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Figure 4 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 4. Shells of Hyalorisia. A. Hyalorisia galea, MNHN-IM-2013-60195, N of Grande-Terre, Guadeloupe (L = 13 mm). B. Hyalorisia neocaledonica n. sp., holotype, MNHN-IM-2013-65645, Lord Howe Rise, New Caledonia (L = 9.5 mm). C. Hyalorisia tosaensis, MNHN-IM-2013-58352, New Ireland, Papua New Guinea (L = 15 mm). D. Hyalorisia nupta n. sp., holotype, MNHN-IM-2007-34010, Bellona Reefs, New Caledonia (L = 18.5 mm). Scale bars = 2 mm.
Figure 5 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 5. Shells of Hyalorisia. A. Hyalorisia lehibe n. sp., holotype, MNHN-IM-2007-39212, off Mahajanga, Madagascar (L = 15 mm). B. Hyalorisia nanhaiensis n. sp., holotype, MNHN-IM-2013-59534, S of Dongsha (=Pratas) Islands, South China Sea (L = 8.5 mm). C. Hyalorisia kely n. sp., holotype, MNHN-IM-2007-39091, off Mahajanga, Madagascar (L = 6.5). D. Hyalorisia melanesica n. sp., holotype, MNHN-IM-2007-33873, Bellona Reefs, New Caledonia (L = 6.6 mm). Scale bars = 2 mm.
Figure 9 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 9. Bivalve hosts (Propeamussium spp.) with foot mark (black arrows) and notch (white arrows) of Hyalorisia. A. Propeamussium sibogai, MNHN-IM-2007- 33954 (L = 46.7 mm), host of H. nupta n. sp. (MNHN-IM-2007-34010). B. Propeamussium caducum, MNHN-IM-2007-39095 (L = 17.8 mm), host of H. kely n. sp. (MNHN-IM-2007-39091). C, D. Propeamussium dalli, MNHN-IM-2013-60196 (L = 83 mm) with H. galea (MNHN-IM-2013-60195) still attached. Photo credits: MNHN; taken by Yves Terryn (A, B) and Laurent Charles (C). Scale bars = 5 mm.
Figure 7 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 7. Radulae of Hyalorisia (A–I) and detail of the rachidian tooth (J–R). A, J. Hyalorisia galea MNHN-IM-2013-60195. B, K. Hyalorisia neocaledonica n. sp., MNHN-IM-2013-65647. C, L. Hyalorisia tosaensis, MNHN-IM-2013-58352. D, M. Hyalorisia nupta n. sp., MNHN-IM-2013-68952. E, N. Hyalorisia nanhaiensis n. sp., MNHN-IM-2013-59697. F, O. Hyalorisia kely n. sp., MNHN-IM-2007-38809. G, P. Hyalorisia melanesica n. sp., MNHN-IM-2007-34205. H, Q. Hyalorisia madagascarensis n. sp., MNHN-IM-2007-39090. I, R. Hyalorisia solomonensis n. sp., MNHN-IM-2007-34215. Scale bars = 100 µm.
Figure 2 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 2. Phylogenetic relationships of the genus Hyalorisia (Bayesian tree based on the combined dataset). Boxes indicate the three lineages, A, B and C, of Hyalorisia. Numbers at nodes are PP and UFb branch support values, respectively; only values higher than 80% are reported, and black dots indicate maximally supported branches. Scale bar indicates substitutions per site.
Figure 1 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 1. Phylogenetic relationships of the genus Hyalorisia (Bayesian tree based on the COI dataset). Numbers at nodes indicate branch support values (PP and UFb values, respectively); only values ≥95% are shown. Boxes indicate the final species hypotheses (MOTUs) for the genus. The histogram displays the distribution of the pairwise genetic distances (K2P) for the MOTUs, as based on the COI alignment; the black bars on the left are intraspecific distances and the yellow bars on the right are interspecific distances. The last two letters in the sample codes indicate the relevant general area of origin: ANT, Antarctica; JP, Japan; AK, Alaska; WA, Washington State; CA, California; PH, Philippines; NC, New Caledonia; SE, Sweden; IT, Italy; FR, Corsica; CNSea, South China Sea; MZChannel, Mozambique Channel; MG, Madagascar; PG, Papua New Guinea; SB, Solomon Islands; GP, Guadeloupe. Scale bar indicates substitutions per site.
Figure 3 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 3. Protoconchs of Hyalorisia. A. Hyalorisia galea, MNHN-IM-2013-61536. B. Hyalorisia neocaledonica n. sp., MNHN-IM-2013-65907. C. Hyalorisia tosaensis, MNHN-IM-2007-34794. D. Hyalorisia nupta n. sp., MNHN-IM-2007-34005. E. Hyalorisia lehibe n. sp., MNHN-IM-2007-39212. F. Hyalorisia nanhaiensis n. sp., MNHN-IM-2013-34796. G. Hyalorisia kely n. sp., MNHN-IM-2007-38809. H. Hyalorisia melanesica n. sp., MNHN-IM-2013-58359. I. Hyalorisia profunda n. sp., MNHN-IM-2007-33828. J. Hyalorisia madagascarensis n. sp., MNHN-IM-39292. K. Hyalorisia solomonensis n. sp., MNHN-IM-2007-34215. Scale bars = 100 µm.
Data from: Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.)
Cryptic sex has been argued to explain the exceptional longevity of certain parthenogenetic vertebrate lineages, yet direct measurements of genetic exchange between sexual and apparently parthenogenetic forms are rare. Female unisexual mole salamanders (Ambystoma sp.) are the oldest known unisexual vertebrate lineage (~5 million years), and one hypothesis for their persistence is that allopolyploid female unisexuals periodically exchange haploid genomes 'genome exchange' during gynogenetic reproduction with males from sympatric sexual species. We test this hypothesis by using genome-specific microsatellite DNA markers to estimate the rates of genome exchange between sexual males and unisexual females in two ponds in NE Ohio. We also test the prediction that levels of gene flow should be higher for 'sympatric' (sexual males present) genomes in unisexuals compared to 'allopatric' (sexual males absent) unisexual genomes. We used a model testing framework in the coalescent-based program MIGRATE-N to compare models where unidirectional gene flow is present and absent between sexual species and unisexuals. As predicted, our results show higher levels of gene flow between sexuals and sympatric unisexual genomes compared to lower (likely artefactual) levels of gene flow between sexuals and allopatric unisexual genomes. Our results provide direct evidence that genome exchange between sexual and unisexual Ambystoma occurs and demonstrate that the magnitude depends on which sexual species are present. The relatively high levels of gene flow suggest that unisexuals must be at a selective advantage over sexual forms so as to avoid extinction due to genetic swamping through genome exchange.
Data from: The mating behaviour of the seed shrimp Parapolycope spiralis (Ostracoda: Cladocopina), with insight into the evolution of mating systems in cryptic interstitial habitats
The mating behaviour of the interstitial ostracod Parapolycope spiralis Tanaka & Tsukagoshi, 2010 is reported here for the first time. This species is adapted to an interstitial environment, and is typified by having tiny body size and being completely blind. In this paper it is presumed that the characteristics of the mating behaviour are typical for species in an interstitial environment. Observations by microscopy on mating behaviour in the laboratory showed various distinct stages: (1) the male captures the female by a sucker on the antennula; (2) the male clasps and maintains the mating position using the endopodite, the endopodite claw, and the exopodite of the antenna; (3) the male makes contact using the distal part of the upper lip; and (4) copulation takes place. These observations indicate that the sequence of stages of the mating behaviour of miniaturized animals is not necessarily always a simplified process. During the process, it seems that the male upper lip establishes physical contact stimuli with the female. Because the interstitial environment is cryptic and consists of a three-dimensional space with reduced connectivity, direct physical contact is likely to be one of the most effective and successful courtship behaviours.
Data from: Cryptic diversity hides host and habitat specialization In a gorgonian-algal symbiosis
Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts coevolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations. Here, we used ribosomal, organelle, and nuclear sequences, along with microsatellite variation, to study the relationship between lineages of a common Caribbean gorgonian and its algal symbionts. The gorgonian Eunicea flexuosa is a broadcast spawner, composed of two recently diverged, genetically distinct lineages largely segregated by depth. We sampled colonies of the two lineages across depth gradients at three Caribbean locations. We find that each host lineage is associated with a unique Symbiodinium B1/184 phylotype. This relationship between host and symbiont is maintained when host colonies are reciprocally transplanted, although cases of within phylotype switching were also observed. Even when the phylotypes of both partners are present at intermediate depths, the specificity between host and symbiont lineages remained absolute. Unrecognized cryptic diversity may mask host-symbiont specificity and change the inference of evolutionary processes in mutualistic associations. Symbiotic specificity thus likely contributes to the ecological divergence of the two partners, generating species diversity within coral reefs.
Data from: In the shadows: phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)
The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.
Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male-biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal-biased X-chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.
Data from: Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers
Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties. The application of newly developed methods for analyzing this dominant marker may not be entirely clear in the context of species delimitation. In this study, we use AFLPs and mtDNA to investigate cryptic speciation in the Trimeresurus macrops complex that belongs to a taxonomically difficult lineage of Asian pitvipers. We analyze AFLPs using population genetic, phylogenetic, multivariate statistical, and Bayes Factor Delimitation methods. A gene tree from three mtDNA markers provided additional evidence. Our results show that the inferences about species boundaries that can be derived from population genetic analysis of AFLPs have certain limitations. In contrast, four multivariate statistical analyses produced clear clusters that are consistent with each other, as well as with Bayes Factor Delimitation results, and with mtDNA and total evidence phylogenies. Furthermore, our results concur with allopatric distributions and patterns of variation in individual morphological characters previously identified in the three proposed species: T. macrops sensu stricto, T. cardamomensis, and T. rubeus. Our study provides evidence for reproductive isolation and genetic distinctiveness that define these taxa as full species. In addition, we re-emphasize the importance of examining congruence of results from multiple methods of AFLP analysis for inferring species diversity.
Data from: Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex
Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.
Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene dataset, we estimated phylogeny and used multilocus genetic networks, analysis of population structure, and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages, and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g., morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists, and conservationists.
Data from: Cryptic diversity in a fig wasp community – morphologically differentiated species are sympatric but cryptic species are allopatric
A key debate in ecology centres on the relative importance of niche and neutral processes in determining patterns of community assembly with particular focus on whether ecologically similar species with similar functional traits are able to coexist. Meanwhile, molecular studies are increasingly revealing morphologically indistinguishable cryptic species with presumably similar ecological roles. Determining the geographic distribution of such cryptic species provides opportunities to contrast predictions of niche versus neutral models. Discovery of sympatric cryptic species increases alpha diversity and supports neutral models, while documentation of allopatric/parapatric cryptic species increases beta diversity and supports niche models. We tested these predictions using morphological and molecular data, coupled with environmental niche modelling analyses, of a fig wasp community along its 2700 km latitudinal range. Molecular methods increased previous species diversity estimates from eight to eleven species, revealing morphologically cryptic species in each of the four wasp genera studied. Congeneric species pairs that were differentiated by a key morphological functional trait (ovipositor length) coexisted sympatrically over large areas. In contrast, morphologically similar species, with similar ovipositor lengths, typically showed parapatric ranges with very little overlap. Despite parapatric ranges, environmental niche models of cryptic congeneric pairs indicate large regions of potential sympatry, suggesting that competitive processes are important in determining the distributions of ecologically similar species. Niche processes appear to structure this insect community and cryptic diversity may typically contribute mostly to beta rather than alpha diversity.
Data from: 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.
Data from: Shedding light on a cryptic cavernicole: a second species of Zenkevitchia Birstein (Crustacea: Amphipoda: Typhlogammaridae) discovered via molecular techniques
The Abkhazian region, in the southern foothills of the Caucasus Mountain Range, comprises a unique natural environment containing numerous subterranean habitats with relict and endemic lineages of obligate stygofauna. We aimed to assess the molecular phylogenetic relationships of Typhlogammaridae species from Balkan and Transcaucasian caves using the mitochondrial cytochrome c oxidase I (COI) in hopes of discovering previously undetected biodiversity. Our results showed molecular divergence within the genus Zenkevitchia Birstein, with two distinct groups located in the karstic regions Gudauta-Sukhumi and Gulripshi, respectively. These data indicated the existence of a new species (sequence divergences between groups of >14.3%) within the hitherto monotypic genus Zenkevitchia and allowed us to estimate the taxonomic relationship between Zenkevitchia admirabilis and Z. yakovi sp. n., based on examined morphological features and molecular phylogenetic relationships. We were unable to detect reliable morphological differences between Z. yakovi sp. n. and Z. admirabilis, highlighting the cryptic nature of the new species and the value of inclusion of molecular data in taxonomic studies.
Data from: Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?
Aphidiinae are mostly composed of specialist parasitoids and the few species described as generalist are suspected to be composed of cryptic specialists, almost indistinguishable based on morphological characteristics. The use of molecular markers has proven to be a useful tool for revealing cryptic species complexes and here we use seven mitochondrial and nuclear gene fragments to study possible genetic differentiation among seven Aphidiinae generalists. Maximum likelihood (ML) trees and Bayesian Poisson tree processes (bPTP) models were conducted on each gene separately and on the seven genes together. The standard cytochrome c oxidase I barcode region appeared to be the most polymorphic and probably the best marker to reveal putative cryptic species. However, we showed with ML trees and bPTP models that a complementary use of mitochondrial and nuclear genes was the most relevant approach to reliably identify cryptic genetic clades in the Aphidiinae. Overall, most of the analysed generalist morphospecies were shown to be composed of subgroups related to the aphid host, some of them revealed as cryptic species by the species delimitation analysis. Further studies are needed to reveal the generality of this result in Aphidiinae.
Data from: Heterospecific courtship, minority effects and niche separation between cryptic butterfly species.
Species interacting in varied ecological conditions often evolve in different directions in different local populations. The butterflies of the cryptic Leptidea complex are sympatrically distributed in different combinations across their Eurasian range. Interestingly, the same species is a habitat generalist in some regions and a habitat specialist in others, where a sibling species has the habitat generalist role. Previous studies suggest that this geographically variable niche divergence is generated by local processes in different contact zones. By varying the absolute and relative densities of Leptidea sinapis and Leptidea juvernica in large outdoor cages, we show that female mating success is unaffected by conspecific density, but strongly negatively affected by the density of the other species. Whereas 80% of the females mated when a conspecific couple was alone in a cage, less than 10% mated when the single couple shared the cage with five pairs of the other species. The heterospecific courtships can thus affect the population fitness, and for the species in the local minority, the suitability of a habitat is likely to depend on the presence or absence of the locally interacting species. If the local relative abundance of the different species depends on the colonization order, priority effects might determine the ecological roles of interacting species in this system.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.