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50 results for “ecomorph”
Supplemental data from: Nature or nurture: A genetic basis for the behavioral selection of depth in siscowet and lean lake charr (Salvelinus namaycush) ecomorphs
<p>These files contain the raw depth and temperature sensor data from siscowet and lean lake charr (<em>Salvelinus namaycush</em>) ecomorphs tagged with pop-up satellite archival tags (PSATs). These fish were produced from wild gametes taken from Lake Superior and reared in a common garden study for nine years and then tagged with PSATs and released in southern Lake Superior. The dataset is supplemental to:</p> <p>Goetz, F., Sitar, S., Seider, M., and Jasonowicz, A. 2022. Nature or nurture: A genetic basis for the behavioral selection of depth in siscowet and lean lake charr (<em>Salvelinus namaycush</em>) ecomorphs. Canadian Journal of Fisheries and Aquatic Sciences. (in press).</p> <p><strong>Data description for metadata.csv:</strong></p> <p>This file contains the metadata associated with each tag deployment. This includes biological data as well as key mission paramters.</p> <table> <thead> <tr> <td>Column</td> <td>Type</td> <td>Description</td> </tr> </thead> <tbody> <tr> <td>mission_id</td> <td>integer</td> <td>mission identifier</td> </tr> <tr> <td>tag_sn</td> <td>integer</td> <td>tag serial number</td> </tr> <tr> <td>ecotype</td> <td>string</td> <td>lake trout ecotype</td> </tr> <tr> <td>release_date</td> <td>string</td> <td>date of tag release</td> </tr> <tr> <td>length_mm</td> <td>float</td> <td>total length in mm</td> </tr> <tr> <td>weight_g</td> <td>float</td> <td>weight in g</td> </tr> <tr> <td>lipid</td> <td>float</td> <td>lipid level meadured by Distell fatmeter set in research mode</td> </tr> <tr> <td>release_site</td> <td>string</td> <td>release site (deep or shallow site)</td> </tr> <tr> <td>sampling_rate</td> <td>string</td> <td>sampling interval of tag (format=HH:MM:SS)</td> </tr> <tr> <td>mission_end_utc</td> <td>datetime</td> <td>programmed tag pop off date and time in UTC time (format=YYYY-MM-DD HH:MM:SS)</td> </tr> <tr> <td>notes</td> <td>string</td> <td>notes and comments</td> </tr> </tbody> </table> <p> </p> <p><strong>Data description for the raw sensor data files:</strong></p> <p>The raw sensor data is found in the files that are prefixed with "raw-sensor-data". The data for each tag is in contained in a seperate file and the files are named as follows "raw-sensor-data-{<em><strong>mission_identifier</strong></em>}-{<em><strong>tag_serial_number</strong></em>}.csv".</p> <table> <thead> <tr> <td>Column</td> <td>Type</td> <td>Description</td> </tr> </thead> <tbody> <tr> <td>mission_id</td> <td>integer</td> <td>mission identifier</td> </tr> <tr> <td>tag_sn</td> <td>integer</td> <td>tag serial number</td> </tr> <tr> <td>timestamp_utc</td> <td>datetime</td> <td>timestamp of sensor reading (format=YYYY-MM-DD HH:MM:SS)</td> </tr> <tr> <td>depth_m</td> <td>string</td> <td>depth in meters</td> </tr> <tr> <td>temperature_c</td> <td>string</td> <td>temperature in degrees celcius</td> </tr> </tbody> </table>
Data from: Postcranial diversity and recent ecomorphic impoverishment of North American gray wolves
Recent advances in genomics and palaeontology have begun to unravel the complex evolutionary history of the gray wolf, Canis lupus. Still, much of their phenotypic variation across time and space remains to be documented. We examined the limb morphology of the fossil and modern North American gray wolves from the late Quaternary (< ca.70 ka) to better understand their postcranial diversity through time. We found that the late-Pleistocene gray wolves were characterised by short-leggedness on both sides of the Cordilleran-Laurentide ice sheets, and that this trait survived well into the Holocene despite the collapse of Pleistocene megafauna and disappearance of the "Beringian wolf" from Alaska. In contrast, extant populations in the Midwestern United States and north-western North America are distinguished by their elongate limbs with long distal segments, which appear to have evolved during the Holocene possibly in response to a new level or type of prey depletion. One of the consequences of recent extirpation of the Plains (C. l. nubilus) and Mexican wolves (C. l. baileyi) from much of the United States is an unprecedented loss of postcranial diversity through removal of short-legged forms. Conservation of these wolves is thus critical to restoration of the ecophenotypic diversity and evolutionary potential of gray wolves in North America.
Data from: Postcranial diversity and recent ecomorphic impoverishment of North American gray wolves
Open the record for dataset details and reuse information.
Data from: Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations
Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole-genome resequencing to examine genomic patterns of divergence in three sympatric cichlid species pairs with very similar functional and ecological differentiation, but different ages. We find a strong signature of increasing genomic divergence with time in both the mitochondrial genome and the nuclear genome. In contrast to many other systems, we find that in these cichlids regions of elevated relative differentiation also exhibit increased absolute differentiation. We detect a signature of convergent evolution in a comparison of outlier regions across all three species pair comparisons but the extent of it is modest, and regions that are strongly divergent in any one pair tend to be only slightly elevated in the other pairs, consistent with a repeatable but polygenic basis of traits that characterize the ecomorphs. Our results suggest that strong functional phenotypic differentiation, as seen in all three species pairs, is generally associated with a clear signature of genomic divergence, even in the youngest species pair.
Data from: Do convergent ecomorphs evolve through convergent morphological pathways? Cranial shape evolution in fossil hyaenids and borophagine canids (Carnivora, Mammalia)
Cases of convergent evolution, particularly within ecomorphological contexts, are instructive in identifying universally adaptive morphological features across clades. Tracing of evolutionary pathways by which ecomorphological convergence takes place can further reveal mechanisms of adaptation, which may be strongly influenced by phylogeny. Ecomorphologies of carnivorous mammals represent some of the most outstanding cases of convergent evolution in the Cenozoic radiation of mammals. This study examined patterns of cranial shape change in the dog (Canidae) and hyena (Hyaenidae) families, in order to compare the evolutionary pathways that led to the independent specialization of bone-cracking hypercarnivores within each clade. Geometric morphometrics analyses of cranial shape in fossil hyaenids and borophagine canids provided evidence for deep-time convergence in morphological pathways toward the independent evolution of derived bone-crackers. Both clades contained stem members with plesiomorphic generalist/omnivore cranial shapes, which evolved into doglike species along parallel pathways of shape change. The evolution of specialized bone-crackers from these doglike forms, however, continued under the constraint of a full cheek dentition and restriction on rostrum length reduction in canids, but not hyaenids. Functionally, phylogenetic constraint may have limited borophagine canids to crack bones principally with their carnassial instead of the third premolar as in hyaenids, but other cranial shape changes associated with durophagy nevertheless evolved in parallel in the two lineages. Size allometry was not a major factor in cranial shape evolution in either lineage, supporting the interpretation of functional demands as drivers for the observed convergence. The comparison between borophagines and hyaenids showed that differential effects of alternative functional "solutions" that arise during morphological evolution may be multiplied with processes of the "macroevolutionary ratchet" already in place to further limit the evolutionary pathways available to specialized lineages.
Data from: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.
Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of measurements that define corallite architecture, and could partition additive and non-additive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h² estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h² were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.
Data from: Recent rapid speciation and ecomorph divergence in Indo-Australian sea snakes
The viviparous sea snakes (Hydrophiinae) are a young radiation of at least 62 species that display spectacular morphological diversity and high levels of local sympatry. To shed light on the mechanisms underlying sea snake diversification, we investigated recent speciation and eco-morphological differentiation in a clade of four nominal species with overlapping ranges in Southeast Asia and Australia. Analyses of morphology and stomach contents identified the presence of two distinct ecomorphs: a 'macrocephalic' ecomorph that reaches >2 m in length, has a large head and feeds on crevice-dwelling eels and gobies; and a 'microcephalic' ecomorph that rarely exceeds 1 m in length, has a small head and narrow fore-body and hunts snake eels in burrows. Mitochondrial sequences show a lack of reciprocal monophyly between ecomorphs and among putative species. However, individual assignment based on newly developed microsatellites separated co-distributed specimens into four significantly differentiated clusters corresponding to morphological species designations, indicating limited recent gene flow and progress towards speciation. A coalescent species tree (based on mitochondrial and nuclear sequences) and isolation-migration model (mitochondrial and microsatellite markers) suggest between one and three transitions between ecomorphs within the last approximately 1.2 million to approximately 840 000 years. In particular, the macrocephalic 'eastern' population of Hydrophis cyanocinctus and microcephalic H. melanocephalus appear to have diverged very recently and rapidly, resulting in major phenotypic differences and restriction of gene flow in sympatry. These results highlight the viviparous sea snakes as a promising system for speciation studies in the marine environment.
FIGURE 6 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 6. Niphargus mirocensis, sp. n., female 17.95 mm (holotype), Rakin ponor: aI–II=antennas I–II; md–R=right mandibula; md–L= left mandibula; mxp=maxilliped; mx1–2=maxilla I and II.
FIGURE 4 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 4. Niphargus mirocensis, sp. n., female 17.95 mm (holotype), Rakin ponor: ppIII–VII=pereopods III–VII.
FIGURE 5 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 5. Niphargus mirocensis, sp. n., female 17.95 mm (holotype), Rakin ponor: plpII=plepopod II; T=telson; upI– upIII=uropods i–III.
FIGURE 3 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 3. Niphargus mirocensis, sp. n., female 17.95 mm (holotype), Rakin ponor: gI–II=gnathopods I–II.
FIGURE 2 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 2. Niphargus mirocensis, sp. n., female 17.95 mm (holotype), Rakin ponor. Head and pleosoma I–III are digitally positioned on a drawing, compared with a real holotype. Holotype`s left ppV (damaged) is reconstructed based on the right ppV from the same specimen.
FIGURE 1 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 1. Distribution map of cave lake ecomorphs belonging to two major clades on Balkan Peninsula. Symbols indicate clade affiliation; closed circles for "Northern orcinus group ", triangles for "Southern orcinus group" and red circles for newly described species. Note a long distance between N. mirocensis sp. n. and species from the same phylogenetic lineage (400 km) and N. mirocensis sp. n. and closest representative of cave lake ecomorphs (280 km). Data were obtained from SubBio database (http://subbio.net/db/).
FIGURE 7 in Description of a new species of Niphargus (Crustacea: Amphipoda: Niphargidae): the first record of a lake ecomorph in the Carpathian Mountains
FIGURE 7. Phylogenetic relationships as inferred from Bayesian analysis. Color of nodes indicates range of posterior probabilities (Black circles = 1, gray circles = 0.95–0.99, white circles = 0.90–.94). Clade with focal N. mirocensis sp. n. is indicated.
Fig. 20 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 20. Phaneropterinae group (continued). Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Arthur Anker.
Fig. 17 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 17. Pseudophyllinae group: supertribe 'Pseudophylliti'. Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Nigel Voaden.
Fig. 19 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 19. Phaneropterinae group (partial). Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credits are as follows: (Barbitistes ocskayi) (Charpentier, 1850) Orthoptera species file online and (Phaneroptera sp. (Serville, 1831)) Arthur Anker.
Fig. 15 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 15. Tettigoniinae group:Terpandrini,Austrosaginae, and HolarcticTettigoniinae.Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Joseph Mugleston.
Fig. 14 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 14. Tettigoniinae group: Requenini, Hexacentrinae, Meconematini, Australian Nedubini, Phisidini (sans Arachnoscelis), Arytropteridini, and Hetrodinae. Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credits are as follows: (Hexacentrus sp.) (Serville, 1831) Hojun Song, (Oediphisis sp.) (Jin, 1992) Arthur Anker, (Hetrodes sp.) (Fischer von Waldheim, 1833) Joseph Mugleston.
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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.
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.