Presentation on the application and impact of next generation sequencing in studies of cave animals and other subterranean species. Held at the 23rd International Conference on Subterranean Biology in the Department of Biology at the University of Arkansas, 13-17 June 2016, Fayetteville, Arkansas.

1. Cave animals
at the dawn of speleogenomics
Markus Friedrich
Wayne State University
friedrichwsu@gmail.com

2. Cave animals
at the dawn of speleogenomics
● Spelling correct?
○ I think so
○ Spelleochecked this morning...

3. Cave animals
at the dawn of speleogenomics
● What does it mean?
○ Concepts and approaches

4. Cave animals
at the dawn of speleogenomics
● Transcriptome or genome sequence based analyses of
cave faunas:
■ Viruses
■ Bacteria
■ Algae
■ Plants
■ Obligate cave animals
● Extant
● Extinct

5. Cave animals
at the dawn of speleogenomics
● Transcriptome or genome sequence based analyses of
cave faunas:
■ Specimen samples
■ Environmental samples

6. Cave animals
at the dawn of speleogenomics
● Transcriptome or genome sequence based analyses of:
■ Regressive traits
Protas & William R. Jeffery WIREs Dev Biol 2012. doi: 10.1002/wdev.61

7. Cave animals
at the dawn of speleogenomics
● Transcriptome or genome sequence based analyses of:
■ Regressive traits
■ Relaxed vs positive selection
Protas & William R. Jeffery WIREs Dev Biol 2012. doi: 10.1002/wdev.61

8. Cave animals
at the dawn of speleogenomics
● Transcriptome or genome sequence based analyses of:
■ Regressive traits
■ Relaxed vs positive selection
■ Constructive (elaborated) traits
Protas & William R. Jeffery WIREs Dev Biol 2012. doi: 10.1002/wdev.61

9. Cave animals
at the dawn of speleogenomics
● Transcriptome or genome sequence based analyses of:
■ Regressive traits
■ Relaxed vs positive selection
■ Constructive (elaborated) traits
■ Convergent vs parallel evolution
Protas &
William R.
Jeffery
WIREs Dev
Biol 2012.
doi:
10.1002/wd
ev.61

10. Candidate gene studies harvesting
molecular key signatures of the evolutionary process
○ Crandall, K. A., & Hillis, D. M. (1997). Rhodopsin evolution in the dark. Nature,
387(6634), 667–668.
○ Buhay, J. E., & Crandall, K. A. (2005). Subterranean phylogeography of
freshwater crayfishes shows extensive gene flow and surprisingly large
population sizes. Molecular Ecology, 14(14), 4259–4273.
○ Leys, R., Cooper, S. J. B., Strecker, U., & Wilkens, H. (2005). Regressive
evolution of an eye pigment gene in independently evolved eyeless
subterranean diving beetles. Biology Letters, 1(4), 496–499.
○ Aspiras, A. C., Prasad, R., Fong, D. W., Carlini, D. B., & Angelini, D. R. (2012).
Parallel reduction in expression of the eye development gene hedgehog in
separately derived cave populations of the amphipod Gammarus minus.
Journal of Evolutionary Biology, 25(5), 995–1001.
○ Niemiller, M. L., Fitzpatrick, B. M., Shah, P., Schmitz, L., & Near, T. J. (2013).
Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid
cavefishes (Teleostei: Amblyopsidae). Evolution; International Journal of
Organic Evolution, 67(3), 732–748.

11. Speleogenomic studies harvest
molecular signatures of evolutionary change
○ Cave-adaptive loss of function:
■ Ortholog of surface genes not detectable
Gene x

12. ○ Cave-adaptive loss of function:
■ Ortholog of surface genes not detectable
Gene x
Speleogenomic studies harvest
molecular signatures of evolutionary change

13. ○ Cave-adaptive loss of function:
■ Orthologs of surface genes not detectable
■ Transcripts with deletions, nonsense or frameshift
mutations
Gene x
Gene x
Speleogenomic studies harvest
molecular signatures of evolutionary change

14. ○ Cave-adaptive loss of function:
■ Orthologs of surface genes not detectable
■ Transcripts with deletions, nonsense or frameshift
mutations
■ Equal numbers of replacement (dN) vs silent
substitutions (dS) mutation ratio (dN/dS = 1)
Gene x
Gene x
dN/dS = 1
dN/dS < 0.2
Speleogenomic studies harvest
molecular signatures of evolutionary change

15. ○ Cave-adaptive gain of function:
■ Orthologs of surface genes expressed at higher level
Gene x
Gene x
Speleogenomic studies harvest
molecular signatures of evolutionary change

16. ○ Cave-adaptive gain of function:
■ Orthologs of surface genes expressed at higher level
Gene x
Gene x
Speleogenomic studies harvest
molecular signatures of evolutionary change

17. ○ Cave-adaptive gain of function:
■ Orthologs of surface genes expressed at higher level
■ Gene family expansions compared to surface forms
Gene x
Gene x 1
Gene x 2
Speleogenomic studies harvest
molecular signatures of evolutionary change

18. ○ Cave-adaptive gain of function:
■ Orthologs of surface genes expressed at higher level
■ Gene family expansions compared to surface forms
■ High replacement vs silent substitution ratio
Gene x
Gene x
dN/dS > 2
dN/dS < 0.2
Speleogenomic studies harvest
molecular signatures of evolutionary change

19. ○ Cave-adaptive gain of function:
■ Orthologs of surface genes expressed at higher level
■ Gene family expansions compared to surface forms
■ High replacement vs silent substitution ratio
■ Selective sweep patterns
Speleogenomic studies harvest
molecular signatures of evolutionary change

20. ○ Purifying selection:
■ Orthologs of surface genes intact
■ Expressed at similar levels
■ Low replacement vs silent substitution ratio
Speleogenomic studies harvest molecular signatures of
evolutionary change or conservation
Gene x
Gene x
dN/dS < 0.2
dN/dS < 0.2

21. ○ Cave-adaptive loss of function
■ Orthologs of surface genes not detectable
■ Transcripts with deletions, nonsense or frameshift
mutations
■ Equal replacement vs silent substitution mutation ratio
○ Cave-adaptive gain of function
■ Orthologs of surface genes expressed at higher level
■ Gene family expansions compared to surface forms
■ High replacement vs silent substitution ratio
■ Selective sweep patterns
○ Purifying selection
○ All of the above identify candidate trait changes
-> Predictive genomics across >5,000 genes
From sequence read to trait discovery:
Predictive speleogenomics

22. Cave animals
at the dawn of speleogenomics
● Spelling correct
● Transcriptome or genome sequence based analyses of
cave adaptation
● What have we learned so far?

23. Welcome
to the age of Next Generation Sequencing!
http://www.slideshare.net/AlagarSuresh/ngs-introduction-51560394/2
2005

24. 2005 2006 2007 2008 2009 2010

25. http://www.cnn.com/2016/03/28/health/cave-man-neanderthal-dna/index.html
2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
Homo n+s

26. (Gross and Wilkens 2013; Bilandžija et al. 2013; Protas et al. 2006)
2005 2006 2007 2008 2009 2010 2011
OCA2 His615Arg
OCA2
OCA2
OCA2 1252G
Convergent evolution of pigment reduction
in human and cavefish populations
Humans
Astyanax

27. 2005 2006 2007 2008 2009 2010
Green et al. (2010)

28. Kim et al. (2011): Genome sequencing reveals insights into physiology and longevity of
the naked mole rat. Nature, doi:10.1038/nature10533
● Strictly subterranean
o Tolerate low oxygen and high carbon dioxide concentrations
● Eusocial
o Reside in large colonies with a single breeding female (queen), who
suppresses the sexual maturity of her subordinate.
● Extraordinarily long-lived (>30 years)
o Negligible senescence
▪ No age-related increase in mortality
▪ High fecundity until death
▪ Resistant to both spontaneous cancer and experimentally induced
tumorigenesis
● Unable to sustain thermogenesis
● Insensitivity to certain types of pain
● Microphthalmic
2005 2006 2007 2008 2009 2010 2011

29. ● 2,4 Gb large genome
● 22,500 genes
● Apparent lack of age related expression level changes
● 39 Proteins with unique amino acid changes
compared to 36 vertebrate genomes
○ Thermoregulation
○ DNA repair
○ Oncogenesis
○ Vision
2005 2006 2007 2008 2009 2010 2011
Kim et al. (2011): Genome sequencing reveals insights into physiology and longevity of
the naked mole rat. Nature, doi:10.1038/nature10533

30. ● Pain reception related neuropeptide gene ACT1
intact but ancestral promoter missing
● 244 pseudogenes:
○ 183 frameshift events
○ 119 premature termination events
Functional categories enriched for
pseudogenes:
Spermatogenesis
Olfactory receptor activity
Visual perception
2005 2006 2007 2008 2009 2010 2011
Kim et al. (2011): Genome sequencing reveals insights into physiology and longevity of
the naked mole rat. Nature, doi:10.1038/nature10533

31. Kim et al. (2011): Genome sequencing reveals insights into physiology and longevity of
the naked mole rat. Nature, doi:10.1038/nature10533
2005 2006 2007 2008 2009 2010 2011
Lack of function mutations in visual system genes:

32. 2005 2006 2007 2008 2009 2010 2011
Friedrich et al. (2011): SB. 2011. Phototransduction and clock gene expression in the
troglobiont beetle Ptomaphagus hirtus of Mammoth cave. J Exp Biol 214:3532–41.

33. 2005 2006 2007 2008 2009 2010 2011
Friedrich et al. (2011): Phototransduction and clock gene expression in the troglobiont
beetle Ptomaphagus hirtus of Mammoth cave. J Exp Biol 214:3532–41.
Bottom
Surface

34. Academy
1839-1905
Alpheus Spring Packard 1888. The cave fauna of North America, with
remarks in the anatomy of brain and the origin of blind species.
Memoirs of the National Academy of Sciences (USA) 4, 1-156

35. Academy
Alpheus Spring Packard 1888. The cave fauna of North America, with
remarks in the anatomy of brain and the origin of blind species.
Memoirs of the National Academy of Sciences (USA) 4, 1-156
"Transverse and horizontal
sections of the head of
Adelops (=Ptomaphagus)
hirtus, from Mammoth
Cave, reveal no traces of
the optic ganglia or the
optic nerve."

36. Academy
Alpheus Spring Packard 1888. The cave fauna of North America, with
remarks in the anatomy of brain and the origin of blind species.
Memoirs of the National Academy of Sciences (USA) 4, 1-156
"Transverse and horizontal
sections of the head of
Adelops (=Ptomaphagus)
hirtus, from Mammoth
Cave, reveal no traces of
the optic ganglia or the
optic nerve."
"It thus appears that
Adelops must be blind
though the eyes exist in a
degenerate state."

37. Ommatidium
Schistocerca
Tribolium
Drosophila
A lens without photoreceptors?

38. A lens without photoreceptors?
Drosophila
Schistocerca
Tribolium

39. Schistocerca
Tribolium
Drosophila
A lens without photoreceptors?

40. RNA-seq: Deep sequencing transcriptome analysis
• NSF award NSF Award #0951886: Pax6 and the genetic regulation of eye
development in Tribolium
• Rui Chen, Bryce Daines (Baylor College)

41. 25 dissected P. hirtus heads minus antennae
Deep sequencing of the P. hirtus head transcriptome
• NSF award NSF Award #0951886: Pax6 and the genetic regulation of eye
development in Tribolium
• Rui Chen, Bryce Daines (Baylor College)

42. ● 27,428,409 short reads (75 bp) produced
● 5,476,803 (19.97%) aligned by blastx to Tribolium refseq proteins
● Orthologs of 8718 Tribolium transcripts observed with >10 reads
● Concatemerization of blastx hit group reads
Drosophila (Adams et al 2000)
Ptomaphagus
Tribolium (TGSC 2008)
100200300 Mya
Deep sequencing of the P. hirtus head transcriptome

43. The insect phototransduction protein machinery
R
opsin
Gqα
β
PLCβ PKC 53E
γ
INAD INAD
5
Arrestin 1
Arrestin 2
Gqα Gqα
R
opsin
R
opsin
PLCβ PKC 53E
2
TRP
4
3
1
5
2
4
3
1
Ca2+

44. The insect phototransduction protein machinery
R
opsin
Gqα
β
PLCβ PKC 53E
γ
INAD INAD
5
Arrestin 1
Arrestin 2
Gqα Gqα
R
opsin
R
opsin
PLCβ PKC 53E
2
TRP
4
3
1
5
2
4
3
1
Ca2+

45. Conserved expression of the insect phototransduction
protein machinery in P. hirtus
R
opsin
Gqα
β
PLCβ PKC 53E
γ
INAD INAD
5
Arrestin 1
Arrestin 2
Gqα Gqα
R
opsin
R
opsin
PLCβ PKC 53E
2
4
3
1
5
2
4
3
1
TRP
Ca2+

46. Transcript conservation predicts
a functional visual system in P. hirtus
•Structural evidence
•Behavioral evidence
Phototaxis
Circadian rhythm

47. Our first light-dark choice assay
Friedrich et al. (2011) The Journal of Experimental Biology 214: 3532-3541.

48. Light vs dark choice of P. hirtus in response to desktop
lamp illumination
Friedrich et al. (2011) The Journal of Experimental Biology 214: 3532-3541.

49. Speleogenomic approach revealed:
Conservation of functional vision
Presence of photoreceptor cells
Negative photoresponse
Differential wavelength specificity
Conservation of circadian gene expression
Preliminary evidence of circadian activity
rhythms
Genetic regression of the visual system:
Loss of UV opsin
Loss of eye specific pigmentation genes:
cinnabar
scarlet
white
2005 2006 2007 2008 2009 2010 2011
Friedrich et al. (2011): Phototransduction and clock gene expression in the troglobiont
beetle Ptomaphagus hirtus of Mammoth cave. J Exp Biol 214:3532–41.

50. 2005 2006 2007 2008 2009 2010 2011 2012
● Genome size: 174 Mb
● ~13,500 genes
● “Dark-fly”: Drosophila melanogaster maintained in constant darkness > 60 years =
1,500 years
○ Dark-fly produce more offspring in dark than in light
○ Preserved strong phototactic behavior and circadian locomotor rhythm
○ Nonsense mutation in the Rhodopsin7 (not expressed in eye)
○ Functional conservation of Rhodopsin 1-6 (all expressed in the eye)
Izutsu et al. (2012): Genome features of "Dark-fly", a Drosophila line reared long-term in
a dark environment. PLoS One. 7(3):e33288.

51. 2005 2006 2007 2008 2009 2010 2011 2012 2013
Hinaux et al (2011): De novo sequencing of Astyanax mexicanus surface fish and
Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye
genes. PLoS One. 8(1):e53553.
Gross et al. (2011): An integrated transcriptome-wide analysis of cave and surface
dwelling Astyanax mexicanus. PLoS One. 8(2):e55659

52. 2005 2006 2007 2008 2009 2010 2011 2012 2013
● 44,145 contigs assembled from expressed
sequence tags generated by Sanger sequencing
● 8 eight cDNA libraries
■ 4 from a surface stream population
■ 4 from the Pachon cave population
● For both populations, libraries were
generated from four developmental
stages.
Hinaux et al (2011): De novo sequencing of Astyanax mexicanus surface fish and
Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye
genes. PLoS One. 8(1):e53553.

53. 2005 2006 2007 2008 2009 2010 2011 2012 2013
Hinaux et al (2011): De novo sequencing of Astyanax mexicanus surface fish and
Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye
genes. PLoS One. 8(1):e53553.
● 31 non-conservative amino-acid changes specific to the
lineage of the cave population.
○ The significant majority function in carbohydrate
metabolism
○ No enrichment of eye developmental genes
● 79 non-conservative amino-acid differences between the
genes of surface and cave morphotypes tentative
evidence of suggested accelerated evolution of vision
genes

54. 2005 2006 2007 2008 2009 2010 2011 2012 2013
Gross et al. (2011): An integrated transcriptome-wide analysis of cave and surface
dwelling Astyanax mexicanus. PLoS One. 8(2):e55659
● 22,596 contigs from 454 sequencing data from Pachon
and surface animals
○ > 600 transcripts were unique to cave or surface
populations
■ 10% of which were related to genes known from
zebrafish
○ Two classes of gene functions overrepresented in
the conserved population-specific subsamples:
■ Metabolic genes were specific for, or
transcriptionally elevated in cave morphotype
■ 16 homologs associated with visual functions
specifically missing or reduced in the cave
morphotype

55. 2005 2006 2007 2008 2009 2010 2011 2012 2013
Meng et al. (2013): Evolution of the eye transcriptome under constant darkness in
Sinocyclocheilus cavefish. Molecular Biology and Evolution 30 :1527-1543
● Compared the mature retinal histology of surface and cave
species
○ Reduction in number and length of photoreceptor cells
● Generated transcriptomes for surface and cave species
● Transcriptional downregulation of eye fate promoting
transcriptional factors

56. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
Yang et al. (2016): The Sinocyclocheilus cavefish genome provides insights into cave
adaptation. BMC Biol. 2016 Jan 4;14:1.
●Whole-genome sequencing and comparative analysis of:
○ Macrophthalmous S. grahami, 1.75 Gb
○ Micophthalmous S. rhinocerous 1.73 Gb
○ Anophthalmous S. anshuiensis.and 1.68 Gb
●~40,000 genes in each species
●Several opsin genes missing in all three species:
○ Lws2, Rh2-1 and Rh2-2 (middle wavelength-sensitive)

57. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
Yang et al. (2016): The Sinocyclocheilus cavefish genome provides insights into cave
adaptation. BMC Biol. 2016 Jan 4;14:1.
● Anophthalmous S. anshuiensis:
○ Genetic regression related to pigmentation:
■ Reduced transcript levels of Oca2 and melanogenesis
pathway genes
■ Loss of Mpv17
○ Genetic regression related to vision:
■ Opsin gene Rh2-4 lost specifically in anophthalmic species
(Sa)
■ Nine eye developmental regulators transcriptionally
downregulated

58. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
Yang et al. (2016): The Sinocyclocheilus cavefish genome provides insights into cave
adaptation. BMC Biol. 2016 Jan 4;14:1.
● Anophthalmous S. anshuiensis:
○ Gain of function changes related to taste reception:
■ Duplication of taste receptor genes, such as Tas1r1 and
Tas2r200-2
○ Gain of function changes related to taste reception:
■ Hsp90α1
● Duplicated
● Higher expression level

59. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
Tierney et al. (2013): Opsin transcripts of predatory diving beetles: a comparison of
surface and subterranean photic niches. R Soc Open Sci. 2015 Jan 28;2(1):140386.

60. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
● Identified transcripts for UV, LW, and c-opsins
from surface beetle transcriptomes
● 3 out of 3 subterranean beetles presented
evidence of parallel loss of all opsin transcription
● Documents genetic regression of the visual
system
Tierney et al. (2013): Opsin transcripts of predatory diving beetles: a comparison of
surface and subterranean photic niches. R Soc Open Sci. 2015 Jan 28;2(1):140386.

61. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
McGaugh et al. (2014): The cavefish genome reveals candidate genes for eye loss. Nat
Communications 5:5307. doi: 10.1038/ncomms6307
● First de novo genome assembly for Astyanax mexicanus
○ ~1 Gb large genome
○ ~23,000 genes
■ ~16,000 1:1 orthologs to zebrafish
● Identifies candidate genes underlying previously mapped quantitative trait
loci (QTL)

62. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
McGaugh et al. (2014): The cavefish genome reveals candidate genes for eye loss. Nat
Communications 5:5307. doi: 10.1038/ncomms6307
● Identifies and tests developmental eye reduction candidate genes
● Assays cave adaptive candidate genes for potential functional and
expression differences between surface and cave morphotype
○ RT-PCR experiments define morphotype candidate gene losses as
false negatives

63. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
McGaugh et al. (2014): The cavefish genome reveals candidate genes for eye loss. Nat
Communications 5:5307. doi: 10.1038/ncomms6307
● RT-PCR confirmation of species-generic candidate gene losses in several
gene families:
○ Retinol dehydrogenases
○ Crystallins
○ Sine oculis homeoboxes
○ Opsins
○ Fibroblast growth factors
○ Gamma-aminobutyric acid A
○ Dopamine receptors
Vision
Sleep and circadian clock

64. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
Stahl et al. (2015): A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod
Crustaceans of the Species Asellus aquaticus. PLoS One. 10:e0140484.
● Deep sequenced cDNA libraries
○ Cave morphotype
○ Surface morphotype
○ Hybrid
● ~25,000 transcripts
○ >4,000 with orthologs in “other” or non-model
species
● Identifies candidate morphotype-specific alleles

65. Welcome to the tree of speleogenomic animal
life!
Astyanax mexicanus Sinocyclocheilus
Heterocephalus
glaber
P. hirtus
Paroster
macrosturtensis
Asellus aquaticus
Homo n+s

66. Speleogenomic coverage
of cave animal species so far
2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016

67. 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
Speleogenomic coverage
of cave animal species so far

68. Coverage of animal genomes so far
2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
http://www.ncbi.nlm.nih.gov/genome/browse/

69. Cave animals
at the dawn of speleogenomics
● What have we learned so far?
○ A lot
● What is the future holding?
○ Genetic surveys of vanishing diversity
○ High resolution genetic analysis of cave invasion
○ High resolution analysis of troglomorphism
○ Value of close relationship to model organisms
○ Impact of genetic drift: population genomics
○ Impact of time: Young vs old troglobites
○ Quest for the oldest and the youngest troglobite...