• Population substructure and signals of divergent adaptive selection despite admixture in the sponge Dendrilla antarctica from shallow waters surrounding the Antarctic Peninsula

      Leiva, Carlos; Taboada, Sergi; Kenny, Nathan J.; Combosch, David; Giribet, Gonzalo; Jombart, Thibaut; Riesgo, Ana (Wiley, 2019-05-24)
      Antarctic shallow‐water invertebrates are exceptional candidates to study population genetics and evolution, because of their peculiar evolutionary history and adaptation to extreme habitats that expand and retreat with the ice sheets. Among them, sponges are one of the major components, yet population connectivity of none of their many Antarctic species has been studied. To investigate gene flow, local adaptation and resilience to near‐future changes caused by global warming, we sequenced 62 individuals of the sponge Dendrilla antarctica along the Western Antarctic Peninsula (WAP) and the South Shetlands (spanning ~900 km). We obtained information from 577 double digest restriction site‐associated DNA sequencing (ddRADseq)‐derived single nucleotide polymorphism (SNP), using RADseq techniques for the first time with shallow‐water sponges. In contrast to other studies in sponges, our 389 neutral SNPs data set showed high levels of gene flow, with a subtle substructure driven by the circulation system of the studied area. However, the 140 outlier SNPs under positive selection showed signals of population differentiation, separating the central–southern WAP from the Bransfield Strait area, indicating a divergent selection process in the study area despite panmixia. Fourteen of these outliers were annotated, being mostly involved in immune and stress responses. We suggest that the main selective pressure on D. antarctica might be the difference in the planktonic communities present in the central–southern WAP compared to the Bransfield Strait area, ultimately depending on sea‐ice control of phytoplankton blooms. Our study unveils an unexpectedly long‐distance larval dispersal exceptional in Porifera, broadening the use of genome‐wide markers within nonmodel Antarctic organisms.
    • Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species

      Plese, Bruna; Rossi, Maria Eleonora; Kenny, Nathan James; Taboada, Sergi; Koutsouveli, Vasiliki; Riesgo, Ana (Wiley, 2019-05-09)
      Mitochondrial resources are of known utility to many fields of phylogenetic, population and molecular biology. Their combination of faster and slower‐evolving regions and high copy number enables them to be used in many situations where other loci are unsuitable, with degraded samples and after recent speciation events.The advent of next‐generation sequencing technologies (and notably the Illumina platform) has led to an explosion in the number of samples that can be studied at transcriptomic level, at relatively low cost. Here we describe a robust pipeline for the recovery of mitochondrial genomes from these RNA‐sequencing resources. This pipeline can be used on sequencing of a variety of depths, and reliably recovers the protein coding and ribosomal gene complements of mitochondria from almost any transcriptomic sequencing experiment. The complete sequence of the mitochondrial genome can also be recovered when sequencing is performed in sufficient depth. We show the efficacy of our pipeline using data from eight nonmodel invertebrates of six disparate phyla. Interestingly, among our poriferan data, where microbiological symbionts are known empirically to make mitochondrial assembly difficult, this pipeline proved especially useful. Our pipeline will allow the recovery of mitochondrial data from a variety of previously sequenced samples, and add an additional angle of enquiry to future RNA‐sequencing efforts, simplifying the process of mitochondrial genome assembly for even the most recalcitrant clades and adding these data to the scientific record for a range of future uses.