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61 results for “giraffes”
Data from: Genomic analysis reveals limited hybridization among three giraffe species in Kenya
<p>The data deposited here was generated by and reported in Coimbra <em>et al.</em> (2023).</p> <p><em>SNP calling and linkage pruning</em></p> <ul> <li><strong>snp_calling_per_species.tar.gz:</strong> includes a genotype likelihoods (GL) file estimated with ANGSD for each giraffe species.</li> <li><strong>sampled_ld.tar.gz:</strong> contains a random sample of estimated pairwise <em>r<sup>2</sup></em> values for each species used to fit linkage disequilibrium (LD) decay curves.</li> <li><strong>ld_pruned_snps.tar.gz:</strong> contains an LD-pruned ANGSD GL file per species.</li> <li><strong>snp_calling_combined.tar.gz:</strong> includes a single LD-pruned ANGSD GL file comprising all sampled individuals of the three giraffe species analyzed in this study.</li> </ul> <p><em>Relatedness</em></p> <ul> <li><strong>relatedness.tar.gz:</strong> contains the input and output files used with NGSremix to estimate relatedness among giraffe in the dataset.</li> <li><strong>snp_calling_combined_unrelated.tar.gz:</strong> includes a single LD-pruned ANGSD GL file comprising all unrelated individuals of the three giraffe species analyzed in this study.</li> </ul> <p><em>Population structure and admixture</em></p> <ul> <li><strong>pcangsd.tar.gz:</strong> contains the covariance matrix generated by PCAngsd.</li> <li><strong>ngsadmix.tar.gz:</strong> includes run likelihood lists for each K value ranging from 1 to 11, as well as the admixture proportions (stored in '.qopt' files) inferred from the run with the highest log-likelihood for each K in NGSadmix.</li> <li><strong>evaladmix.tar.gz:</strong> contains the pairwise correlation of residuals between individuals estimated with evalAdmix for the NGSadmix runs with the highest log-likelihood run for each K.</li> </ul> <p><em>SNP-based phylogenomic inference</em></p> <ul> <li><strong>snp_phylogeny.tar.gz:</strong> contains the input PHYLIP file and the IQ-TREE output tree and log files.</li> </ul> <p><em>Phylogeny of mitochondrial genomes</em></p> <ul> <li><strong>mtdna_phylogeny.tar.gz:</strong> includes the 13 mitochondrial protein-coding gene alignments, the partitions file, and the IQ-TREE output tree and log files.</li> </ul> <p><em>Inference of migration events</em></p> <ul> <li><strong>admixture_graphs.tar.gz:</strong> contains the TreeMix / OrientAGraph input file ('treemix.frq.strat.gz'), the output files for all TreeMix and OrientAGraph runs, and the OptM summary table of TreeMix runs ('optm.tsv').</li> </ul> <p><em>Test for introgression</em></p> <ul> <li><strong>dsuite_introgression.tar.gz:</strong> includes the input VCF, the admixture graph topology reconstructed by OrientAGraph, and the Dsuite output files for the estimation of Patterson's D, f4-ratio, and f-branch statistics.</li> </ul> <p><em>Contemporary migration rates</em></p> <ul> <li><strong>ba3-snps.tar.gz:</strong> contains the input and output files for the BA3-SNPs-autotune and BA3-SNPs runs.</li> </ul> <p><em>Demographic reconstruction</em></p> <ul> <li><strong>demographic_inference.tar.gz:</strong> includes the SFS files generated with ANGSD and realSFS and the StairwayPlot2 blueprint and output files.</li> </ul> <p>Other:</p> <ul> <li><strong>metadata.csv:</strong> a companion file containing sample information used in conjunction with R scripts to plot the figures in the paper.</li> </ul>
Fig. 5 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 5. Giraffe subspecies of the Nile region. The map (extracted from Google Earth; https://www.google.com/intl/de/earth/) shows the geographical barriers (rivers and mountains) that may have isolated (at least temporarily) the subspecies Giraffa camelopardalis camelopardalis (Linnaeus, 1758) (red), G. c. antiquorum (Jardine, 1835) (yellow), G. c. rothschildi Lydekker, 1903 (green) and G. c. reticulata de Winton, 1899 (magenta). The question mark refers to the uncertain geographic origin of Zarafa (left) and the two specimens from Abyssinia (right) (see Discussion for more details).
Fig. 2 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 2. Illustrations of historical giraffe specimens. A. The ʻGiraffe of Levaillantʼ, anonymous painting made in the late 18th century and early 19th century, exhibited in ʻhôtel de Magnyʼ, Jardin des Plantes in Paris (France). B. The ʻGiraffe from Sennaarʼ, representing a lithography of Zarafa (MNHN-1845-211) and the skull of a giraffe from the Cape region (Geoffroy Saint-Hilaire 1827). C. Drawing of the holotype of Giraffa camelopardalis congoensis Lydekker, 1903 (RMCA-452), housed in the Royal Museum of Central Africa, Tervuren (Belgium) (Lydekker 1904). D. Head drawings of the holotypes of G. c. cottoni Lydekker, 1904 (NHMUK-1904.1.21.1, left) and G. g. wardi Lydekker, 1904 (NHMUK-1903.11.18.1, right) (Lydekker 1914).
Table 1 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
<p><b>Table 1.</b> Currently accepted giraffe subspecies (Muller <i>et al.</i> 2018) with their synonyms (modified after Shorrocks 2016).</p><table><tbody><tr><th><b>Subspecies</b></th><th><b>Description</b></th><th><b>Type specimen</b></th><th><b>Type locality</b></th><th><b>Synonyms</b></th></tr></tbody><tbody><tr><th><i>camelopardalis</i></th><td>Linnaeus 1758</td><td>Living giraffe illustrated by Belon du Mans (1553), never deposited in a museum collection.</td><td>Sennar (Sudan) and Ethiopia</td><td><i>Camelopardalis biturigum</i> Duvernoy, 1844 <i>Camelopardalis aethiopica</i> Ogilby, 1837 <i>Giraffa camelopardalis typica</i> Bryden, 1899</td></tr><tr><th><i>giraffa</i></th><td>Boddaert 1784</td><td>Specimens of the Prince of Orange Museum (The Hague) and of Vosmaer (1787) (Museum Leiden), Netherlands.</td><td>Cape of Good Hope, South Africa</td><td><i>Camelopardalis</i> <i>capensis</i> Lesson, 1842 <i>Camelopardalis</i> <i>australis</i> Swainson, 1835 <i>Camelopardalis maculata</i> Weinland, 1863 <i>Giraffa camelopardalis wardi</i> Lydekker, 1904</td></tr><tr><th><i>antiquorum</i></th><td>Jardine 1835</td><td>SMF-498: unspec. type and SMF-497: paratype</td><td>South of Darfour, Sudan</td><td><i>Giraffa camelopardalis senaariensis</i> Trouessart, 1898 <i>Giraffa camelopardalis congoensis</i> Lydekker, 1903</td></tr><tr><th><i>peralta</i></th><td>Thomas 1898</td><td>NHMUK-1898.2.18.1</td><td>Lokoja junction Niger and Benue rivers, Nigeria</td><td>–</td></tr><tr><th><i>tippelskirchi</i></th><td>Matschie 1898</td><td>ZMB-084951 (syntype); second specimen might be considered lost</td><td>Lake Eyasi, Tanzania</td><td><i>Giraffa schillingsi</i> Matschie, 1898</td></tr><tr><th><i>reticulata</i></th><td>de Winton 1899</td><td>NHMUK-18971.30.1</td><td>Loroghi Mountains, Kenya</td><td><i>Giraffa hagenbecki</i> Knottnerus-Meyer, 1910 <i>Giraffa reticulata nigrescens</i> Lydekker, 1911 <i>Giraffa camelopardalis australis</i> Rhoads, 1896</td></tr><tr><th><i>rothschildi</i></th><td>Lydekker 1903</td><td>NHMUK-1903.4.15.1</td><td>Guasin-gisha Plateau east of Mount Elgon, Kenya</td><td><i>Giraffa camelopardalis cottoni</i> Lydekker, 1904</td></tr><tr><th><i>angolensis</i></th><td>Lydekker 1903</td><td>NHMUK- 1939.480</td><td>Cunene River, Angola</td><td><i>Giraffa camelopardalis infumata</i> Noack, 1908</td></tr><tr><th><i>thornicrofti</i></th><td>Lydekker 1911</td><td>NHMUK-1910.10.17.1</td><td>Petauke district, Zambia</td><td>–</td></tr></tbody></table>
Figure 8 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 8. These graphs compare the measured individual cervical vertebrae lengths of fossil Giraffids (Table 4), compared with extant giraffes and the 'other ungulate' group used in this study. The measurement of total vertebral column lengths (TVLs) for the fossil giraffids were generated from the regressions derived for extant giraffes or 'other ungulates', whereas the lengths of the individual cervical vertebrae were taken from the literature (see Table 4). Note that the specimens for Giraffa sp., Samotherium, and Paleotragus germaini appear to scale in a manner similar to extant giraffes, whereas those of Paleotragus primaevus, Climacoceras, and Canthumeryx appear to fall within the range of ungulates that do not demonstrate cervical elongation.
Figure 6 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 6. Graphs of total vertebral column length plotted against the body lengths of C2–C7 vertebrae of all of the extant specimens studied. Other ungulates represent all species studied except the giraffe, camel, and llama. Note that for all specimens of the giraffe the vertebral lengths are longer than one would predict on the basis of a generalized ungulate regression, and scale more steeply than the ungulates. The dotted line on the ungulate plot is an extension of the ungulate regression that allows us to establish a comparison with the camel.
Figure 9 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 9. These graphs compare the measured individual cervical vertebrae lengths of fossil Giraffids (Table 4) with extant giraffes and the 'other ungulate' group used in this study. The measurement of normalized vertebral column lengths for the fossil giraffids were generated from the regressions derived for extant giraffes or 'other ungulates', whereas the lengths of the individual cervical vertebrae were taken from the literature (see Table 4). Note that the specimens for Giraffa sp., Samotherium, and Paleotragus germaini appear to scale in a manner similar to extant giraffes, whereas those of Paleotragus primaevus, Climacoceras, and Canthumeryx appear to fall within the range of ungulates that do not demonstrate cervical elongation.
Figure 5 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 5. Graph of total cervical vertebral length (TCL) vs. individual vertebral length of all the extant specimens studied. Note the way in which the giraffe cervical vertebrae scale in accordance with those seen in the other extant ungulates studied, with the only exception being the youngest giraffe (which was excluded from the regression analysis, but was placed on the graph for comparison).
Figure 2 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 2. Photographs of the lateral aspect of non-articulated giraffe vertebrae C6, C7, T1, and T2, demonstrating the osteological differences between cervical and thoracic vertebrae. Note the size of the transverse foramen in C7, the lack of a transverse foramina in T1 and T2, and the longer spinous process of T1 compared with C6 and C7.
Figure 4 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 4. Upper panel: the percentage contribution of the remaining vertebral regions to the vertebral column length minus that of the cervical of giraffes aged from calf to adult (ages are estimates). Lower panel: the percentage contributions of the remaining vertebral regions to the vertebral column length minus that of the cervical of the extant ungulates studied, in comparison with the adult giraffes. The percentage occupied by the various spinal regions in the giraffe falls into the same ranges observed in other ungulates when the cervical vertebrae are not included. Key: l, lumbar; s, sacral; t, thoracic.
Figure 3 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 3. Upper panel: the percentage contribution of the vertebral regions to the entire length of the vertebral column of giraffes aged from calf to adult (ages are estimates). In the calf, the cervical vertebrae occupy approximately 45% of the total vertebral length. As the animal matures, this increases to between 52 and 54%. Lower panel: the percentage contribution of the vertebral regions to the entire length of the vertebral column of the extant ungulates studied, compared with the adult giraffe. Note that only in the giraffes do the cervical vertebrae occupy more than half of the entire vertebral column. Key: c, cervical; l, lumbar; s, sacral; t, thoracic.
Figure 1 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 1. Photograph of the left aspect of giraffe vertebrae C6–T2, demonstrating how they are articulated in a living individual, and the differences between cervical and thoracic vertebrae. Note the size of the transverse foramen in C7 and the longer spinous process of T1 compared with C6 and C7.
Data from: Seasonality and growth in tropical freshwater ectotherm vertebrates: results from one-year experimentation in the African grey bichir, giraffe catfish, and the West African mud turtle
<p>Growth in ectotherm vertebrates is strongly rhythmed by seasonal variation in environmental parameters. To track the seasonal variation in ancient times in a continental and tropical context, we aim to develop a method based on the use of the growth rate of fossil ectotherm vertebrates (actinopterygians and chelonians) influenced by seasonal environmental fluctuations they experienced in their lifetime. However, the impact of environmental parameters on growth, positive or negative, and its intensity, depends on the taxa considered and data are scarce for tropical species. For one year, an experiment was conducted to better understand the effect of seasonal variation in environmental parameters (food abundance, temperature, and photoperiod) on the somatic growth rate of three species of tropical freshwater ectotherm vertebrates: the fishes <em>Polypterus senegalus</em> and <em>Auchenoglanis occidentalis</em> and the turtle <em>Pelusios castaneus</em>. Mimicking seasonal shifts expected to be experienced by the animals in the wild, the experiment highlighted the preponderant effect of food abundance on the growth rate of those three species. Water temperature variation had a significant effect on the growth rate of <em>Po. senegalus</em> and <em>Pe. castaneus</em>. Moreover, the photoperiod demonstrated no significant effect on the growth of the three species. The duration of application of starvation or cool water conditions, ranging from 1 to 3 months, did not affect the growth rate of the animals. However, <em>Pe. castaneus</em> showed a temporary sensitivity to the return of ad libitum feeding or of warm water, after a period of starvation or cool water, by a period of compensatory growth. Finally, this experiment revealed, in the three species, fluctuations in the growth rate under controlled and constant conditions. This variation, similar to the variation in precipitation and temperature observed in their native environment, could be linked to a strong effect of an internal rhythm controlling somatic growth rate.</p>
Data from: Seasonality and growth in tropical freshwater ectotherm vertebrates: results from one-year experimentation in the African grey bichir, giraffe catfish, and the West African mud turtle
Open the record for dataset details and reuse information.
Fine-scale habitat heterogeneity influences browsing damage by elephant and giraffe
Effects of large mammalian herbivores on woody vegetation tend to be heterogeneous in space and time, but the factors that drive such heterogeneity are poorly understood. We examined the influence of fine-scale habitat heterogeneity on the distribution and browsing effects of two of the largest African terrestrial mammals, the elephant and giraffe. We conducted this study within a 120-ha (500 x 2400 m) ForestGEO long-term vegetation monitoring plot located at Mpala Research Center, Kenya. The plot traverses three distinct topographic habitats ('plateau', 'steep slopes', and 'valley') with contrasting elevation, slope, soil properties, and vegetation composition. To quantify browsing damage, we focused on Acacia mellifera, a palatable tree species that occurs across the three habitat categories. Overall tree density, species richness, and diversity was highest on the steep slopes and lowest on the plateau. Acacia mellifera trees were tallest and had the lowest number of stems per tree on the steep slopes. Both elephant and giraffe avoided the steep slopes and their activity was higher during the wet season than during the dry season. Browsing damage on Acacia mellifera was lowest on the steep slopes. Elephant browsing damage was highest in the valley whereas giraffe browsing damage was highest on the plateau. Our findings suggest that fine-scale habitat heterogeneity is an important factor in predicting the distribution of large herbivores and their effects on vegetation and may interact with other drivers such as edaphic variations to influence local variation in vegetation structure and composition.
The five digits of the giraffe metatarsal
<p>Evolution has shaped the limbs of hoofed animals in specific ways. In artiodactyls, it is the common assumption that the metatarsal is composed of the fusion of digits III and IV, while the other three digits have been lost or are highly reduced. However, evidence from the fossil record and internal morphology of the metatarsal challenges these assumptions. Further, only a few taxonomic groups have been analyzed. In giraffes, we discovered that all five digits are present in the adult metatarsal and are highly fused and modified rather than lost. We used high resolution µCT-scans of the metatarsals of two mid and late-Miocene giraffid fossils and the extant giraffe and okapi. In all the Giraffidae analyzed, we find a combination of four morphologies: (1) four articular facets, (2) four, and in most cases, five separate medullary cavities internally, (3) a clear, small digit I, and (4) in the two fossil taxa of unknown genus the presence of external elongated grooves where the fusions of II and V have taken place. <i>Giraffa</i> and <i>Okapia</i>, the extant Giraffidae, show a difference from all the extinct taxa in having more flattened digits tightly packed together, suggesting convergent highly fused digits despite divergent ecologies and locomotions. These discoveries provide evidence for new understandings as to how bones fuse and question current hypotheses of digit loss.</p>
Magnetic Resonance Imaging Scan of the Brain of a Giraffe (Giraffa camelopardalis)
<p>Magnetic Resonance Imaging Scan of the Brain of a Giraffe (<i>Giraffa camelopardalis</i>) from http://braincatalogue.org/Giraffe</p>
Souvenir model giraffe
This plaster of Paris model is the only surviving souvenir from the Royal Surrey Zoological Gardens. In 1843 five young giraffes were purchased for the Zoological Gardens. They travelled from Africa to Walworth, London, where they were the first giraffes on public display in Britain. This model dipicts one of them. It was added to the collection by Henry Syer Cuming in the mid-1800s. The discolouration of the plaster is due to the item being badly damaged during a fire at the museum in 2013. You can read about its restoration, as well as the zoo and its real giraffes, in [our blog](https://southwarkheritage.wordpress.com/2016/09/09/the-last-giraffe-of-walworth/). You can see more images and information about this object on [our website](http://heritage.southwark.gov.uk/objects/16645/model?ctx=cf10d151-0f55-4d3a-9002-c211b9b36b44&idx=3). Source: Objaverse 1.0 / Sketchfab
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
<p>The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.</p>
History of the Giraffe Pipe locality inferred from microfossil remains: A thriving freshwater ecosystem near the Arctic Circle during the warm Eocene
<p>How will freshwater lakes in the Arctic respond to climate change, especially if polar amplification results in even greater warming at these northern latitudes? Deep-time analogs offer opportunities to understand the potential impacts of future climate warming on Arctic environments. The Giraffe Pipe fossil locality located in the Northwest Territories of Canada offers a window into the life of a thriving Arctic freshwater ecosystem in the Eocene under greenhouse conditions. The remains of an extensive deposit of microfossils, including photosynthetic protists (chrysophytes, diatoms and green algae), heterotrophic protists (euglyphids, heliozoans, paraphysomonads, and rotosphaerids), and sponges, were used to reconstruct the history of the ancient water body. The concentrations and diversity of chrysophyte taxa were extensive throughout the core, accounting for over 70 % of the microfossil remains. The ratio of chrysophyte cysts to diatom valves, with a mean value near 14 throughout the core, further emphasized the dominance of the chrysophytes, and given the high diversity of taxa the locality represents a "paleo-hotspot" for this eukaryote lineage. Based on the totality of fossil evidence, the waterbody within the Giraffe Pipe crater represented a series of relatively shallow aquatic habitats, with changing physical and chemical conditions and varying water depths. Five major zones were identified, each found to be stable for an extended period of time, but with distinct transitions between successive zones signaling significant shifts in environmental conditions. The study provides valuable insight into how Arctic freshwater ecosystems responded to past warm climates, and to the organisms that could potentially thrive in these environments under future warming scenarios.</p>
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