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175 results for “cryptic speciation”
Data from: New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)
Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA samples from three sampling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled sample of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172 837 raw reads (17.4 Mbp) were retrieved, 95 500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA samples genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern sampling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST = 0.0025) can be resolved with a likely power ≥67% by using standard sample sizes of 50 and validated subsets of available markers.
Data from: Barcoding of ancient lake ostracods (Crustacea) reveals cryptic speciation with extremely low distances
Ostracods are drastically reduced crustaceans, with never more than eight appendages enclosed between two valves, leaving only a limited number of morphological characters for species delineation. Conservative morphology of characters used to define genera, along with high variability of characters used to define species are creating problems in applying a morphospecies concept. A high intraspecific variability in a Lake Biwa (Japan) endemic, Physocypria biwaensis (Okubo, 1990), has been observed previously but was never studied in detail. Two sympatric forms, differing in pigmentation and size, suggest a presence of reproductive isolation. The aim of this study is to employ molecular and morphometric tools to aid in species delineation within P. biwaensis complex and reconstruct their phylogenetic relationships. A fragment of the mtCOI gene was amplified from 30 specimens, and an additional 37 specimens were studied for morphological characters. Resulting phylogenies showed that each morphologically distinct form is associated with a distinct phylogenetic group based on mtDNA. The average pairwise distance is very low (5%), indicating a recent divergence time. I speculate that there is a possibility that one of them originated in the lake, while the other probably colonized it afterwards. This seems to be supported with an apparent niche partitioning at different depths. In spite of the fact that traditionally used sexual characters are highly variable in these two species, the morphometric analysis of shell and soft part related characters clearly delineates them and suggests that such characters may be useful for future detection of seemingly cryptic ostracod species.
Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus)
Migratory species that alternate between sympatry and allopatry over the course of an annual cycle are promising subjects for studies seeking to understand the process of speciation in the absence of strict geographic isolation. Here we sought to identify cryptic species and assess rates of gene flow in a clade of neotropical migrant songbirds in which geography and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus) Species Complex. Phylogenetic, clustering, and statistical species delimitation analyses found that V. olivaceus includes two non-sister lineages migrating in opposite directions across the equator. Analyses of gene flow identified low levels of introgression between two species pairs, but none between northern and southern olivaceus. We also identified substantial well-supported conflicts between nuclear and mitochondrial topologies. Although the geographic distribution of mito-nuclear discordance is suggestive of hybridization and mitochondrial capture, we found no evidence of introgression in the nuclear genome of populations with discordant mitochondrial gene trees. Our study finds that species boundaries match breeding range and migratory phenology rather than the existing taxonomy in this group, and demonstrates the utility of genomic data in inferring species boundaries in recently diverged clades.
FIGURE 5 in Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation
FIGURE 5. Upper: adult male Hemiphyllodactylus titiwangsaensis (LSUDPC 6708) from the type locality of Cameron Highlands, Pahang. Middle: adult male H. cf. titiwangsaensis (LSUDPC 2868) from Fraser's Hill, Pahang. Lower: adult male H. cf. titiwangsaensis (LSUDPC 6444) from Genting Highlands, Pahang.
FIGURE 3 in Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation
FIGURE 3. Male Holotype (LSUCH 11762) of Hemiphyllodactylus cicak sp. nov. from Penang Hill, Penang Island, Penang, Peninsular Malaysia.
FIGURE 1 in Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation
FIGURE 1. Distribution of the species of the Hemiphyllodactylus harterti group in Peninsular Malaysia.
FIGURE 2 in Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation
FIGURE 2. Maximum-likelihood phylogram of the Hemiphyllodactylus harterti group with Bayesian posterior probabilities followed by maximum likelihood bootstrap values.
Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S-DIVA algorithm using ultrametric COI tree calculated in BEAST 2.4 software. Numbers at the tips of the trees correspond to the sampling locations on the map (designated as in Fig. 1). Letters represent most likely ancestral range. Sectors in circles indicate the percent of total range probability. Biogeographical regions in the map as in Piepenburg et al. (2011), Ekimova et al. (2019), Laakkonen et al. (2021).
Fig. 2 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 2. Morphology of Arctic Priapulus caudatus. A. Individual WS19002 from the intertidal of the White Sea, showing the body division into introvert (in), trunk (tr) and caudal appendage (ca). B. Frontal scanning electron microscopical (SEM) image of individual WS19002 from the White Sea showing the longitudinal rows of scalids (sc) and the pentagons of pharyngeal teeth (the first five pentagons are labelled with numbers. C. Individual XZ4889 from the Barents Sea, for abbreviations see A. D, E. Frontal view on individual XZ5288 from the Laptev Sea with light microscopy (D) and SEM (E). F. Lateral view on everted pharyngeal teeth in individual XZ5496 from the East-Siberia Sea. Pharyngeal teeth of pentagons 1 to 6 are labelled. G, H. Individual XZ5374 from the Laptev Sea, for abbreviations in G see figure A. H is a magnification showing the ring papillae (rp), posterior warts (pw) and the vesicles (ves) of the caudal appendage.
Fig. 1 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 1. Sampling locations: 1 – Northwest Atlantic (Cobscook Bay), 2 – North Sea (Scotland), 3 – North Sea (Bergen), 4 – Skagerrak (Kristineberg), 5 – Baltic Sea (Oresund), 6 – Norwegian Sea (Tromsø), 7 – Barents Sea (Dalnie Zelentsy), 8 – White Sea, 9 – Barents Sea (Russkaya Gavan), 10 – Kara Sea (Abrosimov Bay), 11 – Gulf of Ob, 12 – Laptev Sea (Severnaya Zemlya), 13 – Laptev Sea (Vilkitsky Strait), 14 – shelf of the Laptev Sea, 15 – Laptev Sea (Buor- Haya), 16 – shallow of the East Siberian Sea, 17 – East Siberian Sea (Chaunskaya Bay), 18 – Chuckchi Sea (Gerold Island), 19 – Sea of Okhotsk (Magadan), 20 – North Pacific (Kamchatka), 21 – North Pacific (Alaska). Green circles indicate individuals from GenBank, yellow circles indicate our samples. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6. Single-gene Bayesian trees for 16S and FoxQ2 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 6. Single-gene Bayesian trees for 16S and FoxQ2 markers. Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 60 are shown.
Fig. 9 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 9. Divergence time estimates from BEAST analysis for major Priapulus caudatus clades with different calibration scenarios (CS). Dates are in millions of years. Green dots indicate the main divergence nodes, orange dots show Okhotsk clade divergence node. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 7. Haplotype TCS network from COI for Priapulus caudatus (including available sequences from GenBank). Frames indicate the main haplogroups, tick marks between haplotypes indicate number of substitutions, relative size of the circles reflects the number of individuals in the haplotype. Colors indicate sample location. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 4. Distribution of five main COI clades around the studied area (including available sequences from GenBank).
Fig. 5 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 5. Right: Bayesian phylogenetic tree of Priapulus caudatus based on COI dataset (without sequences from GenBank). Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 60 are shown. Blue and yellow boxes show 28S + 18S genotypes. Individuals in yellow boxes belong to the intertidal genotype, individuals in blue boxes belong to the subtidal genotype; individuals in half-yellow-half-blue boxes are heterozygotes. Asterisks mark individuals collected in the intertidal (0 m), the rest are from the subtidal (5–500 m). Left: intertidal (yellow worms) and subtidal (blue worms) populations of Priapulus caudatus. Some larvae from intertidal populations pass to the subtidal with the tide. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 3. Single-gene Bayesian trees for COI marker (including all available sequences from GenBank). Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 50 are shown.
Fig. 8 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 8. Ultrametric COI tree calculated in BEAST 2.4 software under the Birth-Death model in 107 MCMC generations (including available sequences from GenBank). Black numbers above branches indicate millions of years (Mya); white numbers below indicate posterior probabilities. On the left side: classic subdivision of the Pliocene-Pleistocene according to Horikawa et al. (2015), M¨oller et al. (2019), and Astakhov and Semionova (2021). Grey boxes indicate glacial periods.
Data from: Hidden island endemic species, and their implications for cryptic speciation within soil arthropods
<p><strong>Aim:</strong> Specialisation to the soil environment is expected to constrain the spatial scale of diversification within animal lineages. In this context, the existence of flightless arthropod lineages, adapted to soil environments, but with broad geographic ranges, represent something of an anomaly. Here we investigate the diversification process within one such 'anomalous' soil specialist: <em>Geomitopsis franzi </em>Coiffait, 1978, an eyeless and flightless beetle species strongly adapted to the endogean environment but distributed across several oceanic islands.</p> <p><strong>Location:</strong> Canary Islands</p> <p><strong>Taxon:</strong> <em>Geomitopsis</em> (Coleoptera, Staphylinidae)</p> <p><strong>Methods:</strong> We performed an integrative study, including molecular phylogenetics, population genomics, and morphometry. Four DNA regions (two mitochondrial and two nuclear) were amplified and sequenced for 159 specimens from 58 localities sampled across five islands for phylogenetic analyses, and a dated phylogenetic tree was obtained using a mitogenome dataset<em>. </em>ddRAD-seq data was generated to evaluate mtDNA lineages in sympatry against the biological species concept.</p> <p><strong>Results:</strong> We found high levels of genetic differentiation (>8% COI gene divergence) among populations from different islands and among geographically coherent lineages within single islands. Lineages within Tenerife presented significant patterns of isolation by distance, with ddRAD-seq providing evidence that lineages represent biological species. Morphometric analyses revealed limited variation, with most lineages lacking diagnostic characters.</p> <p><strong>Main conclusions:</strong> <em>Geomitopsis franzi</em> is comprised of at least seven lineages that merit consideration as biological species, and is best considered as a complex of cryptic species. The limited morphological variation across these lineages is consistent with adaptation to the endogean environment placing strong constraints on morphological change. The evolution of cryptic species should be favoured when such constraints are coupled with limited dispersal ability, which characterises <em>G. franzi</em>, and is a trait that broadly characterises the soil mesofauna. We suggest that cryptic species diversity is likely to be a recurrent feature across soil adapted arthropod species with range sizes that appear inconsistent whith a low potential for dispersal.</p>
Figure 5 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 5. Example song spectrograms and photos for each of the three warbling vireo genetic groups used in our DFA of songs. The colours of the outlines of the spectrograms and photos correspond to DFA results in Figure 4. Photos were taken by the first author.
Figure 4 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)
Figure 4. Plots of the first two canonical axes based on DFA of warbling vireo songs. Colours and shapes correspond to three of the four microsatellite genetic groups (Black Hills are not included): eastern (red/circle), north-western (green/ square) and south-western (blue/triangle). The largest shape represents the mean centroid for each genetic group.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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.