Mutations that provide environment-dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates achieved through symmetric or asymmetric mutation processes and are abundant in both coding and non-coding regions in positions that could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from five closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5′UTRs and coding regions compared to 3′UTRs and non-coding transcripts among Helianthus spp. Furthermore, allele frequency differences measured by pairwise F_ST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.

Cyclura carinata, a Bahamian rock iguana, currently has two recognized subspecies. Cyclura c. carinata is found on numerous islands and cays throughout the Turks and Caicos Islands. The second subspecies, C. c. bartschi, is now only known to exist on Booby Cay, a small island off of Mayaguana Island, Bahamas, which is also within the subspecies historic range. Support for subspecific status is weak. Geographic isolation appears to be the only strong indicator of genetic isolation. Recent conservation attempts made on the species behalf have raised questions regarding the validity of subspecific designations. We used mtDNA sequence data to ask whether there is any genetic variation that distinguishes C. c. bartschi from ten sampled populations of C. c. carinata. Our findings show that the Booby Cay population is fixed for a common mtDNA haplotype found in Caicos Island populations of C. carinata. In contrast, four different haplotypes were found among populations designated C. c. carinata. We conclude that there is insufficient evidence to support C. c. bartshi as a subspecies and recommend that the Booby Cay population be included in ongoing conservation efforts currently focused on the Turks and Caicos Islands.

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura, restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the 2 currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than 2. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

Cyclura ricordii is an endemic iguana from Hispaniola Island and is threatened on the IUCN Red List. The main threats are predation by introduced mammals, habitat destruction, and hunting pressure. The present study focused on two nesting sites from Pedernales Province in the Dominican Republic. The hypothesis that natal philopatry influences dispersal and nest‐site selection was tested. Monitoring and sampling took place in 2012 and 2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley's K revealed that nests were significantly clustered at multiple scales, when both nesting sites were considered and within each nesting site. This suggests a patchy, nonrandom distribution of nests within nest sites. Hierarchical AMOVA revealed that nest‐site aggregations did not explain a significant portion of genetic variation within nesting sites. However, a small but positive correlation between geographic and genetic distance was detected using a Mantel's test. Hence, the relationship between geographic distance and genetic distance among hatchlings within nest sites, while detectable, was not strong enough to have a marked effect on fine‐scale genetic structure. Spatial and genetic data combined determined that the nesting sites included nesting females from multiple locations, and the hypothesis of “natal philopatry” was not supported because females nesting in the same cluster were no more closely related to each other than to other females from the same nesting site. These findings imply that nesting aggregations are more likely associated with cryptic habitat variables contributing to optimal nesting conditions.

Short tandem repeat (STR) variation is rarely explored as a contributor to adaptive evolution. An intriguing mechanism involving STRs suggests that STRs function as “tuning knobs” of adaptation whereby stepwise changes in STR allele length have stepwise effects on phenotypes. Previously, we tested the predictions of the “tuning knob” model at the gene expression level by conducting an RNA-Seq experiment on natural populations of common sunflower (Helianthus annuus L.) transecting a well-defined cline from Kansas to Oklahoma. We identified 479 STRs with significant allele length effects on gene expression (eSTRs). In this study, we expanded the range to populations further north and south of the focal populations and used a targeted approach to study the relationship between STR allele length and gene expression in five selected eSTRs. Seeds from 96 individuals from six natural populations of sunflower from Nebraska and Texas were grown in a common garden. The individuals were genotyped at the five eSTRs, and gene expression was quantified with qRT-PCR. Linear regression models identified that eSTR length in comp26672 was significantly correlated with gene expression. Further, the length of comp26672 eSTR was significantly correlated with latitude across the range from Nebraska to Texas. The eSTR locus comp26672 was located in the CHUP1 gene, a gene associated with chloroplast movement in response to light intensity, which suggests a potential adaptive role for the eSTR locus. Collectively, our results from this targeted study show a consistent relationship between allele length and gene expression in some eSTRs across a broad geographical range in sunflower and suggest that some eSTRs may contribute to adaptive traits in common sunflower.