of evolution by natural selection.
On the Galápagos Islands and afterward, Darwin thought in terms of "centres of creation" and rejected ideas concerning the transmutation of species. From Henslow's teaching, he was interested in the geographical distribution of species, particularly links between species on oceanic islands and on nearby continents. On Chatham Island, he recorded that a mockingbird was similar to those he had seen in Chile, and after finding a different one on Charles Island he carefully noted where mockingbirds had been caught. In contrast, he paid little attention to the finches. When examining his specimens on the way to Tahiti, Darwin noted that all of the mockingbirds on Charles Island were of one species, those from Albemarle of another, and those from James and Chatham Islands of a third. As they sailed home about nine months later, this, together with other facts, including what he had heard about Galápagos tortoises, made him wonder about the stability of species.
Following his return from the voyage, Darwin presented the finches to the Geological Society of London at their meeting on 4 January 1837, along with other mammal and bird specimens that he had collected. The bird specimens, including the finches, were given to John Gould, the famous English ornithologist, for identification. Gould set aside his paying work and at the next meeting, on 10 January, reported that the birds from the Galápagos Islands that Darwin had thought were blackbirds, "gross-beaks" and finches were actually "a series of ground Finches which are so peculiar [as to form] an entirely new group, containing 12 species". This story made the newspapers.
Darwin had been in Cambridge at that time. In early March, he met Gould again and for the first time got a full report on the findings, including the point that his Galápagos "wren" was another closely allied species of finch. The mockingbirds that Darwin had labelled by island were separate species rather than just varieties. Gould found more species than Darwin had expected, and concluded that 25 of the 26 land birds were new and distinct forms, found nowhere else in the world but closely allied to those found on the South American continent. Darwin now saw that, if the finch species were confined to individual islands, like the mockingbirds, this would help to account for the number of species on the islands, and he sought information from others on the expedition. Specimens had also been collected by Captain Robert FitzRoy, FitzRoy’s steward Harry Fuller and Darwin's servant Covington, who had labelled them by island. From these, Darwin tried to reconstruct the locations from where he had collected his own specimens. The conclusions supported his idea of the transmutation of species.
Text from The Voyage of the Beagle
At the time that he rewrote his diary for publication as Journal and Remarks (later The Voyage of the Beagle), he described Gould's findings on the number of birds, noting that "Although the species are thus peculiar to the archipelago, yet nearly all in their general structure, habits, colour of feathers, and even tone of voice, are strictly American". In the first edition of The Voyage of the Beagle, Darwin said that "It is very remarkable that a nearly perfect gradation of structure in this one group can be traced in the form of the beak, from one exceeding in dimensions that of the largest gros-beak, to another differing but little from that of a warbler".
In 1839, Darwin conceived of his theory of natural selection, and by the time of the second edition in 1845 Darwin had brought together his theory. He now added two closing sentences: "Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends".
The remaining land-birds form a most singular group of finches, related to each other in the structure of their beaks, short tails, form of body and plumage: there are thirteen species, which Mr. Gould has divided into four subgroups. All these species are peculiar to this archipelago; and so is the whole group, with the exception of one species of the sub-group Cactornis, lately brought from Bow Island, in the Low Archipelago. Of Cactornis, the two species may be often seen climbing about the flowers of the great cactus-trees; but all the other species of this group of finches, mingled together in flocks, feed on the dry and sterile ground of the lower districts. The males of all, or certainly of the greater number, are jet black; and the females (with perhaps one or two exceptions) are brown. The most curious fact is the perfect gradation in the size of the beaks in the different species of Geospiza, from one as large as that of a hawfinch to that of a chaffinch, and (if Mr. Gould is right in including his sub-group, Certhidea, in the main group) even to that of a warbler. The largest beak in the genus Geospiza is shown in Fig. 1, and the smallest in Fig. 3; but instead of there being only one intermediate species, with a beak of the size shown in Fig. 2, there are no less than six species with insensibly graduated beaks. The beak of the sub-group Certhidea, is shown in Fig. 4. The beak of Cactornis is somewhat like that of a starling, and that of the fourth subgroup, Camarhynchus, is slightly parrot-shaped. Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends. In a like manner it might be fancied that a bird originally a buzzard, had been induced here to undertake the office of the carrion-feeding Polybori of the American continent.
Text from On the Origin of Species
Darwin discussed the divergence of species of birds in the Galápagos more explicitly in his chapter on geographical distribution in On the Origin of Species:
The most striking and important fact for us in regard to the inhabitants of islands, is their affinity to those of the nearest mainland, without being actually the same species. [In] the Galapagos Archipelago... almost every product of the land and water bears the unmistakable stamp of the American continent. There are twenty-six land birds, and twenty-five of these are ranked by Mr. Gould as distinct species, supposed to have been created here; yet the close affinity of most of these birds to American species in every character, in their habits, gestures, and tones of voice, was manifest.... The naturalist, looking at the inhabitants of these volcanic islands in the Pacific, distant several hundred miles from the continent, yet feels that he is standing on American land. Why should this be so? why should the species which are supposed to have been created in the Galapagos Archipelago, and nowhere else, bear so plain a stamp of affinity to those created in America? There is nothing in the conditions of life, in the geological nature of the islands, in their height or climate, or in the proportions in which the several classes are associated together, which resembles closely the conditions of the South American coast: in fact there is a considerable dissimilarity in all these respects. On the other hand, there is a considerable degree of resemblance in the volcanic nature of the soil, in climate, height, and size of the islands, between the Galapagos and Cape de Verde Archipelagos: but what an entire and absolute difference in their inhabitants! The inhabitants of the Cape de Verde Islands are related to those of Africa, like those of the Galapagos to America. I believe this grand fact can receive no sort of explanation on the ordinary view of independent creation; whereas on the view here maintained, it is obvious that the Galapagos Islands would be likely to receive colonists, whether by occasional means of transport or by formerly continuous land, from America; and the Cape de Verde Islands from Africa; and that such colonists would be liable to modification;—the principle of inheritance still betraying their original birthplace.
Polymorphism in Darwin's finches
Whereas Darwin spent just five weeks in the Galápagos, and David Lack spent three months, Peter and Rosemary Grant and their colleagues have made research trips to the Galápagos for about thirty years, particularly studying Darwin's finches. Here, we look briefly at the case of the large cactus finch Geospiza conirostris on Isla Genovesa (formerly Tower Island), which is formed from a shield volcano, and is home to a variety of birds. These birds, like all well-studied groups, show various kinds of morphism.
Males are dimorphic in song type: songs A and B are quite distinct. Also, males with song A have shorter bills than B males. This is also a clear difference. With these beaks, males are able to feed differently on their favourite cactus, the prickly pear Opuntia. Those with long beaks are able to punch holes in the cactus fruit and eat the fleshy aril pulp, which surrounds the seeds, whereas those with shorter beaks tear apart the cactus base and eat the pulp and any insect larvae and pupae (both groups eat flowers and buds). This dimorphism clearly maximises their feeding opportunities during the non-breeding season when food is scarce.
If the population is panmixic, then Geospiza conirostris exhibits a balanced genetic polymorphism and not, as originally supposed, a case of nascent sympatric speciation. The selection maintaining the polymorphism maximises the species' niche by expanding its feeding opportunity. The genetics of this situation cannot be clarified in the absence of a detailed breeding program, but two loci with linkage disequilibrium is a possibility.
Another interesting dimorphism is for the bills of young finches, which are either 'pink' or 'yellow'. All species of Darwin's finches exhibit this morphism, which lasts for two months. No interpretation of this phenomenon is known.
For some decades, taxonomists have placed these birds in the family Emberizidae along with the New World sparrows and Old World buntings (Sulloway 1982). However, the Sibley–Ahlquist taxonomy puts Darwin's finches with the tanagers (Monroe and Sibley 1993), and at least one recent work follows that example (Burns and Skutch 2003). The American Ornithologists' Union, in its North American check-list, places the Cocos finch in the Emberizidae but with an asterisk indicating that the placement is probably wrong (AOU 1998–2006); in its tentative South American check-list, the Galápagos species are incertae sedis, of uncertain place (Remsen et al. 2007).
- Genus Geospiza
- Large cactus finch (Geospiza conirostris)
- Sharp-beaked ground finch (Geospiza difficilis)
- Vampire finch (Geospiza difficilis septentrionalis)
- Medium ground finch (Geospiza fortis)
- Small ground finch (Geospiza fuliginosa)
- Large ground finch (Geospiza magnirostris)
- Darwin's large ground finch (Geospiza magnirostris magnirostris) – possibly extinct (1957?)
- Common cactus finch (Geospiza scandens)
- Genus Camarhynchus
- Genus Certhidea
- Genus Pinaroloxias
- Cocos finch (Pinaroloxias inornata)
- Genus Platyspiza
- Vegetarian finch (Platyspiza crassirostris)
Molecular basis of beak evolution
Developmental research in 2004 found that bone morphogenetic protein 4 (BMP4), and its differential expression during development, resulted in variation of beak size and shape among finches. BMP4 acts in the developing embryo to lay down skeletal features, including the beak. The same group showed that the development of the different beak shapes in Darwin's finches are also influenced by slightly different timing and spatial expressions of a gene called calmodulin (CaM). Calmodulin acts in a similar way to BMP4, affecting some of the features of beak growth. The authors suggest that changes in the temporal and spatial expression of these two factors are possible developmental controls of beak morphology.
In a recent study genode sequencing revealed a 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity.
- Grant & Grant 2008, p. 3
- Lack, David. 1947. Darwin's Finches. Cambridge University Press (reissued in 1961 by Harper, New York, with a new preface by Lack; reissued in 1983 by Cambridge University Press with an introduction and notes by Laurene M. Ratcliffe and Peter T. Boag). ISBN 0-521-25243-1
- Steinheimer 2004, p. 300
- Grant, K. Thalia and Estes, Gregory B. 2009 "Darwin in Galapagos: Footsteps to a New World" Princeton University Press, Princeton.
- Steinheimer 2004, pp. 301–303
- Keynes 2000, p. xix.
- Gordon Chancellor; Randal Keynes (October 2006), Darwin's field notes on the Galapagos: 'A little world within itself', Darwin Online
- Eldredge 2006
- Desmond & Moore 1991, p. 209
- Sulloway 1982, pp. 57–58
- Desmond & Moore 1991, p. 248
- Sulloway 2006
- Darwin 1839, pp. 461–462
- Darwin 1839, p. 462.
- Darwin 1845, pp. 379–380
- Darwin 1887
- Darwin 1845, p. 380.
- Darwin 1859, pp. 397–398.
- Huxley J. 1955. Morphism in birds. 11th Int Ornith Cong (Basel 1954, p309-328) touches on this theme.
- B. Rosemary Grant and Peter R. Grant 1989. Evolutionary dynamics of a natural population: the large cactus finch of the Galápagos. Chicago, p241 first para.
- Grant, Peter R. 1999. Ecology and evolution of Darwin's finches. Princeton NJ, p428 in Afterword.
- Maynard Smith J. 1998. Evolutionary genetics. 2nd ed, Chapter 5, Oxford.
- Grant, Peter R. 1999. Ecology and evolution of Darwin's finches. Princeton NJ. (see plate 7)
- Abzhanov, Arhat; Meredith Protas, B. Rosemary Grant, Peter R. Grant, Clifford J. Tabin (September 3, 2004), "Bmp4 and Morphological Variation of Beaks in Darwin's Finches", Science (USA: AAAS) 305 (5689): 1462–1465, Bibcode:2004Sci...305.1462A, doi:10.1126/science.1098095, ISSN 0036-8075, OCLC 1644869, PMID 15353802, retrieved 2008-03-08
- Abzhanov, Arhat; Winston P. Kuo, Christine Hartmann, B. Rosemary Grant, Peter R. Grant and Clifford J. Tabin (August 3, 2006), "The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches", Nature (UK: Nature Publishing Group) 442 (7102): 563–567, Bibcode:2006Natur.442..563A, doi:10.1038/nature04843, ISSN 0028-0836, OCLC 1586310, PMID 16885984, retrieved 2008-03-08
- Andersson, Leif; Sangeet Lamichhaney, Jonas Berglund, Markus Sällman Almén, Khurram Maqbool, Manfred Grabherr, Alvaro Martinez-Barrio, Marta Promerová, Carl-Johan Rubin, Chao Wang, Neda Zamani, B. Rosemary Grant, Peter R. Grant, Matthew T. Webster (February 11, 2015), "Evolution of Darwin’s finches and their beaks revealed by genome sequencing", Nature (UK: Nature Publishing Group) 518 (7102), Bibcode:2006Natur.442..563A, doi:10.1038/nature04843, ISSN 0028-0836, OCLC 1586310, PMID 16885984, retrieved 2008-03-08
- Darwin, Charles (1839), Narrative of the surveying voyages of His Majesty's Ships Adventure and Beagle between the years 1826 and 1836, describing their examination of the southern shores of South America, and the Beagle's circumnavigation of the globe. Journal and remarks. 1832–1836 III, London: Henry Colburn
- Darwin, Charles (1845), Journal of researches into the natural history and geology of the countries visited during the voyage of H.M.S. Beagle round the world, under the Command of Capt. Fitz Roy, R.N (2nd. ed.), London: John Murray
- Darwin, Charles (1859), On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (1st ed.), London: John Murray
- Darwin, Francis (1887), "Chapter 1, The Foundations of the 'Origin of Species'", in Darwin, Francis, The life and letters of Charles Darwin, including an autobiographical chapter 2, London: John Murray
- Desmond, Adrian; Moore, James (1991), Darwin, London: Michael Joseph, Penguin Group, ISBN 0-7181-3430-3, OCLC 185764721
- Eldredge, Niles (2006), "Confessions of a Darwinist", The Virginia Quarterly Review (Spring 2006): 32–53, retrieved 2008-11-04
- Grant, Peter R.; Grant, B. Rosemary (2008), How and Why Species Multiply: The Radiation of Darwin's Finches, Princeton University Press, ISBN 978-0-691-13360-7
- Lack, David (1940), "Evolution of the Galapagos Finches", Nature (7 September 1940) 146 (146): 324–327, Bibcode:1940Natur.146..324L, doi:10.1038/146324a0, retrieved 2013-12-06
- Check-list of North American Birds, American Ornithologists' Union, 1998–2006, archived from the original on April 4, 2007, retrieved 2007-04-09
- Burns, Kevin J.; Skutch, Alexander F. (2003), "Tanagers and Tanager-Finches", in Christopher Perrins, ed., The Firefly Encyclopedia of Birds, Firefly Books, pp. 629–631, ISBN 1-55297-777-3, retrieved 2007-04-09 It is not clear whether this placement was made by Burns and Skutch or by Perrins.
- Keynes, Richard (2000), Charles Darwin's zoology notes & specimen lists from H.M.S. Beagle, Cambridge University Press, retrieved 2008-12-08
- Sibley, Charles G. (1993), A World Checklist of Birds, New Haven, Conn.: Yale University Press, ISBN 0-300-07083-7, retrieved 2013-12-06 Monroe and Sibley consider the tanagers to be a tribe (Thraupini) of a big family Fringillidae rather than a family of their own (Thraupidae).
- Zimmer, J. (2007-04-05), A classification of the bird species of South America, American Ornithologists' Union, retrieved 2007-04-09
- Steinheimer, F. D. (2004), "Charles Darwin's bird collection and ornithological knowledge during the voyage of H.M.S. Beagle, 1831–1836", Journal of Ornithology 145 (4): 300–320, doi:10.1007/s10336-004-0043-8, retrieved 2008-12-08
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- Sulloway, Frank J. (2006), "Why Darwin Rejected Intelligent Design", in Brockman, John, Intelligent Thought: Science versus the Intelligent Design Movement, New York: Vintage, pp. 107–126
The tanagers (singular //) comprise the bird family Thraupidae, in the order Passeriformes. The family has an American distribution. The Thraupidae are the second-largest family of birds and represent about 4% of all avian species and 12% of the Neotropical birds. Traditionally, about 240 species of tanagers were described, but the taxonomic treatment of this family's members is currently in a state of flux. As more of these birds are studied using modern molecular techniques, some genera are expected to be relocated elsewhere. Already, species in the genera Euphonia and Chlorophonia, which were once considered part of the tanager family, are now treated as members of Fringillidae, in their own subfamily (Euphoniinae). Likewise, the genera Piranga (which includes the scarlet tanager, summer tanager, and western tanager), Chlorothraupis, and Habia appear to be members of the cardinal family, and have been reassigned to that family by the AOU.
Tanagers are small to medium-sized birds. The shortest-bodied species, the white-eared conebill, is 9 cm (3.8 in) long and weighs 7 grams, barely smaller than the short-billed honeycreeper. The longest, the magpie tanager is 28 cm (11 in) and weighs 76 grams (2.7 oz). The heaviest is the white-capped tanager which weighs 114 grams (4 oz) and measures about 24 cm (9.5 in). Both sexes are usually the same size and weight. Tanagers are often brightly colored, but some species are black and white. Birds in their first year are often duller or a different color altogether. Males are typically more brightly colored than females. Most tanagers have short, rounded wings. The shape of the bill seems to be linked to the species' foraging habits.
Tanagers are restricted to the New World and mainly to the tropics. About 60% of tanagers live in South America, and 30% of these species live in the Andes. Most species are endemic to a relatively small area.
Most tanagers live in pairs or in small groups of three to five individuals. These groups may consist simply of parents and their offspring. Birds may also be seen in single-species or mixed flocks. Many tanagers are thought to have dull songs, though some are elaborate.
Tanagers are omnivorous, and their diets vary from genus to genus. They have been seen eating fruits, seeds, nectar, flower parts, and insects. Many pick insects off branches. Other species look for insects on the undersides of leaves. Yet others wait on branches until they see a flying insect and catch it in the air. Many of these particular species inhabit the same areas, but these specializations alleviate competition.
The breeding season is March through June in temperate areas and in September through October in South America. Some species are territorial, while others build their nests closer together. Little information is available on tanager breeding behavior. Males show off their brightest feathers to potential mates and rival males. Some species' courtship rituals involve bowing and tail lifting.
Most tanagers build cup nests on branches in trees. Some nests are almost globular. Entrances are usually built on the side of the nest. The nests can be shallow or deep. The species of the tree in which they choose to build their nests and the nests' positions vary among genera. Most species nest in an area hidden by very dense vegetation. No information is yet known regarding the nests of some species.
The clutch size is three to five eggs. The female incubates the eggs and builds the nest, but the male may feed the female while she incubates. Both sexes feed the young. Five species have helpers assist in feeding the young. These helpers are thought to be the previous year's nestlings.
Phylogenetic studies suggest the true tanagers form three main groups, two of which consist of several smaller, well-supported clades. The list below is an attempt using information gleaned from the latest studies to organize them into coherent related groups, and as such may contain groupings not yet accepted by or are under review by the various ornithological taxonomy authorities.
Mainly dull-colored forms
a) Conebill and flowerpiercer group (Also contains Haplospiza, Catamenia, Acanthidops, Diglossa, Diglossopis, Phrygilus and Sicalis traditionally in the Emberizidae) This group despite having a rather varied bill morphology shows marked plumage similarities. Most are largely gray, blue, or black, and numerous species have rufous underparts:
- Genus Conirostrum – typical conebills (10 species)
- Genus Oreomanes – giant conebill
- Genus Xenodacnis – tit-like dacnis
- Genus Catamenia (three species)
- Genus Diglossa – typical flowerpiercers (14 species)
- Genus Diglossopis – blue flowerpiercers (four species)
- Genus Haplospiza (two species), paraphyletic with two species of sierra-finch Phrygilus
- Genus Acanthidops – peg-billed finch
- Genus Phrygilus - sierra finches (11 species)
- Genus Sicalis – yellow finches (12 species), paraphyletic with Phrygilus
- Genus Sporophila – typical seedeaters (some 55 species)
- Genus Oryzoborus (six species)
- Genus Dolospingus – white-naped seedeater
- Genus Charitospiza – coal-crested finch
c) "Yellow-rumped" clade:
- Genus Heterospingus (two species)
- Genus Chrysothlypis (two species)
- Genus Hemithraupis (three species)
- Genus Ramphocelus – silver-billed tanagers (nine species)
- Genus Lanio – shrike-tanagers (four species)
- Genus Eucometis – gray-headed tanager
- Genus Tachyphonus (eight species)
- Genus Trichothraupis – black-goggled tanager
- Genus Stephanophorus – diademed tanager
- Genus Coryphospingus (two species)
- Genus Volatinia – blue-black grassquit
f) The Poospiza clade - a diverse but close-knit group containing both warbler- and finch-like forms:
- Genus Poospiza – warbling-finches (15 species)
- Genus Compsospiza - mountain finches (two species)
- Genus Cnemoscopus – gray-hooded bush tanager
- Genus Hemispingus – hemispinguses (12 species)
- Genus Thlypopsis (six species)
- Genus Pyrrhocoma – chestnut-headed tanager
- Genus Cypsnagra – white-rumped tanager
- Genus Nephelornis – pardusco
g) Grass and pampa-finches, relationships within Thraupidae are uncertain, but together form a well-supported clade:
h) A miscellaneous and likely polyphyletic group of unplaced "tanager-finches" (which may or may not include the species called tanager-finch) whose members when studied will no doubt be relocated to other clades:
- Genus Melanodera (two species)
- Genus Rowettia – Gough Island finch
- Genus Nesospiza (two species)
- Genus Gubernatrix – yellow cardinal
- Genus Idiopsar – short-tailed finch
- Genus Piezorina – cinereous finch
- Genus Xenospingus – slender-billed finch
- Genus Incaspiza – Inca finches (five species)
- Genus Coryphaspiza – black-masked finch
- Genus Rhodospingus – crimson-breasted finch
- Genus Donacospiza – long-tailed reed finch (may be related to Poospiza)
i) Basal forms in group 1:
"Typical" colorful tanagers
a) Tropical canopy tanagers:
- Genus Thraupis - T. abbas & episcopus at least
- Genus Pipraeidea (two species)
- Genus Tangara (about 50 species)
- Genus Geospiza – ground finches (six species)
- Genus Camarhynchus – tree finches (five species)
- Genus Platyspiza - vegetarian finch
- Genus Certhidea – warbler-finches (two species)
- Genus Pinaroloxias – Cocos finch
- Genus Melopyrrha – Cuban bullfinch
- Genus Coereba – bananaquit - formerly placed in its own family Coerebidae
- Genus Tiaris – grassquits (five species) - polyphyletic
- Genus Loxipasser – yellow-shouldered grassquit
- Genus Euneornis – orangequit
- Genus Melanospiza – St. Lucia black finch
- Genus Loxigilla – Antillean bullfinches (three species) - polyphyletic
c) Mountain tanagers:
- Genus Cyanicterus – blue-backed tanager
- Genus Bangsia – (five species)
- Genus Buthraupis – (two species)
- Genus Cnemathraupis – (two species)
- Genus Chlorornis – grass-green tanager
- Genus Wetmorethraupis – orange-throated tanager
- Genus Anisognathus – (five species)
- Genus Dubusia – (two species)
- Genus? Saltator rufiventris - rufous-bellied saltator
d) Typical tanagers:
- Genus Diuca (two species)
- Genus Lophospingus (two species)
- Genus Neothraupis – white-banded tanager
- Genus Cissopis – magpie tanager
- Genus Paroaria (five or six species)
- Genus Schistochlamys (two species)
f) Green and golden-collared honeycreepers:
g) Typical honeycreepers and relatives:
- Genus Tersina – swallow tanager
- Genus Cyanerpes, the typical honeycreepers (four species)
- Genus Pseudodacnis – turquoise dacnis-tanager
- Genus Dacnis, the dacnises (eight species)
h) Basal lineages within group 2:
- Genus Chlorochrysa (three species)
- Genus Parkerthraustes – yellow-shouldered grosbeak (traditionally in Cardinalidae, but biochemical evidence suggests it is a tanager)
- Genus Nemosia – (two species)
- Genus Compsothraupis – scarlet-throated tanager
- Genus Sericossypha – white-capped tanager
- Genus Saltator (16 species; traditionally placed in Cardinalidae, but biochemical evidence suggests they may be tanagers or a sister group)
- Genus Saltatricula – many-colored Chaco finch - traditionally placed in the Emberizidae, but may be related to one of the saltators
Thraupidae incertae sedis
- Genus Mitrospingus (two species)
- Genus Orthogonys – olive-green tanager
- Genus Calochaetes – vermilion tanager
- Genus Catamblyrhynchus – plushcap
- Genus Oreothraupis – tanager finch
- Genus Urothraupis – black-backed bush tanager
- Genus Rhodinocichla – rosy thrush-tanager
- Genus Lamprospiza – red-billed pied tanager
- Genus Phaenicophilus – palm tanagers (two species)
- Genus Xenoligea – white-winged warbler
- Genus Microligea – green-tailed warbler
- Genus Calyptophilus – chat-tanagers (two species)
- Genus Nesospingus – Puerto Rican tanager
- Genus Incaspiza - Inca finches (five species)
Recently split from Thraupidae
Related to Arremonops and other American sparrows in Emberizidae:
- Genus Chlorospingus – bush-tanagers (around 10 species)
- Genus Piranga – northern tanagers (nine species)
- Genus Habia – ant-tanagers or habias (five species)
- Genus Chlorothraupis (three species)
- Genus Amaurospiza (four species; apparently very close to Cyanocompsa)
- Genus Spindalis – spindalises (four species).
- Burns, K.J. et al. (2014) Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution.
- Yuri & Mindell (2002)
- Fjeldså & Rahbek (2006) & Klicka et al. (2007)
- See http://www.museum.lsu.edu/~Remsen/SACCBaseline.html
- Burns et al. (2003) & Klicka et al. (2007)
- See Webster & Webster (1999). If the presence of a free lacrimal bone as found in Haplospiza, Acanthidops, and two of the three Catamenias has any phylogenetic significance then this clade may also include several other "tanager-finches" that share this feature
- Klicka (2007)
- Webster & Webster (1999) & Klicka et al. (2007), probably polyphyletic
- Klicka et al. (2007)
- Clark (1986)
- See Lijtmaer et al. (2004) & Robbins et al. (2005). Polyphyletic. Members of this genus are paraphyletic with various members of Sporophila
- See Robbins et al. (2005). This species is nested within a group containing both Sporophila and Oryzoborus
- Burns et al. (2003)
- (See below: Group 1f)
- Klicka et al. (2007). This species formerly placed near Passerina in the Cardinalidae is related to Phrygilus alaudinus a tanager-finch
- Klicka et al. (2007). This genus is very likely polyphyletic within its clade
- Ridgely & Tudor (1989) p.472
- Klicka et al. (2007). Some members of this genus paraphyletic with respect to certain Tangara
- See Burns et al. (2002) for the circumscription of this group the "domed nest clade" or "Tholospiza".
- See Burns et al. (2002). Exact affinities uncertain but probably sister species to Tiaris olivacea in the "Tholospiza"
- See http://www.museum.lsu.edu/~Remsen/SACCBaseline10.html Apparently close to mountain-tanagers Dubusia and Delothraupis
- See Burns et al. (2003) for close relationship of these species
- See Burns et al. (2003), Klicka et al. (2007) - may be closer to group 1
- Klicka & Spellman (2007)
- See http://www.museum.lsu.edu/~Remsen/SACCBaseline10.html
- Klicka et al. (2007). Apparently closest to Saltator atricollis and this species may require moving to Saltatricula
- See http://www.museum.lsu.edu/~Remsen/SACCBaseline10.html. May be related to the emberizine genus Atlapetes
- See http://www.museum.lsu.edu/~Remsen/SACCBaseline11.html
- Bent, A. Life Histories of Blackbirds, Orioles, Tanagers, and Allies. New York:Dover Publications:1965. 549 p.
- Burns, K. J., S. J. Hackett, and N. K. Klein. 2002. Phylogenetic relationships and morphological diversity in Darwin's finches and their relatives. Evolution 56: 1240-1252.
- Burns, K. J., S. J. Hackett, and N. K. Klein. 2003. Phylogenetic relationships of Neotropical honeycreepers and the evolution of feeding morphology. J. Avian Biology 34: 360-370.
- Clark, G. A., JR. 1986. Systematic interpretations of foot-scute patterns of Neotropical finches. Wilson Bull. 98: 594-597.
- Fjeldså J. and Rahbek C. (2006). Diversification of tanagers, a species rich bird group, largely follows lowlands to montane regions of South America. Integrative and Comparative Biology 46(1):72-81. Download - http://intl-icb.oxfordjournals.org/cgi/reprint/46/1/72.
- Greeney, H. 2005. Nest and eggs of the Yellow-whiskered Bush Tanager in Eastern Ecuador. Ornitologia Neotropical 16: 437- 438.
- Hellmayr, C. E. 1935. Catalogue of birds of the Americas and the adjacent islands in Field Museum of Natural History. Fieldiana Zoology v.13, pt.8. - for "Coerebidae". (Download available at https://archive.org/details/catalogueofbirds138hell)
- Hellmayr, C. E. 1936. Catalogue of birds of the Americas and the adjacent islands in Field Museum of Natural History. Fieldiana Zoology v.13, pt.9. Tersinidae - Thraupidae. (Download available at https://archive.org/details/catalogueofbirds139hell)
- Hellmayr, C. E. 1938. Catalogue of birds of the Americas and the adjacent islands in Field Museum of Natural History. Fieldiana Zoology v.13, pt.11. Ploceidae - Catamblyrhynchidae - Fringillidae. (Download available at https://archive.org/details/catalogueofbirdso1311hell)
- Infonatura. 2005 June. Birds, mammals, and amphibians of Latin America Accessed 2006 March 4.
- Isler M. Isler P. The Tanagers a Natural History, Distribution, and Identification. Washington D.C.: Smithsonian Institution Press: 1987. 404 p.
- Klicka, J., K. Burns, & G. M. Spellman. 2007. Defining a monophyletic Cardinalini: A molecular perspective. Molecular Phylogenetics and Evolution 45: 1014-1032
- Latta, S. 2006. et al. Aves de la República Dominicana y Haití. Princeton University Press.
- Lijtmaer, D. A., N. M. Sharpe, P. L. Tubaro & S. C. Lougheed. 2004. Molecular phylogenetics and diversification of the genus Sporophila (Aves: Passeriformes). Mol. Philo. Evol. 33:562-579.
- Lougheed, S. C., J. R. Freeland, P. Handford, & I. T. Boag. 2000. A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a Neotropical emberizid genus. Molecular Phylogenetics and Evolution 17: 367-378.
- Montereybay. 2000 July. 6-11. Tanagers: Thraupidae Accessed 2006 March 4.
- Naoki, K. 2003. Evolution of Ecological Diversity in the Neotropical Tanagers of the Genus Tangara (Aves: Thraupidae). Dissertation available online, given to Louisiana State University.
- Ridgely, R. S., & G. Tudor. 1989. The Birds of South America, vol. 1. Univ. Texas Press, Austin.
- Robbins, M. B., M. J. Braun, C. J. Huddleston, D. W. Finch, & C. M. Milensky (2005). First Guyana records, natural history, and systematics of the White-winged Seedeater (Dolospingus fringilloides). Ibis 147:334-341.
- Sato, A., C. O'Huigin, F. Figueroa, P. R. Grant, B. R. Grant, H. Tichy, and J. Klein. 1999. Phylogeny of Darwin's finches as revealed by mtDNA sequences. Proc. Nat. Acad. Sci. 96: 5101-5106.
- Webster, J.D. & Webster, J.R. 1999. Skeletons and the genera. of sparrows (Emberizinae). Auk 116: 1054–1074.
- Yuri, T., and D. P. Mindell. 2002. Molecular phylogenetic analysis of Fringillidae, "New World nine-primaried oscines" (Aves: Passeriformes) Mol. Phylogen. Evol. 23:229-243.
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