Repetitive DNA sequences as an indicator of the level of genetic isolation in fish

Abstract

Although the functional role is still unknown for most types of nuclear noncoding repetitive sequences, some of them proved to provide adequate phylogenetic and taxonomic markers for studying the genetic relationships of organisms at the species and within species levels. Several markers were used in this work. First, microsatellite markers were used to examine populations varying in the extent of genetic subdi vision in marine and anadromous fish, including the Chilean jack mackerel Trachurus murphyi, anadromous brown trout Salmo trutta, and isolated and anadromous char populations. Locus polymorphism was propor tional to the gene flow between populations in all cases. Second, satellite DNA was used to study the phylo genetic relationships within the genera Salmo, Oncorhynchus, Salvelinus, and Coregonus. Genetic distances agreed well with the taxonomic relationships based on morphological traits and various biochemical markers and correlated with the evolutionary ages estimated for the groups by other markers. Third, RAPD PCR with a set of 20 mer primers was performed to study the genus Coregonus and anadromous and isolated popula tions and species of the genus Salvelinus. The resulting phylogenetic trees may help to resolve some disputable taxonomic issues for the groups. A comparison showed that several RAPD detected sequences contain con served fragments of coding sequences and polymorphic repeats (minisatellites) from intergenic regions or introns. The finding point to a nonrandom nature of repetitive DNA divergence and may reflect the evolution of the fish groups examined. Heterochromatic satellite repeats were assumed to contribute to generating a reproductive barrier.

Identification and characterization of repetitive DNA in the genus Didelphis Linnaeus, 1758 (Didelphimorphia, Didelphidae) and the use of satellite DNAs as phylogenetic markers

“…In this study, we used Illumina NGS technologies to perform a low pass shot-gun genome sequencing of Didelphini taxa of all Didelphis species and Lutreolina crassicaudata Desmarest 1804, combined with computational pipelines in order to identify the most abundant repetitive DNA families. With this approach we aimed to characterize the identified putative satDNA families and assess their utility in the phylogenetic inference of the genus Didelphis ( De La Herrán et al, 2001 ; López-Flores et al, 2004 ; Shubina et al, 2015 ), comparing it to previous molecular-based studies (e.g. Dias and Perini, 2018 ; Dias et al ., 2020 ).…”

Relaciones evolutivas de los peces Prochilodus reticulatus y Prochilodus magdalenae (Characiformes: Prochilodontidae)

“…(10) . Para el Catatumbo, P. reticulatu era la especie de mayor contribución a las capturas totales, según los monitoreos realizados entre 1989 y 1995 por la Asociación Cravo Norte (11) , sin embargo, en la actualidad su aporte ha disminuido.…”

“…Las metodologías moleculares han revolucionado el análisis genético permitiendo la identificación de especies implementando diversas técnicas moleculares. La técnica para detectar polimorfismo en el ADN amplificado al azar (RAPD) en ictiología, es un método basado en la PCR, en el que se emplea un cebador corto, generalmente de 10 bases, para amplificar secuencias arbitrarias de ADN (11) . Con esta técnica no se busca ningún fragmento de ADN específico, ya que el cebador se adhiere al ADN patrón en secuencias complementarias de ubicación desconocida.…”