The importance of naming cryptic species and the conservation of endemic subterranean amphipods

Abstract

Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu lato. Using uni- and multilocus delineation methods we show that it consists of 15 parapatric and sympatric species, which we describe using molecular diagnoses. The new species are not mere “taxonomic inflation” as they originate from several distinct branches within the genus and coexist with no evidence of lineage sharing. They are as evolutionarily distinct as average nominal species of the same genus. Ignoring these cryptic species will underestimate the number of subterranean endemics in Slovenia by 12 and in Croatia by four species, although alpha diversity of single caves remains unchanged. The new taxonomy renders national Red Lists largely obsolete, as they list mostly large-ranged species but omit critically endangered single-site endemics. Formal naming of cryptic species is critical for them to be included in conservation policies and faunal listings.

Cryptic species as a window into the paradigm shift of the species concept

“…Alternative species delimitations suggested by different methods were not in conflict with each other, but differed in the degree of splitting; distance methods typically turned to be more conservative (Copilaş‐Ciocianu & Petrusek, ; Delić, Trontelj, Rendoš, & Fišer, ; Delić, Švara, et al., ; Eme et al., ; Katouzian et al., ; Weiss et al., ). In such cases, authors either provided a rough estimate of species number (Copilaş‐Ciocianu & Petrusek, ; Weiss et al., ), opted for a particular species hypothesis by ranking the efficiency of different methods (e.g., conservative ABGD was preferred over PTP and bGMYC; Katouzian et al., ), reconsidered the results within spatial context (presence of syntopy (Delić, Trontelj, et al., )) or drew on other studies to justify the choice of a particular threshold value. Unfortunately, cross‐referencing is not always appropriate because the value of thresholds depend on how genetic distances are calculated (e.g., uncorrected p, K2P, patristic distances) (Richards et al., ).…”

“…In other words, DNA‐complemented taxonomy contributed only 1% to the total number of described amphipod species. Only two studies relied solely upon DNA sequences to diagnose species (Delić, Trontelj, et al., ; Murphy et al., ), and one study complemented morphological diagnoses with diagnostic COI sequences (King & Leys, ).…”

“…First, range sizes of many species are much smaller than previously conceived. Species with small range sizes are much more vulnerable to external disturbances than broadly distributed species and even local perturbations can lead to biodiversity loss (Bland & Collen, ; Delić, Trontelj, et al., ). Second, ignoring the vulnerability of cryptic species to multiple stressors can underestimate threats to local populations and ultimately biodiversity.…”

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

“…It is also effective in other taxonomic groups such as amphipods (Bastos‐Pereira & Ferreira, ; García‐Dávila, Magalhães, & Guerrero, ) or isopods (KamilarI & Sfenthourakis, ). When no morphological differences are found, species delimitation and description may be accomplished solely based on molecular data (Churchill, Valdés, & Foighil, ; Delić, Trontelj, Rendoš, & Fišer, ). In these cases, new sequence data may subsequently lead to emended molecular diagnoses as new morphological information may lead to emendations of a morphological diagnosis (Nygren & Pleijel, ).…”

An integrated pathway for building regional phylogenies for ecological studies

“…Usually each species is represented by the sequences available without regard to their geographical origin (Antonelli et al, ; Pearse & Purvis, ; Smith et al, ). Most studies show that cryptic species complexes are made up of species with ranges that rarely overlap, are smaller than the original species range, and do not necessarily form a monophyletic clade (Delić et al, ; Eme et al, ; Fenessy et al, ; Trontelj et al, ). One way to avoid potential errors introduced by undescribed cryptic taxa is to select sequences that are either within or are spatially proximate to the region of interest, thereby increasing the probability of the sequence representing the correct taxon.…”