Gene network variation and alternative paths to convergent evolution in turtles

Abstract

Diversification of the turtle's shell comprises remarkable phenotypic transformations. For instance, two divergent species convergently evolved shell-closing systems with shoulder blade (scapula) segments that enable coordinated movements with the shell. We expected these unusual structures to originate via similar changes in underlying gene networks, as skeletal segment formation is an evolutionarily conserved developmental process. We tested this hypothesis by comparing transcriptomes of scapula tissue across three stages of embryonic development in three emydid turtles from natural populations. We found that alternative strategies for skeletal segmentation were associated with interspecific differences in gene co-expression networks. Notably, mesenchyme homeobox 2 (MEOX2) and HOXA3-5 were central hubs driving the activity of 2,806 genes in a candidate network for scapula segmentation, albeit in only one species. Even so, scapula muscle overgrowth corresponded to the activity of similar myogenic networks in both species. This and other derived developmental processes were not observed in the third species, which displayed the ancestral (unsegmented) scapula condition. Differential gene expression tests against this reference lineage supported histological and network analyses. Our findings illustrate that molecular underpinnings of convergent evolution, including during the diversification of the atypical turtle "body plan," are influenced by variation in underlying developmental processes.

Delayed trait development and the convergent evolution of shell kinesis in turtles

“…Early shell development in kinetic-shelled turtles does not appear to differ from akinetic turtles [11,19], congruent with our analyses on hatchling shell tissue. However, the fibrous plastral hinge that enables shell kinesis develops gradually [46 -48].…”

“…Indeed, major advances in formulating a theoretical framework for the study of convergent evolution were achieved in recent years [5,6]. However, hypotheses targeting the role of developmental processes are rarely addressed (but see [7][8][9][10][11]).…”

Transcriptomic similarities and differences between the limb bud AER and unique carapacial ridge of turtle embryos

“…Read counts per gene were calculated using the featureCounts package of R Bioconductor (Liao, Smyth, & Shi, 2014). Overall mapping rates were 88%-90% and rates of unambiguously assigned reads per library were 53%-60%, similar to previous studies on C. picta (Cordero, Liu, et al, 2018;Radhakrishnan, Literman, Neuwald, Severin, & Valenzuela, 2017).…”

The postembryonic transformation of the shell in emydine box turtles

“…Such a narrow window over which evolutionary morphological change may originate often favors the production of certain phenotypic variants over others, that is, developmental biases (Arthur, ; Maynard Smith et al, ). Turtles are rather unusual as developmental interactions of the shell and limb girdles likely limit skeletal trait diversification, particularly during the late stages of embryonic development when the shell has formed and interspecific differences are generally expected to emerge (Cordero & Quinteros, ; Cordero et al, ). Still, adaptive shell diversification is feasible via heterochronic shifts in bone ossification centers coupled with disproportionate size and shape changes (allometry) during juvenile life stages (Cordero et al, ; Kordikova, , ; Pritchard, ; Salmon, Coppenrath, & Higgins, ).…”

“…Active plastral kinesis is enabled by modified muscle connections and articulations of the limb girdles, as defined by Pritchard (), is the most common type of shell kinesis in living turtles and it is readily recognizable by the presence of a flexible hinge joint that enables elevation of part of the plastron in response to potential predators (Agassiz, ; Bramble, ; Pritchard, , ). Neck and limb girdle musculoskeletal specializations, which begin to develop in embryos, act as biomechanical linkages that power kinesis as turtles grows (Bramble, ; Cordero & Quinteros, ; Cordero et al, ). Consequently, the kinetic plastral hinge develops gradually in juveniles (Cordero et al, ; Legler, ; Richmond, ).…”