@article{wiegmann_trautwein_winkler_barr_kim_lambkin_bertone_cassel_bayless_heimberg_et al._2011, title={Episodic radiations in the fly tree of life}, volume={108}, number={14}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Wiegmann, B. M. and Trautwein, M. D. and Winkler, I. S. and Barr, N. B. and Kim, J. W. and Lambkin, C. and Bertone, M. A. and Cassel, B. K. and Bayless, K. M. and Heimberg, A. M. and et al.}, year={2011}, pages={5690–5695} }
 @article{chapman_kirkness_simakov_hampson_mitros_weinmaier_rattei_balasubramanian_borman_busam_et al._2010, title={The dynamic genome of Hydra}, volume={464}, number={7288}, journal={Nature}, author={Chapman, J. A. and Kirkness, E. F. and Simakov, O. and Hampson, S. E. and Mitros, T. and Weinmaier, T. and Rattei, T. and Balasubramanian, P. G. and Borman, J. and Busam, D. and et al.}, year={2010}, pages={592–596} }
 @article{sperling_vinther_moy_wheeler_semon_briggs_peterson_2009, title={MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record}, volume={276}, number={1677}, journal={Proceedings of the Royal Society of London. Series B}, author={Sperling, E. A. and Vinther, J. and Moy, V. N. and Wheeler, B. M. and Semon, M. and Briggs, D. E. G. and Peterson, K. J.}, year={2009}, pages={4315–4322} }
 @article{wheeler_heimberg_moy_sperling_holstein_heber_peterson_2009, title={The deep evolution of metazoan microRNAs}, volume={11}, ISSN={["1525-142X"]}, DOI={10.1111/j.1525-142X.2008.00302.x}, abstractNote={SUMMARYmicroRNAs (miRNAs) are approximately 22‐nucleotide noncoding RNA regulatory genes that are key players in cellular differentiation and homeostasis. They might also play important roles in shaping metazoan macroevolution. Previous studies have shown that miRNAs are continuously being added to metazoan genomes through time, and, once integrated into gene regulatory networks, show only rare mutations within the primary sequence of the mature gene product and are only rarely secondarily lost. However, because the conclusions from these studies were largely based on phylogenetic conservation of miRNAs between model systems likeDrosophilaand the taxon of interest, it was unclear if these trends would describe most miRNAs in most metazoan taxa. Here, we describe the shared complement of miRNAs among 18 animal species using a combination of 454 sequencing of small RNA libraries with genomic searches. We show that the evolutionary trends elucidated from the model systems are generally true for all miRNA families and metazoan taxa explored: the continuous addition of miRNA families with only rare substitutions to the mature sequence, and only rare instances of secondary loss. Despite this conservation, we document evolutionary stable shifts to the determination of position 1 of the mature sequence, a phenomenon we call seed shifting, as well as the ability to post‐transcriptionally edit the 5′ end of the mature read, changing the identity of the seed sequence and possibly the repertoire of downstream targets. Finally, we describe a novel type of miRNA in demosponges that, although shows a different pre‐miRNA structure, still shows remarkable conservation of the mature sequence in the two sponge species analyzed. We propose that miRNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation.}, number={1}, journal={EVOLUTION & DEVELOPMENT}, author={Wheeler, Benjamin M. and Heimberg, Alysha M. and Moy, Vanessa N. and Sperling, Erik A. and Holstein, Thomas W. and Heber, Steffen and Peterson, Kevin J.}, year={2009}, pages={50–68} }