Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

Abstract

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species‐specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species‐specific changes in many pregnancy‐related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

A chromosome-level genome assembly of the yellow-throated marten (Martes flavigula)

“…Among these, long interspersed elements (LINE) that accounted for 26.13% of the whole genome were the most abundant (Table 4 ). These results are supported by similar findings in published mustelids genomes 22 , 34 , 35 .…”

Tayra

“…Tayras are non-seasonal breeders with several estrous cycles each year. The genes associated with reproduction that may be involved in the non-seasonal breeding include ETV2, MUC15, SLC38A2, HSD17B10, RBP2, and RNASEH2B (Derežanin et al 2022). The copulation of a pair of wild tayras was recorded through remote cameras in Altos de Campana National Park (Panama); the event occurred diurnally and for 43 min, although in the first video, the male was already mounting the female, so the exact duration of coitus was unknown (Fuentes et al 2021).…”

“…Apparently, tayras exhibit prospective cognition due to their constant visits to a known source of food, which also implies spatial memory (Tallei et al 2021), and that they are capable of collecting and storing immature fruits for consumption once ripe (Soley and Alvarado-Díaz 2011). The evolution of their caching behavior may have been consequence of the presence of genes related to memory and learning (e.g., SLC38A1 [Qureshi et al 2019]; CRBN [Higgins et al 2010]; Derežanin et al 2022). The diet of this species in not fully understood by region, season, sex, or age.…”

“…Apparently, the eyesight of the tayra may be relatively poor (Defler 1980). The presence, quantity, and variation in several genes (e.g., ANKRD13A [Avellino et al 2013]; RBP2 [D'Ambrosio et al 2011]) implicated with lens-fiber formation and retinal vascularization suggests that tayras might have poor eyesight (Derežanin et al 2022). The tongue of the tayra has mechanical (filiform and conical), and gustative (fungiform and circumvallated) lingual papillaes (Gonçalves et al 2020).…”

Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China

“…Over thousands of years, species have acquired their ecological niches through adaptations to local phenological conditions and competition with other species [ 1 – 3 ]. With the advent of the anthropocene, the balance of competition among species has been disrupted.…”