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846 results for “homologs”
Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals
Accurate modeling of the complexity of morphological evolution is crucial for morphological phylogenetics and for performing tests on a wide variety of evolutionary scenarios. In this context, morphological integration and the problem of correlated categorical characters represent a major challenge. In particular, the magnitude and implications of correlations among serially homologous structures such as teeth have been much debated but were never tested statistically within a broad phylogenetic context. Here, we present a large-scale empirical study analyzing the serial variation of cingular crests on successive molars (M1, M2 and M3) of 274 placental species in a phylogenetic context. Both likelihood analyses and analysis of phylogenetic co-distributions demonstrated highly correlated evolution in the entire sample and thus the non-independence of these serial features at a macroevolutionary scale. Likelihood analyses show that their serial variation should be better scored within a single composite character model with constrained paths for transitions enabling simultaneous changes on all three molars, which suggests a strong developmental or genetic integration. These results are congruent with current molecular and developmental knowledge related to dental morphological variation and call into question the frequent use of separate characters scored on serially homologous structures of the dentition in phylogenetic analyses. Overall, they provide long-overdue and clear empirical evidence that in-depth studies of patterns of integration constitute an essential step towards more realistic character construction and modeling. This approach is critical for more accurate morphological phylogenetics and, more generally, for testing macroevolutionary scenarios on groups of correlated characters.
Data from: Phylogenetic relationships of the Early Miocene diving and flightless duck Cayaoa bruneti (Aves, Anatidae) from Patagonia: homology or convergence?
Cayaoa bruneti, coming from the early Miocene of Gaiman Formation (Chubut, Argentina) is interpreted as one of the earliest examples of diving behaviour and the earliest example of flight loss within Anseriformes, being also the only known diving duck from South America. Herein is presented the first phylogeny of Anatidae with Cayaoa bruneti. It was made by the methodology of parsimony and by using characters previously defined by other authors, redefined in the present work as well as new characters. The phylogenetic analysis using all the characters and without considering the information contributed by analyses using molecular characters puts Cayaoa bruneti as part of a single radiation of diving ducks within Anatinae, as sister group to the Erismaturinae. Analyzing the different bones as different partitions show that the humerus and femur have the most effect, while the skull characters result in groupings closer to those seen in analyses with molecular characters. When making the analysis with a molecular backbone for the topology, Cayaoa bruneti arises as a basal branch within the Erismaturinae. These results make Cayaoa bruneti an independent and early example of the recurring evolution of flightlessness in large marine Anatidae.
Data from: Stronger convex (stabilizing) selection on homologous sexual display traits in females than in males: a multipopulation comparison in Drosophila serrata
Mutual mate choice for homologous sexual display traits has been demonstrated in Mutual mate choice for homologous sexual display traits has been demonstrated in several recent studies yet little attention has been given to quantitative comparison of the strength and form of mate preferences between the sexes. Such comparisons may provide important insight into the evolution of mate choice for honest signals. In particular, because females generally provide the majority of resources for initial offspring development, female displays may trade-off with fecundity, causing preference evolution to differ between the sexes. Recent theory suggests that adaptive male preferences for honest displays in females are possible under certain conditions and may result in preferences that are convex (i.e. stabilizing) in form. We compared sexual selection on a suite of contact pheromones arising from mutual mate choice using nine separate geographic populations of Drosophila serrata. We show that the convex selection is stronger on females than on males overall in these populations, and that convex selection is the predominate form of nonlinear selection on females but not males.
Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data ("gene tree") approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently—within the last two million years—and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases.
FIGURES 1–9 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 1–9. Stenichnus godarti. Mature larva patrolling the arena (1–2) and eating an oribatid mite (3–4); pupa five days after pupation (5, 8–9), teneral adult eating uropodine mite (6), and prepupa (7).
FIGURES 23–24 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 23–24. Alternative cephalic setal homology between Stenichnus godarti (23) and St. collaris (24; after Jałoszyński 2013). Setae are organize in presumably homologous groups: labrofrontal I (Lbf1), labrofrontal II (Lbf2), mediolateral (Ml), prestigmal-postantennal (Prs), poststigmal (Pst), dorsal epicranial I (Dep1), dorsal epicranial II (Dep2), and dorsal epicranial posterior (Depp). Abbreviations: AnI, antennal insertion; Es, frontal arm of epicranial suture; Est, epicranial stem; sEs, hypothetically 'shifted' epicranial suture; St, stemma.
FIGURES 21–22 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 21–22. Larva of Stenichnus godarti. Abdomen in dorsal (21) and ventral (22) view (if one half of tergite or sternite bears more setae, setation of the other half is treated as incomplete). Abbreviations: AM, anal membrane; L, lateral seta; l, lentiform structure; mt, microtrichion; P, posterior seta; Sp, spiracle; V, ventral seta.
FIGURES 19–20 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 19–20. Larva of Stenichnus godarti. Thorax in dorsal (19) and ventral (20) views. Abbreviations: A, anterior seta; Cxc, coxal cavity; D, dorsal seta; L, lateral seta; l, lentiform structure; P, posterior seta; Sp, spiracle; T1d, pronotum; T1v, prosternum; T2d, mesonotum; T2v, mesosternum; T3d, metanotum; T3v, metasternum; V, ventral seta; Vl, ventrolateral seta.
FIGURES 29–32 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 29–32. Alternative mesonotal (29, 31) and metanotal (30, 32) setal homology between Stenichnus godarti (29–30) and St. collaris (31–32; after Jałoszyński 2013). Setae are organized in presumably homologous rows: dorsal (D), lateral (L) and posterior (P). Within incomplete rows hypothetically absent setae are marked by asterisks (*).
FIGURES 16–18 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 16–18. Larva of Stenichnus godarti. Left fore leg in posterior view (16), right middle leg in posterior view (17) and right hind leg in anterior view (18). Abbreviations: A, anterior seta; Cx, coxa; D, dorsal seta; Fe, femur; Pd, posterodorsal seta; Pr, pretarsus; Pv, posteroventral seta; sp, spines; Ti, tibiotarsus; Tr, trochanter; V, ventral seta.
FIGURES 25–28 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 25–28. Alternative pronotal setal homology between Stenichnus godarti (25–26) and St. collaris (27–28; after Jałoszyński 2013); variant I (25, 27) and variant II (26, 28) discussed in the text. Setae are organized in presumably homologous rows: dorsal (D) and lateral (L).
FIGURES 10–15 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 10–15. Larva of Stenichnus godarti. Head in dorsal (10) and ventral (11) views; left (12) and right (13) antenna in dorsal view; right (14) and left (15) maxilla in ventral view. Abbreviations: Ag, antennal gland; An1–3, antennomere I–III; Cd, cardo; Da, dorsoanterior seta; De, dorsoepicranial seta; Df, dorsofrontal seta; Dl, dorsolateral seta; Dp, dorsoposterior seta; Es, frontal arm of epicranial suture; Est, epicranial stem; L, lateral seta; l, lentiform structure; La, labral anterior seta; Ma, mala; Md. mandible; MdS, mandibular seta; Mn, mentum; Mxp1–3, maxillary palpomere II–III; Ptp, posterior tentorial pit; SA, sensory appendage; Smn, submentum; sol, solenidion; St, stemma; Stp, stipes; V, ventral seta; Va, ventroanterior seta; Vl, ventrolateral seta.
Differential responses of Medicago truncatula NLA homologs to nutrient deficiency and arbuscular mycorrhizal symbiosis
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Fig. 23. Principal Components Analysis plot for 23 and 25 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 23. Principal Components Analysis plot for 23 and 25 measurements taken from males and females, respectively. First and second PCA for males were body size and metasoma length (97% of variance explained), and for females it was patella and carapace lengths (92% of variance explained) [upper plate]. The variable vector dimensions that separate the principal components of males and females are shown in the lower plate.
Fig. 22 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 22. Map of Central Mexico and Aguascalientes state showing the distribution of Vaejovis aguazarca Díaz-Plascencia and Gonz´alez-Santill´an sp. nov. (gray circles), Vaejovis aquascalentensis Ch´avez-Samayoa and Gonz´alez-Santill´an sp. nov. (red diamonds), Vaejovis tenamaztlei Contreras-F´elix, Francke and Bryson, 2015 (green stars), Vaejovis coalcoman Contreras-F´elix and Francke 2014 (orange square), and Vaejovis dugesi Pocock, 1902 (blue triangle). Mountain ranges are indicated as: Sierra Fria (1), Sierra del Laurel (2) and Juan el Grande foothills (3). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 21 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 21. Pedipalp chela of Vaejovis tenamaztlei Contreras-Felix´, Francke and Bryson, 2015 under UV light (6). A. Dorsal, B. Retrolateral, C. Ventral, and D. Prolateral aspects.
Fig. 20 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 20. Pedipalp patella of Vaejovis tenamaztlei Contreras-F´elix, Francke and Bryson, 2015 under UV light (6). A. Dorsal, B. Retrolateral, C. Ventral, and D. Prolateral aspects.
Fig. 16 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 16. Pedipalp femur of Vaejovis aquascalentensis Ch´avez-Samayoa and Gonz´alez-Santill´an sp. nov. under UV light (6). A. Dorsal, B. Retrolateral, C. Ventral, and D. Prolateral aspects.
Fig. 19 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 19. Pedipalp femur of Vaejovis tenamaztlei Contreras-Felix´, Francke and Bryson, 2015 under UV light (6). A. Dorsal, B. Retrolateral, C. Ventral, and D. Prolateral aspects.
Fig. 17 in Two new species of Vaejovis (Scorpiones: Vaejovidae) belonging to the mexicanus group from Aguascalientes, Mexico, with comments on the homology and function of the hemispermatophore
Fig. 17. Pedipalp patella of Vaejovis aquascalentensis Ch´avez-Samayoa and Gonz´alez-Santill´an sp. nov. under UV light (6). A. Dorsal, B. Retrolateral, C. Ventral, and D. Prolateral aspects.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.