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Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq:Apalone spinifera(ZZ/ZW, 2n= 66) andStaurotypus triporcatus(XX/XY, 2n= 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling inApalone(Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions inStaurotypus(Kinosternidae) andTrachemys scripta(Emydidae). Furthermore, we identified a chromosome folding pattern that enables “centromere–telomere interactions” previously undetected in turtles. The combined turtle pattern of “centromere–telomere interactions” (discovered here) plus “centromere clustering” (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome. 

Abstract To promote survival and fitness, organisms use a suite of physiological systems to respond to both predictable and unpredictable changes in the environment. These physiological responses are also influenced by changes in life history state. The continued activation of physiological systems stemming from persistent environmental perturbations enable animals to cope with these challenges but may over time lead to significant effects on the health of wildlife. In the present study, we tested how varying environmental perturbations driven by tourism and associated supplemental feeding affects the energetics, corticosterone and immunity of six discrete populations of the northern Bahamian rock iguana (Cyclura cychlura inornata and Cyclura cychlura figginsi). We studied populations within and outside the reproductive season and quantified tourist numbers during sample collection. Specifically, we measured clutch size, body condition, plasma energy metabolites, reactive oxygen species, baseline corticosterone concentrations and immune function of male and female iguanas from each population to address whether (i) disparate physiologies are emerging across a gradient of tourism and feeding, (ii) both subspecies respond similarly and (iii) responses vary with season/reproductive condition. We found significant effects of tourism level, season and their interaction on the physiology of both C. c. inornata and C. c. figginsi, supporting the idea that tourism is leading to the divergence of phenotypes. Specifically, we found elevated plasma energy metabolites, oxidative stress and a measure of innate immunity (bactericidal ability), but reduced corticosterone concentrations with increasing tourism in both subspecies of rock iguanas. These physiological metrics differ according to the level of tourism in both subspecies and persist across seasons despite variation with natural seasonal and reproductive changes. These findings suggest that anthropogenic disturbance results in disparate physiologies in northern Bahamian rock iguanas. 

ABSTRACT There is great interspecific variation in the nutritional composition of natural diets, and the varied nutritional content is physiologically tolerated because of evolutionarily based balances between diet composition and processing ability. However, as a result of landscape change and human exposure, unnatural diets are becoming widespread among wildlife without the necessary time for evolutionary matching between the diet and its processing. We tested how a controlled, unnatural high glucose diet affects glucose tolerance using captive green iguanas, and we performed similar glucose tolerance tests on wild Northern Bahamian rock iguanas that are either frequently fed grapes by tourists or experience no such supplementation. We evaluated both short and longer-term blood glucose responses and corticosterone (CORT) concentrations as changes have been associated with altered diets. Experimental glucose supplementation in the laboratory and tourist feeding in the wild both significantly affected glucose metabolism. When iguanas received a glucose-rich diet, we found greater acute increases in blood glucose following a glucose challenge. Relative to unfed iguanas, tourist-fed iguanas had significantly lower baseline CORT, higher baseline blood glucose, and slower returns to baseline glucose levels following a glucose challenge. Therefore, unnatural consumption of high amounts of glucose alters glucose metabolism in laboratory iguanas with short-term glucose treatment and free-living iguanas exposed to long-term feeding by tourists. Based on these results and the increasing prevalence of anthropogenically altered wildlife diets, the consequences of dietary changes on glucose metabolism should be further investigated across species, as such changes in glucose metabolism have health consequences in humans (e.g. diabetes).