Biology subjects

Rios-Touma, B.

Publications and source records attributed to Rios-Touma, B..

4 recordsLinked to original sources

bioRxiv2023

Evolution of Opsin Genes in Caddisflies (Insecta: Trichoptera)

Insects have evolved complex and diverse visual systems in which light-sensing protein molecules called opsins couple with a chromophore to form photopigments. Insect photopigments group into three major gene families based on wavelength sensitivity: long wavelength (LW), short wavelength (SW), and ultraviolet wavelength (UV). Here, we identified 123 opsin sequences from whole genome assemblies across 25 caddisfly species (Insecta: Trichoptera). We discovered the LW opsins have the most diversity across species and form two separate clades in the opsin gene tree. Conversely, we observed a loss of the SW opsin in half of the trichopteran species in this study, which might be associated with the fact that caddisflies are active during low-light conditions. Lastly, we found a single copy of the UV opsin in all the species in this study, with one exception: Athripsodes cinereus has two copies of the UV opsin and resides within a clade of caddisflies with colorful wing patterns. SignificanceWhile opsin evolution in some insect groups has been well-characterized, it has never been studied across caddisflies. Our findings provide insight into the diversity of opsins in caddisflies and form a basis for further research into the evolutionary drivers and complex visual systems in Trichoptera.

genomics↗

bioRxiv2022

Uncovering hidden genetic diversity: allelic resolution of insect and spider silk genes

Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we show that there is extensive variation--both in terms of length and repeat motif order--between alleles of silk genes within individual arthropods. Further, this variation exists across two deep, independent origins of silk which diverged more than 500 million years ago--(1) the insect clade containing caddisflies and butterflies and (2) spiders. This remarkable convergence in previously overlooked patterns of allelic variation across multiple origins of silk suggests mechanisms for the generation and maintenance of structural protein-coding genes. Future genomic efforts to connect genotypes to phenotypes should account for such allelic variation.

genomics↗

bioRxiv2022

Structural diversity of silk heavy-chain fibroins across major caddisfly (Trichoptera) clades

BackgroundLarvae of Trichoptera produce silk to build various underwater structures allowing them to exploit a wide range of aquatic environments. The heavy chain fibroin (h-fibroin) gene encodes the primary protein component of their silk. Studies on this long (>20 kbp) and highly repetitive gene have been limited by difficulties in its sequence assembly. Recently, high-quality long-read sequencing techniques have been successfully applied to obtain the full-length h-fibroin sequence. ResultsWe used three new and five previously published genomes to identify eight full-length h-fibroin gene and protein sequences of h-fibroin across the order Trichoptera covering various endpoints of the diversity of ecological silk use in caddisflies. We analyze these together with four existing high-quality h-fibroin sequences. Across the order, we observed conserved patterns in h-fibroin (high similarity of amino(n)-/carboxyl(c)-termini, presence of characteristic repeating structural modules). However, the sequence, number, and arrangement of these repeating modules varied across clades with increasing structural complexity of h-fibroin in fixed retreat and tube-case builders compared to cocoon-builders. We also found a higher percentage of proline in fixed-retreat makers. ConclusionThis study provides characterizations of the primary structure of h-fibroin from a diverse set of caddisflies. The interplay of conserved termini and basic motif structure with high variation in repeating modules as well as the variation in the percentage of proline might be linked to differences in mechanical properties (i.e., tensile strength, toughness) related to the different silk usage. This sets a starting point for future studies to screen and correlate amino acid motifs and other sequence features with quantifiable silk properties.

genomics↗

bioRxiv2018

New mining concessions will severely decrease biodiversity and ecosystem services in Ecuador

Ecuador has the worlds highest biodiversity, despite being a tiny fraction of the worlds land area. The threat of extinction for much of this biodiversity has dramatically increased since April 2016, during which time the Ecuadorian government has opened approximately 2.9 million hectares of land for mining exploration, with many of the concessions in previously protected forests. Herein, we describe the system of protected lands in Ecuador, their mining laws, and outline the scale of threat by comparing the mammals, amphibians, reptiles, birds, and orchids from several now threatened protected areas, classed as \"Bosques Protectores\" (BPs), in the NW montane cloud forests. We examine two large (>5,000 ha) BPs, Los Cedros and El Chontal, and two medium BPs, Mashpi (1,178 ha) and Maquipucuna (2,474 ha). Since BP El Chontal is so poorly explored, we used several other small reserves (<500 hectares) in the Intag Valley to gain an idea of its biodiversity. Together, these BPs and reserves form a buffer and a southern corridor for the still-protected Cotacachi-Cayapas Ecological Reserve, which is otherwise now surrounded by mining concessions. We gathered published literature, \"gray literature\", information from reserve records and websites, and our previously unpublished observations to make comparative species tables for each reserve. Our results from these still incompletely known reserves reveal the astonishing losses that mining will incur: eight critically endangered species, including two primates (brown-headed spider monkey and white-fronted capuchin), 37 endangered species, 149 vulnerable and 85 near threatened and a large number of less threatened species Our data show that each of the reserves protects a unique subset of taxa in this land of highly localized endemics. Each of the reserves also generates sustainable income for the local people. The short-term national profits from mining will not compensate for the permanent biodiversity losses, and the long-term ecosystem service and economic losses at the local and regional level.

ecology↗