Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

Abstract

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation‐related actions.

Complex cycles of divergence and migration shape lineage structure in the common kingsnake species complex

“…This is an increasingly common pattern across many taxa (e.g. Burbrink et al, 2021; Chan & Levin, 2005; Firneno et al, 2021; Myers et al, 2020; Streicher et al, 2016; Toews & Brelsford, 2012), as the relatively recent ability to obtain 1,000s of nuclear loci has greatly expanded our power to make complex population genetic inferences. We identify three discrete lineages within the common kingsnake complex, corresponding to L. californiae, L. splendida and a single eastern lineage composed of the rest of the complex.…”

“…This is an increasingly common pattern across many taxa (e.g. Burbrink et al, 2021;Chan & Levin, 2005;Firneno et al, 2021;Myers et al, 2020;Streicher et al, 2016;Toews & Brelsford, 2012),…”

Ancistroceruswasps (Hymenoptera, Vespidae) from the Centre of Europe: Phylogeny, cryptic species, neutral and non‐neutral markers

“…An integrative approach in the characterisation of cryptic species, along with the phylogenetic relationships, should involve the data on ecology, development, and behaviour. Peculiarities in these species traits allow assessing the specificity of ecological niche, that is, differences in ecosystem resource exploitation and serving as a resource for natural enemies, as well as the specificity of mate recognition system and reproductive compatibility in the sexually reproducing cryptic species, including the cases of incompatibility induced by Wolbachia (Firneno et al, 2021; Fišer et al, 2018; Hernández‐Roldán et al, 2016; Kiourtsoglou et al, 2021; Lecocq et al, 2015; Pfingstl et al, 2021; Schlick‐Steiner et al, 2010). Such empirical studies may combine several aspects of speciation and species delimitation (Magoga et al, 2021; Parslow et al, 2020; Pentinsaari et al, 2017; Sabadini et al, 2020), including a focus on cryptic species (Jusoh et al, 2020; Moraes et al, 2021; Zhou et al, 2019).…”

Lineage and role in integrative taxonomy of a heterotrophic orchid complex

“…We tested four species versus three species delimitations, which in the latter case accessions from the Coast/Cascades and Sierra Nevada were considered a single species. Delimitations were coded as dummy variables (0/1; Zapata & Jiménez, 2012; Papakostas et al, 2016; Firneno et al, 2021), and were used as potential explanatory variables in four RDA scenarios with different data sets as the response variables (representing role): (1) morphology only, (2) abiotic niche only, (3) fungal associates only (Abouheif distance, as above), and (4) combined extended data (excluding SNP data). We ran RDA and variance partitioning (Legendre et al, 2011; Peres‐Neto et al, 2006) to quantify the unique and shared contributions among delimitations and test the significance of the adjusted R 2 values for each data set.…”

“…We tested four species versus three species delimitations, which in the latter case accessions from the Coast/Cascades and Sierra Nevada were considered a single species. Delimitations were coded as dummy variables (0/1; Zapata & Jiménez, 2012;Papakostas et al, 2016;Firneno et al, 2021), and were used as potential ex- S2). For K = 3, there were three distinct groupings corresponding to var.…”