Literature Review: Whole Genome Comparisons

by Carl Strang

Another hot area of biological research these days is the comparative study of whole genomes, the entire DNA sequences of different species. Birds received a lot of this sort of attention in 2014 publications, but the following notes also include interesting studies of insects and crocodilians.

Zhang, Guojie, et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-1320. They compared whole genomes of 48 species across the range of living species. Of the 37 orders, 34 are represented, the missing ones being some of the ratite groups (only tinamous and ostrich included). The genome is smaller than those of other amniotes, through loss of repetitive sections and large deletions. There are large areas shared by all birds, but plenty of areas where genes vary according to lifestyles, as well as convergences. They looked at vocal learning, which occurs in songbirds, parrots and hummingbirds, and earlier had been shown to have common brain circuits for song learning not present in other birds. Genomes showed convergence in the underlying protein-coding and regulatory genes, absent in birds that don’t learn songs. They also identified genes associated with bird skeletal development, lung structure, and feathers. Teeth were absent in the common ancestor of all modern birds, rather than being lost more than once. Birds have more genes for color vision than mammals, and the ancestral bird is supported as tetrachromatic.

Among the many interesting points from the following study is that falcons like this kestrel are more closely related to parrots than they are to hawks and eagles.

Among the many interesting points from the following study is that falcons like this kestrel are more closely related to parrots than they are to hawks and eagles.

Jarvis, Erich D., et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331. Whole genomes proved problematic in phylogenetic analysis, thanks to convergences in protein coding portions and the jumble of rapid diversification in the early Paleogene. Non-coding sections, however, provided a more consistent picture. Some highlights: Anseriformes (ducks, geese, etc.) plus Galliformes (chickens etc.) are closest (sister) to one another, their combined Galloanseres group separate from “Neoaves” (together with them forming “Neognathae,” separate from Palaeognathae or ratites). Flamingoes and grebes are sister groups, confirming the earlier Field Museum study, with the next-closest local birds the pigeons and doves, all combined into “Columbea” vs. “Passerea” as the divisions of Neoaves. Hummingbirds are sister to swifts, then nightjars. Cranes are sister to shorebirds. Loons are sister to a cluster of water bird orders including pelicans, herons, tube-nosed seabirds, and penguins. New World vultures are sister to eagles and other Accipitriformes. Owls are sister to a cluster of orders with only woodpeckers represented locally. Oscines are sister to suboscines, together to parrots, then falcons. Groups charted as existing by the end of the Mesozoic are Palaeognathae, Galloanseres, Columbea, and Passerea, with nearly all orders in existence by 50 million years ago. The splits more recent than that are those between hummingbirds and swifts (both contained within order Caprimulgiformes), Coraciiformes (including kingfishers) and Piciformes (including woodpeckers), and oscines and suboscines within Passeriformes.

Romanov, Michael N., et al. 2014. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15 (1): 1060 DOI: 10.1186/1471-2164-15-1060  Their portion of the avian whole-genome comparison project found that chickens and turkeys most resemble the computed common ancestor of birds and other dinosaurs.

Mitchell, Kieren J., et al. 2014. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science 344:898-900. They sequenced elephant bird DNA (extinct species from Madagascar) and found, surprisingly, that this was the New Zealand kiwi’s nearest relative. Their study concluded that the ratites (emu, ostrich, rhea, kiwi, etc.) descended from flying ancestors that once were widespread and dispersed easily. After the dinosaurs were gone, the larger ratites were able to fill some large-herbivore niche space and the various groups independently evolved into large flightless forms. That evolutionary window closed as the mammals caught up, except for isolated islands where, for instance, the dodo evolved. Continental drift separated some large flightless ratites geographically, but ancestral flight also contributed as indicated by the New Zealand-Madagascar connection.

Insect flight was fostered by the first forests, which created the 3-dimensional framework that made flight advantageous.

Insect flight was fostered by the first forests, which created the 3-dimensional framework that made flight advantageous.

Misof, B., et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763-767. They did a massive genomic comparison across the insect class, and highlights include indications that insects first appeared 479mya (million years ago, Early Ordovician), coincident with the first land plants. They first developed wings 406mya (Early Devonian; the oldest insect fossils date to 412mya), becoming the first flying animals, at about the same time plants grew larger and began to produce forests, creating a 3D environment in which flight would be especially advantageous. Major lineages of today trace back to the Mississippian (345mya), and the major diversification of insects with complete metamorphic development happened in the Early Cretaceous.

American alligators are genetically very close to the other crocodilians.

American alligators are genetically very close to the other crocodilians.

Green, R.E., et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346 (6215): 1254449 DOI: 10.1126/science.1254449  Whole-genome comparisons found that crocodilians are very similar to one another (93% similarity among species), and have changed very slowly. This slow evolutionary pace, shared with the nearest outgroup of crocodilians + birds, the turtles, indicates that the shared ancestor likewise evolved slowly, and that some time after the split, avian ancestors evolved the capacity for rapid evolution that set the stage for rapid diversification after the other dinosaurs went extinct.

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