Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Abstract

Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species ( L. campechanus ). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favour the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. Despite finding evidence of introgression in geographically neighbouring populations in northern South America, our genomic analyses strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.

One, two or more species? Mitonuclear discordance and species delimitation

“…This suggests that no divergent selection or genetic incompatibilities evolved during the allopatric phase, and that the nuclear genomes freely admixed during secondary contact (lineage fusion). However, it cannot be excluded that some genomic regions are under divergent selection and less permeable to introgression than mtDNA, as recently shown in red snappers where two biological species appear to be maintained despite sharing of deeply divergent mt lineages across nuclear genomes (Pedraza‐Marrón et al, ). Recent statistical developments including Bayesian inference and approximate Bayesian computation (ABC) applied to NGS data sets, now allow testing for sophisticated demographic scenarios, such as population expansion/contraction over time, divergence between lineages, but also admixture (hybridization) and introgression.…”

Taxonomical study of Trichomycterus (Siluriformes: Trichomycteridae) from the Ribeira de Iguape River basin reveals a new species recorded in the early 20th century

“…Thus, these species may not be distinguished by mitochondrial molecular data due to the lack of reciprocal monophyly between them, as previously reported for other Neotropical freshwater fish groups with a complex taxonomic history (Pereira et al , ; Costa‐Silva et al ., 2015; Henriques et al , ). There are cases in which mitochondrial markers failed to distinguish taxa traditionally recognized as separated species based on morphology (Pedraza‐Marrón et al , ). Genetic similarity in mitochondrial markers between T. jacupiranga and T. alternatus may also be associated with mitochondrial introgression because of hybridization.…”

“…There are cases in which mitochondrial markers failed to distinguish taxa traditionally recognized as separated species based on morphology (Pedraza-Marrón et al, 2019). Genetic similarity in mitochondrial markers between T. jacupiranga and T. alternatus may also be associated with mitochondrial introgression because of hybridization.…”

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

“…These population genetic studies provided substantial evidence for the existence of two phylogeographic lineages. However, a handful of genetic markers is not appropriate for inferring fine-scale population structure and genetic differentiation, especially in cryptic species (Struck et al, 2018;Pedraza-Marrón et al, 2019). Recent rapid developments in nextgeneration sequencing (NGS) have provided many extraordinary tools with which to study population divergence (Davey et al, 2011;Xu et al, 2016;Clucas et al, 2018;Friedline et al, 2019;Rincon-Sandoval et al, 2019;Vendrami et al, 2019).…”