Three routes to crypsis: Stasis, convergence, and parallelism in the Mastigias species complex (Scyphozoa, Rhizostomeae)

Integrating cryptic diversity into coral evolution, symbiosis and conservation

Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.

Cryptic diversity begets challenges and opportunities in biodiversity research

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

Complete mitochondrial genome of Mastigias papua (Scyphozoa: Rhizostomeae: Mastigiidae) based on next-generation sequencing and phylogenetic analysis

We assembled the complete mitochondrial genome (mitogenome) of Mastigias papua (Scyphozoa: Rhizostomeae: Mastigiidae) by the data generated from the next-generation sequencing platform. The complete mitogenome of M. papua was 16,560 bp in length, containing 14 protein-coding genes, two transfer RNA genes, and two ribosomal RNA genes. The base compositions were A 30.65%, C 15.16%, G 16.34%, and T 37.86%, with a gene arrangement similar to the mitogenomes derived from other representatives of Scyphozoa. Based on the 13 common protein-coding genes of 16 species within Scyphozoa, we constructed the phylogenetic tree and found that M. papua has a close relationship with Cassiopea andromeda and Cassiopea xamachana. All these species belong to an order of jellyfish Rhizostomeae, which have similar morphological characteristics. This is agreement with the conclusion we got by the phylogenetic relationship analysis using molecular data. This research has practical implications for advancing understanding of the phylogenetic relationships, taxonomic classifications, and phylogeography within Scyphozoa.

How we study cryptic species and their biological implications: A case study from marine shelled gastropods

Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency of cryptic species among taxonomic groups is not well documented. The term "cryptic species" is imprecisely used in scientific literature, causing ambiguity when interpreting their evolutionary and ecological significance. This study reviews how cryptic species have been defined, discussing implications for taxonomy and biology, and explores these implications with a case study based on recently published literature on extant shelled marine gastropods. Reviewed gastropods were recorded by species. Records of cryptic gastropods were presented by authors with variable levels of confidence but were difficult to disentangle from inherent biases in the study effort. These complexities notwithstanding, most gastropod species discussed were not cryptic. To the degree that this review's sample represents extinct taxa, the results suggest that a high proportion of shelled marine gastropod species are identifiable for study in the fossil record. Much additional work is needed to provide a more adequate understanding of the relative frequency of cryptic species in shelled marine gastropods, which should start with more explicit definitions and targeted case studies.

Integrative Taxonomy Approach Reveals Cryptic Diversity within the Phoretic Pseudoscorpion Genus Lamprochernes (Pseudoscorpiones: Chernetidae)

Pseudoscorpions represent an ancient, but homogeneous group of arachnids. The genus Lamprochernes comprises several morphologically similar species with wide and overlapping distributions. We implemented an integrative approach combining molecular barcoding (cox1), with cytogenetic and morphological analyses in order to assess species boundaries in European Lamprochernes populations. The results suggest ancient origins of Lamprochernes species accompanied by morphological stasis within the genus. Our integrative approach delimited three nominal Lamprochernes species and one cryptic lineage Lamprochernes abditus sp. nov. Despite its Oligocene origin, L. abditus sp. nov. can be distinguished from its closest relative only by molecular and cytogenetic differences, or alternatively, by a complex multivariate morphometric analysis involving other Lamprochernes species. The population structure and common haplotype sharing across geographically distant populations in most Lamprochernes species suggest that a phoretic manner of dispersal is efficient in this group.

Demystifying Cassiopea species identity in the Florida Keys: Cassiopea xamachana and Cassiopea andromeda coexist in shallow waters

The phylogeny of the Upside-Down Jellyfish (Cassiopea spp.) has been revised multiple times in its history. This is especially true in the Florida Keys, where much of the Cassiopea stock for research and aquarium trade in the United States are collected. In August 2021, we collected 55 Cassiopea medusae at eight shallow water sites throughout the Florida Keys and sequenced COI, 16S, and 28S genes. Mitochondrial genes demonstrate that the shallow waters in Florida are inhabited by both Cassiopea xamachana and a non-native Cassiopea andromeda lineage, identified in multispecies assemblages at least thrice. While C. xamachana were present at all sites, the C. andromeda-mitotype individuals were present at only a minority of sites. While we cannot confirm hybridization or lack thereof between the C. xamanchana and C. andromeda lineages, these previously unknown multispecies assemblages are a likely root cause for the confusing and disputed COI-based species identities of Cassiopea in the Florida Keys. This also serves as a cautionary note to all Cassiopea researchers to barcode their individuals regardless of the location in which they were collected.

Revealing the cryptic diversity of the widespread and poorly known South American blind snake genus Amerotyphlops (Typhlopidae: Scolecophidia) through integrative taxonomy

Morphological stasis is generally associated with relative constancy in ecological pressures throughout time, producing strong stabilizing selection that retains similar shared morphology. Although climate and vegetation are commonly the main key factors driving diversity and phenotypic diversification in terrestrial vertebrates, fossorial organisms have their morphology mostly defined by their fossorial lifestyle. Among these secretive fossorial organisms, blind snakes of the South American genus Amerotyphlops are considered poorly studied when compared to other taxa. Here, we evaluate the cryptic diversity of Amerotyphlops using phylogenetic and multivariate approaches. We based our phylogenetic analysis on a molecular dataset composed of 12 gene fragments (eight nuclear and four mitochondrial) for 109 species of Typhlopidae. The multivariate analysis was implemented using 36 morphological variables for 377 specimens of Amerotyphlops. Additionally, we contrast our phylogenetic result with the morphological variation found in cranial, external and hemipenial traits. Our phylogenetic results recovered with strong support the following monophyletic groups within Amerotyphlops: (1) a clade formed by A. tasymicris and A. minuisquamus; (2) a clade composed of A. reticulatus; (3) a north-eastern Brazilian clade including A. yonenagae, A. arenensis, A. paucisquamus and A. amoipira; and (4) a clade composed of A. brongersmianus and a complex of cryptic species. Based on these results we describe four new species of Amerotyphlops from north-eastern and south-eastern Brazil, which can be distinguished from the morphologically similar species, A. brongersmianus and A. arenensis.

Revealing hidden diversity among upside-down jellyfishes (Cnidaria: Scyphozoa: Rhizostomeae:

Morphological variability within Cassiopea is well documented and has led to inaccuracies in the establishment of species boundaries in this taxon. Cassiopea medusae specimens from the Western Pacific (Japan and the Philippines) were analysed using multiple lines of complementary evidence, including types of cnidae, macro-morphology and molecular data. These observations lead to the recognition of two distinct species: Cassiopea mayeri, sp. nov. and a previously synonymised variety now raised to species level (Cassiopea culionensis, stat. nov.). These species can be distinguished from each other using morphological features. Herein, sexually dimorphic traits are included for the first time in the descriptions of Cassiopea species. Nematocyst types not previously observed in the genus are also reported. Molecular analyses, based on individual and combined markers (16S + cytochrome c oxidase I, COI), also support two distinct species; they are not sister taxa, and both are nested together within a clade of other Cassiopea members from the Australian and Indo-Pacific regions. Species richness is underestimated in the Western Pacific region, and integrative approaches are helpful to reveal and describe species. The systematics of Cassiopea is far from completely understood, but the present study represents an important further step. http://www.zoobank.org/References/B1A66787-009D-4465-954A-412C6878FCB4.

Homoplasy and morphological stasis revealed through multilocus phylogeny of new myrmecophilous species in Armadillidiidae (Isopoda: Oniscidea)

The terrestrial isopod family Armadillidiidae presents higher diversity in karstic areas, with fewer species present in areas with reduced suitable subterranean habitats, such as siliceous sandy soils. Myrmecophily, although not widespread in the family Armadillidiidae, can help these animals to colonize sandy substrates, as is observed in several populations of myrmecophilous Armadillidiidae species in central and southern Spain. Morphological examination and multilocus phylogenetic analyses, including mitochondrial DNA (Cox1) and nuclear DNA (18S, 28S and H3) markers, indicate that these myrmecophilous populations represent four new taxa: Iberiarmadillidium pinicola gen. & sp. nov., Iberiarmadillidium psammophilum sp. nov., Iberiarmadillidium sakura sp. nov. and Cristarmadillidium myrmecophilum sp. nov. Some of the main diagnostic characters used in the taxonomy of Armadillidiidae are not clearly apomorphic. Among head morphologies, Eluma type seems to be the ancestral state, being typical of several unrelated lineages; duplocarinate and Armadillidium types are derived states observed in unrelated lineages. The presence of a schisma is a convergent character state, because it has been identified in several taxa nested in unrelated clades. The newly described taxa present patterns of morphological stasis and homoplasy, likely to be associated with their shared myrmecophilous habits. The generic taxonomy of the family needs a deep revision including phylogenetic approaches and thorough taxon sampling.

Larger scyphozoan species dwelling in temperate, shallow waters show higher blooming potential

142 scientific publications have been reviewed on the characteristics of the scyphozoans with respect to their ability to develop blooms and the most significant environmental characteristics that determine them. Special attention was paid to depth, temperature, salinity, chlorophyll concentration, and the habitat of the 39 registered blooming genera. After the review, we find that over the past decades, the number of scyphozoan blooming-species is higher than previously recorded, increasing from circa 14% to 25% of the class. Species that inhabit depths less than 27.1 m are prone to produce blooms, particularly in semienclosed areas with low rates of water renewal and high thermal amplitudes. Temperature appears as the main environmental factor controlling blooms, but food availability is essential to sustain the proliferations. Interspecies variability in the response to environmental factors observed in this work suggest that bloom predictive models should be constructed species-habitat-specific.

The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa)

Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.

Long-term stasis in acariform mites provides evidence for morphologically stable evolution: Molecular vs. morphological differentiation in Linopodes (Acariformes; Prostigmata)

Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY.

Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.

Another stripe on the tiger makes no difference? Unexpected diversity in the widespread tiger tarantula Davus pentaloris (Araneae: Theraphosidae: Theraphosinae)

Integrative taxonomy is relevant for the discovery and delimitation of cryptic species by incorporating different sources of evidence to construct rigorous species hypotheses. The genus Davus was recently revised and it was found that Davus pentaloris presents high morphological variation across its widespread distribution. However, tarantulas usually present low dispersal capabilities that occasionally result in local endemism. In order to evaluate species boundaries within this taxon, we examine the morphological variation and, additionally, employ four strategies based on mtDNA data (COI): two distance-based [automatic barcode gap discovery (ABGD) and Neighbor-Joining (NJ)] and two tree-based methods [general mixed Yule coalescent (GMYC) and Bayesian Poisson tree process (bPTP)]. Available morphological evidence recovers 13 putative morphospecies, but the different methods based on molecular data recover a variable number of candidate species (16–18). Based on the congruence across all analyses and the available morphological data, we recognize 13 clearly diagnosable species, 12 of them new to science. We conclude that the underestimation of the diversity in D. pentaloris was mainly caused by deficient practices in taxonomy, rather than by the presence of cryptic diversity. Although COI is a functional barcoding marker and it gives reliable results in our study, we recommend combining multiple sources of evidence and strategies to construct better species delimitation hypotheses.

Demographic, Environmental, and Phenotypic Change but Genetic Consistency in the Jellyfish Mastigias papua

AbstractSpatiotemporal environmental change can produce phenotypic differences within and between populations. For scyphozoans, the effect of environmental variation on phenotype has been unclear because of multiple challenges, including difficulties delimiting populations. Marine lakes, bodies of seawater entirely surrounded by land, provide an opportunity to study discrete populations and capture responses to perturbations. We use this opportunity to compare Mastigias papua (Lesson, 1830) medusae before and after a demographic and environmental perturbation. We reconstructed mitochondrial DNA haplotype networks, measured morphological variation, and assessed swimming behavior of pre- and post-perturbation samples to evaluate two hypotheses about the source of variation: recolonization from an alternate location or endemic phenotypic variation. We found significant differences between samples in morphology (F > 9.5, P < 0.001) and in two of three behaviors (F > 8.45, P < 0.005) but no substantial genetic differentiation (Φ_ST = 0.03, P = 0.09). We reject the hypothesis of recolonization because pre- and post-perturbation lake medusae were genetically similar to each other and also significantly different from any potential source locations (Φ_ST > 0.48, P > 0.001). We could not distinguish the source of endemic variation; this will require genomic or experimental analyses. Increasing climatic variability emphasizes the need for understanding population-level responses to environmental change and how responses may be modified by sources of intraspecific variation.

Recognizing peripheral ecosystems in marine protected areas: A case study of golden jellyfish lakes in Raja Ampat, Indonesia

Peripheral marine ecosystems can harbor endemic diversity and attract tourism attention, yet are generally not included in conservation management plans due to their remoteness or inland positioning. A case study in Raja Ampat of seven landlocked marine lakes containing golden jellyfish (Mastigias spp.) was conducted to address the lack of fundamental insights into evolutionary, ecological and social contexts of these ecosystems. An interdisciplinary approach was taken towards identifying the jellyfish lakes as distinct management units in order to incorporate them into existing Marine Protected Areas. Mastigias papua populations showed strong genetic (ϕ_ST: 0.30-0.86) and morphological (F = 28.62, p-value = 0.001) structure among lakes, with putative new subspecies. Risks arising from rapid increase in tourism to Raja Ampat (30-fold since 2007) warrant restrictions on jellyfish lake use. Recommendations are provided for adaptive management and science-based conservation policies for jellyfish lakes across Indonesia.

Evolution of morphological crypsis in the Tetramorium caespitum ant species complex (Hymenoptera: Formicidae)

Cryptic species are morphologically very similar to each other. To what extent stasis or convergence causes crypsis and whether ecology influences the evolution of crypsis has remained unclear. The Tetramorium caespitum complex is one of the most intricate examples of cryptic species in ants. Here, we test three hypotheses concerning the evolution of its crypsis: H1: The complex is monophyletic. H2: Morphology resulted from evolutionary stasis. H3: Ecology and morphology evolved concertedly. We confirmed (H1) monophyly of the complex; (H2) a positive relation between morphological and phylogenetic distances, which indicates a very slow loss of similarity over time and thus stasis; and (H3) a positive relation between only one morphological character and a proxy of the ecological niche, which indicates concerted evolution of these two characters, as well as a negative relation between p-values of correct species identification and altitude, which suggests that species occurring in higher altitudes are more cryptic. Our data suggest that species-specific morphological adaptations to the ecological niche are exceptions in the complex, and we consider the worker morphology in this complex as an adaptive solution for various environments.

Hidden and cryptic species reflect parallel and correlated evolution in the phylogeny of the genus Callyntra (Coleoptera: Tenebrionidae) of Central Chile

The origin of cryptic species has traditionally been associated with events of recent speciation, genetic constraints, selection of an adaptive character, sexual selection and/or convergent evolution. Species of the genus Callyntra inhabit coastal terraces, mountain slopes, and peaks; their elytral designs are associated with each of these habitats. However, cryptic species have been described within each of these habitats; the taxonomy of this group has been problematic, thus establishing the phylogenetic relationships in this group is fundamental to clarify the systematics and evolutionary patterns of Callyntra. We reconstructed the phylogeny of this group using two mitochondrial genes (COI, 16S) and one nuclear gene (Mp20). We also performed species delimitation using PTP based methods (PTP, mlPTP, bPTP) and GMYC, and evaluated the evolution of the elytral design related to habitat preference. The results showed a tree with five clades, that together with the different methods of species delimitation recovered the described species and suggested at least five new species. The elytral design and habitat preference showed phylogenetic signals. We propose a new classification based on monophyletic groups recovered by phylogenetic analyses. We also suggest that parallel evolution in different habitats and later stasis in the elytral design would be the cause of the origin of cryptic species in this group from central Chile.

Species richness of jellyfishes (Scyphozoa : Discomedusae) in the Tropical Eastern Pacific: missed taxa, molecules, and morphology match in a biodiversity hotspot

Species richness in the seas has been underestimated due to the combined challenges presented by the taxonomic impediment, delimitation of species, preponderance of cryptic species, and uneven sampling effort. The mismatch between actual and estimated diversity varies by region and by taxon, leaving open questions such as: are hotspots for well-known taxa also hotspots for poorly known taxa? We address these challenges and this question for shallow-water scyphozoan jellyfishes in the Tropical Eastern Pacific (TEP). We increased sampling effort at 34 coastal locations along the TEP, and combined analyses of four molecular markers and up to 53 morphological characters. We applied phylogenetic analyses under Bayesian and maximum likelihood frameworks, barcoding, and statistical multivariate analyses of morphological data to estimate species richness. Where only five Discomedusae were reported previously, we found a total of 25 species. Of these, 22 species are new to science, two are non-indigenous, and one is a previous record; the other four prior records had been misidentified. The new discoveries evince the need to evaluate the evolutionary relationships with neighbouring regions to understand fully the origins of jellyfish diversity in the TEP and will lead to revision of the systematics and taxonomy of Scyphozoa.