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opencc-by-4.0Feb 2023View details →

Table 1 in Hiding in plain sight: Integrative analyses uncover a cryptic Salvia species in Europe

Table 1. Biometric data (floral and vegetative) of morphological characters for Salvia austriaca Jacq. (N = 29) and Salvia FDPD (N = 35).<table><tbody><tr><th>Variable Floral traits</th><th>Salvia austriaca Values in mm</th><th>Salvia FDPD Values in mm</th></tr></tbody><tbody><tr><th>ch* (corolla height)</th><td>(6.24) 10.69 ± 0.55 (17)</td><td>(8.36) 12.38 ± 0.54 (21.33)</td></tr><tr><th>cl* (corolla length)</th><td>(14.27) 17.7 ± 0.26 (20.4)</td><td>(19) 22.75 ± 0.4 (26.34)</td></tr><tr><th>a* (absolute length of the abaxial lever arm)</th><td>(12.79) 14.44 ± 0.22 (17.23)</td><td>(16.04) 20.71 ± 0.31 (24)</td></tr><tr><th>b (distance between joint and pollen-sacs)</th><td>(11.25) 14.06 ± 0.35 (18.57)</td><td>(9.69) 13.69 ± 0.39 (18.27)</td></tr><tr><th>c* (absolute length of the adaxial lever arm)</th><td>(2.15) 2.72 ± 0.07 (3.54)</td><td>(2.23) 3.06 ± 0.09 (4.04)</td></tr><tr><th>cal* (calyx length) Vegetative traits</th><td>(7.4) 8.22 ± 0.15 (9.86) Values in cm, except stlp</td><td>(8.05) 9.54 ± 0.15 (10.82) Values in cm, except stlp</td></tr><tr><th>sth (stem height)</th><td>(24) 56.23 ± 2.27 (79)</td><td>(8) 61.2 ± 3.65 (104)</td></tr><tr><th>stlp* (number of stem leaf pairs)</th><td>(1) 1.53 ± 0.14 (3)</td><td>(1) 1.69 ± 0.09 (3)</td></tr><tr><th>lpet (length of petiole of rosette leaf)</th><td>(1.8) 3.67 ± 0.32 (7.5)</td><td>(1) 4.46 ± 0.44 (12)</td></tr><tr><th>lobl (length of leaf blade of rosette leaf)</th><td>(5.2) 11.61 ± 0.53 (14.5)</td><td>(8.5) 13.83 ± 0.77 (25)</td></tr></tbody></table>Values represent (minimum) mean ± standard error (maximum). * indicates significant differences between measurements (p <0.05).

opencc-zeroJun 2021View details →

Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species

Marine ecosystems formed by kelp forests are severely threatened by global change and local coastline disturbances in many regions. In order to take appropriate conservation, mitigation and restoration actions, it is crucial to identify the most diverse populations which could serve as a "reservoir" of genetic diversity. This requires the development of specific tools, such as microsatellite markers to investigate the level and spatial distribution of genetic diversity. Here, we tested new polymorphic microsatellite loci from the genome of the kelp, Laminaria digitata, and tested them for cross-amplification and polymorphism in four closely related congeneric species (Laminaria hyperborea, Laminaria ochroleuca, Laminaria rodriguezii and Laminaria pallida). Adding these 20 new microsatellite loci to the ten L. digitata loci previously developed by Billot et al. (1998) and Brenan et al. (2014) and to the ten L. ochroleuca loci previously developed by Coelho et al. (2014), we retained a total of 30 polymorphic loci for L. digitata, 19 for L. hyperborea, 16 for L ochroleuca, 19 for L. rodriguezii and 12 for L. pallida. These markers have been tested for the first time in the last two species. As predicted, the proportion of markers that cross-amplified between species decreased with increasing genetic distance. In addition, as problems of species identification were reported in this genus, mainly between L. digitata and Hedophyllum nigripes, but also between L. digitata, L. hyperborea and L. ochroleuca in areas where their range distributions overlap, we report a rapid PCR identification method based on species-specific cox1 mitochondrial primers that allows these four species of kelp to be rapidly distinguished.

opencc-by-4.0Nov 2009View details →

Fig. 3 in The Use of Molecular Phylogenetic and Morphological Tools to Identify Cryptic and Paraphyletic Species: Examples from the Diminutive Long-fingered Bats (Chiroptera: Miniopteridae: Miniopterus) on Madagascar

Fig. 3. Photograph of living Miniopterus brachytragos captured near Ambanizana, Masoala Peninsula

opencc-by-4.0Mar 2014View details →

Fig. 39 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters

Fig. 39. Boaedon fuliginosus (Boie), skull of AMNH R-11996, ×3.7.

opencc-by-4.0Mar 2014View details →

Fig. 5 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters

Fig. 5. Eutrachelophis steinbachi (Boulenger). Adult female shown approximately life size (BMNH

opencc-by-4.0Mar 2014View details →

Fig. 17 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters

Fig. 17. The tips of diverse bilobed hemipenes. A. Apical discs on the hemipenis of Liophis

opencc-by-4.0Apr 2009View details →

Figure 4 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon

Figure 4. Wing centroid size in male and female Merodon avidus A and M. avidus B.

opencc-by-4.0Apr 2009View details →

Figure 1 in Cryptic speciation at organic-rich marine habitats: a new bacteriovore annelid from whale-fall and fish farms in the North-East Atlantic

Figure 1. Map showing collection sites in Sweden and Norway for the new species.

opencc-by-4.0Apr 2009View details →

Figure 2 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon

Figure 2. Positions of the wing landmarks used in the geometric morphometric analyses.

Data from: Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

Previous work, using morphological characters, identified a generalist copepod parasite (Pharodes tortugensis) at high prevalence on two common gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin Islands (BVI). DNA barcoding subsequently revealed C. glaucofraenum to be three morphologically similar species (C. glaucofraenum, C. venezuelae and C. tortugae), casting doubt on host identities in the BVI and the classification of the parasite as a single species. Mitochondrial cytochrome c oxidase subunit I (COI) data from 67 gobies in the BVI showed that, in addition to C. dicrus, host gobies were a mix of C. glaucofraenum and C. venezuelae, while C. tortugae was unexpectedly absent from the study area. COI data (n = 70) indicated that the copepod infecting all three hosts was a single species, almost certainly P. tortugensis. The pharodes–coryphopterus interaction has a strong impact on host dynamics in the BVI, and a revised understanding of these dynamics must account for any differences among the three newly confirmed hosts in transmission of, and susceptibility to, the shared parasite. No other infected hosts were discovered at our sites, but P. tortugensis is reportedly widespread and infects 12 additional host species elsewhere. Further DNA barcoding is thus needed to test whether P. tortugensis is truly a widespread generalist, or instead represents a group of more specialized cryptic species.

Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus)

Knowledge of genetic structure is essential for the long-term management and conservation of endangered species. We report the results from a genetic examination of the federally endangered Florida bonneted bat (Eumops floridanus) sampled from its range in southern Florida, USA. Bonneted bats are primarily found in four regions separated by approximately 100 to 250 kms, including three western natural areas (BW, PC, and CC) and one urban population on the east coast [Miami-Dade County (MD)]. We used 22 microsatellite loci and cytochrome b sequences to assess the extent of connectivity and levels of genetic diversity. Regional populations were highly differentiated (FST = 0.178) and model-based and multivariate analyses showed that MD was the most distinct among pairwise comparisons. Regional populations are small (i.e., Ne < 100) but demographically stable. Estimates of contemporary migration and historic gene flow suggest that regional populations do not frequently exchange migrants, but simulations suggest that the divergence among western regions is likely a result of recent genetic drift rather than long-term isolation. Significantly, mitochondrial DNA revealed that haplotypes from MD were similar or shared with those recognized as Eumops ferox from Cuba and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in Florida. Our data support the management of each of the four populations as distinct population segments, and that BW, PC and CC combined are on an independent evolutionary trajectory from bats in MD. Critically, bonneted bats in Florida appear to harbor cryptic diversity that will require a reassessment of their taxonomy.

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

Variation among functionally similar species in their response to environmental stress buffers ecosystems from changing states. Functionally similar species may often be cryptic species representing evolutionarily distinct genetic lineages that are morphologically indistinguishable. However, the extent to which cryptic species differ in their response to stress, and could therefore provide a source of response diversity, remains unclear because they are often not identified or are assumed to be ecologically equivalent. Here, we uncover differences in the bleaching response between sympatric cryptic species of the common Indo-Pacific coral, Pocillopora. In April 2019, prolonged ocean heating occurred at Moorea, French Polynesia. 72% of pocilloporid colonies bleached after 22 days of severe heating (>8°C-days) at 10 m depth on the north shore fore reef. Colony mortality ranged from 11% to 42% around the island four months after heating subsided. The majority (86%) of pocilloporids that died from bleaching belonged to a single haplotype, despite twelve haplotypes, representing at least five species, being sampled. Mitochondrial (open reading frame) sequence variation was greater between the haplotypes that experienced mortality versus haplotypes that all survived than it was between nominal species that all survived. Colonies >30 cm in diameter were identified as the haplotype experiencing the most mortality, and in 1125 colonies that were not genetically identified, bleaching and mortality increased with colony size. Mortality did not increase with colony size within the haplotype suffering the highest mortality, suggesting that size-dependent bleaching and mortality at the genus level was caused instead by differences among cryptic species. The relative abundance of haplotypes shifted between February and August, driven by declines in the same common haplotype for which mortality was estimated directly, at sites where heat accumulation was greatest, and where larger colony sizes occurred. The identification of morphologically indistinguishable species that differ in their response to thermal stress, but share a similar ecological function in terms of maintaining a coral-dominated state, has important consequences for uncovering response diversity that drives resilience, especially in systems with low or declining functional diversity.

Going against the flow: barriers to gene flow impact patterns of connectivity in cryptic coral reef gobies throughout the western Atlantic

Aim: Complex oceanographic features have historically caused difficulty in understanding gene flow in marine taxa. Here, we evaluate the impact of potential phylogeographic barriers to gene flow and assess demography and evolutionary history of a coral reef goby species complex. Specifically, we test how the Amazon River outflow and ocean currents impact gene flow. Location: Western Atlantic. Taxon: The bridled goby (Coryphopterus glaucofraenum) and sand-canyon goby (C. venezuelae) species complex. Methods: We used mitochondrial DNA and 2401 genomic SNPs to investigate evolutionary history and test hypotheses of how major barriers impact species-level differentiation. We used clustering algorithms and pairwise FST to assess population differentiation caused by minor barriers within and among regions. Finally, we tested alternate hypotheses of demographic history via coalescent simulations to determine the most plausible spread across the Western Atlantic. Results: We found two unique clades of C. glaucofraenum along the Brazilian coast and Atol das Rocas (AR) that are more closely related to C. venzuelae. Further genetic structure within the Caribbean and separately along the Brazilian coast led to at least two distinct populations in each location. Coalescent simulations indicated that an ancestral population of C. venezuelae split from C. glaucofraenum in the Caribbean, dispersed to Brazil, then spread to AR. Main Conclusions: Species-level genetic differentiation has resulted from the Amazon River outflow and isolation of AR. Population differentiation within the Caribbean matched previous studies indicating an east-west pattern of divergence. Brazilian population differentiation was impacted by the cold-water upwelling at Cabo Frio. Overall, this research highlights how barriers to gene flow impact speciation and genetic structure within western Atlantic gobies and provides insight into the role oceanographic features have in the speciation process of fishes.

opencc-zeroNov 2022View details →

Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions is critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking and hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected and high host densities were found to have lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.

opencc-zeroNov 2022View details →

Unraveling the myotis norass: Ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Using sequences from 2615 UCE loci and multiple methodologies we inferred phylogenies for the largest genetic dataset of New World Myotis to date. The resulting phylogenetic trees were populated with short branch lengths and widespread conflict, hallmarks consistent with rapid adaptive radiations. The degree of conflict observed in Myotis has likely contributed to difficulties disentangling deeper evolutionary relationships. Unlike earlier phylogenies based on 1-2 gene sequences, this UCE dataset places M. brandtii outside the New World clades. Introgression testing of a small subset of our samples revealed evidence of historical but not contemporary gene flow, suggesting that hybridization occurs less frequently in the Neotropics than in the Nearctic. We identified several instances of cryptic lineages within described species as well as several instances of potential taxonomic over-splitting. Evidence from Central and South American localities suggests that diversity in those regions is not fully characterized. In light of the accumulated evidence of the evolutionary complexity in Myotis and our survey of the taxonomic implications from our phylogenies it is apparent that the definition of species and regime of species delimitation need to be re-evaluated for Myotis. This will require substantial collaboration and sample sharing between geneticists and taxonomists to build a system that is both robust and applicable in a genus as diverse as Myotis.

opencc-zeroNov 2022View details →

Phenotypic traits evolution and morphological traits associated with echolocation calls in cryptic horseshoe bats (Rhinolophidae)

Bats provide an excellent case study for studying evolution due to their remarkable flight and echolocation capabilities. In this study, we sought to understand the phenotypic evolution of key traits in Rhinolophidae (horseshoe bats) using phylogenetic comparative methods. We aim to test the phylogenetic signals of traits and evaluated the best-fit evolutionary models given the data for each trait considering different traits may evolve under different models (i.e., Brownian Motion (BM), Ornstein-Uhlenbeck (OU) and Early Burst (EB)) and reconstruct ancestral character states. We examined how phenotypic characters are associated with echolocation calls and minimum detectable prey size. We measured 34 traits of 10 Asian rhinolophids species (187 individuals). We found that the majority of traits showed a high phylogenetic signal based on Blomberg's K and Pagel's λ, but each trait may evolve under different evolutionary models. Sella traits were shown to evolve under stabilizing selection based on OU models, indicating sella traits have the tendency to move forward along the branches toward some medial value in equilibrium. Our findings highlight the importance of sella characters in association with echolocation call emissions in Rhinolophidae, as calls are important for spatial cognition and also influence dietary preferences. Minimum detectable prey size in Rhinolophidae was associated with call frequency, bandwidth, call duration, wingspan and wing surface area. Ultimately, understanding trait evolution requires sensitivity due to the differential selective pressures which may apply to different characteristics.

opencc-zeroApr 2023View details →

Data from: Cryptic male mate choice for high-quality females reduces male postcopulatory success in future matings

Cryptic male mate choice occurs when males differentially allocate resources to females during or after copulation. When male resources are limited, males may benefit by strategically allocating more resources toward higher-quality females. In the fruit fly, Drosophila melanogaster, males mate for longer and may transfer more sperm and more seminal proteins when they mate with larger females compared to smaller females. It is unclear, however, whether this increased investment in large females has any impact on the males' later matings. We mated D. melanogaster males sequentially to females of large or small body size in all possible combinations to test whether cryptic male mate choice for large females is costly to the males' subsequent matings. Second matings were shorter for males compared to their first matings, but there were no differences in fecundity between females mated first or second by a male. Interestingly, male success at defensive sperm competition declined between his first and second matings only when his first mating had been with a large female. This suggests that the higher initial investment in large females reduced male postcopulatory success in their subsequent matings. Cryptic male mate choice may carry underappreciated costs to males that could limit their reproductive potential.

opencc-zeroJun 2023View details →

Hierarchical drivers of cryptic biodiversity on coral reefs

Declines in habitat structural complexity have marked ecological outcomes, as currently observed in many of the world's ecosystems. Coral reefs have provided a model for such changes in marine ecosystems, but our understanding has been centred on corals and fishes at broad spatial scales when metazoan diversity on coral reefs is dominated by small cryptic taxa (herein: 'cryptofauna'). Given the paucity of studies and high taxonomic complexity of the cryptofauna, both of which limit a priori hypotheses, we asked whether hierarchical structuring theory provides a compelling framework to impose order and quantify pattern. In general terms, we explored whether cryptic communities are sufficiently described by broad seascape parameters or limited by a set of processes operating at their distinctly nested microhabitat scale. To address this theory and gaps in knowledge for the cryptofauna, we characterised community structure in coral rubble, an eroded coral condition where biodiversity proliferates. Rubble was sampled along a depth and exposure gradient at Heron Island on the Great Barrier Reef, Australia, to parameterise environmental and morphological indicators of sessile taxa and motile cryptofauna communities. We employed a hierarchical study framework from microhabitat to seascape scales, which were evaluated using non-structured multivariate analyses and Bayesian structural equation modelling. While the non-structured analyses showed the effects of seascape on the cryptobenthos and its community, this approach overlooked the finer hierarchical patterns in rubble ecology revealed only in the structured model. Seascape parameters (exposure and depth) influenced microhabitat complexity (i.e., rubble branchiness), which determined the cover of sessile organisms on rubble pieces, which shaped the motile cryptofauna community. Rubble is likely to be increasingly prevalent on coral reefs in the Anthropocene and is typically associated with low seascape-level complexity and reduced macrofaunal richness. Parallel with hierarchical structuring theory, we show a similar response operating at the microhabitat scale whereby low rubble complexity (i.e., branchiness) reduces cryptobenthic structure, diversity and size spectra. We expect there may be an initial increase in biodiversity and trophodynamic processes derived from branching rubble, but a delay in ecosystem-scale outcomes if coral, and thus rubble, generation and complexity cannot be sustained in a future ocean.

opencc-zeroJun 2023View details →

Supplementary datasets to: Molecular species delimitation and morphometry in the Melampus bidentatus (Panpulmonata, Ellobiidae) cryptic species complex

The coffee bean snail Melampus bidentatus occurs in coastal salt marshes along the North American Atlantic and Gulf coasts and in the Caribbean. It was recently found that this large geographical span is actually occupied by a complex of three apparently cryptic species (preliminarily called "North", "South", and "Gulf") with partially overlapping distributions. Until now, it was not clear whether there are any morphological differences between the three species or which of the available names can be applied to each of the cryptic species. We used the already-known distribution patterns of the cryptic species as well as new barcode sequences to assign available names to the three cryptic species. We then compared morphological characters from 264 specimens using two approaches: an analysis based on 11 landmark points on the shell and another based on the entire shell outline. We were able to assign a nominal name to each of the three cryptic species: Melampus bidentatus for "North", Melampus jaumei for "South", and Melampus gundlachi for "Gulf". The morphometric analyses did not yield any diagnostic differentiating features; these cryptic species are hence diagnosable solely by genetic analysis but may phenotypically differ in some unseen internal features or in their physiology.