1. Cell Biology
  2. Epidemiology and global health
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Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa

  1. Lee R Berger
  2. John Hawks
  3. Darryl J de Ruiter
  4. Steven E Churchill
  5. Peter Schmid
  6. Lucas K Delezene
  7. Tracy L Kivell
  8. Heather M Garvin
  9. Scott A Williams
  10. Jeremy M DeSilva
  11. Matthew M Skinner
  12. Charles M Musiba
  13. Noel Cameron
  14. Trenton W Holliday
  15. William Harcourt-Smith
  16. Rebecca R Ackermann
  17. Markus Bastir
  18. Barry Bogin
  19. Debra Bolter
  20. Juliet Brophy
  21. Zachary D Cofran
  22. Kimberly A Congdon
  23. Andrew S Deane
  24. Mana Dembo
  25. Michelle Drapeau
  26. Marina C Elliott
  27. Elen M Feuerriegel
  28. Daniel Garcia-Martinez
  29. David J Green
  30. Alia Gurtov
  31. Joel D Irish
  32. Ashley Kruger
  33. Myra F Laird
  34. Damiano Marchi
  35. Marc R Meyer
  36. Shahed Nalla
  37. Enquye W Negash
  38. Caley M Orr
  39. Davorka Radovcic
  40. Lauren Schroeder
  41. Jill E Scott
  42. Zachary Throckmorton
  43. Caroline VanSickle
  44. Christopher S Walker
  45. Pianpian Wei
  46. Bernhard Zipfel
  1. University of the Witwatersrand, South Africa
  2. University of Wisconsin-Madison, United States
  3. Texas A&M University, United States
  4. Duke University, United States
  5. University of Zurich, Switzerland
  6. University of Arkansas, United States
  7. University of Kent, United Kingdom
  8. Max Planck Institute for Evolutionary Anthropology, Germany
  9. Mercyhurst University, United States
  10. New York University, United States
  11. New York Consortium in Evolutionary Primatology, United States
  12. Dartmouth College, United States
  13. University of Colorado Denver, United States
  14. Loughborough University, United Kingdom
  15. Tulane University, United States
  16. Lehman College, United States
  17. American Museum of Natural History, United States
  18. University of Cape Town, South Africa
  19. Museo Nacional de Ciencias Naturales, Spain
  20. Modesto Junior College, United States
  21. Louisiana State University, United States
  22. Nazarbayev University, Kazakhstan
  23. University of Missouri, United States
  24. University of Kentucky College of Medicine, United States
  25. Simon Fraser University, Canada
  26. Université de Montréal, Canada
  27. Australian National University, Australia
  28. Biology Department, Universidad Autònoma de Madrid, Spain
  29. Midwestern University, United States
  30. Liverpool John Moores University, United Kingdom
  31. University of Pisa, Italy
  32. Chaffey College, United States
  33. University of Johannesburg, South Africa
  34. George Washington University, United States
  35. University of Colorado School of Medicine, United States
  36. Croatian Natural History Museum, Croatia
  37. University of Iowa, United States
  38. Lincoln Memorial University, United States
  39. Smithsonian Institution, United States
  40. Institute of Vertebrate Paleontology and Paleoanthropology, China
Research article
Cite this article as: eLife 2016;5:e16370 doi: 10.7554/eLife.16370

Figures

Figure 1 with 2 supplements
Meaningful alt text here please.
Perturbation of Hh signaling affects gene expression in the cephalic ganglia.

(AB) Double fluorescent RNA in situ hybridization (FISH) for hh (magenta) and neuronal markers (A) pc2 or (B) chat (green) in wild-type animals. Main panels show cephalic ganglia. Lower panels show high magnification images of, from left to right, hh (magenta), pc2 or chat (green), DAPI (gray), and merged channels from a representative double-positive neuron. (C) Excision of cephalic ganglia tissue from acid-killed animals for RNA isolation. The left panel shows incision in the dorsal epidermis. Middle panel shows detail of the boxed region in the left panel after removal of dorsal epidermis. The right panel shows the detail of the boxed region in the middle panel after removal of gut tissue overlying the cephalic ganglia and ventral nerve cords. Abbreviations: inc, incision; gut, gut branches; phx, pharynx; CG, cephalic ganglia; VNC, ventral nerve cords. See methods for dissection protocol. (D) Representative image of amputation used to collect tissue for generating the head fragment Illumina libraries. Circle indicates the portion of the animal taken for RNA isolation. (E) Bar graph depicting log2 fold enrichment of selected markers in cephalic ganglia transcriptome over the head fragment transcriptome. Experimentally-verified neural markers and non-neural markers identified by brackets. Average log2 fold enrichment of all 7 CNS genes listed in Figure 1—source data 2 in cephalic ganglia transcriptome is 2.57. Average log2 fold depletion of all 22 non-CNS genes listed in Figure 1—source data 2 in cephalic ganglia transcriptome is 1.22. Statistically significant log2 fold change indicated by asterisks (*padj≤0.05, **padj≤0.001). For a list of all analyzed genes, see Figure 1—source data 1. (F) Bar graph depicting log2 fold enrichment of transcript expression level in the cephalic ganglia tissue of hh(RNAi) animals (blue bars) or ptc(RNAi) animals (red bars) over cephalic ganglia tissue from control(RNAi) animals. (G) Intersection of CNS-enriched genes (n = 2237) and Hh-dependent genes (n = 30) reveals 7 CNS genes misregulated following Hh pathway perturbation. Bar graph shows CNS enrichment (green bar) and relative expression following RNAi of hh (blue bar) or ptc (red bar) for if-1 and cali (*padj≤0.05, **padj≤ 0.01). (HI) WISH for (H) if-1 and (I) cali. Dorsal surface shown on left, ventral surface shown on the right. Anterior up, maximum intensity projection of the ventral domain shown for A, B. Anterior up for H, I. Scale bars: 50 um for overviews, 10 um for insets for A, B; 500 um for H, I.

https://doi.org/10.7554/eLife.16996.002
Figure 1—figure supplement 1
Meaningful alt text here please.
Analysis of RNA-seq libraries.

(A) Volcano plot of differential expression between head fragment transcriptome and cephalic ganglia transcriptome. Dots represent the magnitude of differential expression versus the significance for each gene with an average RPKM over 100. A horizontal dotted line indicates significance cutoff and vertical lines indicate the differential expression magnitude cutoff. Number of genes significantly enriched (purple dots) or depleted (blue dots) in cephalic ganglia tissue listed in the upper right and left corners, respectively. (B) Column scatter plot of differential expression of neural markers between conditions. Each dot represents one neural marker. The solid red line indicates mean log2 fold change of all analyzed neural markers for each condition.

https://doi.org/10.7554/eLife.16996.007
Figure 1—figure supplement 2
Meaningful alt text here please.
Hh signaling pathway perturbation does not affect regional expression of transcription factors in the central nervous system.

FISH of orthologs of vertebrate CNS development transcription factors following perturbation of Hh signaling pathway components. Schematic indicates a region of the animal displayed in images. Inhibition of hh (center column) or ptc (right column) shows no change in the expression pattern of nkx2 (top row), nkx6 (middle row), or pax6b (bottom row) from controls (left column). Anterior up, maximum intensity projection of ventral side shown. Scale bars: 100 um for all.

https://doi.org/10.7554/eLife.16996.008
Figure 1 with 2 supplements
Meaningful alt text here please.
Perturbation of Hh signaling affects gene expression in the cephalic ganglia.

(AB) Double fluorescent RNA in situ hybridization (FISH) for hh (magenta) and neuronal markers (A) pc2 or (B) chat (green) in wild-type animals. Main panels show cephalic ganglia. Lower panels show high magnification images of, from left to right, hh (magenta), pc2 or chat (green), DAPI (gray), and merged channels from a representative double-positive neuron. (C) Excision of cephalic ganglia tissue from acid-killed animals for RNA isolation. The left panel shows incision in the dorsal epidermis. Middle panel shows detail of the boxed region in the left panel after removal of dorsal epidermis. The right panel shows the detail of the boxed region in the middle panel after removal of gut tissue overlying the cephalic ganglia and ventral nerve cords. Abbreviations: inc, incision; gut, gut branches; phx, pharynx; CG, cephalic ganglia; VNC, ventral nerve cords. See methods for dissection protocol. (D) Representative image of amputation used to collect tissue for generating the head fragment Illumina libraries. Circle indicates the portion of the animal taken for RNA isolation. (E) Bar graph depicting log2 fold enrichment of selected markers in cephalic ganglia transcriptome over the head fragment transcriptome. Experimentally-verified neural markers and non-neural markers identified by brackets. Average log2 fold enrichment of all 7 CNS genes listed in Figure 1—source data 2 in cephalic ganglia transcriptome is 2.57. Average log2 fold depletion of all 22 non-CNS genes listed in Figure 1—source data 2 in cephalic ganglia transcriptome is 1.22. Statistically significant log2 fold change indicated by asterisks (*padj≤0.05, **padj≤0.001). For a list of all analyzed genes, see Figure 1—source data 1. (F) Bar graph depicting log2 fold enrichment of transcript expression level in the cephalic ganglia tissue of hh(RNAi) animals (blue bars) or ptc(RNAi) animals (red bars) over cephalic ganglia tissue from control(RNAi) animals. (G) Intersection of CNS-enriched genes (n = 2237) and Hh-dependent genes (n = 30) reveals 7 CNS genes misregulated following Hh pathway perturbation. Bar graph shows CNS enrichment (green bar) and relative expression following RNAi of hh (blue bar) or ptc (red bar) for if-1 and cali (*padj≤0.05, **padj≤ 0.01). (HI) WISH for (H) if-1 and (I) cali. Dorsal surface shown on left, ventral surface shown on the right. Anterior up, maximum intensity projection of the ventral domain shown for A, B. Anterior up for H, I. Scale bars: 50 um for overviews, 10 um for insets for A, B; 500 um for H, I.

https://doi.org/10.7554/eLife.16996.002
Figure 1—figure supplement 1
Meaningful alt text here please.
Analysis of RNA-seq libraries.

(A) Volcano plot of differential expression between head fragment transcriptome and cephalic ganglia transcriptome. Dots represent the magnitude of differential expression versus the significance for each gene with an average RPKM over 100. A horizontal dotted line indicates significance cutoff and vertical lines indicate the differential expression magnitude cutoff. Number of genes significantly enriched (purple dots) or depleted (blue dots) in cephalic ganglia tissue listed in the upper right and left corners, respectively. (B) Column scatter plot of differential expression of neural markers between conditions. Each dot represents one neural marker. The solid red line indicates mean log2 fold change of all analyzed neural markers for each condition.

https://doi.org/10.7554/eLife.16996.007
Figure 1—figure supplement 2
Meaningful alt text here please.
Hh signaling pathway perturbation does not affect regional expression of transcription factors in the central nervous system.

FISH of orthologs of vertebrate CNS development transcription factors following perturbation of Hh signaling pathway components. Schematic indicates a region of the animal displayed in images. Inhibition of hh (center column) or ptc (right column) shows no change in the expression pattern of nkx2 (top row), nkx6 (middle row), or pax6b (bottom row) from controls (left column). Anterior up, maximum intensity projection of ventral side shown. Scale bars: 100 um for all.

https://doi.org/10.7554/eLife.16996.008

Additional files

Table 1 - source data 1.

Is the species name mentioned in the title, impact statement, abstract and digest of eLife papers (July–Sept 2014)?

some more details here
https://example.com/a-non-doi-link
Table 1 - source data 1.

Is the species name mentioned in the title, impact statement, abstract and digest of eLife papers (July–Sept 2014)?

some more details here
https://doi.org/10.7554/eLife.10181.001