'How would you calibrate a molecular clock for the phylogeny of Hylobatidae and Hominidae, and what would the results be?

1. 'How would you calibrate a molecular clock
for the phylogeny of Hylobatidae and
Hominidae, and what would the results be?
What does the fossil record have to say about
it?'
By: Roya Shariati
The Australian National University (ANU)

2. phylogenetic relationships among these four major groups are still unknown. Most previous studies
have been based on morphology, vocalization, electrophoretic protein evidence, and karotyping and
have differed in their conclusions (Bruce and Ayala, 1979; Creel and Preuschoft, 1984; Geissmann,
1993, 2001; Groves, 1972; Haimoff et al., 1982; Liu et al., 1987; Shafer, 1986).
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Although the monophyly of the gibbons
(family Hylobatidae) is widely accepted,
this is not the case for the taxonomy
adopted within the family
.In early studies on gibbon systematics,
the Hylobatidae were grouped into two
distinct genera, including the siamang
(Symphalangus)
on the one hand and all the remaining
gibbons (Hylobates) on the other (e.g.,
Napier and Napier, 1967; Schultz, 1933;
Simonetta, 1957). When gibbons were
studied in more detail,
however, it became clear that four, not
two, major hylobatid divisions needed to
be recognized.
These groups are generally accepted now
as four distinct subgenera (i.e.,
Symphalangus, Nomascus, Bunopithecus,
and Hylobates)

3. Even the use of molecular techniques based mainly on
mitochondrial DNA sequences was not able to resolve the
evolutionary relationships among the gibbon subgenera
Furthermore,
 Most molecular studies did not include the subgenus
Bunopithecus and therefore presented an incomplete view on
gibbon evolution.
 The mitochondrial control region is known to evolve faster
than other parts of mtDNA and may therefore be more suited
to resolve a radiation which evolved over a short time span
than sequences used in previous studies (Garza and
Woodruff, 1992; Hall et al., 1998)
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Therefore determined the DNA sequence of the complete
mitochondrial control region and adjacent phenylalaninetRNA (Phe-tRNA) of the four gibbon subgenera with the
intention of :
1-resolving the evolutionary relationships between the
subgenera and
2-comparing the distances between them with those between
the great ape genera Homo and Pan. (Garza and Woodruff,
1992; Hall et al., 1998; Hayashi et al., 1995; Zehr, 1999;
Zhang, 1997).

4. A New Generic Name for the Hoolock Gibbon (Hylobatidae)
Alan Mootnick1 and Colin Groves
 The generic nomen Bunopithecus is not applicable to hoolock gibbons. Groves
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(1968),
The concolor gibbons (formerly regarded simply as a species of Hylobates: H.
concolor) were at least as different from Hylobates and Symphalangus as they were
from each other.
Each subgenus has a distinctive karyotype.
The type of Bunopithecus sericu s is outside the range of modern Hylobatidae in its
dental characters.
The anterior fovea is much larger and less sharply demarcated in general, but with a
larger mesial crest; the entoconid is reduced; the hypoconulid is very large
the wide central basin so characteristic of modern gibbons is undeveloped and
encroached on by the surrounding cusps and grooves (Groves 2004), .

5. Five gibbon species representing the four major groups
within the Hylobatidae clade, Hylobates, Hoolock
(Bunopithecus),Symphalangus, and Nomascus, were
studied. All study animals or their parents were identified
by us using fur coloration and vocal characteristicsas
described in Geissmann (1995).

7. Gibbons produce single offspring; twins are
very rare (Dal Pra & Geissmann, 1994;
Dielentheis et al., 1991; Geissmann,
1989).
Gibbon birth weights (mean ± standard
deviations) are 406±55 g (n=7)
for the genus Hylobates, 487±87 g
(n=3)
for Nomascus, and 551±88 g
for Symphalangus (Geissmann &
Orgeldinger, 1995).
The differences in birth weights between
the genera parallel those observed in
adult body weights.
No birth weights are available
for Hoolock but, to judge by adult body
weights, those can be expected be
similar to the birth weights
of Nomascus. Gestation length in all
gibbons appears to be around 7 months
(Geissmann, 1991), but no data are
available for Hoolock.
Ontogeny

8. Genetic Variances
Evolutionary shaping of the human α2- α1globin duplication units by retroposition
of Alu family repeats and
by simple DNA deletion events. The proposed
scheme of evolution has been deduced
from sequence comparison of the
duplication units between human and
gibbon.
The ancestral unit consisted of blocks X, I, IV,
II, Y, and Z.
The evolutionary origin of block III is
uncertain at the present time.
It could belong to the ancestral unit, but was
deleted from the α2-, but not α1-, globin
unit. Alternatively, it could have been
inserted into the α1-globin unit after the
duplication event.

9. Like other hominoids, gibbons exhibit relatively long pre-adult developmental
phases
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After tandem duplication, independent
retroposition of different Alu family
repeats into the adult α-globin locus
occurred.
Of the four depicted repeats, Alu1, Alu2,
and Alu3 were inserted in the
human/gibbon ancestor, with the insertion
timing of Alu3 as early as prior to the
separation of gibbon/human from the Old
World monkeys (9, 14).
Alu4 is present in the gibbon lineage,
prior to or after the human/gibbon
divergence is unknown,
since the DNA region containing its
insertion site has been deleted from the
human genome.

11. DNA was extracted from periphereal blood lymphocytes and hair samples (H. hoolock) by the
standard methods outlined in Sambrook et al. (1989) and Walsh et al. (1991), respectively. The
complete mitochondrial control region and adjacent Phe-tRNA from one individual each of H.
(Bunopithecus) hoolock, H. (Nomascus) leucogenys leucogenys, H. (Nomascus) gabriellae, and
H. (Symphalangus) syndactylus and two individuals of H. (Hylobates) lar were PCR-amplified
(Saiki et al., 1988) with the oligonucleotide primers L16007(59CCCAAAGCTAAAATTCTAA39) and H00651 (59-TAACTGCAGAAGGCTAGGACCAAACCT- 39) According to Kocher et
al. (1989), with H and L designating the heavy- and light-strand sequences of the mitochondrial
genome and the numbers indicating the 39 end of the primers according to the human reference
sequence (Anderson et al., 1981).
homo/1-954
CCTGAGTTGTAAAAAACTCCAGTTGACAC..AAAATAGACTACGAAAGTGGCTTTAACAT
gorilla/1-949
CCTGAGTTGTAAAAAACTCCAGCTGATAT..AAAATAAACTACGAAAGTGGCTTTAATAT
chimp/1-949
CCTGAGTTGTAAAAAACTCCAGCTGATAC..AAAATAAACTACGAAAGTGGCTTTAACAC
bonono/1-950
CCTGAGTTGTAAAAAACTCCAGCTGATAC..AAAATAAACTACGAAAGTGGCTTTAACAC
pongo/1-953
CCTGAGTTGTAGAAAACTTAAGTTAATAC..AAAATAAACTACGAAAGTGGCTTTAATAT
gibbon/1-951
TCCAAGTCGTAAAAAACTCTGGCTGCTAT..AAAATAAACTACGAAAGTGGCTTTAACAC
macaque/1-946
TCTAAACTGT..AAAACCCTAGCTGATGT..AAAATAAACTACGAAAGTGGCTTTAAAGC
monkey/1-958
ACTAAGTTGTGGAAAACTCCAGTTATAGT..GAAATACCCTACGAAAGTGGCTTTAATAT

12. Considering the fast pace of sequence evolution pertaining to the mitochondrial control
region,
 Only great ape sequences were taken into account for the sequence comparisons and
phylogenetic analyses. The gorilla (Gorilla gorilla, NC001645) and orang-utan (Pongo
pygmaeus, NC001646) (Horai et al., 1995)
 Sequences were excluded from the analyses since both of the sequences exhibit a major
deletion in the mitochondrial control region.
 Thus, the herein determined sequences were compared with the homologous sequences
obtained from human (Homo sapiens, NC001807) (Anderson et al., 1981), pygmy
chimpanzee (Pan paniscus, NC001644) (Horai et al., 1995), and common chimpanzee (Pan
troglodytes, X93335) (Arnason et al., 1996).
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13. Phylogenetic Analyses
The expected monophylies of both the
Homo–Pan and the gibbon clades are
supported by bootstrap values of
100%.
 The Hylobatidae, Nomascus is the
most basal group, followed by
Symphalangus, whereas Bunopithecus
and Hylobates were the last to diverge.
 Nomascus as the deepest split is
supported by high bootstrap values in
all three tree reconstruction methods
used.
 Results about the relationships among
Bunopithecus, Hylobates, and
Symphalangus are contradictive;
whereas maximum likelihood and
neighbor-joining link Bunopithecus
and Hylobates, maximum-parsimony
groups Bunopithecus with
Symphalangus.
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Pure observed sequence distances and not
taking different generation times into
account,
It is obvious that the distances among the
four gibbon subgenera are in the same
range as those between Homo and Pan, or
even higher.
The uncorrected average distances are
10.3%
between
Hylobates
and
Bunopithecus,
10.6%
between
Symphalangus and the Bunopithecus–
Hylobates clade, and 12.8% between
Nomascus and the other three subgenera.
In contrast, the distance between Homo
and Pan is only 9.6%. Based on these
findings, it would be justified to elevate all
four gibbon subgenera to genus rank.
The data depict evolutionary relationships
among the gibbon genera that are
supported by high bootstrap values.
However, more extensive stretches of
mitochondrial and nuclear DNA may need
to be sequenced to definitively establish
the branching order of the four gibbon
clades.

15. Times of catarrhine divergences in million years before present

16. The monophyly of the hylobatids and their basal position within the phylogeny of
living Hominoidea are well established top Figure.
The monophyly of the group consisting of the African apes (genera Pan and Gorilla)
and humans (Homo), but excluding the Asian orang-utans (Pongo), is also well
supported.
The term "great apes" does not represent a systematic unit. It is often used to represent
a group consisting of the African apes and the orang-utans, but excluding humans.
These apes have traditionally been united in the family "Pongidae".
This grouping is based on similarity.Humans are more closely related to some of its
members (i.e. the African apes) than to its other members (i.e. the Asian orang-utans),
the great apes do not represent a monophyletic group.

17. In 1967 molecular differences among the
hominoids were transferred to divergence
times by Sarich and Wilson,
‘‘.If man and Old World monkeys last shared a
common ancestor 30 million years ago, then
man and African apes shared a common
ancestor 5 million years ago (Sarich and
Wilson).
The original arguments for recent hominoid
divergences have been supported in other
studies applying local primate calibration
points: the split between Platyrrhini (New
World monkeys) and Catarrhini (Old World
monkeys, great apes, and Homo) set at 35–40
MYBP (Goodman et al. 1998), the split
between Cercopithecoidea and Hominoidea
set at 30 MYBP or 25 MYBP (Porter et al.
1997),
and that between Pongo and the lineage leading
to Gorilla/Pan/Homo set at 14–17 MYBP
(Sibley and Ahlquist 1987; Adachi and
Hasegawa1995.

18. Family Hylobatidae
Genus: Hylobates
Genus: Hoolock
Hoolocks
Genus: Nomascus
Characteristics
Small or dwarf
gibbons, lar group
Crested
gibbons, concolor group
Genus: Symphalangus Siamangs
1.
2.
Family Hominidae
Genus: Homo
Humans
Genus: Gorilla
Gorillas
Genus: Pan
Chimpanzees
Genus: Pongo
Orangutans
3.
4.
The Hominoidea share several
primitive characteristics of catarrhine
primates with their sister group, the
Cercopithecoidea ("Old World
monkeys"), including:
As in all catarrhine primates, the
ektotympanic ring is drawn out to
form an external bony auditory
meatus.
The bony palate and the nasal
apertures are relatively broad relativ
broad.
The dental formula in hominoids is
the same as in all other catarrhine
primates: 2.1.2.3 / 2.1.2.3.

19. Photograph of buff cheeked gibbon courtesy of Alan R. Thomson,
copyright The Royal Zoological Society of Scotland.
1. Skull of Hylobates hoolock, white-browed
or hoolock gibbon, from South East Asia
– Bangladesh, Burma, Assam.
2. Skull of Pongo pygmaeus, the Bornean
orang-utan.
3. Skulls of male and female Gorilla gorilla,
the Western gorilla, from Equatorial
Africa.
4. Skull of Pan troglodytes, the common
chimpanzee, from West and Central
Africa.
5. Skulls of Homo sapiens, a human being;
one skull prepared to show brain case.

20.  Gibbon skulls (1) are relatively light and there is little difference in the
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skulls of males and females, they have the largest canines, relatively
speaking, of all apes.
The skulls of the heavier great apes and humans (2-5) are robust to protect
the brain from damage.
Orangutan skulls (2) slope markedly backwards, unlike the skulls of gorillas
(3) and chimpanzees (4).
The skulls of male gorillas (3) and orangutans are much more heavily built
than the females and also have substantial midline (sagittal) and neck
(nuchal) crests to provide additional attachment surfaces for neck muscles.
The human cranium (5) is smooth-domed and lacks crests; the brain cavity
is very large.
The skull of the chimpanzee (4) is very like a human skull .

21. Molar pattern: Living homioid primates exhibit a simple Y5-pattern in the lower dentition; the upper molars
have 4 cusps with a diagonal crest (crista obliqua). Compared to the Cercopithecoidea, the Hominoidea
exhibit a more primitive molar pattern without bilophodont shearing crests. The lower molars are
distinguished by an enlarged talonid section and by 5 main cusps. If viewed from the lingual side, the grooves
between the cusps take a y-shaped form, which explains the name Y5-pattern.The upper molars are of a more
or less square shape. They are derived from the hypothetical primitve molar pattern of anthropoid primates in
that the originally three-cusped tooth was "upgraded" to a four-cusped tooth through the enlargement of a
minor supplementary cusp (hypoconus), which, however, remained separated from the rest of the occusal
surface by an oblique shearing crest, the crista obliqua.
The anterior lower premolar varies in its form from a long shearing blade in gibbons (sectorial front dentition)
to a two-cusped "molarised" tooth in humans. Most hominoid primates have relatively broad incisors. The
canines are more variable than those of the Cercopithecoidea, both in their shape and in the extent of their
sexual dimorphism.

22. The thorax is broadened and the vertebral column is slightly shifted away
from a dorsal position towards the center of the thoracal cavity. The latter
characteristic is most strongly developed in humans.
The scapulae are shifted away from a position lateral of the thorax to a more
dorsal position, and the claviculae, which connect with the scapulae, are
elongated to match the new position of the latter

23. Various genera of the Catarrhini, sorted by their intermembral
indices (indices from Fleagle, 1999)
Homo
H
72
Chlorocebus
Ce
83
Papio
Ce
95-97
Presbytis
Co 75-78 Miopithecus
Ce
83
Theropithecus
Ce
100
Lophocebus
Ce 78
Ce
83-84 Pan
H
102-106
Colobus
Co 78-79 Macaca
Ce
84100
Gorilla
H
116
Cercopithecus Ce 79-86 Piliocolobus
Co
87
Hylobates
H
126-130
Procolobus
Ce
92
Hoolock
H
129
Semnopithecus Co 80-83 Nasalis
Co
94
Pongo
H
139
Trachypithecus Co 82-83 Pygathrix
Co
95
Nomascus
H
140
Allenopithecus Ce 83
Ce
95
Symphalangus
H
147
Co 80
Cercocebus
Erythrocebus
Mandrillus
Intermembral index = (humerus length + radius length) x 100 / (femur length + tibia length); Abbreviations: Ce=Cercopithecinae, Co=Colobinae,
H=Hominoidea

24. Some vertebral numbers of selected members of the Anthropoidea
(average values, after Schultz, 1961).

25. Ventral view of the rump skeleton of an adult female macaque compared
to selected members of the Hominoidea, all brought to the same size (after
Schultz, 1969, p. 78).

26. · Ischial callosities reduced in size (Hylobatidae) or absent
· Femur with broad condyles.
· Feet with robust big toe (Hallux), excpet in orangutans (genus Pongo

27. Hominoids also differ from
cercopithecoid primates in
several behavioral and
ecological characteristics. It is
often unknown, however,
whether these are derived
hominoid traits or pimitive
anthropoid features.
 In general (relative to their body
size) hominoid primates exhibit
a longer gestation period and a
longer maturation period (i.e.
the time until they reach sexual
maturity).
 Hominoid social structure is
normally organized around
matrilines, and the females don't
usually stay in their natal
groups. When forageing for
food, several species appear to
adopt a fission-fusionorganisation.
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28. Body Size
dwarf gibbons (genus Hylobates) 5-7 kg,
hoolocks (Hoolock) and
crested gibbons (Nomascus) 7-10 kg,
siamangs (Symphalangus) 10-12 kg.
There is virtually no sexual dimorphism in
either the canine teeth or body size.
relatively simple molar teeth with low,
rounded cusps, sectorial front teeth and long,
dagger like canines in both sexes
· short snout, large orbits, relatively wide
inter-orbital distance, globular braincase,
shallow mandibula with broad ascending
ramus

29. o
Thescientificnames Symphalangus a
nd syndactylus both mean 'fingers
that have grown together'.
o In the feet of the siamang, the
second and third digit are actually
joined by connective tissue at the
base. This condition is known as
syndactyly.
o
It occasionally occurs in other
gibbon species, as well, but is quite
rare and the connection is usually
less extensive.
o Gibbons are the only apes, that
consistently
exhibit
ischial
callosities. In addition, the females
have noticeable sexual swellings,
during which the Labiae majorae
undergo cyclic changes in their
colour and form.

30. Locomotion
1. In order to prevent the whole body from rotating with each step during bipedal
2.
3.
4.
5.
walking, a counter-rotation of the upper body in the opposite direction is needed.
In humans, this counter-rotation this takes place in the chest area. In gibbons,
however, this counter-rotation occurs in the hip, which makes the movement look
more awkward.
The complete upright posture observed in humans is possible because of two
curvatures in the spinal column, the so-called lordoses. This brings the body's
center of gravity directly over the bearing area of the feet.
The gibbon lacks these curvatures of the spinal column and achieves a similar
result be bending both his hip-joint and his knee joints when standing upright .
The bended knees further help to cushion the forces of forward locomotion
during walking, whereas humans resolve this by the rolling motion of their feet.

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