Marphysa (Eunicidae,polychaete, Annelida) species of the Sanguinea group from Australia,with comments on pseudo‐cryptic species

The genus Marphysa is widely collected for bait by recreational fishermen in Australia, and yet the number of species remains unresolved. A new species is described together with additional information on a previously described species. This study reveals that while species of Marphysa superficially resemble one another, detailed studies on the distribution of different types of chaetae along the body, together with molecular studies, uncover species which may co‐occur. Correct identification is critical for management of these largely intertidal species. This study also highlights the increasing awareness of the presence of pseudo‐cryptic species in polychaetes.     

Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera,Monogononta) in mountain lakes

1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements. 2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino‐South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy. 3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies. 4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental‐based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.     

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

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new “species” paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category—which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a “process” counterpart to the long‐studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance‐based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large‐scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.     

Global analysis reveals that cryptic diversity is linked with habitat but not mode of life

The ubiquity of genetically distinct, cryptic species is limiting any attempt to estimate local or global biodiversity as well as impeding efforts to conserve species or control pests and diseases. Environmental factors or biological traits promoting rapid diversification into morphologically similar species remain unclear. Here, using a meta‐analysis of 1230 studies using DNA sequences to search for cryptic diversity in metazoan taxa, we test two hypotheses regarding the frequency of cryptic taxa based on mode of life and habitat. First, after correcting for study effort and accounting for higher taxonomic affinities and biogeographical region of origins, our results do not support the hypothesis that cryptic taxa are more frequent among parasitic than free‐living taxa. Second, in contrast, the results support the hypothesis that cryptic taxa are more common in certain habitats than others: for a given study effort, more cryptic taxa are found in freshwater than in terrestrial or marine taxa. These findings suggest that the greater heterogeneity and fragmentation of freshwater habitats may promote higher rates of genetic differentiation among its inhabitants, a general pattern with serious implications for freshwater conservation biology.     

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in‐depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy.     

Cost‐benefit analysis of acoustic recorders as a solution to sampling challenges experienced monitoring cryptic species

The inferences that can be made from any study are limited by the quality of the sampling design. By bad luck, when monitoring species that are difficult to detect (cryptic), sampling designs become dictated by what is feasible rather than what is desired. We calibrated and conducted a cost‐benefit analysis of four acoustic recorder options that were being considered as potential solutions to several sampling restrictions experienced while monitoring the Australasian bittern, a cryptic wetland bird. Such sampling restrictions are commonly experienced while monitoring many different endangered species, particularly those that are cryptic. The recorder options included mono and stereo devices, with two sound file processing options (visual and audible analysis). Recording devices provided call‐count data similar to those collected by field observers but at a fraction of the cost, which meant that “idealistic” sampling regimes, previously thought to be too expensive, became feasible for bitterns. Our study is one of the few to assess the monetary value of recording devices in the context of data quality, allowing trade‐offs (and potential solutions) commonly experienced while monitoring cryptic endangered species to be shown and compared more clearly. The ability to overcome challenges of monitoring cryptic species in this way increases research possibilities for data deficient species and is applicable to any species with similar monitoring challenges.     

Comparative physiological studies on the growth of cryptic species of Bostrychia intricata (Rhodomelaceae,Rhodophyta) in various salinity and temperature conditions

Inter‐ and intra‐specific physiological variations of intertidal macroalgae have been well investigated. However, studies on physiological responses of cryptic algal species have been poorly documented. Bostrychia intricata is a widespread marine red alga in the Southern Hemisphere, and has many cryptic species. We investigated the effect of different salinities and temperatures on the specific growth rate of three cryptic species (N2, N4 and N5) of B. intricata from New Zealand. Our data indicated that all cryptic species grew at the full range of salinities and temperatures tested, but exhibited a significant difference in their specific growth rates. Cryptic species N4 had a higher growth rate than the other two cryptic species under all experimental conditions, whereas cryptic species N2 occasionally showed a higher growth rate than cryptic species N5 at high salinities and lower temperatures. The distinct physiological properties of these cryptic species may explain their distribution pattern (a wider distribution of cryptic species N4 than N2 and N5) in New Zealand. The physiological divergence between the cryptic species could be related to their levels of evolutionary divergence, with more similar physiology between cryptic species, which share a more recent common ancestor (N2 and N5). Our findings underline that morphologically indistinguishable cryptic algal species are different in many other aspects and are truly independent entities.     

A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal capabilities were not as important.     

Geographic pattern of cranial differentiation in the Asian Midday Jird Meriones meridianus (Rodentia: Muridae: Gerbillinae) and its taxonomic implications

The existence of cryptic species in the midday jird (Meriones meridianus) has been suggested in literature, although based on little empirical data to support this hypothesis. In this study, a two‐dimensional landmark‐based geometric morphometric approach was used to investigate whether patterns in intraspecific variation in skull shape and size exist, using 110 skull specimens from more than 20 different localities along the distribution range of M. meridianus. This is the first study of morphological differences on such a big sample size and geographical range, and it tries to find whether skull shape variation in this species is best described as being clinal or rather reflecting cryptic diversity. The latter seems to be the case, as a dimorphic skull phenotype was found, reflecting a geographic disparity between the Middle East and the Far East specimens both in shape and in size. Distinct cranial differences were found in the overall cranial size and, also at the level of the inflation of the bulla, the elongation of the nasal, the length of the teeth row and the incisive foramen, as well as the distance in between the latter two. It thus seems that M. meridianus from Middle East is morphologically distinct from that of the Far East. Furthermore, our results also demonstrate that clinal variation could explain variation within Middle East populations, whereas a more heterogenous pattern is found for those of the Far East. The hypothesis that the observed phenotypic variation may reflect cryptic species is discussed, with the recommendation for a thorough taxonomical revision of the genus in the region.     

Cuticular hydrocarbon profiles as a taxonomic tool: advantages,limitations and technical aspects

Cuticular hydrocarbons (CHCs) are expressed on an insect's cuticle and are one of the major factors allowing insects to identify members of their own species, colony and gender. As a result of their species‐specificity, CHCs are increasingly used to delimit species in addition to more conventional methods, such as morphology or genetic markers, and so play an important role in chemotaxonomy. Species vary in the type of CHCs that they produce, as well as in the relative quantities of shared compounds. This review summarizes not only how taxonomists may differentiate between species based on CHC profiles, but also the incentive for using CHC composition as taxonomic tool. Benefits regarding the identification of cryptic species and early signs of reproductive isolation are then discussed, giving examples from studies of taxonomy, behaviour and biosynthesis. For taxonomic characters to reliably indicate species boundaries, their limitations need to be known. Potential problems caused by environmental effects, intra‐species variation in profiles and other technical issues are highlighted, and suggestions are made regarding their avoidance. It remains a challenge to determine the variation beyond which two species can be called independent; a problem shared by most methods of delimitation. Recently, there has been a shift towards using a combination of different taxonomic tools, both molecular and non‐molecular, to test observed species differences.     

Some ‘ant’swers: Application of a layered barcode approach to problems in ant taxonomy

DNA barcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test the DNA barcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomal DNA and long‐wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character‐based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character‐based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character‐based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character‐based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character‐based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost‐efficient approach to estimate presence, absence or frequency of cryptic species.     

Identifying species of moths (Lepidoptera) from Baihua Mountain,Beijing, China,using DNA barcodes

DNA barcoding has become a promising means for the identification of organisms of all life‐history stages. Currently, distance‐based and tree‐based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a “character‐based” method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA‐barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree‐based, distance‐based, and diagnostic character‐based methods to identify the taxa. The tree‐based method divided the 393 specimens into 79 taxa (species), and the distance‐based method divided them into 84 taxa (species). Although the diagnostic character‐based method found only 39 so‐identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree‐based and distance‐based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character‐based method performs well in small data sets and can also be used as the foundation of species‐specific biochips.     

Taxonomic surrogacy in biodiversity assessments,and the meaning of Linnaean ranks

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.     

DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago

DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese‐breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour‐joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan‐specific cryptic species from trans‐Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans‐Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.     

Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods

Terrestrial arthropods comprise the most species‐rich communities on Earth, and grassland flowers provide resources for hundreds of thousands of arthropod species. Diverse grassland ecosystems worldwide are threatened by various types of environmental change, which has led to decline in arthropod diversity. At the same time, monitoring grassland arthropod diversity is time‐consuming and strictly dependent on declining taxonomic expertise. Environmental DNA (eDNA) metabarcoding of complex samples has demonstrated that information on species compositions can be efficiently and non‐invasively obtained. Here, we test the potential of wild flowers as a novel source of arthropod eDNA. We performed eDNA metabarcoding of flowers from several different plant species using two sets of generic primers, targeting the mitochondrial genes 16S rRNA and COI. Our results show that terrestrial arthropod species leave traces of DNA on the flowers that they interact with. We obtained eDNA from at least 135 arthropod species in 67 families and 14 orders, together representing diverse ecological groups including pollinators, parasitoids, gall inducers, predators, and phytophagous species. Arthropod communities clustered together according to plant species. Our data also indicate that this experiment was not exhaustive, and that an even higher arthropod richness could be obtained using this eDNA approach. Overall, our results demonstrate that it is possible to obtain information on diverse communities of insects and other terrestrial arthropods from eDNA metabarcoding of wild flowers. This novel source of eDNA represents a vast potential for addressing fundamental research questions in ecology, obtaining data on cryptic and unknown species of plant‐associated arthropods, as well as applied research on pest management or conservation of endangered species such as wild pollinators.     

Hidden diversity in the non‐caryophyllaceous plant‐parasitic members of Microbotryum (Pucciniomycotina: Microbotryales)

Abstract

Members of the fungal genus Microbotryum are well‐known parasites on eudicotyledonous plant hosts. However, recent studies focused exclusively on Microbotryum species being parasites in the anthers of Caryophyllaceae in which strong host‐specificity was confirmed by molecular analyses. Consequently, species numbers have risen considerably as multi‐host parasites were split up in so‐called cryptic species. We subjected three non‐caryophyllaceous Microbotryum groups to molecular phylogenetic analyses to see whether we would confirm multi‐host morphospecies or if host‐specific cryptic species in these selected groups could be revealed as well (i.e. a group of non‐caryophyllaceous anther smuts, parasites on different Fallopia species, and parasites on Polygonum bistorta and Polygonum vi‐viparum). We applied a multiple analysis strategy to correct for varying alignment effects on a two‐locus dataset (ITS and LSU rDNA). The results obtained by the different approaches are uniform; high host‐specificity exists in the non‐ caryophyllaceous anther smuts, but overlapping host ranges occur in the parasites of Fallopia species. Results for the parasites of Polygonum are similar, with Microbotryum bistortarum being separated into three lineages and M. marginale forming a lineage on P. bistorta which apparently is conspecific with M. bistortarum p.p. Our study shows that phylogenetic patterns within Microbotryum are much more complicated than deduced from morphological observations alone. Even though Microbotryum species are highly host‐specific, it is impossible to identify species based solely on host taxa affiliation. Species status is reinstated for the anther smut on Salvia pratensis.     

When rare species become endangered: cryptic speciation in myrmecophilous hoverflies

The myrmecophilous hoverfly, Microdon mutabilis, is listed as a ‘Rare’ or ‘Nationally Notable Species’ in UK Red Data Books. As an obligate social parasite, feeding only from ant colonies, its life‐style satisfies theoretical conditions under which cryptic speciation is predicted to evolve; namely, strong selection for nonmorphological adaptations that enhance its exploitation of a local subspecies or populations of its host. Samples of larvae and pupae in Ireland, Scotland and England showed that M. mutabilis exploits a single and different host ant species on different sites across its range. In nine southern English colonies, 95.6% of infested nests were of Myrmica scabrinodis whereas in six Irish and two Scottish colonies 100% and 94.2%, respectively, of the infested nests were of Formica lemani, despite M. scabrinodis being common at all sites. Although the adults from ‘scabrinodis’ (and lemani) populations are cryptic, morphometric measurements of pupae showed consistent diagnostic characters that were sufficiently distinct for these ecotypes to be classed as separate species. We conclude that M. mutabilis is the ‘lemani‐type’ and designate the ‘scabrinodis‐type’ as a new species, Microdon myrmicae spec. nov. Thus, one of the listed threatened species of the British Isles becomes two species, each possessing about half the number of populations and occupying half the range of the original ‘species’. Each also inhabits a different serai stage within grassland or heathland, and will require a different management regime if its declining populations are to be conserved. ‘M. mutabilis’ is reported with other host ant species on the European continent. In the light of our results, these may prove to be additional cryptic species. We suggest that cryptic speciation is apt to evolve in species, such as myrmecophiles, endoparasites and koinobiont parasitoids, whose life‐styles result in strong selection on their physiological or behavioural characters. The implications for Red Data Book classifications and for practical conservation are discussed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75 , 291–300.     

On the Myths of Indicator Species: Issues and Further Consideration in the Use of Static Concepts for Ecological Applications

The use of static indicator species, in which species are expected to have a similar sensitivity or tolerance to either natural or human-induced stressors, does not account for possible shifts in tolerance along natural environmental gradients and between biogeographic regions. Their indicative value may therefore be considered at least questionable. In this paper we demonstrate how species responses (i.e. abundance) to changes in sediment grain size and organic matter (OM) alter along a salinity gradient and conclude with a plea for prudency when interpreting static indicator-based quality indices. Six model species (three polychaetes, one amphipod and two bivalves) from the North Sea, Baltic Sea and the Mediterranean Sea region were selected. Our study demonstrated that there were no generic relationships between environment and biota and half of the studied species showed different responses in different seas. Consequently, the following points have to be carefully considered when applying static indicator-based quality indices: (1) species tolerances and preferences may change along environmental gradients and between different biogeographic regions, (2) as environment modifies species autecology, there is a need to adjust indicator species lists along major environmental gradients and (3) there is a risk of including sibling or cryptic species in calculating the index value of a species.