Transcriptomic insights into the genetic basis of mammalian limb diversity

Abstract

BackgroundFrom bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species.ResultsWe assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species.ConclusionsTaken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.

Timing the developmental origins of mammalian limb diversity

“…This is of note, as BAR116 is located near the Hoxd cluster, and, as described above, Hoxd genes have been shown to be differentially expressed in bat wings (Booker et al, 2016;Chen et al, 2005;Eckalbar et al, 2016;Maier et al, 2017;Wang et al, 2014). Future research in this area has the potential to tease apart the genomic basis of morphological innovation and evolution in bats and, more broadly, in mammals.…”

“…This hypothesis is supported by data from numerous sources including candidate gene studies, transcriptomic analyses, morphometric quantifications of developing and adult limbs, and cellular assays (e.g., Cooper et al, 2014;Maier et al, 2017;Ross et al, 2013;Sears et al, 2015;Thewissen et al, 2006). This hypothesis is supported by data from numerous sources including candidate gene studies, transcriptomic analyses, morphometric quantifications of developing and adult limbs, and cellular assays (e.g., Cooper et al, 2014;Maier et al, 2017;Ross et al, 2013;Sears et al, 2015;Thewissen et al, 2006).…”

“…Results of these studies suggested that the effective sizes of the two major signaling centers of the limb, the AER (assayed via Fgf signaling) and zone of polarizing activity (ZPA; assayed via Shh signaling) are larger in the bat forelimb (i.e., wing) than in the bat hind limb or in the forelimbs of nonvolant species such as mice (Cretekos et al, 2007;Cooper, Cretekos, & Sears, 2012;Hockman et al, 2008). Additional in situ hybridization (ISH) assays revealed that the expression patterns of several Hox genes important to limb patterning, including Hoxa13, Hoxd12, and Hoxd13, also differ in bat forelimbs relative to bat hind limbs and/ or mouse forelimbs (Chen, Cretekos, Rasweiler, & Behringer, 2005;Maier et al, 2017). Researchers have suggested that the enlarged signaling centers and second wave of Shh signaling help generate the larger size of the bat forelimb.…”

“…), Fgf8, and Shh in bat fore-and hind limbs (Eckalbar et al, 2016;Maier et al, 2017;Wang et al, 2014), and of Bmp's and associated genes in developing bat digits of differing lengths (Eckalbar et al, 2016;Maier et al, 2017;Wang et al, 2010). These assays largely support the results of previous candidate gene approaches.…”

“…In these studies, they compared the transcriptomes of bat, mouse, pig, and opossum limbs at the ridge, bud, and paddle stages of development (Maier et al, 2017;Sears et al, 2015). exist for the developmental evolution of mammalian limbs.…”