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38 results for “geographic sampling”
Fig. 1 in Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics
Fig. 1 Type localities for recognized species of Rhinolophus (black circles), as well as subspecies and synonyms (white circles); label names represent the specific epithets of currently recognized species. Biomes of Africa and neighboring regions indicated by color shading, dark yellow: Tropical and subtropical moist broadleaf forests; orange: Flooded grasslands and savannas; gray: Tropical and subtropical grasslands, savannas, and shrublands; olive brown: Deserts and xeric shrublands; gray-green: Tropical and subtropical moist broadleaf forests; peach: Mangroves; ochre: Mediterranean forests, woodlands, and shrub; dark tan: Tropical and subtropical dry broadleaf forests [14]
Fig. 5 in Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics
Fig. 5 Species tree estimated in StarBEAST2 using the four nuclear intron dataset. Numbers adjacent to nodes indicate posterior probabilities. Terminal tips in the tree that are statistically well-supported (PP ≥ 0.95) from BPP are indicated by "*" preceding the clade name, and terminal tips that had PP <0.95 are indicated by "?" preceding the clade name. Species groups are from [13]
FIGURE 3 Morphological trait sampling for all bird families. AVONET contains 718,662 in AVONET: morphological, ecological and geographical data for all birds
FIGURE 3 Morphological trait sampling for all bird families. AVONET contains 718,662 individual trait measurements, all of which are used to calculate species averages. However, sampling per species varies across families depending on taxonomy. Upper phylogram shows sampling under BirdLife International (11,009 species in 243 families). Families where sampling completeness is below 75% indicated by lighter shading. Most families with lower sampling are species poor (numbers in black circles show species richness). Lower panels show that sampling improves under more conservative taxonomic treatments of eBird (10,661 species in 249 families) and BirdTree (9993 species in 194 families). Coloured bars indicate the proportion of species in each family measured to different levels of completeness. 'Complete set' means a full set of all 9 core morphological traits (not necessarily from the same individual). 'Individuals' means any individual bird with one or more traits measured
Рис. 2. Распредение биомассы Mytilus trossulus septentrionalis на литорали дальневоcточных морей России. Здесь и далее на гистограммах по оси абцисс после географических пунктов в скобках укаЗана выборка (число иЗученных проб), по оси ординат – максимальные ЗначениЯ биомассы вида. Под Значением биомассы 0.1 г/м² подраЗумеваютсЯ качественные пробы. СокраЩениЯ (бмп) и (топ) оЗначают соответственно беринговоморское и тихоокеанское побережьЯ Восточной Камчатки. Побережье Зал. Петра Великого от устьЯ р. Туманной к северу до м. Поворотного условно отноcитсЯ к южному Приморью; побережье к северу от м. Поворотного (пос. Преображение, б. СоколовскаЯ) до б. Ольга, включительно, условно относитсЯ к среднему Приморью; побережье к северу от б. Ольга до м. Белкина и материковое побережье Татарского пролива относим к северному Приморью. Fig. 2. The distribution of biomass of Mytilus trossulus septentrionalis in the intertidal zone of the Far Eastern seas of Russia. Here and throughout on histograms, on the abcissa is the number of studied samples (numbers in parentheses following the names geographic localities), on the ordinate is the maximum biomass of species. The number 0.1 g wet wt m-2 means the qualitative samples. Abbreviations (bmp) and (top) mean the Bering Sea coast and the Pacific coast of eastern Kamchatka. The coast of Peter the Great Bay from the mouth of the Tumannaya River to Cape Povorotny is conditionally referred to as southern Primorye; the area north of Cape Povorotny (Preobrazhenie Settlement, Sokolovskaya Bay) to Olga Bay inclusive is conditionally referred to as middle Primorye; north of Olga Bay to Cape Belkin and the mainland coast of the Tatar Strait to as northern Primorye. in Bivalve mollusks of the intertidal zone of the Far Eastern seas of Russia
Рис. 2. Распредение биомассы Mytilus trossulus septentrionalis на литорали дальневоcточных морей России. Здесь и далее на гистограммах по оси абцисс после географических пунктов в скобках укаЗана выборка (число иЗученных проб), по оси ординат – максимальные ЗначениЯ биомассы вида. Под Значением биомассы 0.1 г/м² подраЗумеваютсЯ качественные пробы. СокраЩениЯ (бмп) и (топ) оЗначают соответственно беринговоморское и тихоокеанское побережьЯ Восточной Камчатки. Побережье Зал. Петра Великого от устьЯ р. Туманной к северу до м. Поворотного условно отноcитсЯ к южному Приморью; побережье к северу от м. Поворотного (пос. Преображение, б. СоколовскаЯ) до б. Ольга, включительно, условно относитсЯ к среднему Приморью; побережье к северу от б. Ольга до м. Белкина и материковое побережье Татарского пролива относим к северному Приморью. Fig. 2. The distribution of biomass of Mytilus trossulus septentrionalis in the intertidal zone of the Far Eastern seas of Russia. Here and throughout on histograms, on the abcissa is the number of studied samples (numbers in parentheses following the names geographic localities), on the ordinate is the maximum biomass of species. The number 0.1 g wet wt m-2 means the qualitative samples. Abbreviations (bmp) and (top) mean the Bering Sea coast and the Pacific coast of eastern Kamchatka. The coast of Peter the Great Bay from the mouth of the Tumannaya River to Cape Povorotny is conditionally referred to as southern Primorye; the area north of Cape Povorotny (Preobrazhenie Settlement, Sokolovskaya Bay) to Olga Bay inclusive is conditionally referred to as middle Primorye; north of Olga Bay to Cape Belkin and the mainland coast of the Tatar Strait to as northern Primorye.
Text-fig. 13. Scatter diagram of m1 length vs SDQ for pre-Eemian (time slice 5) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 13. Scatter diagram of m1 length vs SDQ for pre-Eemian (time slice 5) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 11. Scatter diagram of m1 length vs SDQ for Würmian/Weichselian (time slice 3) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and extant Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 11. Scatter diagram of m1 length vs SDQ for Würmian/Weichselian (time slice 3) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and extant Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 12. Scatter diagram of m1 length vs SDQ for Eemian (time slice 4) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 12. Scatter diagram of m1 length vs SDQ for Eemian (time slice 4) Arvicola samples from different geographical provenances compared with M. savini-A. mosbachensis and Arvicola sapidus. Empty dotted ovals indicate the range of extant Arvicola ex gr. amphibius samples from Italy (cyan) and from the other European locations (green) Abbreviations: FR – France, GE – Germany, IT – Italy, SP – Spain.
Text-fig. 10. Scatter diagram of m1 length vs SDQ for Extant (time slice 1 and 2) Arvicola samples of different geographical provenances compared with M. savini-A. mosbachensis. Abbreviations: EU – Europe, GE – Germany, IT – Italy, SP – Spain. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 10. Scatter diagram of m1 length vs SDQ for Extant (time slice 1 and 2) Arvicola samples of different geographical provenances compared with M. savini-A. mosbachensis. Abbreviations: EU – Europe, GE – Germany, IT – Italy, SP – Spain.
Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.
A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
<p>Tropical ecosystems are often biodiversity hotspots, and invertebrates represent the main underrepresented component of diversity in large-scale analyses. This problem is partly related to the scarcity of data widely available to conduct these studies and the lack of systematic organization of knowledge about invertebrates' distributions in biodiversity hotspots. Here, we introduce and analyze a comprehensive data compilation of Amazonian ant diversity. Using records from 1817 to 2020 from both published and unpublished sources, we describe the diversity and distribution of ant species in the Brazilian Amazon Basin. Further, using high-definition images and data from taxonomic publications, we build a comprehensive database of morphological traits for the ant species that occur in the region. In total, we recorded 1,067 nominal species in the Brazilian Amazon Basin, with sampling locations strongly biased by access routes, urban centers, research institutions, and major infrastructure projects. Large areas where ant sampling is non-existent represent about 52% of the basin and are concentrated mainly in the North, Southeastern, and Western Brazilian Amazon. We found that distance to roads is the main driver of ant sampling in the Amazon. Contrary to our expectations, morphological traits had lower predictive power in predicting sample bias than purely geographic variables. However, when geographic predictors were controlled, habitat stratum and traits contribute to explain the remaining variance. More species were recorded in better-sampled areas, but species richness estimation models suggest that areas in South Amazonian edge forests are associated with especially high species richness. Our results represent the first trait-based, large-scale study for insects in Amazonian forests and a starting point for macroecological studies focusing on insect diversity in the Amazon Basin.</p>
A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
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Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
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Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified), western Europe (domesticus, DOM), and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia, and Korea, are inferred, with the possibility of several different routes.
Extended Data Fig. 2-27 Geographical information of bioinformatic predicted samples based on the analysis of 16S rRNA gene in four PE degrading bacteria
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Supplementary material 1 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Gazetteer : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Supplementary information figure : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Name and DNA sequences of pairs of primers used for amplification and sequencing of the CYTB gene : Data type: molecular data
FIGURE 2. Bromeliad species sampled. A in Ciliate species from tank-less bromeliads in a dry tropical forest and their geographical distribution in the Neotropics
FIGURE 2. Bromeliad species sampled. A=Tillandsia dasyliriifolia, B=T. rothii, C=Bromelia pinguin, D=T. polystachia and E=B. karatas.
FIGURE 3 in Broad geographic sampling and DNA barcoding do not support the presence of Helobdella stagnalis (Linnaeus, 1758) (Clitellata: Glossiphoniidae) in North America
FIGURE 3. Best scoring maximum likelihood tree recovered from the analysis of the COI alignment (lnL = -100106.195003). Likelihood bootstrap support values and parsimony bootstrap support values are denoted above and below each node, respectively. Branches are drawn proportionate to the amount of change and GenBank accession numbers are noted before each taxon. Taxon names on tip labels of GenBank sequences are based on identifications made by previous studies. The neotype specimen of H. stagnalis is indicated in bold. Dagger (†) indicates non-scute-bearing specimens.
FIGURE 1 in Broad geographic sampling and DNA barcoding do not support the presence of Helobdella stagnalis (Linnaeus, 1758) (Clitellata: Glossiphoniidae) in North America
FIGURE 1. Helobdella stagnalis (Linnaeus, 1758). Neotype (SMNH Type-9177) and non-type (ROMIZ I11710). A. Dorsal view (SMNH Type-9177). B. Dissection of the genital region (ROMIZ I11710). C. Ventral view (SMNH Type-9177). D. Dissection of median region of the body (ROMIZ I11710). E. Ventral surface of the genital region (SMNH Type-9177). F. Dorsal view of the nuchal region (SMNH Type-9177). Abbreviations: A, atrium; E, eyespots; FG, female gonopore; GC, gastric caeca; MG, male gonopore; O, ovisacs; P, pharynx; PC, post caeca; Sc, nuchal scute.
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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.