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Australia: The Land Where Time Began |
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Gorilla Genome Sequence – Insights into Hominid Evolution
According to Scally et al.
Gorillas are the closet living relatives after chimpanzees, and are of
comparable importance for the study of human origins and evolution. In
this paper they present the assembly and analysis of a genome sequence
for the western lowland gorilla, and compare the entire genomes of all
extant great ape genera. They proposed a synthesis of genetic and fossil
evidence that was consistent with placing the human-chimpanzee and
human-chimpanzee-gorilla speciation events at approximately 6 and 10
Million years ago (Ma). Gorilla is closer to human or chimpanzee than
the latter are to each other; but it is rarer around coding genes, which
indicates pervasive selection throughout the evolution of great apes,
and the functional consequences in gene expression. It was revealed by a
comparison of coding genes that approximately 500 genes displayed
accelerated evolution on each of the lineages, gorilla, human and
chimpanzee, and there is evidence for parallel acceleration, especially
for genes that are involved in hearing. Western and eastern species of
gorilla were also compared, and it was estimated that the average
sequence divergence time as 1.75 Ma, though with evidence of more recent
genetic exchange and a population bottleneck in the eastern species. A
greater understanding of great ape evolution and biology will be
promoted by the use of genome sequence in these as well as future
analyses.
Many elements of anatomy and physiology are shared between humans with
gorillas and chimpanzees, the similarity of humans to these species was
emphasised by Darwin and Huxley in the first evolutionary accounts of
human origins (Huxley, 1863). It was confirmed by molecular studies that
we are closer to the African apes than to orang-utans and on average
closer to chimpanzees than to gorillas (King & Wilson, 1975). There are
functional differences between the great apes and their relevance to
human evolution, which have been assisted by reference genome sequences
for chimpanzee (Chimpanzee Sequencing and Analysis Consortium, 2005) and
orang-utan (Locke et al.,
2011), have been explored by subsequent analyses (Locke et
al., 2011). In this paper
Scally et al. have provided
reference assembly and initial analysis for the gorilla genome sequence,
which establishes a foundation for future study of the great ape
evolution and genetics. The costs of sequencing have been substantially
reduced by recent technological development, though the assembly of
whole vertebrate genomes has remained a challenging computational
problem. They used a single female western gorilla (Gorilla
gorilla gorilla) named Kamilah to generate a reference assembly,
using
5.4 x 109 base pairs (5.4 Bbp) of capillary sequence
combined with 166.8 Gdp of illumine read pairs. Genes, transcripts and
predictions of gene orthologues and paralogues were annotated by Ensembl
(Hubbard et al., 2009), and evidence that was found by additional
analysis for 498 functional long (>200 bp) intergenic RNA transcripts.
It was found by an assessment of assembly quality using finishing fosmid
sequences that a typical (N50) of error free sequence are 7.2 kbp long,
that have errors clustered in repetitive regions. The total rate of
single base and indel errors is 0.13 kbp, outside repeat masked regions
and away from contig ends. In order to enable a comparison of species
within the
Gorilla genus, Scally et
al. also collected less
extensive sequence data for 3 other gorillas. At present gorillas are
found only within several isolated and endangered populations whose
evolutionary relationships are uncertain. As well as Kamilah the
analysis of Scally et al.
included 2 western lowland gorillas, Kwanza (male) and EB(JC) (female)
and 1 eastern lowland gorilla, Mukisi (male).
Speciation of the great apes
In this study the Kamilah assembly was included with human, chimpanzee (Pan
troglodytes) orang-utan (Pongo
abelii) and macaque (Macaca
mulatta) I a 5-way whole-genome alignment using the Ensembl EPO
pipeline (Paten et al.,
2008). When low quality regions of the chimpanzee assembly and regions
with many alignment gaps were filtered out, the results obtained was
2.01 Gdp of 1:1:1:1 orthologous alignment blocks to which were then
applied a coalescence inference model, CoalHMM, in order to estimate the
timescales and population sizes involved in the speciation of hominins
with orang-utan as an out-group.
In the interpretation of the results from CoalHMM there are 2 issues
that need to be addressed.
1)
The results themselves are obtained in units of sequence divergence
rather than years, and therefore need to be scaled by an appropriate
yearly mutation rate.
2)
CoalHMM makes several simplifying assumptions, as does any model, the
consequences of which need to be understood in the context of realistic
demography. These issues were discussed in turn.
The results of CoalHMM would correspond to speciation time estimates THC
(for human-chimpanzee) and THCG
(for human-chimpanzee-gorilla) of 3.7 and 5.95 Ma, respectively, using a
rate of 10-9 mutations/bp/year derived from human-macaque
sequence divergence and as used as in
previous calculations. These dates are consistent with other
recent molecular estimates (Bradley, 2008; Burgess & Yang, 2008), though
they are at variance with certain aspects of the fossil record, which
includes several fossils which have been proposed, though not accepted
universally (Wood & Harrison, 2011), to be hominins, and therefore to
post-date the human-chimpanzee split. The relationship between molecular
and fossil evidence has indeed remained difficult to resolve in spite of
the accumulation of genetic data (Steiper & Young, 2008). Direct
estimates of mutation rate per generation in population of modern
humans, based on the incidence of disease-causing mutations (Lynch,
2010) or sequencing of familial trios (The 1000 Genome Project
Consortium, 2011; 2011; Roach et
al., 2010), indicate that a lower value of (0.5 to 0.6) x 10-9
bp/year is plausible, based on average hominine generation times of
20-25 years. This would give estimates of about 6 and 10 Ma for
THC and
THCG, potentially
in better agreement with the fossil record.
This timetable for hominine speciation must, however, also be reconciled
with older events, such as the speciation of orang-utan, which is
believed to have occurred no earlier than the Middle Miocene (12-16 Ma),
as prior to this, fossil apes differed substantially from what might be
expected for an early great ape (Hartwig et
al., 2002). If the changing
of mutation rates over time is allowed for this becomes possible, with a
mutation rate of 1 x 10-9 bp/year in the common ancestor of
great apes, which decreases to lower values in all extant species.
Comparable changes in rate of mutations have been observed previously in
primate evolution on larger timescales, including a branch length of
decrease of about 30% in humans compared to baboons since their common
ancestor (Kim et al., 2006).
Within the great apes a decrease is also a predicted consequence of the
increase in body sizes that has been observed over this period of time
and the associated small size with shorter generation times in other
primates (Fleagle et al.,
1998), is consistent with deviations from the molecular clock that are
seen in sequence divergence of the great apes and macaque. It was noted
by Scally et al., however,
that
Sahelanthropus and
Chororapithecus have
remained difficult to incorporate in this model, and can be in hominin
and gorilla genera only if most of the decrease occurred early in the
evolution of the great apes.
That ancestral demography may have affected the genetic inferences is an
alternative explanation for the discrepancy that is apparent in fossil
and genetic dates (if the issue of whether or not the fossil taxa have
been placed correctly). Certainly CoalHMM’s model does not fit the model
in all respects. Possibly of most importance, it assumes that the
ancestral population sizes are constant in time, and that there was no
gene flow between populations that were separated, approximations that
may not hold in reality. It is suggested by simulations that an
ancestral population would have had limited impact on the inference of THC
on the ancestral population bottleneck, its influence having been
largely captured by changes in the effective population size of the
model. The speciation time that is estimated by CoalHMM represents an
average that is weighted by gene flow over the period of separation,
under conditions of genetic exchange between populations following the
main separation of the Chimpanzee and human lineages. In some cases this
can mean that it can be substantially older than the most recent
exchange. It would, however, be more recent than the speciation time
inferred from fossils if there had been strong gene flow between
populations following the development of derived fossil characteristics.
E.g., for the extent that this is plausible as part of a
non-allopatric speciation process, it constitutes an alternative
explanation for the discrepancy of the data while not requiring a change
in mutation rate.
Summary
The inability to observe mutation rates in the past means that the
timing of events from genetic data has remained uncertain, though
whole-genome comparisons can be strongly conclusive about the ordering
of speciation events. Scally et
al. state that in their view possible variation in mutation rates
allows hominid genomic data to be consistent with values of
THC from 5.5 Ma to
7 Ma and THCG from
8.5 Ma to 12 Ma with the potential of ancestral demographic structure
adding inherent ambiguity to both events.
Better resolution may be provided by further integrated analysis
of fossil and genetic evidence.
Discussion
The prevailing pattern of ape evolution has been one of fragmentation
and extinction (Begun, 2007), since the Middle Miocene which was an
epoch of abundance and diversity for apes throughout Eurasia and Africa.
The distribution at the present of non-human great apes, which exist
only as endangered and subdivided populations in equatorial forest
refugia (The IUCN Red List of Threatened Species. Version, 2010. 1,
2010), is a legacy of that process. Even humans, that are now spread
around the world and occupying habitats that were previously
inaccessible to any primate, bear the genetic legacy of past population
crises. All other branches of the
Homo genus have gone
extinct. Scally et al.
suggest it may be that we see some echo of our own ancestors prior to
the last 100,000 years in the condition of Gorilla,
Pan
and
Pongo, and possibly a
condition experienced many times over several million years of
evolution. It is notable that species of at least these genera continued
to exchange genetic material long after separation (Locke et
al., 2011; Green et
al., 2010), a deposition that
may have aided their survival in the face of diminishing numbers. As
well as teaching about human evolution, the study of the great apes
connects us to a time when our own existence was more tenuous, and in
doing so, highlights the importance of protecting and conserving these
remarkable species.
Scally, A., et al. (2012). "Insights into hominid evolution from the
gorilla genome sequence." Nature 483(7388): 169-175.
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Author: M.H.Monroe Email: admin@austhrutime.com Sources & Further reading |