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Special section on bird genomes in Science (1 Viewer)

Fred Ruhe

Well-known member
Netherlands
The new issue of Science has a special section on a new study of avian and crocodile genomes and relates to many vert-paleo topics.

http://www.sciencemag.org/content/current

Particular papers of interest:

Xing Xu, Zhonghe Zhou, Robert Dudley, Susan Mackem, Cheng-Ming Chuong, Gregory M. Erickson, and David J. Varricchio (2014) An integrative approach to understanding bird origins.
Science 346 (6215): 1253293
DOI: 10.1126/science.1253293
http://www.sciencemag.org/content/346/6215/1253293.abstract

Background
The origin of birds is one of the most enduring and dramatic evolutionary debates. The hypothesis that the primarily small-sized birds are nested within a theropod dinosaur group that includes the gigantic Tyrannosaurus rex has been supported by strong fossil evidence, but until recently, several important issues remained unresolved, including the origins of feathers and flight, the “temporal paradox” (the coelurosaurian theropods occur too late in the fossil record to be ancestral to the Jurassic bird Archaeopteryx), and supposed homological incongruities (e.g., the suggested homologies of three fingers in tetanuran theropods are different from those of living birds). Recent discoveries of spectacular dinosaur fossils from China and elsewhere provide new information to address these issues, and also prompt numerous studies in disciplines other than paleontology that help explain how bird characteristics originated and evolved.

Graphic
Evolutionary history of selected bird features inferred from multidisciplinary data. Recent studies demonstrate that major bird characteristics have evolved in a sequential way, and many of them initiated transformation early in dinosaur evolution, with some approaching modern conditions well before the origin of birds, whereas others appear only near the origin of the crown group birds.

Advances
The discoveries of feathered dinosaur fossils from the Jurassic and Cretaceous sediments of China and elsewhere document a diverse range of feathers from monofilamentous feathers to highly complex flight feathers, which show a general evolutionary trend of increasing complexity leading to the cladogenesis of birds. The wide occurrence of foot feathers in Mesozoic theropods (i.e., short filamentous forms in relatively basal theropods and large vaned forms in derived theropods, including early birds) clarifies feather-scale relations and integumentary evolution pertinent to flight origins and also shows that bird flight likely had evolved through a four-winged stage. With numerous discoveries of well-preserved dinosaur fossils covering a wide range of geological periods, the morphological, functional, and temporal transition from ground-living to flight-capable theropod dinosaurs is now one of the best-documented major evolutionary transitions. Meanwhile, studies in disciplines other than paleontology provide new insights into how bird characteristics originated and evolved—such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and an unusual pulmonary system. The iconic features of extant birds, for the most part, evolved in a gradual and stepwise fashion throughout theropod evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree.
Research into bird origins provides a model example of how an integration of paleontological and neontological data can be used to gain a comprehensive understanding of the complexity surrounding major evolutionary transitions and to set new research directions.

Outlook
A refined, more robust phylogeny will be imperative to move our studies forward. A larger data set will help to increase the accuracy of phylogenetic reconstructions, but better character formulation and more accurate scorings are imperative at the current stage. In terms of character evolution, an integrative approach combining paleontological, neontological, developmental, temporal, and even paleoenvironmental data is particularly desirable. Greater examination of fossils pertaining to molecular information is also a potentially fruitful avenue for future investigation. Evolutionary scenarios for various aspects of the origin of birds have sometimes been constructed from neontological data, but any historical reconstruction must ultimately be tested using the fossil record. Consequently, dense fossil sampling along the line to modern birds and better understanding of transitional forms play key roles in such reconstructions.


Robert W. Meredith, Guojie Zhang, M. Thomas P. Gilbert, Erich D.
Jarvis, and Mark S. Springer (2014)
Evidence for a single loss of mineralized teeth in the common avian ancestor.
Science 346 (6215): 1254390
DOI: 10.1126/science.1254390
http://www.sciencemag.org/content/346/6215/1254390.abstract

The absence of teeth or edentulism has evolved on multiple occasions within vertebrates, including birds, turtles, and a few groups of mammals (anteaters, baleen whales, and pangolins). There are also mammals with enamelless teeth (aardvarks, sloths, and armadillos). All toothless/enamelless vertebrates are descended from ancestors with enamel-capped teeth. In the case of birds, it is theropod dinosaurs.
Instead of teeth, modern birds use a horny beak (rhamphotheca) and part of their digestive tract (muscular gizzard) to grind up and process food. The fossil record of early birds is fragmentary, and it is unclear whether tooth loss evolved in the common ancestor of all modern birds or convergently in two or more independent lineages.

INTRODUCTION
The absence of teeth or edentulism has evolved on multiple occasions within vertebrates, including birds, turtles, and a few groups of mammals (anteaters, baleen whales, and pangolins). There are also mammals with enamelless teeth (aardvarks, sloths, and armadillos). All toothless/enamelless vertebrates are descended from ancestors with enamel-capped teeth. In the case of birds, it is theropod dinosaurs.
Instead of teeth, modern birds use a horny beak (rhamphotheca) and part of their digestive tract (muscular gizzard) to grind up and process food. The fossil record of early birds is fragmentary, and it is unclear whether tooth loss evolved in the common ancestor of all modern birds or convergently in two or more independent lineages.

Graphic
Observed shared inactivating mutations in tooth formation. Related genes were mapped onto a time tree depicting evolutionary relationships and times of divergence between modern birds, the closely related extinct taxon Ichthyornis, and the American alligator.
The hypothesized loss of mineralized teeth on the modern bird branch at 116 million years ago (Ma) is based on frameshift mutation rates.
Observed shared inactivating mutations in tooth formation. Related genes were mapped onto a time tree depicting evolutionary relationships and times of divergence between modern birds, the closely related extinct taxon Ichthyornis, and the American alligator.
The hypothesized loss of mineralized teeth on the modern bird branch at 116 million years ago (Ma) is based on frameshift mutation rates.

RATIONALE
Tooth formation in vertebrates is a complicated process that involves many different genes. Of these genes, six are essential for the proper formation of dentin (DSPP) and enamel (AMTN, AMBN, ENAM, AMELX, and MMP20). We examined these six genes in the genomes of 48 bird species, which represent nearly all living bird orders, as well as the American alligator, a representative of Crocodylia (the closest living relatives of birds), for the presence of inactivating mutations that are shared by all 48 birds. The presence of such shared mutations in dentin and enamel-related genes would suggest a single loss of mineralized teeth in the common ancestor of all living birds. We also queried the genomes of additional toothless/enamelless vertebrates, including three turtles and four mammals, for inactivating mutations in these genes. For comparison, we looked at the genomes of mammalian taxa with enamel-capped teeth.

RESULTS
All edentulous vertebrate genomes that were examined are characterized by inactivating mutations in DSPP, AMBN, AMELX, AMTN, ENAM, and MMP20, rendering these genes nonfunctional. The dentin-related gene DSPP is functional in vertebrates with enamelless teeth (sloth, aardvark, and armadillo). All six genes are functional in the American alligator and mammalian taxa with enamel-capped teeth. More important, 48 bird species share inactivating mutations in both dentin-related (DSPP) and enamel-related genes (ENAM, AMELX, AMTN, and MMP20), indicating that the genetic machinery necessary for tooth formation was lost in the common ancestor of all modern birds. Furthermore, the frameshift mutation rate in birds suggests that the outer enamel covering of teeth was lost about 116 million years ago.

CONCLUSIONS
We postulate, on the basis of fossil and molecular evidence, a two-step scenario whereby tooth loss and beak development evolved together in the common ancestor of all modern birds. In the first stage, tooth loss and partial beak development commenced on the anterior portion of both the upper and lower jaws. The second stage involved concurrent progression of tooth loss and beak development from the anterior portion of both jaws to the back of the rostrum. We propose that this progression ultimately resulted in a complete horny beak that effectively replaced the teeth and may have contributed to the diversification of living birds.


Richard E. Green, Edward L. Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W. Vandewege, John A. St. John, Salvador Capella-Gutiérrez, Todd A. Castoe, Colin Kern, Matthew K. Fujita, Juan C. Opazo, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Robert M.
Hubley, Arian F. Smit, Roy N. Platt, Christine A. Lavoie, Meganathan P. Ramakodi, John W. Finger Jr., Alexander Suh, Sally R. Isberg, Lee Miles, Amanda Y. Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C. Burgess, Scott V. Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T. Howard, Cathy R. Gresham, Daniel G. Peterson, Jürgen Schmitz, David D. Pollock, David Haussler, Eric W. Triplett, Guojie Zhang, Naoki Irie, Erich D. Jarvis, Christopher A. Brochu, Carl J. Schmidt, Fiona M. McCarthy, Brant C. Faircloth, Federico G. Hoffmann, Travis C.
Glenn, Toni Gabaldón, Benedict Paten, and David A. Ray (2014)

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
Science 346 (6215): 1254449
DOI: 10.1126/science.1254449
http://www.sciencemag.org/content/346/6215/1254449.abstract

INTRODUCTION
Crocodilians and birds are the two extant clades of archosaurs, a group that includes the extinct dinosaurs and pterosaurs. Fossils suggest that living crocodilians (alligators, crocodiles, and
gharials) have a most recent common ancestor 80 to 100 million years ago. Extant crocodilians are notable for their distinct morphology, limited intraspecific variation, and slow karyotype evolution. Despite their unique biology and phylogenetic position, little is known about genome evolution within crocodilians.

Graphic
Evolutionary rates of tetrapods inferred from DNA sequences anchored by ultraconserved elements. Evolutionary rates among reptiles vary, with especially low rates among extant crocodilians but high rates among squamates. We have reconstructed the genomes of the common ancestor of birds and of all archosaurs (shown in gray silhouette, although the morphology of these species is uncertain).

RATIONALE
Genome sequences for the American alligator, saltwater crocodile, and Indian gharial—representatives of all three extant crocodilian families—were obtained to facilitate better understanding of the unique biology of this group and provide a context for studying avian genome evolution. Sequence data from these three crocodilians and birds also allow reconstruction of the ancestral archosaurian genome.

RESULTS
We sequenced shotgun genomic libraries from each species and used a variety of assembly strategies to obtain draft genomes for these three crocodilians. The assembled scaffold N50 was highest for the alligator
(508 kilobases). Using a panel of reptile genome sequences, we generated phylogenies that confirm the sister relationship between crocodiles and gharials, the relationship with birds as members of extant Archosauria, and the outgroup status of turtles relative to birds and crocodilians.

We also estimated evolutionary rates along branches of the tetrapod phylogeny using two approaches: ultraconserved element–anchored sequences and fourfold degenerate sites within stringently filtered orthologous gene alignments. Both analyses indicate that the rates of base substitution along the crocodilian and turtle lineages are extremely low. Supporting observations were made for transposable element content and for gene family evolution. Analysis of whole-genome alignments across a panel of reptiles and mammals showed that the rate of accumulation of micro-insertions and microdeletions is proportionally lower in crocodilians, consistent with a single underlying cause of a reduced rate of evolutionary change rather than intrinsic differences in base repair machinery. We hypothesize that this single cause may be a consistently longer generation time over the evolutionary history of Crocodylia.

Low heterozygosity was observed in each genome, consistent with previous analyses, including the Chinese alligator. Pairwise sequential Markov chain analysis of regional heterozygosity indicates that during glacial cycles of the Pleistocene, each species suffered reductions in effective population size. The reduction was especially strong for the American alligator, whose current range extends farthest into regions of temperate climates.

CONCLUSION
We used crocodilian, avian, and outgroup genomes to reconstruct 584 megabases of the archosaurian common ancestor genome and the genomes of key ancestral nodes. The estimated accuracy of the archosaurian genome reconstruction is 91% and is higher for conserved regions such as genes. The reconstructed genome can be improved by adding more crocodilian and avian genome assemblies and may provide a unique window to the genomes of extinct organisms such as dinosaurs and pterosaurs.


Guojie Zhang, Cai Li, Qiye Li, Bo Li, Denis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou, Zhiyong Huang, Na An, Jie Wang, Qiumei Zheng, Yingqi Xiong, Guangbiao Wang, Bo Wang, Jingjing Wang, Yu Fan, Rute R. da Fonseca, Alonzo Alfaro-Núñez, Mikkel Schubert, Ludovic Orlando, Tobias Mourier, Jason T. Howard, Ganeshkumar Ganapathy, Andreas Pfenning, Osceola Whitney, Miriam V. Rivas, Erina Hara, Julia Smith, Marta Farré, Jitendra Narayan, Gancho Slavov, Michael N Romanov, Rui Borges, João Paulo Machado, Imran Khan, Mark S. Springer, John Gatesy, Federico G.
Hoffmann, Juan C. Opazo, Olle Håstad, Roger H. Sawyer, Heebal Kim, Kyu-Won Kim, Hyeon Jeong Kim, Seoae Cho, Ning Li, Yinhua Huang, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Mads F. Bertelsen, Elizabeth Derryberry, Wesley Warren, Richard K Wilson, Shengbin Li, David A. Ray, Richard E. Green, Stephen J. O’Brien, Darren Griffin, Warren E. Johnson, David Haussler, Oliver A. Ryder, Eske Willerslev, Gary R. Graves, Per Alström, Jon Fjeldså, David P. Mindell, Scott V.
Edwards, Edward L. Braun, Carsten Rahbek, David W. Burt, Peter Houde, Yong Zhang, Huanming Yang, Jian Wang, Avian Genome Consortium, Erich D. Jarvis, M. Thomas P. Gilbert, and Jun Wang (2014)

Comparative genomics reveals insights into avian genome evolution and adaptation.
Science 346 (6215): 1311-1320
DOI: 10.1126/science.1251385
http://www.sciencemag.org/content/346/6215/1311.abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.


Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T.
Howard, Alexander Suh, Claudia C. Weber, Rute R. da Fonseca, Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, Ganesh Ganapathy, Bastien Boussau, Md. Shamsuzzoha Bayzid, Volodymyr Zavidovych, Sankar Subramanian, Toni Gabaldón, Salvador Capella-Gutiérrez, Jaime Huerta-Cepas, Bhanu Rekepalli, Kasper Munch, Mikkel Schierup, Bent Lindow, Wesley C. Warren, David Ray, Richard E.
Green, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Shengbin Li, Ning Li, Yinhua Huang, Elizabeth P. Derryberry, Mads Frost Bertelsen, Frederick H. Sheldon, Robb T. Brumfield, Claudio V. Mello, Peter V.
Lovell, Morgan Wirthlin, Maria Paula Cruz Schneider, Francisco Prosdocimi, José Alfredo Samaniego, Amhed Missael Vargas Velazquez, Alonzo Alfaro-Núñez, Paula F. Campos, Bent Petersen, Thomas Sicheritz-Ponten, An Pas, Tom Bailey, Paul Scofield, Michael Bunce, David M. Lambert, Qi Zhou, Polina Perelman, Amy C. Driskell, Beth Shapiro, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Qiuemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnea Smeds, Frank E. Rheindt, Michael Braun, Jon Fjeldsa, Ludovic Orlando, F. Keith Barker, Knud Andreas Jønsson, Warren Johnson, Klaus-Peter Koepfli, Stephen O’Brien, David Haussler, Oliver A. Ryder, Carsten Rahbek, Eske Willerslev, Gary R.
Graves, Travis C. Glenn, John McCormack, Dave Burt, Hans Ellegren, Per Alström, Scott V. Edwards, Alexandros Stamatakis, David P. Mindell, Joel Cracraft, Edward L. Braun, Tandy Warnow, Wang Jun, M. Thomas P.
Gilbert, and Guojie Zhang (2014)

Whole-genome analyses resolve early branches in the tree of life of modern birds.
Science 346 (6215): 1320-1331
DOI: 10.1126/science.1253451
http://www.sciencemag.org/content/346/6215/1320.abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.


Elizabeth Pennisi (2014)
Bird genomes give new perches to old friends.
Comparing genomes clarifies family relations and pinpoints genes for song learning.
Science 346 (6215): 1275-1276
DOI: 10.1126/science.346.6215.1275
http://www.sciencemag.org/content/346/6215/1275.summary

The placement of a strange South American bird called the hoatzin in the avian family tree is one of the many findings revealed this week from a massive international project analyzing the sequenced genomes of 48 bird species representing nearly every order of bird. The effort, involving 200 people from 80 labs and weeks of supercomputer time, has yielded the most definitive avian family tree yet. It has also pinpointed gene networks underlying the traits that make birds birds, such as feathers and beaks instead of teeth. In one provocative finding, a team has identified the gene network that underlies complex singing in birds—and found that the same network operates in humans, where it is presumably crucial to language. Already, 200 more bird genomes have been sequenced, with more waiting in the wings.


News stories:

http://news.ucsc.edu/2014/12/crocodile-genomes.html

http://phys.org/news/2014-12-penguin-genomes.html

http://www.washingtonpost.com/news/.../we-finally-know-when-birds-lost-their-teeth/

http://www.washingtonpost.com/news/...-bird-genomes-unlocking-their-dinosaur-pasts/

http://www.latimes.com/science/scie...mes-bird-evolution-20141210-story.html#page=1


Enjoy,

Fred
 

Richard Klim

-------------------------
Nadachowska-Brzyska et al 2015

Nadachowska-Brzyska, Li, Smeds, Zhang & Ellegren 2015. Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Curr Biol 25(10): 1375–1380. [article & pdf]

Toews 2015. Evolution: a genomic guide to bird population history. Curr Biol 25(11): R465–R467. [pdf]
 

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