Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species. We discuss how application of a more rigorous definition of cryptic species in taxonomic practice will lead to more accurate estimates of their prevalence in nature, better understanding of their distribution patterns on the tree of life, and increased abilities to resolve the processes underlying their evolution.

Many interstitial species were first described as widely distributed, often cosmopolitan or amphi-oceanic, contrasting with descriptions of a sedentary life style and the general absence of pelagic dispersal stages. These inconsistencies became known as the "meiofauna paradox". In this review we present a literature review investigating these inconsistencies and address the assumptions of the meiofauna paradox. We break the paradox down to two aspects including species distribution and dispersal. Focusing on distribution, we demonstrate that wide distributions are seldom given and false records likely stem from biological phenomena like stasis or recent speciation. These phenomena account for morphological similarity, ultimately represented by the pronounced occurrence of cryptic species with restricted distribution ranges. Additionally, taxonomic artefacts such as the erroneous application of taxonomic keys contribute to the report of widely distributed species. Considering dispersal, we point out the mismatch between traditional assumptions of meiofaunal sedentarism and growing experimental and empirical evidences suggesting higher dispersal potential. These evidences include not only indications for dispersal by pelagic stages, but further consider ecological and life-history traits in shaping distribution ranges. We conclude that the meiofauna paradox sensu strictu most likely does not exist and provide a roadmap for future research, suggesting a focus on morphological similarity and marine connectivity. Meiofaunal research should concentrate on evolutionary factors resulting in morphological similarity, improving the taxonomic resolution of species complexes and conducting more sophisticated experimental experiments to meiofaunal dispersal. In all cases meiofaunal research will benefit from high-throughput sequencing such as genome scanning approaches, metagenomics or metatranscriptomics.

No abstract

Cryptic species are detected at an ever-increasing rate, mainly due to the application of molecular data. While the impact of this hidden diversity on macro-ecology and conversation biology is widely recognized, its evolutionary significance is rarely. In recent years it became apparent that definitions of cryptic species are too ambiguous to allow the differentiation between natural phenomena from human-made artefacts. Hence, recently a unifying conceptual framework has been proposed highlighting the necessity to test the degree of reduced phenotypic disparity in cryptic species. Within this reduced disparity also lies the evolutionary significance, as cryptic species can be regarded as the opposite of adaptive radiations. Specifically, studies on evolutionary stasis can substantially benefit from including these by addressing both patterns of reduced disparity and processes resulting in the lack of phenotypic evolution. Additionally, this will allow connecting macro-evolutionary and paleontological studies with micro-evolutionary investigations of genotype-phenotype linkage.

The restriction site‐associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time‐efficient way for obtaining thousands of genomic markers. However, when working with non‐model taxa with few genomic resources, optimization of RADseq wet‐lab and bioinformatic tools may be challenging, often resulting in allele dropout—that is when a given RADseq locus is not sequenced in one or more individuals resulting in missing data. Additionally, as datasets include divergent taxa, rates of dropout will increase since restriction sites may be lost due to mutation. Mitigating the impacts of allele dropout is crucial, as missing data may lead to incorrect inferences in population genetics and phylogenetics. Here, we demonstrate a simple pipeline for the optimization of RADseq datasets which involves partitioning datasets into subgroups, namely by reducing and analysing the dataset at a population or species level. By running the software Stacks at a subgroup level, we were able to reliably identify and remove individuals with high levels of missing data (bad apples) likely stemming from artefacts in library preparation, DNA quality or sequencing artefacts. Removal of the bad apples generally led to an increase in loci and decrease in missing data in the final datasets. The biological interpretability of the data, as measured by the number of retrieved loci and missing data, was considerably increased.