[dinosaur] Komodo dragon genome + turkey inner ear + bird femurs + hyaenodont brains + more

Ben Creisler
[email protected]

Some recent non-dino papers that may be of interest:

==========
Free pdf:

Abigail L. Lind, Yvonne Y. Y. Lai, Yulia Mostovoy, Alisha K. Holloway,
Alessio Iannucci, Angel C. Y. Mak, Marco Fondi, Valerio Orlandini, Walter
L. Eckalbar, Massimo Milan, Michail Rovatsos, Ilya G. Kichigin, Alex I.
Makunin, Martina Johnson Pokorná, Marie Altmanová, Vladimir A. Trifonov,
Elio Schijlen, Lukáš Kratochvíl, Renato Fani, Petr Velenský, Ivan Rehák,
Tomaso Patarnello, Tim S. Jessop, James W. Hicks, Oliver A. Ryder, Joseph
R. Mendelson III, Claudio Ciofi, Pui-Yan Kwok, Katherine S. Pollard, and
Benoit G. Bruneau (2019)
Genome of the Komodo dragon reveals adaptations in the cardiovascular and
chemosensory systems of monitor lizards.
Nature Ecology & Evolution (2019)
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1038_s41559-2D019-2D0945-2D8&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=dysVYW3mbaaAtqjc94fD0NgzICzt2QIoduq3C-du4Bk&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_s41559-2D019-2D0945-2D8&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=ZFcc66WPE17ENWLPY0BiYoU5-XZSDIJRro2fCZiYdkI&e= 
Free pdf:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_s41559-2D019-2D0945-2D8.pdf&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=Z-52Wsr42oNoaRuqkKJ3-E7fG1qjXJqCu2u6kh86yP4&e= 

Monitor lizards are unique among ectothermic reptiles in that they have
high aerobic capacity and distinctive cardiovascular physiology resembling
that of endothermic mammals. Here, we sequence the genome of the Komodo
dragon Varanus komodoensis, the largest extant monitor lizard, and generate
a high-resolution de novo chromosome-assigned genome assembly for V.
komodoensis using a hybrid approach of long-range sequencing and
single-molecule optical mapping. Comparing the genome of V. komodoensis
with those of related species, we find evidence of positive selection in
pathways related to energy metabolism, cardiovascular homoeostasis, and
haemostasis. We also show species-specific expansions of a chemoreceptor
gene family related to pheromone and kairomone sensing in V. komodoensis
and other lizard lineages. Together, these evolutionary signatures of
adaptation reveal the genetic underpinnings of the unique Komodo dragon
sensory and cardiovascular systems, and suggest that selective pressure
altered haemostasis genes to help Komodo dragons evade the anticoagulant
effects of their own saliva. The Komodo dragon genome is an important
resource for understanding the biology of monitor lizards and reptiles
worldwide.

***********
News:

Komodo dragon genome reveals clues about its evolution

https://urldefense.proofpoint.com/v2/url?u=https-3A__phys.org_news_2019-2D07-2Dkomodo-2Ddragon-2Dgenome-2Dreveals-2Dclues.html&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=7nSlBFKsp9fVLZQsn3phO9CY-x1g9MrRyHEnbQCFQXY&e= 

https://urldefense.proofpoint.com/v2/url?u=https-3A__gladstone.org_about-2Dus_news_dragon-2Dheart&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=gjcQNQYB1hPHt8z3Wy4R_N3EdbR0NQNvPVUGXeQiEoQ&e= 

How Komodo dragons survive deadly bites from other Komodos

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.sciencemag.org_news_2019_07_how-2Dkomodo-2Ddragons-2Dsurvive-2Ddeadly-2Dbites-2Dother-2Dkomodos&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=Yi43OCAo4mMQg_qFxMNXk_3SvfkdpEhgndmR2iB0UUE&e= 

What makes this dragon fierce

https://urldefense.proofpoint.com/v2/url?u=https-3A__cosmosmagazine.com_biology_the-2Dgenes-2Dof-2Da-2Ddragon&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=svP3OMYip-Ek4K77cj46RdCWK5DT3kVFSegMcBWqxRg&e= 


====

Free pdf:

Donald G. Cerio & Lawrence M. Witmer (2019)
Intraspecific variation and symmetry of the inner-ear labyrinth in a
population of wild turkeys: implications for paleontological
reconstructions.
PeerJ 7:e7355
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.7717_peerj.7355&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=lfwgMVeya4hw-Z8aJNIMVg5GJJQWbOu2v-o0pC92lEE&e= 

https://urldefense.proofpoint.com/v2/url?u=https-3A__peerj.com_articles_7355_&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=_hBXb4EXhnHfTGhvspL7vUFgfOM55PxbTd-ihKg-n8Y&e= 

Free pdf:

https://urldefense.proofpoint.com/v2/url?u=https-3A__peerj.com_articles_7355.pdf&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=LeOlUN9EtfCMu5_aBozUobRHLyzlHmjFnWnjFEpwK4Q&e= 


The cochlea and semicircular canals (SCCs) of the inner ear are vital
neurosensory devices. There are associations between the anatomy of these
sensorineural structures, their function, and the function of related
biological systems, for example, hearing ability, gaze stabilization,
locomotor agility, and posture. The endosseous labyrinth is frequently used
as a proxy to infer the performance of the hearing and vestibular systems,
locomotor abilities, and ecology of extinct species. Such fossil inferences
are often based on single specimens or even a single ear, representing an
entire species. To address whether a single ear is representative of a
population, we used geometric morphometrics to quantitatively assess the
variation in shape and symmetry in a sample of endosseous labyrinths of
wild turkeys Meleagris gallopavo of southern Ohio. We predicted that ears
would be symmetrical both within individuals and across the sample; that
labyrinth shape and size would covary; that labyrinth shape would vary with
the size of the brain, measured as width of the endocranium at the
cerebellum; and that labyrinths would be morphologically integrated. To
test these predictions, we microCT-scanned the heads of 26 cadaveric
turkeys, digitally segmented their endosseous labyrinths in Avizo, and
assigned 15 manual landmarks and 20 sliding semilandmarks to each digital
model. Following Procrustes alignment, we conducted an analysis of
bilateral symmetry, a Procrustes regression analysis for allometry and
other covariates including side and replicate, and analyses of global
integration and modularity. Based on Procrustes distances, no individual’s
left and right ears were clearly different from each other. When comparing
the ears of different specimens, statistically clear differences in shape
were found in only 66 of more than 1,300 contrasts. Moreover, effects of
both directional and fluctuating asymmetry were very small--generally, two
orders of magnitude smaller than the variance explained by individual
variation. Statistical tests disagreed on whether these asymmetric effects
crossed the threshold of significance, possibly due to non-isotropic
variation among landmarks. Regardless, labyrinths appeared to primarily
vary in shape symmetrically. Neither labyrinth size nor endocranial width
was correlated with labyrinth shape, contrary to our expectations. Finally,
labyrinths were found to be moderately integrated in a global sense, but
four weakly separated modules--the three SCCs and cochlea--were recovered
using a maximum-likelihood analysis. The results show that both fluctuating
and directional asymmetry play a larger role in shape variation than
expected--but nonetheless, endosseous labyrinths are symmetrical within
individuals and at the level of the population, and their shape varies
symmetrically. Thus, inferences about populations, and very possibly
species, may be confidently made when only a single specimen, or even a
single ear, is available for study.

====


Xinsen Wei & Zihui Zhang (2019)
Ontogenetic changes of geometrical and mechanical characteristics of the
avian femur: a comparison between precocial and altricial birds.
Journal of Anatomy (advance online publication)
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1111_joa.13062&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=eBIjqJuUYclpA78db8xtjilMQBVMV0IzUzVvgmi_Nbc&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__onlinelibrary.wiley.com_doi_10.1111_joa.13062&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=wy3Y3i4QAj_usuKR6JtyAuC1oRoXbxcFPkeBODyNWa4&e= 


The mechanical performance of limb bones is closely associated with an
animal's locomotor capability and is thus important to our understanding of
animal behaviour. This study combined a geometrical analysis and
three‐point bending tests to address the question of how the mechanical
performance of the femurs of Japanese quail (Coturnix coturnix japonica)
and pigeon (Columba livia domestica) respond to changing functional demands
during ontogeny. Results showed that hatchling quails had stiff bone
tissues, and the femoral ultimate loads scaled negatively with body mass,
corresponding to high functional demands during early growth. The hatchling
pigeon femora had weak material properties but they showed a dramatic
increase in Young's modulus during growth. Consequently, although femoral
cross‐sectional geometry showed negative allometry, the ultimate loads
scaled positively with body mass. Older pigeons had more circular bone
cross‐sections than younger pigeons, probably due to load stimulation
changes occurred shortly after the onset of locomotion. Negative allometry
and isometry of the cross‐sectional geometry of hind limb bones were
observed in flying birds and ground‐dwelling birds, respectively. The
correspondence between geometrical change and locomotor pattern suggests
that ontogenetic changes in cross‐sectional geometry may be an effective
indicator of avian locomotor behaviour.


====

Morgane Dubied,  Floréal Solé &  Bastien Mennecart (2019)
The cranium of Proviverra typica (Mammalia, Hyaenodonta) and its impact on
hyaenodont phylogeny and endocranial evolution.
Palaeontology (advance online publication)
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1111_pala.12437&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=3hVfs1qJMkXjKD1OFd88v8tulxf2IHLcaXhyvKxjcP8&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__onlinelibrary.wiley.com_doi_10.1111_pala.12437&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=uizn3fVGj2Pzgiz7daniiGDfjyYwk1v93mbWrXTcgq0&e= 


Raw X‐ray microtomographic data files are archived at the Naturhistorisches
Museum Basel; additional data for this study are available in the Dryad
Digital Repository: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.5061_dryad.rt1385v&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=AWQ8VwcE7qGHANELS9hS6TNnsc1a_xjR32v7FwTeCr8&e=  and on the
MorphoMuseuM website: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.18563_journal.m3.74&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=gXNtJtHVKmN5uD8Pvycbh63k8uhZjYfpfodWamySNkw&e= .

We describe the first endocast reconstruction of a hyaenodont mammal based
on X‐ray microtomography. The endocast belongs to the type material of the
European hyaenodont Proviverra typica. We performed phylogenetic analysis
to contextualize the evolution of endocranial size and complexity in
Hyaenodonta. We added several European hyaenodonts and modified several
codings of the most recent character–taxon matrix established to question
the relationships within Hyaenodonta. Including these new species in a
phylogenetic analysis reveals a new clade: Hyaenodontoidea. Comparisons
with several previously described endocasts show that there was an increase
in complexity in the convolutions of the encephalon within Hyaenodontidae
history. Moreover, the analysis of the encephalization quotient reveals
that the endocranium of the Hyaenodonta is not smaller than those of fossil
Carnivora or some extant Carnivora. Therefore, the extinction of
Hyaenodonta may not be linked to the relative size of hyaenodont brains.

===


Jacob D. Gardner, Michel Laurin & Chris L. Organ (2019)
The Relationship Between Genome Size and Metabolic Rate in Extant
Vertebrates.
bioRxiv
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1101_659094&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=Xz536RlStBXC6UVoOgZ8_2M4sgtdMTdEl1yugC8bEsY&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_659094v1&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=pYzfZoNYny4UMYtE4t305WAEBHlPn3mN8W3Ml2a2_DE&e= 
free pdf:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_biorxiv_early_2019_07_25_659094.full.pdf&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=WemjrrkwQ7kw7jwLtN8mt2XpaKLbaxx3tlpZHVHtdCs&s=Ws3Nvt4ZIBRk4FRcOh0U2vZqqM1uTABmw_ZR9buKVsY&e= 


Genome size has long been hypothesized to affect metabolic rate in various
groups of animals. The mechanism behind this proposed association is the
nucleotypic effect, in which large nucleus and cell sizes influence
cellular metabolism through surface-to-volume ratios. Here, we provide a
review of the recent literature on the relationship between genome size and
metabolic rate. We also conduct an analysis using phylogenetic comparative
methods and a large sample of extant vertebrates. We find no evidence that
the effect of genome size improves upon models in explaining metabolic rate
variation. Not surprisingly, our results show a strong positive
relationship between metabolic rate and body mass, as well as a substantial
difference in metabolic rate between endothermic and ectothermic
vertebrates, controlling for body mass. The presence of endothermy can also
explain elevated rate shifts in metabolic rate. We further find no evidence
for a punctuated model of evolution for metabolic rate. Our results do not
rule out the possibility that genome size affects cellular physiology in
some tissues, but we find little support for a direct functional connection
between genome size and overall metabolism in extant vertebrates.

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