(Non)Parallel developmental pathways to vertebrate appendage reduction and loss

This is the pre-peer reviewed version of the following article: (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss , which has been published in final form at https://doi.org/10.1002/ece3.8226. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Appendages have been reduced or lost hundreds of times independently during vertebrate evolution. This suggests that selection routinely favors appendage reduction. How often are the same developmental and genetic pathways used during loss by independent lineages? We reviewed the developmental and evolutionary literatures of appendage reduction in 12 genera spanning fish, reptiles, birds, and mammals. We found that appendage reduction and loss resulted from modified gene expression in each case but one. However, the genes for which expression was modified were rarely shared. Our findings suggest that adaptive loss of complex traits might proceed relatively easily through changes in gene expression along multiple developmental pathways.

Evolutionary history of the vertebrate Piwi gene family

PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.

(Non)Parallel developmental pathways to vertebrate appenda

This is the pre-peer reviewed version of the following article: (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss , which has been published in final form at https://doi.org/10.1002/ece3.8226. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Appendages have been reduced or lost hundreds of times independently during vertebrate evolution. This suggests that selection routinely favors appendage reduction. How often are the same developmental and genetic pathways used during loss by independent lineages? We reviewed the developmental and evolutionary literatures of appendage reduction in 12 genera spanning fish, reptiles, birds, and mammals. We found that appendage reduction and loss resulted from modified gene expression in each case but one. However, the genes for which expression was modified were rarely shared. Our findings suggest that adaptive loss of complex traits might proceed relatively easily through changes in gene expression along multiple developmental pathways.

Developing Inside a Layer of Germs—A Potential Role for Multiciliated Surface Cells in Vertebrate Embryos

This paper reviews current research on the microbial life that surrounds vertebrate embryos. Several clades are believed to develop inside sterile—or near-sterile—embryonic microhabitats, while others thrive within a veritable zoo of microbial life. The occurrence of embryo-associated microbes in some groups, but not others, is an under-appreciated transition (possibly transitions) in vertebrate evolution. A lack of comparable studies makes it currently impossible to correlate embryo-associated microbiomes with other aspects of vertebrate evolution. However, there are embryonic features that should instruct a more targeted survey. This paper concludes with a hypothesis for the role of multiciliated surface cells in amphibian and some fish embryos, which may contribute to managing embryo-associated microbial consortia. These cells are known to exist in some species that harbor in ovo microbes or have relatively porous egg capsules, although most have not been assayed for embryo-associated microbiota. Whether the currents generated within these extraembryonic microhabitats contribute to culturing consistent microbial communities remains to be seen.

Multiple evolutionary origins and losses of tooth complexity in squamates

Teeth act as tools for acquiring and processing food, thus holding a prominent role in vertebrate evolution. In mammals, dental-dietary adaptations rely on tooth complexity variations controlled by cusp number and pattern. Complexity increase through cusp addition has dominated the diversification of mammals. However, studies of Mammalia alone cannot reveal patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, multiple-cusped teeth evolved over 20 times independently from a single-cusped common ancestor. Squamates frequently lost cusps and evolved varied multiple-cusped morphologies at heterogeneous rates. Tooth complexity evolved in correlation with changes in plant consumption, resulting in several major increases in speciation. Complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental-dietary evolution.

Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.