By
Kevin E. Noonan —

"Genome
projects" for a variety of species (comprising a complete sequence
determination of a species' genomic DNA) has been underway for the past dozen or
so years, in the wake of the completion of the Human Genome Project at the turn
of the century.  While such a sequence
determination remains the "gold standard" for a full appreciation of
the gene structure and complement of a species, partial genome sequences,
focusing on an animal's protein-coding sequences can also be useful in deriving
phylogenetic relationships and understanding how genes are associated with (if
not directly responsible for) shared phenotypic characteristics.

Such
a study was reported recently for the bottlenose dolphin, Tursiops truncates in a paper by Michael McGowen, Lawrence Grossman
and Derek Wildman of the Center for
Molecular Medicine and Genetics, Wayne State University School of Medicine (Proceedings of the Royal Society: Biological Sciences, 279: 3643-3651).   The
paper,"Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown,"
reports the results of a comparison of 10,025 protein-coding genes from
bottlenose dolphins and orthologous genes from cow (Bovis taurus, the closest living mammalian species in the Order
Cetartiodactyla), horse (Equus caballus),
dog (Canis familiaris) (together,
these four species comprising the laurasiatherian species), mouse (Mus muscalus), elephant (Loxodonta africana), opossum (Monodelphis domestica), platypus (Ornithorhynchus anatinus), chicken (Gallus gallus) and man.  The comparison was limited to coding
sequences (CDS) ranging from 26335 bp (SYNE1)
to 150 bp (C20orf196 and FDPS).

Dolphin
genes were found to have the slowest rates of synchronous substitution between
the laurasiatherian species and comparable to rates seen in elephants and humans.  The mean ratio of the number of
non-synonymous substitutions per non-synonymous site to the number of
synonymous substitutions per synonymous site (dN/dS) were highest in
dolphins of all laurasiatherian species, and again close to human rate
ratios.  Within the dolphin genome, 228
genes were identified as having  (dN/dS)
>1 (shown in Table 2), which was interpreted to indicate positive selection
at levels (2.26%) significantly higher than seen in other species (horse, 48 or
0.51%; cow, 32 or 0.32%; dog, 11 or 0.12%).  Moreover, while at least 46% of genes in all other lineages studied were
subject to "purifying selection" (genes having a (dN/dS)
<0.1), only 36.4% (or 3646 dolphin genes) were found with this ratio,
compared with 44-51% in other species.

Of
the 228 dolphin genes (2.26% of total genes sequenced) under positive selection
(having dN/dS > 1), 27 of these genes are related to the nervous system
including genes homologous to human genes known to be involved in sleep,
synaptic plasticity and, when defective, cognitive disability.  These include "[s]even genes [that] are
identified as being involved in intellectual disabilities and/or microcephaly (ERCC8,
AP4S1, MCPH1, TTR), schizophrenia (MAL) or
Alzheimer's susceptibility (AGER, RNF182)[; f]ive genes []
involved in neuroendocrine function, neuropeptide hormonal activity, or
function as hormones that affect the brain (AGRP, C2orf40, EDN2,
NMU, TTR)[; ] genes [that] function in the development of myelin (MAL),
neuronal or brain development (CNPY1, ZNF597, PCP4L1, MCPH1), neural
potassium channel function (KCNK18), neurite growth (CD47, LRFN1,CNPY2)
and synaptic function (BAALC, DBI, SYPL1, AP4S1, LRFN1)."  These results were consistent with
morphological characteristics of dolphin brains, including "high level of
gyrification (cortical folding), expansion of the insular and cingulate
cortices, specialized von Economo neurons, high glia to neuron ratio increase
in synapse number, reduction of the olfactory system and the large relative
size of the cerebral cortex."  This
suggests to the authors that a genetic analysis might uncover evidence of "convergent
evolution" among large-brained mammals.  Further, consistent with the source, the authors report that genes "putatively
related to cetacean adaptations" were also identified, including "the
cardiovascular system (TSPO2, EPGN, PLN, EDN2, PLA2G5,
KCNJ2), sperm function and spermatogenesis (TNP1, USP26,SPAG4,
NANOS3, SPATA9, CDYL, SOX30, SPATA7, AKAP4, SPATA3, GTSF1),
lung development and respiratory function (SCGB3A2, PLUNC, TMPRSS11D),
dermal development and function (KRTDAP, SPINK5, SPINK6, IL20,
PSORS1C2, DMKN), hair (KRT84), olfaction (OR6B1, OR2AK2),
vision (CRYGN), milk (CSN2), glucose and/or glycerol metabolism (OSTN,
SOCS6, AQP9), vitamin B-1 and B-12 binding and metabolism (TCN1, THTPA)
and a multitude of genes involved in lipid transport and metabolism (APOA2,
APOC4, APOO, FABP4, SERINC4, CCDC129, PLA2G5, PNLIPRP3, RARRES2,
NR1I3)."

The
study also examined metabolism-associated genes (a total of 548 genes),
particularly the mitochondrial cellular (genomic) component genes (i.e., genes
residing in the cellular chromosome whose gene products localize in the
mitochondrion).  These genes are believed
to be important for energy metabolism.  8.5%
of these genes (compared with 1.5-5% for other species) were found to have (dN/dS) > 0.5, including the gene for
cytochrome c (CYCS).  This is consistent with the increased energy
needs of mammals with large brains, it being known that "basal metabolic
rates [are correlated] with relative [larger] brain size" [Isler et al., 2006, "Metabolic costs of brain size evolution," Biol. Lett.
2, 557–560] as has been observed in humans [Grossman et al., 2004, "Accelerated evolution of the electron transport chain
in anthropoid primates," Trends Genet. 20, 578–585].  These
results were consistent with increased brain size, which like in humans is
larger than expected when body size is considered.

The
authors conclude that their data is consistent with a slower rate of mutation
that other species (1.4 x 10^-9 substitutions/per site per year
compared with an average mammalian mutation rate of 2.2 x 10^-9
substitutions/per site per year).  These
results are also consistent with "adaptive evolution" of both the
dolphin nervous system and brain, and although the authors have not established
a definitive link between any of the brain-related genes they identified and "morphological
or behavioral" traits in dolphins.  But they point out that they identified six genes (AP4S1encoding a membrane protein
associated with AMPA glutamate receptors; SYPL1encoding a synaptic
molecule differentially regulated during human development; LRFN1encoding a synaptic adhesion molecule;
BAALC encoding a component of postsynaptic complexes; and DBI encoding
a modulator of signal transduction at type A gamma-aminobutyric acid receptors
with implications in sleep regulation) that are thought to be involved in
synaptic function; similar genes "have been implicated in the evolution of
the brain in humans" according to the report.

Genes
involved in DNA repair and associated with intellectual disabilities in humans
were also identified in the study, including "ERCC8 is a gene
involved in transcription-coupled DNA damage repair; mutations in this gene
result in Cockayne's syndrome, whose symptoms include microcephaly,
neurological defects and premature ageing [Rapin et al., 2006, "Cockayne syndrome in adults: Review with clinical and
pathological study of a new case," J. Child Neurol. 21, 991–1006].  ERCC8 shows evidence of positive selection in recent human populations [Voight
et al., 2006, "A map of recent positive
selection in the human genome," PLoS Biol. 4, e72].  MCPH1 is another gene with evidence of function in DNA damage repair as
well as cell cycle regulation.  MCPH1 dysfunction can cause microcephaly
and has been documented to be under positive selection along the human lineage."

Regarding
genes involved in energy metabolism, the positive selection observed by these
authors is consistent with an oxygenation rate of 6.0 mL kg/min, greater than
in humans or elephants.  In this regard
the paper makes the following interesting observation:

During the course of primate evolution,
metabolism evolved to provide a constant supply of energy to the increasing
demands of a larger brain.  [Leonard et al.,
2003, "Metabolic correlates of hominid brain evolution," Comp. Biochem.
Physiol. A 136, 5–15].  Humans have evolved several adaptations,
including an increase in visceral fat and the evolution of tissue-specific
insulin resistance in the brain that protects nervous tissue from energy
shortage; however, malfunctions of this system in humans can cause type 2
diabetes (Kuzawa, 2010 Beyond feast-famine: brain evolution, human life
history, and the metabolic syndrome. In Human evolutionary biology
(ed.
Muehlenbein M.), pp. 518–527. Cambridge, UK: Cambridge University
Press).  Interestingly, recent research has proposed that dolphins
should be seen as a
model for type 2 diabetes, as they possess all the hallmarks of the
disease [Venn-Watson et al., 2011, "Dolphins as animal models for type 2 diabetes:
sustained, post-prandial hyperglycemia and hyperinsulinemia," Gen. Comp.
Endocrinol. 170: 193–99)].  Here, we find genomic signatures of
adaptive evolution in dolphin genes related to control of food intake such as genes
involved in glycerol uptake and/or glucose metabolism (AQP9, OSTN,
SOCS6), and a neuropeptide AGRP that is expressed in the
hypothalamus and involved in increasing appetite, decreasing metabolism and
regulating leptin. In addition, we found several genes under selection related
to lipid transport and metabolism [] that may be associated with the large fat reserves
found in cetaceans.

This paper is just one example of how elucidating
genomic DNA structure can provide insights (including, as set forth above
regarding the relationship between energy metabolism and diabetes, unexpected
insights) into genotype/phenotype relationships in evolutionarily related
species.  These results also indicate
that the "golden age" of genomics is still, really, in its infancy.